ijms-logo

Journal Browser

Journal Browser

Feature Papers in Molecular Plant Sciences

A topical collection in International Journal of Molecular Sciences (ISSN 1422-0067). This collection belongs to the section "Molecular Plant Sciences".

Viewed by 326569

Editor


E-Mail Website
Collection Editor

Topical Collection Information

Dear Colleagues,

This Topical Collection aims to collect high-quality review and original papers on omics techniques in the research fields of molecular plant sciences. Omics techniques include genomics, proteomics, transcriptomics, metabolomics, and so on. Genomics has revealed the static sequences of genes and proteins, and focus has been shifted to their functions, interaction, and modifications. The omics technologies are high-throughput technologies and have identified gene products (transcripts, proteins, and metabolites) present in a specific biological sample. Furthermore, omics technologies have opened new avenues towards biomarker discovery, identification of signaling molecules associated with function of plant growth, and stress responses. This Topical Collection will contain articles describing omics databases, new technology for omics, and system biology.

Since the aim of this Topical Collection is to illustrate, through selected works, frontier research in molecular plant sciences, we encourage Editorial Board Members of the Molecular Plant Sciences Section of the International Journal of Molecular Sciences to contribute papers reflecting the latest progress in their research field, or to invite relevant experts and colleagues to do so.

Prof. Dr. Setsuko Komatsu
Collection Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Omics
  • Plant
  • Plant sciences
  • Food sciences
  • Omics databases
  • New technology for omics
  • System biology

Published Papers (117 papers)

2024

Jump to: 2023, 2022, 2021, 2020, 2019

18 pages, 4285 KiB  
Article
Exploring Seaweed and Glycine Betaine Biostimulants for Enhanced Phenolic Content, Antioxidant Properties, and Gene Expression of Vitis vinifera cv. “Touriga Franca” Berries
by Eliana Monteiro, Gabriella De Lorenzis, Valentina Ricciardi, Miguel Baltazar, Sandra Pereira, Sofia Correia, Helena Ferreira, Fernando Alves, Isabel Cortez, Berta Gonçalves and Isaura Castro
Int. J. Mol. Sci. 2024, 25(10), 5335; https://doi.org/10.3390/ijms25105335 - 14 May 2024
Viewed by 346
Abstract
Climate change will pose a challenge for the winemaking sector worldwide, bringing progressively drier and warmer conditions and increasing the frequency and intensity of weather extremes. The short-term adaptation strategy of applying biostimulants through foliar application serves as a crucial measure in mitigating [...] Read more.
Climate change will pose a challenge for the winemaking sector worldwide, bringing progressively drier and warmer conditions and increasing the frequency and intensity of weather extremes. The short-term adaptation strategy of applying biostimulants through foliar application serves as a crucial measure in mitigating the detrimental effects of environmental stresses on grapevine yield and berry quality. The aim of this study was to evaluate the effect of foliar application of a seaweed-based biostimulant (A. nodosum—ANE) and glycine betaine (GB) on berry quality, phenolic compounds, and antioxidant activity and to elucidate their action on the secondary metabolism. A trial was installed in a commercial vineyard (cv. “Touriga Franca”) in the Cima Corgo (Upper Corgo) sub-region of the Douro Demarcated Region, Portugal. A total of four foliar sprayings were performed during the growing season: at flowering, pea size, bunch closer, and veraison. There was a positive effect of GB in the berry quality traits. Both ANE and GB increased the synthesis of anthocyanins and other phenolics in berries and influenced the expression of genes related to the synthesis and transport of anthocyanins (CHS, F3H, UFGT, and GST). So, they have the potential to act as elicitors of the secondary metabolism, leading to improved grape quality, and also to set the foundation for sustainable agricultural practices in the long run. Full article
Show Figures

Figure 1

25 pages, 6343 KiB  
Article
GhMYB52 Like: A Key Factor That Enhances Lint Yield by Negatively Regulating the Lignin Biosynthesis Pathway in Fibers of Upland Cotton (Gossypium hirsutum L.)
by Yang Yang, Xue Zhou, Xi Zhu, Bo Ding, Linzhu Jiang, Huiming Zhang, Silu Li, Shuyan Cao, Mi Zhang, Yan Pei and Lei Hou
Int. J. Mol. Sci. 2024, 25(9), 4921; https://doi.org/10.3390/ijms25094921 - 30 Apr 2024
Viewed by 411
Abstract
In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), [...] Read more.
In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization. Full article
Show Figures

Figure 1

23 pages, 7639 KiB  
Article
Changes in Phytohormones and Transcriptomic Reprogramming in Strawberry Leaves under Different Light Qualities
by Peng Li, Zhiqiang Wang, Xiaodi Wang, Fengzhi Liu and Haibo Wang
Int. J. Mol. Sci. 2024, 25(5), 2765; https://doi.org/10.3390/ijms25052765 - 27 Feb 2024
Viewed by 684
Abstract
Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the [...] Read more.
Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the phytohormones and transcriptomic reprogramming in strawberry leaves under different light qualities are still unclear. In this study, we treated strawberry plants with sunlight, sunlight covered with a 50% sunshade net, no light, blue light (460 nm), red light (660 nm), and a 50% red/50% blue LED light combination for 3 days and 7 days. Our results revealed that the light quality has an effect on the contents of Chl a and Chl b, the minimal fluorescence (F0), and the Pn of strawberry plants. The light quality also affected the contents of abscisic acid (ABA), auxin (IAA), trans-zeatin-riboside (tZ), jasmonic acid (JA), and salicylic acid (SA). RNA sequencing (RNA-seq) revealed that differentially expressed genes (DEGs) are significantly enriched in photosynthesis antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolisms, carotenoid biosynthesis, tryptophan metabolism, phenylalanine metabolism, zeatin biosynthesis, and linolenic acid metabolism. We then selected the key DEGs based on the results of a weighted gene co-expression network analysis (WGCNA) and drew nine metabolic heatmaps and protein–protein interaction networks to map light regulation. Full article
Show Figures

Figure 1

19 pages, 6228 KiB  
Article
Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation
by Shuqi Zhao, Xiaoman Gao, Xiaolei Yu, Tao Yuan, Guiyu Zhang, Chenlai Liu, Xinzhong Li, Pei Wei, Xiaoyan Li and Xing Liu
Int. J. Mol. Sci. 2024, 25(4), 2193; https://doi.org/10.3390/ijms25042193 - 12 Feb 2024
Viewed by 937
Abstract
The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland [...] Read more.
The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau. Full article
Show Figures

Figure 1

24 pages, 2940 KiB  
Article
DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value
by Konstantinos Paschalidis, Dimitrios Fanourakis, Georgios Tsaniklidis, Ioannis Tsichlas, Vasileios A. Tzanakakis, Fotis Bilias, Eftihia Samara, Ioannis Ipsilantis, Katerina Grigoriadou, Ioulietta Samartza, Theodora Matsi, Georgios Tsoktouridis and Nikos Krigas
Int. J. Mol. Sci. 2024, 25(3), 1891; https://doi.org/10.3390/ijms25031891 - 4 Feb 2024
Cited by 1 | Viewed by 1755
Abstract
Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated [...] Read more.
Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness. Full article
Show Figures

Figure 1

16 pages, 7547 KiB  
Article
Identification and Expression Patterns of WOX Transcription Factors under Abiotic Stresses in Pinus massoniana
by Dengbao Wang, Zimo Qiu, Tao Xu, Sheng Yao, Mengyang Zhang, Xiang Cheng, Yulu Zhao and Kongshu Ji
Int. J. Mol. Sci. 2024, 25(3), 1627; https://doi.org/10.3390/ijms25031627 - 28 Jan 2024
Viewed by 841
Abstract
WUSCHEL-related homeobox (WOX) transcription factors (TFs) play a crucial role in regulating plant development and responding to various abiotic stresses. However, the members and functions of WOX proteins in Pinus massoniana remain unclear. In this study, a total of 11 WOX genes were [...] Read more.
WUSCHEL-related homeobox (WOX) transcription factors (TFs) play a crucial role in regulating plant development and responding to various abiotic stresses. However, the members and functions of WOX proteins in Pinus massoniana remain unclear. In this study, a total of 11 WOX genes were identified, and bioinformatics methods were used for preliminary identification and analysis. The phylogenetic tree revealed that most PmWOXs were distributed in ancient and WUS clades, with only one member found in the intermediate clade. We selected four highly conserved WOX genes within plants for further expression analysis. These genes exhibited expressions across almost all tissues, while PmWOX2, PmWOX3, and PmWOX4 showed high expression levels in the callus, suggesting their potential involvement in specific functions during callus development. Expression patterns under different abiotic stresses indicated that PmWOXs could participate in resisting multiple stresses in P. massoniana. The identification and preliminary analysis of PmWOXs lay the foundation for further research on analyzing the resistance molecular mechanism of P. massoniana to abiotic stresses. Full article
Show Figures

Figure 1

2023

Jump to: 2024, 2022, 2021, 2020, 2019

14 pages, 2399 KiB  
Article
Biochemical Analysis to Understand the Flooding Tolerance of Mutant Soybean Irradiated with Gamma Rays
by Setsuko Komatsu, Tiantian Zhou and Yuhi Kono
Int. J. Mol. Sci. 2024, 25(1), 517; https://doi.org/10.3390/ijms25010517 - 30 Dec 2023
Viewed by 723
Abstract
Flooding stress, which reduces plant growth and seed yield, is a serious problem for soybean. To improve the productivity of flooded soybean, flooding-tolerant soybean was produced by gamma-ray irradiation. Three-day-old wild-type and mutant-line plants were flooded for 2 days. Protein, RNA, and genomic [...] Read more.
Flooding stress, which reduces plant growth and seed yield, is a serious problem for soybean. To improve the productivity of flooded soybean, flooding-tolerant soybean was produced by gamma-ray irradiation. Three-day-old wild-type and mutant-line plants were flooded for 2 days. Protein, RNA, and genomic DNA were then analyzed based on oppositely changed proteins between the wild type and the mutant line under flooding stress. They were associated with cell organization, RNA metabolism, and protein degradation according to proteomic analysis. Immunoblot analysis confirmed that the accumulation of beta-tubulin/beta-actin increased in the wild type under flooding stress and recovered to the control level in the mutant line; however, alpha-tubulin increased in both the wild type and the mutant line under stress. Ubiquitin was accumulated and genomic DNA was degraded by flooding stress in the wild type; however, they were almost the same as control levels in the mutant line. On the other hand, the gene expression level of RNase H and 60S ribosomal protein did not change in either the wild type or the mutant line under flooding stress. Furthermore, chlorophyll a/b decreased and increased in the wild type and the mutant line, respectively, under flooding stress. These results suggest that the regulation of cell organization and protein degradation might be an important factor in the acquisition of flooding tolerance in soybean. Full article
Show Figures

Figure 1

20 pages, 4886 KiB  
Article
Genome-Wide Identification and Characterization of Gibberellic Acid-Stimulated Arabidopsis Gene Family in Pineapple (Ananas comosus)
by Mingzhe Yang, Chaoyang Liu, Wei Zhang, Jing Wu, Ziqin Zhong, Wen Yi, Hui Liu, Yan Leng, Weisheng Sun, Aiping Luan and Yehua He
Int. J. Mol. Sci. 2023, 24(23), 17063; https://doi.org/10.3390/ijms242317063 - 2 Dec 2023
Cited by 1 | Viewed by 1022
Abstract
The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to [...] Read more.
The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to be characterized. In this study, 15 AcGASA genes were identified in pineapple through a genome-wide scan and categorized into three major branches based on a phylogenetic tree. All AcGASA proteins share a common structural domain with 12 cysteine residues, but they exhibit slight variations in their physicochemical properties and motif composition. Predictions regarding subcellular localization suggest that AcGASA proteins are present in the cell membrane, Golgi apparatus, nucleus, and cell wall. An analysis of gene synteny indicated that both tandem and segmental repeats have a significant impact on the expansion of the AcGASA gene family. Our findings demonstrate the differing regulatory effects of these hormones (GA, NAA, IAA, MeJA, and ABA) on the AcGASA genes. We analyzed the expression profiles of GASA genes in different pineapple tissue parts, and the results indicated that AcGASA genes exhibit diverse expression patterns during the development of different plant tissues, particularly in the regulation of floral organ development. This study provides a comprehensive understanding of GASA family genes in pineapple. It serves as a valuable reference for future studies on the functional characterization of GASA genes in other perennial herbaceous plants. Full article
Show Figures

Figure 1

20 pages, 4018 KiB  
Article
SMALL PLANT AND ORGAN 1 (SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice
by Lei Qiao, Qilong Wu, Liuzhen Yuan, Xudong Huang, Yutao Yang, Qinying Li, Nida Shahzad, Haifeng Li and Wenqiang Li
Int. J. Mol. Sci. 2023, 24(23), 16974; https://doi.org/10.3390/ijms242316974 - 30 Nov 2023
Viewed by 873
Abstract
Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and [...] Read more.
Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation. Full article
Show Figures

Figure 1

16 pages, 5619 KiB  
Article
Transcriptome-Wide Identification of TCP Transcription Factor Family Members in Pinus massoniana and Their Expression in Regulation of Development and in Response to Stress
by Mengyang Zhang, Romaric Hippolyte Agassin, Zichen Huang, Dengbao Wang, Sheng Yao and Kongshu Ji
Int. J. Mol. Sci. 2023, 24(21), 15938; https://doi.org/10.3390/ijms242115938 - 3 Nov 2023
Cited by 1 | Viewed by 959
Abstract
Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and [...] Read more.
Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and development processes. At present, TCP TFs have been widely studied in multiple plant species, but research in P. massoniana has not been carried out. In this study, 13 PmTCP TFs were identified from the transcriptomes of P. massoniana. The phylogenetic results revealed that these PmTCP members were divided into two categories: Class I and Class II. Each PmTCP TF contained a conserved TCP domain, and the conserved motif types and numbers were similar in the same subgroup. According to the transcriptional profiling analysis under drought stress conditions, it was found that seven PmTCP genes responded to drought treatment to varying degrees. The qRT-PCR results showed that the majority of PmTCP genes were significantly expressed in the needles and may play a role in the developmental stage. Meanwhile, the PmTCPs could respond to several stresses and hormone treatments at different levels, which may be important for stress resistance. In addition, PmTCP7 and PmTCP12 were nuclear localization proteins, and PmTCP7 was a transcriptional suppressor. These results will help to explore the regulatory factors related to the growth and development of P. massoniana, enhance its stress resistance, and lay the foundation for further exploration of the physiological effects on PmTCPs. Full article
Show Figures

Figure 1

19 pages, 7608 KiB  
Article
Virome Analysis of Aconitum carmichaelii Reveals Infection by Eleven Viruses, including Two Potentially New Species
by Jie Yang, Ping-Xiu Lan, Yun Wang, Jin-Ming Li, Ruhui Li, Steve Wylie, Xiao-Jiao Chen, Gen-Hua Yang, Hong Cai and Fan Li
Int. J. Mol. Sci. 2023, 24(21), 15558; https://doi.org/10.3390/ijms242115558 - 25 Oct 2023
Viewed by 1133
Abstract
Aconitum carmichaelii is a herbaceous herb indigenous to China that has been cultivated for traditional medicine for centuries. Virus-like symptoms of A. carmichaelii plants were observed on leaves in some A. carmichaelii plantations in Zhanyi and Wuding Counties, Yunnan Province, southwest China. High-throughput [...] Read more.
Aconitum carmichaelii is a herbaceous herb indigenous to China that has been cultivated for traditional medicine for centuries. Virus-like symptoms of A. carmichaelii plants were observed on leaves in some A. carmichaelii plantations in Zhanyi and Wuding Counties, Yunnan Province, southwest China. High-throughput sequencing (HTS) was performed on 28 symptomatic plants, and the results revealed infection with 11 viruses, including 2 novel viruses and 9 previously described viruses: Aconitum amalgavirus 1 (AcoAV-1), aconite virus A (AcVA), cucumber mosaic virus (CMV), currant latent virus (CuLV), apple stem grooving virus (ASGV), chilli veinal mottle virus (ChiVMV), tomato spotted wilt orthotospovirus (TSWV), tobacco vein distorting virus (TVDV), and potato leafroll virus (PLRV). Two novel viruses tentatively named Aconitum potyvirus 1 and Aconitum betapartitivirus 1, were supported by sequence and phylogenetic analysis results of their genomes. We proposed the names Potyvirus aconiti and Betapartitivirus aconiti. RT-PCR assays of 142 plants revealed the predominance and widespread distribution of CMV, AcVA, and AcoPV-1 in plantations. The detection of isolates of CuLV, ASGV, ChiVMV, TSWV, TVDV, and PLRV infections for the first time in A. carmichaelii expands their known host ranges. Full article
Show Figures

Figure 1

19 pages, 2344 KiB  
Article
OXPHOS Organization and Activity in Mitochondria of Plants with Different Life Strategies
by Irina V. Ukolova and Gennadii B. Borovskii
Int. J. Mol. Sci. 2023, 24(20), 15229; https://doi.org/10.3390/ijms242015229 - 16 Oct 2023
Viewed by 851
Abstract
The study of the supramolecular organization of the mitochondrial oxidative phosphorylation system (OXPHOS) in various eukaryotes has led to the accumulation of a considerable amount of data on the composition, stoichiometry, and architecture of its constituent superstructures. However, the link between the features [...] Read more.
The study of the supramolecular organization of the mitochondrial oxidative phosphorylation system (OXPHOS) in various eukaryotes has led to the accumulation of a considerable amount of data on the composition, stoichiometry, and architecture of its constituent superstructures. However, the link between the features of system arrangement and the biological characteristics of the studied organisms has been poorly explored. Here, we report a comparative investigation into supramolecular and functional OXPHOS organization in the mitochondria of etiolated shoots of winter wheat (Triticum aestivum L.), maize (Zea mays L.), and pea (Pisum sativum L.). Investigations based on BN-PAGE, in-gel activity assays, and densitometric analysis revealed both similarities and specific OXPHOS features apparently related to the life strategies of each species. Frost-resistant winter wheat was distinguished by highly stable basic I1III2IVa/b respirasomes and V2 dimers, highly active complex I, and labile complex IV, which were probably essential for effective OXPHOS adaptation during hypothermia. Maize, a C4 plant, had the highly stable dimers IV2 and V2, less active complex I, and active alternative NAD(P)H dehydrogenases. The latter fact could contribute to successful chloroplast–mitochondrial cooperation, which is essential for highly efficient photosynthesis in this species. The pea OXPHOS contained detergent-resistant high-molecular respirasomes I1–2III2IVn, highly active complexes IV and V, and stable succinate dehydrogenase, suggesting an active energy metabolism in organelles of this plant. The results and conclusions are in good agreement with the literature data on the respiratory activity of mitochondria from these species and are summarized in a proposed scheme of organization of OXPHOS fragments. Full article
Show Figures

Figure 1

17 pages, 5539 KiB  
Article
Genome-Wide Identification and Characterization of the YTH Domain-Containing RNA-Binding Protein Family in Liriodendron chinense
by Sheng Yao, Jingjing Zhang, Xiang Cheng, Dengbao Wang, Wenya Yu, Kongshu Ji and Qiong Yu
Int. J. Mol. Sci. 2023, 24(20), 15189; https://doi.org/10.3390/ijms242015189 - 14 Oct 2023
Cited by 1 | Viewed by 1320
Abstract
N6-methyladenosine (m6A) is becoming one of the most important RNA modifications in plant growth and development, including defense, cell differentiation, and secondary metabolism. YT521-B homology (YTH) domain-containing RNA-binding proteins, identified as m6A readers in epitranscriptomics, could affect [...] Read more.
N6-methyladenosine (m6A) is becoming one of the most important RNA modifications in plant growth and development, including defense, cell differentiation, and secondary metabolism. YT521-B homology (YTH) domain-containing RNA-binding proteins, identified as m6A readers in epitranscriptomics, could affect the fate of m6A-containing RNA by recognizing and binding the m6A site. Therefore, the identification and study of the YTH gene family in Liriodendron chinense (L. chinense) can provide a molecular basis for the study of the role of m6A in L. chinense, but studies on the YTH gene in L. chinense have not been reported. We identified nine putative YTH gene models in the L. chinense genome, which can be divided into DF subgroups and DC subgroups. Domain sequence analysis showed that the LcYTH protein had high sequence conservation. A LcYTH aromatic cage bag is composed of tryptophan and tryptophan (WWW). PrLDs were found in the protein results of YTH, suggesting that these genes may be involved in the process of liquid–liquid phase separation. LcYTH genes have different tissue expression patterns, but the expression of LcYTHDF2 is absolutely dominant in all tissues. In addition, the expression of the LcYTH genes is changed in response to ABA and MeJA. In this study, We identified and analyzed the expression pattern of LcYTH genes. Our results laid a foundation for further study of the function of the LcYTH gene and further genetic and functional analyses of m6A RNA modification in forest trees. Full article
Show Figures

Figure 1

13 pages, 6107 KiB  
Article
Cloning of PmMYB6 in Pinus massoniana and an Analysis of Its Function
by Yuan He, Qingqing Hao, Peizhen Chen, Yiyun Qin, Manqing Peng, Sheng Yao, Xin He, Qiong Yu, Romaric Hippolyte Agassin and Kongshu Ji
Int. J. Mol. Sci. 2023, 24(18), 13766; https://doi.org/10.3390/ijms241813766 - 6 Sep 2023
Cited by 1 | Viewed by 1367
Abstract
Phenylpropanoids are crucial for the growth and development of plants and their interaction with the environment. As key transcriptional regulators of plant growth and development, MYB-like transcription factors play a vital role in the biosynthesis of phenylpropanoid metabolites. In this study, we functionally [...] Read more.
Phenylpropanoids are crucial for the growth and development of plants and their interaction with the environment. As key transcriptional regulators of plant growth and development, MYB-like transcription factors play a vital role in the biosynthesis of phenylpropanoid metabolites. In this study, we functionally characterized PmMYB6, a Pinus massoniana gene that encodes an R2R3-MYB transcription factor. It was confirmed by qPCR that PmMYB6 was highly expressed in the flowers, xylem, and phloem of P. massoniana. By overexpressing PmMYB6 in tobacco and poplar, we found that transgenic plants had enlarged xylem, increased content of lignin and flavonoids, and up-regulated expression of several enzyme genes of the phenylpropane metabolism pathway to different degrees. The above research results indicate that PmMYB6 is involved in the metabolic flux distribution of different branches of the phenylpropane metabolic pathway, and the results may provide clues for the regulation of metabolic fluxes between flavonoids and the lignin biosynthesis pathways of P. massoniana, as well as provide a basis for the molecular breeding of P. massoniana. Full article
Show Figures

Figure 1

15 pages, 3303 KiB  
Article
Proteomic Analysis Reveals Salt-Tolerant Mechanism in Soybean Applied with Plant-Derived Smoke Solution
by Setsuko Komatsu, Taiki Kimura, Shafiq Ur Rehman, Hisateru Yamaguchi, Keisuke Hitachi and Kunihiro Tsuchida
Int. J. Mol. Sci. 2023, 24(18), 13734; https://doi.org/10.3390/ijms241813734 - 6 Sep 2023
Viewed by 1287
Abstract
Salt stress of soybean is a serious problem because it reduces plant growth and seed yield. To investigate the salt-tolerant mechanism of soybean, a plant-derived smoke (PDS) solution was used. Three-day-old soybeans were subjected to PDS solution under 100 mM NaCl for 2 [...] Read more.
Salt stress of soybean is a serious problem because it reduces plant growth and seed yield. To investigate the salt-tolerant mechanism of soybean, a plant-derived smoke (PDS) solution was used. Three-day-old soybeans were subjected to PDS solution under 100 mM NaCl for 2 days, resulting in PDS solution improving soybean root growth, even under salt stress. Under the same condition, proteins were analyzed using the proteomic technique. Differential abundance proteins were associated with transport/formaldehyde catabolic process/sucrose metabolism/glutathione metabolism/cell wall organization in the biological process and membrane/Golgi in the cellular component with or without PDS solution under salt stress. Immuno-blot analysis confirmed that osmotin, alcohol dehydrogenase, and sucrose synthase increased with salt stress and decreased with additional PDS solution; however, H+ATPase showed opposite effects. Cellulose synthase and xyloglucan endotransglucosylase/hydrolase increased with salt and decreased with additional PDS solution. Furthermore, glycoproteins decreased with salt stress and recovered with additional treatment. As mitochondrion-related events, the contents of ATP and gamma-aminobutyric acid increased with salt stress and recovered with additional treatment. These results suggest that PDS solution improves the soybean growth by alleviating salt stress. Additionally, the regulation of energy metabolism, protein glycosylation, and cell wall construction might be an important factor for the acquisition of salt tolerance in soybean. Full article
Show Figures

Figure 1

15 pages, 4289 KiB  
Article
Association Mapping and Expression Analysis of the Genes Involved in the Wood Formation of Poplar
by Yaolin Wang, Heng Zhang, Sheng Zhu, Tengfei Shen, Huixin Pan and Meng Xu
Int. J. Mol. Sci. 2023, 24(16), 12662; https://doi.org/10.3390/ijms241612662 - 10 Aug 2023
Viewed by 1448
Abstract
Xylogenesis is a complex and sequential biosynthetic process controlled by polygenes. Deciphering the genetic architecture of this complex quantitative trait could provide valuable information for increasing wood biomass and improving its properties. Here, we performed genomic resequencing of 64 24-year-old trees (64 hybrids [...] Read more.
Xylogenesis is a complex and sequential biosynthetic process controlled by polygenes. Deciphering the genetic architecture of this complex quantitative trait could provide valuable information for increasing wood biomass and improving its properties. Here, we performed genomic resequencing of 64 24-year-old trees (64 hybrids of section Aigeiros and their parents) grown in the same field and conducted full-sib family-based association analyses of two growth and six woody traits using GEMMA as a choice of association model selection. We identified 1342 significantly associated single nucleotide polymorphisms (SNPs), 673 located in the region upstream and downstream of 565 protein-encoding genes. The transcriptional regulation network of secondary cell wall (SCW) biosynthesis was further constructed based on the published data of poplar miRNA, transcriptome, and degradome. These provided a certain scientific basis for the in-depth understanding of the mechanism of poplar timber formation and the molecular-assisted breeding in the future. Full article
Show Figures

Figure 1

18 pages, 10534 KiB  
Article
Genome-Wide Identification, Characterization, and Expression Analysis of Long-Chain Acyl-CoA Synthetases in Carya illinoinensis under Different Treatments
by Wenjuan Ma, Kaikai Zhu, Juan Zhao, Mengyun Chen, Lu Wei, Zhenbing Qiao, Pengpeng Tan and Fangren Peng
Int. J. Mol. Sci. 2023, 24(14), 11558; https://doi.org/10.3390/ijms241411558 - 17 Jul 2023
Cited by 1 | Viewed by 1357
Abstract
As crucial enzymes in the lipid metabolic network, long-chain acyl-CoA synthases (LACSs) are members of the acyl-activated enzyme superfamily and play a crucial role in epidermal wax synthesis, plant lipid anabolic metabolism, and stress tolerance. In this study, 11 pecan LACS genes were [...] Read more.
As crucial enzymes in the lipid metabolic network, long-chain acyl-CoA synthases (LACSs) are members of the acyl-activated enzyme superfamily and play a crucial role in epidermal wax synthesis, plant lipid anabolic metabolism, and stress tolerance. In this study, 11 pecan LACS genes were identified and categorized into five groups and located on nine chromosomes. The significant degree of conservation in the AtLACS and CiLACS protein sequences was demonstrated by multiple sequence alignment and conserved motif analysis. Cis-acting element analysis identified numerous stress-responsive and hormone-inducible elements in the promoter regions of CiLACS genes. The expression levels of CiLACS9 and CiLACS9-1 were considerably up-regulated under salt and drought stress, according to the qRT-RCR study. Treatment with ABA also led to increased expression levels of CiLACS1, CiLACS1-1, CiLACS2, and CiLACS9-1. Notably, CiLACS4, CiLACS4-1, CiLACS9, and CiLACS9-1 exhibited peak expression levels at 135 days after anthesis and are likely to have been crucial in the accumulation of seed kernel oil. Moreover, the CiLACS9 gene was shown to be located in the cytoplasm. These findings offer a theoretical framework for clarifying the roles of LACS genes in the processes of pecan kernel oil synthesis and response to abiotic stressors. Full article
Show Figures

Figure 1

32 pages, 20479 KiB  
Article
Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potatoes
by Sergey N. Lomin, Oksana O. Kolachevskaya, Dmitry V. Arkhipov and Georgy A. Romanov
Int. J. Mol. Sci. 2023, 24(14), 11408; https://doi.org/10.3390/ijms241411408 - 13 Jul 2023
Viewed by 1123
Abstract
It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in [...] Read more.
It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in potato (Solanum tuberosum L.). The corresponding genes were retrieved from sequenced genomes of the doubled monoploid S. tuberosum DM1-3-516-R44 (DM) of the Phureja group, the heterozygous diploid line RH89-039-16 (RH), and the autotetraploid cultivar Otava. Both canonical and noncanonical auxin signaling pathways were considered. Phylogenetic and domain analyses of deduced proteins were supplemented by expression profiling and 3D molecular modeling. The canonical and ABP1-mediated pathways of auxin signaling appeared to be well conserved. The total number of potato genes/proteins presumably involved in canonical auxin signaling is 46 and 108 in monoploid DM and tetraploid Otava, respectively. Among the studied potatoes, spectra of expressed genes obviously associated with auxin signaling were partly cultivar-specific and quite different from analogous spectrum in Arabidopsis. Most of the noncanonical pathways found in Arabidopsis appeared to have low probability in potato. This was equally true for all cultivars used irrespective of their ploidy. Thus, some important features of the (noncanonical) auxin signaling pathways may be variable and species-specific. Full article
Show Figures

Figure 1

12 pages, 5726 KiB  
Article
Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species
by Jinliao Chen, Fei Wang, Zhuang Zhao, Minghe Li, Zhongjian Liu and Donghui Peng
Int. J. Mol. Sci. 2023, 24(13), 11167; https://doi.org/10.3390/ijms241311167 - 6 Jul 2023
Cited by 7 | Viewed by 1492
Abstract
Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of Paraphalaenopsis, which limits our studies of this genus. In this study, we reported the chloroplast [...] Read more.
Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of Paraphalaenopsis, which limits our studies of this genus. In this study, we reported the chloroplast genomes of three species of Paraphalaenopsis (P. labukensis, P. denevel, and P. laycockii ‘Semi-alba’) and performed comprehensive comparative analysis. These three chloroplast genomes showed a typical quadripartile structure. Their lengths ranged from 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence in the three chloroplast genomes. In addition, six hypervariable regions were identified (psbM-trnDGUC, psbB, ccsA, trnKUUU, trnSGCU-trnGUCC, rps16-trnQUUG) that can be used as DNA molecular markers. Phylogenetic relationships were determined using the chloroplast genomes of 28 species from 12 genera of Aeridinae. Results suggested that Paraphalaenopsis was a clade of Aeridinae that was sister to the Holcoglossum-Vanda clade, with 100% bootstrap support within Aeridinae. The findings of this study provided the foundation for future studies on the phylogenetic analysis of Aeridinae. Full article
Show Figures

Figure 1

21 pages, 4174 KiB  
Article
Transcriptome Screening of Long Noncoding RNAs and Their Target Protein-Coding Genes Unmasks a Dynamic Portrait of Seed Coat Coloration Associated with Anthocyanins in Tibetan Hulless Barley
by Kaifeng Zheng, Xiaozhuo Wu, Xiuhua Xue, Wanjie Li, Zitao Wang, Jinyuan Chen, Yanfen Zhang, Feng Qiao, Heping Zhao, Fanfan Zhang and Shengcheng Han
Int. J. Mol. Sci. 2023, 24(13), 10587; https://doi.org/10.3390/ijms241310587 - 24 Jun 2023
Cited by 3 | Viewed by 1344
Abstract
Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding [...] Read more.
Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding genes (PCGs). Here, we conducted a comprehensive bioinformatics analysis to identify a total of 9414 long noncoding RNAs (lncRNAs) in the seed coats of purple and white hulless barley along a developmental gradient. Transcriptome-wide profiles of lncRNAs documented several properties, including GC content fluctuation, uneven length, a diverse range of exon numbers, and a wide variety of transcript classifications. We found that certain lncRNAs in hulless barley possess detectable sequence conservation with Hordeum vulgare and other monocots. Furthermore, both differentially expressed lncRNAs (DElncRNAs) and PCGs (DEPCGs) were concentrated in the later seed development stages. On the one hand, DElncRNAs could potentially cis-regulate DEPCGs associated with multiple metabolic pathways, including flavonoid and anthocyanin biosynthesis in the late milk and soft dough stages. On the other hand, there was an opportunity for trans-regulated lncRNAs in the color-forming module to affect seed coat color by upregulating PCGs in the anthocyanin pathway. In addition, the interweaving of hulless barley lncRNAs and diverse TFs may function in seed coat coloration. Notably, we depicted a dynamic portrait of the anthocyanin synthesis pathway containing hulless barley lncRNAs. Therefore, this work provides valuable gene resources and more insights into the molecular mechanisms underlying anthocyanin accumulation in hulless barley from the perspective of lncRNAs, which facilitate the development of molecular design breeding in crops. Full article
Show Figures

Figure 1

15 pages, 2624 KiB  
Article
Exploring Redox Modulation of Plant UDP-Glucose Pyrophosphorylase
by Daniel Decker, Juliette Aubert, Malgorzata Wilczynska and Leszek A. Kleczkowski
Int. J. Mol. Sci. 2023, 24(10), 8914; https://doi.org/10.3390/ijms24108914 - 17 May 2023
Cited by 1 | Viewed by 1657
Abstract
UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro [...] Read more.
UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro through oxidation by hydrogen peroxide or oxidized glutathione (GSSG) and through reduction by dithiothreitol or glutathione. Generally, while oxidative treatment decreased UGPase activity, a subsequent reduction restored the activity. The oxidized enzyme had increased Km values with substrates, especially pyrophosphate. The increased Km values were also observed, regardless of redox status, for UGPase cysteine mutants (Cys102Ser and Cys99Ser for sugarcane and barley UGPases, respectively). However, activities and substrate affinities (Kms) of sugarcane Cys102Ser mutant, but not barley Cys99Ser, were still prone to redox modulation. The data suggest that plant UGPase is subject to redox control primarily via changes in the redox status of a single cysteine. Other cysteines may also, to some extent, contribute to UGPase redox status, as seen for sugarcane enzymes. The results are discussed with respect to earlier reported details of redox modulation of eukaryotic UGPases and regarding the structure/function properties of these proteins. Full article
Show Figures

Figure 1

22 pages, 4340 KiB  
Article
Comparison and Characterization of Phenotypic and Genomic Mutations Induced by a Carbon-Ion Beam and Gamma-ray Irradiation in Soybean (Glycine max (L.) Merr.)
by Zhuo Feng, Yan Du, Jingmin Chen, Xia Chen, Weibin Ren, Lulu Wang and Libin Zhou
Int. J. Mol. Sci. 2023, 24(10), 8825; https://doi.org/10.3390/ijms24108825 - 16 May 2023
Cited by 2 | Viewed by 1564
Abstract
Soybean (Glycine max (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to [...] Read more.
Soybean (Glycine max (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to be highly efficient with high linear energy transfer (LET), and gamma rays have also been widely used for mutation breeding. However, systematic knowledge of the mutagenic effects of these two mutagens during development and on phenotypic and genomic mutations has not yet been elucidated in soybean. To this end, dry seeds of Williams 82 soybean were irradiated with a carbon-ion beam and gamma rays. The biological effects of the M1 generation included changes in survival rate, yield and fertility. Compared with gamma rays, the relative biological effectiveness (RBE) of the carbon-ion beams was between 2.5 and 3.0. Furthermore, the optimal dose for soybean was determined to be 101 Gy to 115 Gy when using the carbon-ion beam, and it was 263 Gy to 343 Gy when using gamma rays. A total of 325 screened mutant families were detected from out of 2000 M2 families using the carbon-ion beam, and 336 screened mutant families were found using gamma rays. Regarding the screened phenotypic M2 mutations, the proportion of low-frequency phenotypic mutations was 23.4% when using a carbon ion beam, and the proportion was 9.8% when using gamma rays. Low-frequency phenotypic mutations were easily obtained with the carbon-ion beam. After screening the mutations from the M2 generation, their stability was verified, and the genome mutation spectrum of M3 was systemically profiled. A variety of mutations, including single-base substitutions (SBSs), insertion–deletion mutations (INDELs), multinucleotide variants (MNVs) and structural variants (SVs) were detected with both carbon-ion beam irradiation and gamma-ray irradiation. Overall, 1988 homozygous mutations and 9695 homozygous + heterozygous genotype mutations were detected when using the carbon-ion beam. Additionally, 5279 homozygous mutations and 14,243 homozygous + heterozygous genotype mutations were detected when using gamma rays. The carbon-ion beam, which resulted in low levels of background mutations, has the potential to alleviate the problems caused by linkage drag in soybean mutation breeding. Regarding the genomic mutations, when using the carbon-ion beam, the proportion of homozygous-genotype SVs was 0.45%, and that of homozygous + heterozygous-genotype SVs was 6.27%; meanwhile, the proportions were 0.04% and 4.04% when using gamma rays. A higher proportion of SVs were detected when using the carbon ion beam. The gene effects of missense mutations were greater under carbon-ion beam irradiation, and the gene effects of nonsense mutations were greater under gamma-ray irradiation, which meant that the changes in the amino acid sequences were different between the carbon-ion beam and gamma rays. Taken together, our results demonstrate that both carbon-ion beam and gamma rays are effective techniques for rapid mutation breeding in soybean. If one would like to obtain mutations with a low-frequency phenotype, low levels of background genomic mutations and mutations with a higher proportion of SVs, carbon-ion beams are the best choice. Full article
Show Figures

Figure 1

13 pages, 4375 KiB  
Article
Genome-Wide Identification and Analysis of OsSPXs Revealed Its Genetic Influence on Cold Tolerance of Dongxiang Wild Rice (DXWR)
by Cheng Huang, Jilin Wang, Dianwen Wang, Jingjing Chang, Hongping Chen, Dazhou Chen, Wei Deng and Chunjie Tian
Int. J. Mol. Sci. 2023, 24(10), 8755; https://doi.org/10.3390/ijms24108755 - 15 May 2023
Viewed by 1460
Abstract
SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential [...] Read more.
SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential functions of other SPX genes in cold stress are unknown. Therefore, in this study, we identified six OsSPXs from the whole genome of DXWR. The phylogeny of OsSPXs has a strong correlation with its motif. Transcriptome data analysis showed that OsSPXs were highly sensitive to cold stress, and real-time PCR verified that the levels of OsSPX1, OsSPX2, OsSPX4, and OsSPX6 in cold-tolerant materials (DXWR) during cold treatment were higher than that of cold-sensitive rice (GZX49). The promoter region of DXWR OsSPXs contains a large number of cis-acting elements related to abiotic stress tolerance and plant hormone response. At the same time, these genes have expression patterns that are highly similar to cold-tolerance genes. This study provides useful information about OsSPXs, which is helpful for the gene-function research of DXWR and genetic improvements during breeding. Full article
Show Figures

Figure 1

12 pages, 752 KiB  
Review
Cross-Kingdom Regulation of Plant-Derived miRNAs in Modulating Insect Development
by Xuepeng Chi, Zhe Wang, Ying Wang, Zhenguo Liu, Hongfang Wang and Baohua Xu
Int. J. Mol. Sci. 2023, 24(9), 7978; https://doi.org/10.3390/ijms24097978 - 28 Apr 2023
Cited by 4 | Viewed by 1896
Abstract
MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial regulatory factors in plants and animals at the post-transcriptional level. These tiny molecules suppress gene expression by complementary oligonucleotide binding to sites in the target messenger. Recently, the discovery of plant-derived miRNAs with [...] Read more.
MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial regulatory factors in plants and animals at the post-transcriptional level. These tiny molecules suppress gene expression by complementary oligonucleotide binding to sites in the target messenger. Recently, the discovery of plant-derived miRNAs with cross-kingdom abilities to regulate gene expression in insects has promoted exciting discussion, although some controversies exist regarding the modulation of insect development by plant-derived miRNAs. Here, we review current knowledge about the mechanisms of miRNA biogenesis, the roles of miRNAs in coevolution between insects and plants, the regulation of insect development by plant-derived miRNAs, the cross-kingdom transport mechanisms of plant-derived miRNAs, and cross-kingdom regulation. In addition, the controversy regarding the modulation of insect development by plant-derived miRNAs also was discussed. Our review provides new insights for understanding complex plant–insect interactions and discovering new strategies for pest management and even crop genetic improvement. Full article
Show Figures

Figure 1

23 pages, 819 KiB  
Review
From Transgenesis to Genome Editing in Crop Improvement: Applications, Marketing, and Legal Issues
by Daniela Marone, Anna Maria Mastrangelo and Grazia Maria Borrelli
Int. J. Mol. Sci. 2023, 24(8), 7122; https://doi.org/10.3390/ijms24087122 - 12 Apr 2023
Cited by 4 | Viewed by 4704
Abstract
The biotechnological approaches of transgenesis and the more recent eco-friendly new breeding techniques (NBTs), in particular, genome editing, offer useful strategies for genetic improvement of crops, and therefore, recently, they have been receiving increasingly more attention. The number of traits improved through transgenesis [...] Read more.
The biotechnological approaches of transgenesis and the more recent eco-friendly new breeding techniques (NBTs), in particular, genome editing, offer useful strategies for genetic improvement of crops, and therefore, recently, they have been receiving increasingly more attention. The number of traits improved through transgenesis and genome editing technologies is growing, ranging from resistance to herbicides and insects to traits capable of coping with human population growth and climate change, such as nutritional quality or resistance to climatic stress and diseases. Research on both technologies has reached an advanced stage of development and, for many biotech crops, phenotypic evaluations in the open field are already underway. In addition, many approvals regarding main crops have been granted. Over time, there has been an increase in the areas cultivated with crops that have been improved through both approaches, but their use in various countries has been limited by legislative restrictions according to the different regulations applied which affect their cultivation, marketing, and use in human and animal nutrition. In the absence of specific legislation, there is an on-going public debate with favorable and unfavorable positions. This review offers an updated and in-depth discussion on these issues. Full article
Show Figures

Figure 1

29 pages, 1980 KiB  
Review
Hairy Root Cultures as a Source of Phenolic Antioxidants: Simple Phenolics, Phenolic Acids, Phenylethanoids, and Hydroxycinnamates
by Janusz Malarz, Yulia V. Yudina and Anna Stojakowska
Int. J. Mol. Sci. 2023, 24(8), 6920; https://doi.org/10.3390/ijms24086920 - 7 Apr 2023
Cited by 7 | Viewed by 2493
Abstract
Plant-derived antioxidants are intrinsic components of human diet and factors implicated in tolerance mechanisms against environmental stresses in both plants and humans. They are being used as food preservatives and additives or ingredients of cosmetics. For nearly forty years, Rhizobium rhizogenes-transformed roots [...] Read more.
Plant-derived antioxidants are intrinsic components of human diet and factors implicated in tolerance mechanisms against environmental stresses in both plants and humans. They are being used as food preservatives and additives or ingredients of cosmetics. For nearly forty years, Rhizobium rhizogenes-transformed roots (hairy roots) have been studied in respect to their usability as producers of plant specialized metabolites of different, primarily medical applications. Moreover, the hairy root cultures have proven their value as a tool in crop plant improvement and in plant secondary metabolism investigations. Though cultivated plants remain a major source of plant polyphenolics of economic importance, the decline in biodiversity caused by climate changes and overexploitation of natural resources may increase the interest in hairy roots as a productive and renewable source of biologically active compounds. The present review examines hairy roots as efficient producers of simple phenolics, phenylethanoids, and hydroxycinnamates of plant origin and summarizes efforts to maximize the product yield. Attempts to use Rhizobium rhizogenes-mediated genetic transformation for inducing enhanced production of the plant phenolics/polyphenolics in crop plants are also mentioned. Full article
Show Figures

Graphical abstract

20 pages, 10614 KiB  
Article
Metabolic Composition and Quality Traits of Polygonatum cyrtonema Hua from Different Germplasms and Age Sections Based on Widely Targeted Metabolomics Analysis
by Qingshuang Wang, Jingjie Ban, Roudi Cai, Xueying Zhang, Chunwang Lai, Yan Chen, Xiaoli Li, Cuirong Chen, Yukun Chen, Zihao Zhang, Zhongxiong Lai and Yuling Lin
Int. J. Mol. Sci. 2023, 24(7), 6077; https://doi.org/10.3390/ijms24076077 - 23 Mar 2023
Viewed by 1417
Abstract
Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values [...] Read more.
Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values of rhizomes, the metabolic composition and quality traits of rhizomes from different germplasms and age sections of P. cyrtonema were analysed by widely targeted metabolomics, and the molecular mechanism of triacylglycerol synthesis was explored. The results showed that the different germplasms and age sections of P. cyrtonema were rich in different nutritional and medicinal components. Of these, the broad-leaved green stem (GK) germplasm is rich in polysaccharides, alkaloids, and lipids; the pointed-leaved green stem (JL) germplasm is rich in flavonoids, steroids, and amino acids, while the pointed-leaved purple stem (JZ) germplasm contains more phenolic acids. The one-year (AT) age section is rich in polysaccharides, steroids, organic acids, and lipids; the three years (CT) age section contains more flavonoids, alkaloids, and amino acid metabolites. Lipids were significantly enriched in the broad-leaved green stem germplasm and the one-year age section. Interestingly, the highest accumulation of triacylglycerols, an important component of lipids, was also found in the GK germplasm and the AT age section. Nineteen, 14, and 13 members of the glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidic acid acyltransferase (LPAT), and diacylglycerol acyltransferase (DGAT) gene families, respectively, involved in triacylglycerol synthesis were also identified. The quantitative real-time PCR (qRT-PCR) results further suggested that the differentially expressed PcDGAT1, PcDGAT2.4, PcGPAT9.1, PcLPAT2.9, and PcLPAT4.3 genes may play important roles in triacylglycerol synthesis in P. cyrtonema. Therefore, this study provides a new theoretical reference for product development and the breeding of new varieties of Polygonatum species. Full article
Show Figures

Graphical abstract

13 pages, 2100 KiB  
Review
“B” Regulatory Subunits of PP2A: Their Roles in Plant Development and Stress Reactions
by Csaba Máthé, Csongor Freytag, Adrienn Kelemen, Márta M-Hamvas and Tamás Garda
Int. J. Mol. Sci. 2023, 24(6), 5147; https://doi.org/10.3390/ijms24065147 - 7 Mar 2023
Cited by 4 | Viewed by 1725
Abstract
Protein phosphatase PP2A is an enzyme complex consisting of C (catalytic), A (scaffold) and B (regulatory) subunits. B subunits are a large family of proteins that regulate activity, substrate specificity and subcellular localization of the holoenzyme. Knowledge on the molecular functions of PP2A [...] Read more.
Protein phosphatase PP2A is an enzyme complex consisting of C (catalytic), A (scaffold) and B (regulatory) subunits. B subunits are a large family of proteins that regulate activity, substrate specificity and subcellular localization of the holoenzyme. Knowledge on the molecular functions of PP2A in plants is less than for protein kinases, but it is rapidly increasing. B subunits are responsible for the large diversity of PP2A functioning. This paper intends to give a survey on their multiple regulatory mechanisms. Firstly, we give a short description on our current knowledge in terms of “B”-mediated regulation of metabolic pathways. Next, we present their subcellular localizations, which extend from the nucleus to the cytosol and membrane compartments. The next sections show how B subunits regulate cellular processes from mitotic division to signal transduction pathways, including hormone signaling, and then the emerging evidence for their regulatory (mostly modulatory) roles in both abiotic and biotic stress responses in plants. Knowledge on these issues should be increased in the near future, since it contributes to a better understanding of how plant cells work, it may have agricultural applications, and it may have new insights into how vascular plants including crops face diverse environmental challenges. Full article
Show Figures

Figure 1

14 pages, 7902 KiB  
Article
Genome-Wide Association Analysis of Fruit Shape-Related Traits in Areca catechu
by Hao Ding, Guangzhen Zhou, Long Zhao, Xinyu Li, Yicheng Wang, Chengcai Xia, Zhiqiang Xia and Yinglang Wan
Int. J. Mol. Sci. 2023, 24(5), 4686; https://doi.org/10.3390/ijms24054686 - 28 Feb 2023
Cited by 2 | Viewed by 1922
Abstract
The areca palm (Areca catechu L.) is one of the most economically important palm trees in tropical areas. To inform areca breeding programs, it is critical to characterize the genetic bases of the mechanisms that regulate areca fruit shape and to identify [...] Read more.
The areca palm (Areca catechu L.) is one of the most economically important palm trees in tropical areas. To inform areca breeding programs, it is critical to characterize the genetic bases of the mechanisms that regulate areca fruit shape and to identify candidate genes related to fruit-shape traits. However, few previous studies have mined candidate genes associated with areca fruit shape. Here, the fruits produced by 137 areca germplasms were divided into three categories (spherical, oval, and columnar) based on the fruit shape index. A total of 45,094 high-quality single-nucleotide polymorphisms (SNPs) were identified across the 137 areca cultivars. Phylogenetic analysis clustered the areca cultivars into four subgroups. A genome-wide association study that used a mixed linear model identified the 200 loci that were the most significantly associated with fruit-shape traits in the germplasms. In addition, 86 candidate genes associated with areca fruit-shape traits were further mined. Among the proteins encoded by these candidate genes were UDP-glucosyltransferase 85A2, the ABA-responsive element binding factor GBF4, E3 ubiquitin-protein ligase SIAH1, and LRR receptor-like serine/threonine-protein kinase ERECTA. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the gene that encoded UDP-glycosyltransferase, UGT85A2, was significantly upregulated in columnar fruits as compared to spherical and oval fruits. The identification of molecular markers that are closely related to fruit-shape traits not only provides genetic data for areca breeding, but it also provides new insights into the shape formation mechanisms of drupes. Full article
Show Figures

Figure 1

13 pages, 1075 KiB  
Review
Crucial Abiotic Stress Regulatory Network of NF-Y Transcription Factor in Plants
by Han Zhang, Shujing Liu, Tianmeng Ren, Mengxue Niu, Xiao Liu, Chao Liu, Houling Wang, Weilun Yin and Xinli Xia
Int. J. Mol. Sci. 2023, 24(5), 4426; https://doi.org/10.3390/ijms24054426 - 23 Feb 2023
Cited by 13 | Viewed by 2768
Abstract
Nuclear Factor-Y (NF-Y), composed of three subunits NF-YA, NF-YB and NF-YC, exists in most of the eukaryotes and is relatively conservative in evolution. As compared to animals and fungi, the number of NF-Y subunits has significantly expanded in higher plants. The NF-Y complex [...] Read more.
Nuclear Factor-Y (NF-Y), composed of three subunits NF-YA, NF-YB and NF-YC, exists in most of the eukaryotes and is relatively conservative in evolution. As compared to animals and fungi, the number of NF-Y subunits has significantly expanded in higher plants. The NF-Y complex regulates the expression of target genes by directly binding the promoter CCAAT box or by physical interaction and mediating the binding of a transcriptional activator or inhibitor. NF-Y plays an important role at various stages of plant growth and development, especially in response to stress, which attracted many researchers to explore. Herein, we have reviewed the structural characteristics and mechanism of function of NF-Y subunits, summarized the latest research on NF-Y involved in the response to abiotic stresses, including drought, salt, nutrient and temperature, and elaborated the critical role of NF-Y in these different abiotic stresses. Based on the summary above, we have prospected the potential research on NF-Y in response to plant abiotic stresses and discussed the difficulties that may be faced in order to provide a reference for the in-depth analysis of the function of NF-Y transcription factors and an in-depth study of plant responses to abiotic stress. Full article
Show Figures

Figure 1

16 pages, 2542 KiB  
Article
Small Cellular Particles from European Spruce Needle Homogenate
by Marko Jeran, Anna Romolo, Vesna Spasovski, Matej Hočevar, Urban Novak, Roman Štukelj, Vid Šuštar, Matic Kisovec, Apolonija Bedina Zavec, Ksenija Kogej, Aleš Iglič, Polonca Trebše and Veronika Kralj-Iglič
Int. J. Mol. Sci. 2023, 24(5), 4349; https://doi.org/10.3390/ijms24054349 - 22 Feb 2023
Cited by 1 | Viewed by 1821
Abstract
Small cellular particles (SCPs) are being considered for their role in cell-to-cell communication. We harvested and characterized SCPs from spruce needle homogenate. SCPs were isolated by differential ultracentrifugation. They were imaged by scanning electron microscope (SEM) and cryogenic transmission electron microscope (cryo TEM), [...] Read more.
Small cellular particles (SCPs) are being considered for their role in cell-to-cell communication. We harvested and characterized SCPs from spruce needle homogenate. SCPs were isolated by differential ultracentrifugation. They were imaged by scanning electron microscope (SEM) and cryogenic transmission electron microscope (cryo TEM), assessed for their number density and hydrodynamic diameter by interferometric light microscopy (ILM) and flow cytometry (FCM), total phenolic content (TPC) by UV-vis spectroscopy, and terpene content by gas chromatography-mass spectrometry (GC-MS). The supernatant after ultracentrifugation at 50,000× g contained bilayer-enclosed vesicles whereas in the isolate we observed small particles of other types and only a few vesicles. The number density of cell-sized particles (CSPs) (larger than 2 μm) and meso-sized particles (MSPs) (cca 400 nm–2 µm) was about four orders of magnitude lower than the number density of SCPs (sized below 500 nm). The average hydrodynamic diameter of SCPs measured in 10,029 SCPs was 161 ± 133 nm. TCP decreased considerably due to 5-day aging. Volatile terpenoid content was found in the pellet after 300× g. The above results indicate that spruce needle homogenate is a source of vesicles to be explored for potential delivery use. Full article
Show Figures

Figure 1

17 pages, 345 KiB  
Review
Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective
by Peiyun Lv, Jinlu Wan, Chunting Zhang, Aiman Hina, G M Al Amin, Naheeda Begum and Tuanjie Zhao
Int. J. Mol. Sci. 2023, 24(4), 4187; https://doi.org/10.3390/ijms24044187 - 20 Feb 2023
Cited by 9 | Viewed by 2992
Abstract
Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, [...] Read more.
Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies. Full article
17 pages, 5205 KiB  
Article
Evolutionary Analysis of Respiratory Burst Oxidase Homolog (RBOH) Genes in Plants and Characterization of ZmRBOHs
by Haiyang Zhang, Xu Wang, An Yan, Jie Deng, Yanping Xie, Shiyuan Liu, Debin Liu, Lin He, Jianfeng Weng and Jingyu Xu
Int. J. Mol. Sci. 2023, 24(4), 3858; https://doi.org/10.3390/ijms24043858 - 14 Feb 2023
Cited by 9 | Viewed by 2435
Abstract
The respiratory burst oxidase homolog (RBOH), as the key producer of reactive oxygen species (ROS), plays an essential role in plant development. In this study, a bioinformatic analysis was performed on 22 plant species, and 181 RBOH homologues were identified. A typical RBOH [...] Read more.
The respiratory burst oxidase homolog (RBOH), as the key producer of reactive oxygen species (ROS), plays an essential role in plant development. In this study, a bioinformatic analysis was performed on 22 plant species, and 181 RBOH homologues were identified. A typical RBOH family was identified only in terrestrial plants, and the number of RBOHs increased from non-angiosperms to angiosperms. Whole genome duplication (WGD)/segmental duplication played a key role in RBOH gene family expansion. Amino acid numbers of 181 RBOHs ranged from 98 to 1461, and the encoded proteins had molecular weights from 11.1 to 163.6 kDa, respectively. All plant RBOHs contained a conserved NADPH_Ox domain, while some of them lacked the FAD_binding_8 domain. Plant RBOHs were classified into five main subgroups by phylogenetic analysis. Most RBOH members in the same subgroup showed conservation in both motif distribution and gene structure composition. Fifteen ZmRBOHs were identified in maize genome and were positioned in eight maize chromosomes. A total of three pairs of orthologous genes were found in maize, including ZmRBOH6/ZmRBOH8, ZmRBOH4/ZmRBOH10 and ZmRBOH15/ZmRBOH2. A Ka/Ks calculation confirmed that purifying selection was the main driving force in their evolution. ZmRBOHs had typical conserved domains and similar protein structures. cis-element analyses together with the expression profiles of the ZmRBOH genes in various tissues and stages of development suggested that ZmRBOH was involved in distinct biological processes and stress responses. Based on the RNA-Seq data and qRT-PCR analysis, the transcriptional response of ZmRBOH genes was examined under various abiotic stresses, and most of ZmRBOH genes were up-regulated by cold stress. These findings provide valuable information for further revealing the biological roles of ZmRBOH genes in plant development and abiotic stress responses. Full article
Show Figures

Figure 1

14 pages, 3629 KiB  
Article
Transcription Factor SiDi19-3 Enhances Salt Tolerance of Foxtail Millet and Arabidopsis
by Shenghui Xiao, Yiman Wan, Shiming Guo, Jiayin Fan, Qing Lin, Chengchao Zheng and Changai Wu
Int. J. Mol. Sci. 2023, 24(3), 2592; https://doi.org/10.3390/ijms24032592 - 30 Jan 2023
Cited by 3 | Viewed by 1664
Abstract
Salt stress is an important limiting factor of crop production. Foxtail millet (Setaria italica L.) is an important model crop for studying tolerance to various abiotic stressors. Therefore, examining the response of foxtail millet to salt stress at the molecular level is [...] Read more.
Salt stress is an important limiting factor of crop production. Foxtail millet (Setaria italica L.) is an important model crop for studying tolerance to various abiotic stressors. Therefore, examining the response of foxtail millet to salt stress at the molecular level is critical. Herein, we discovered that SiDi19-3 interacts with SiPLATZ12 to control salt tolerance in transgenic Arabidopsis and foxtail millet seedlings. SiDi19-3 overexpression increased the transcript levels of most Na+/H+ antiporter (NHX), salt overly sensitive (SOS), and calcineurin B-like protein (CBL) genes and improved the salt tolerance of foxtail millet and Arabidopsis. Six SiDi19 genes were isolated from foxtail millet. Compared with roots, stems, and leaves, panicles and seeds had higher transcript levels of SiDi19 genes. All of them responded to salt, alkaline, polyethylene glycol, and/or abscisic acid treatments with enhanced expression levels. These findings indicate that SiDi19-3 and other SiDi19 members regulate salt tolerance and other abiotic stress response in foxtail millet. Full article
Show Figures

Figure 1

17 pages, 16457 KiB  
Article
Functional Characterization of Potato UBC13-UEV1s Genes Required for Ubiquitin Lys63 Chain to Polyubiquitination
by Weigang Liu, Xun Tang, Xue Fu, Huanhuan Zhang, Cunlan Zhu, Ning Zhang and Huaijun Si
Int. J. Mol. Sci. 2023, 24(3), 2412; https://doi.org/10.3390/ijms24032412 - 26 Jan 2023
Viewed by 1521
Abstract
Ubiquitin-conjugating enzymes (E2s/UBC) are components of the ubiquitin proteasome system (UPS), and the ubiquitin-conjugating enzyme variant (UEV) is one of E2s (ubiquitin-conjugating enzymes, UBC) subfamily. The UEVs and UBC13 play an auxiliary role in mediating Lys63-linked polyUb chain assembly, which is correlated with [...] Read more.
Ubiquitin-conjugating enzymes (E2s/UBC) are components of the ubiquitin proteasome system (UPS), and the ubiquitin-conjugating enzyme variant (UEV) is one of E2s (ubiquitin-conjugating enzymes, UBC) subfamily. The UEVs and UBC13 play an auxiliary role in mediating Lys63-linked polyUb chain assembly, which is correlated with target protein non-proteolytic functions, such as DNA repair or response to stress. However, the collaborative mechanism of StUBC13 (homologue of AtUBC13) and StUEVs (the UEVs in potato) involved in potato are not fully understood understood. Here, we identified two StUBC13 and seven StUEVs from potato genome. We analyzed protein motif and conserved domain, gene structure, phylogenetic features, cis-acting elements of StUBC13 and StUEVs. Subsequently, we screened StUBC13 partners protein and verified interaction between StUBC13 and StUEVs using yeast two-hybrid, split luciferase complementation (SLC) and bimolecular fluorescence complementation (BiFC) approach. The expression profile and qRT-PCR analysis suggested that StUBC13 and StUEVs gene exhibited a tissue-specific expression and were induced by different stress. Overall, this investigative study provides a comprehensive reference and view for further functional research on StUBC13 and StUEV1s in potato. Full article
Show Figures

Figure 1

15 pages, 5435 KiB  
Article
Genome-Wide Identification of Kiwifruit SGR Family Members and Functional Characterization of SGR2 Protein for Chlorophyll Degradation
by Juan Luo, Muhammad Abid, Yi Zhang, Xinxia Cai, Jing Tu, Puxin Gao, Zupeng Wang and Hongwen Huang
Int. J. Mol. Sci. 2023, 24(3), 1993; https://doi.org/10.3390/ijms24031993 - 19 Jan 2023
Cited by 4 | Viewed by 1773
Abstract
The STAY-GREEN (SGR) proteins play an important role in chlorophyll (Chl) degradation and are closely related to plant photosynthesis. However, the availability of inadequate studies on SGR motivated us to conduct a comprehensive study on the identification and functional dissection of SGR superfamily [...] Read more.
The STAY-GREEN (SGR) proteins play an important role in chlorophyll (Chl) degradation and are closely related to plant photosynthesis. However, the availability of inadequate studies on SGR motivated us to conduct a comprehensive study on the identification and functional dissection of SGR superfamily members in kiwifruit. Here, we identified five SGR genes for each of the kiwifruit species [Actinidia chinensis (Ac) and Actinidia eriantha (Ae)]. The phylogenetic analysis showed that the kiwifruit SGR superfamily members were divided into two subfamilies the SGR subfamily and the SGRL subfamily. The results of transcriptome data and RT-qPCR showed that the expression of the kiwifruit SGRs was closely related to light and plant developmental stages (regulated by plant growth regulators), which were further supported by the presence of light and the plant hormone-responsive cis-regulatory element in the promoter region. The subcellular localization analysis of the AcSGR2 protein confirmed its localization in the chloroplast. The Fv/Fm, SPAD value, and Chl contents were decreased in overexpressed AcSGR2, but varied in different cultivars of A. chinensis. The sequence analysis showed significant differences within AcSGR2 proteins. Our findings provide valuable insights into the characteristics and evolutionary patterns of SGR genes in kiwifruit, and shall assist kiwifruit breeders to enhance cultivar development. Full article
Show Figures

Figure 1

22 pages, 3692 KiB  
Article
Biology of Two-Spotted Spider Mite (Tetranychus urticae): Ultrastructure, Photosynthesis, Guanine Transcriptomics, Carotenoids and Chlorophylls Metabolism, and Decoyinine as a Potential Acaricide
by Ambra S. Parmagnani, Giuseppe Mannino, Carla Brillada, Mara Novero, Luca Dall’Osto and Massimo E. Maffei
Int. J. Mol. Sci. 2023, 24(2), 1715; https://doi.org/10.3390/ijms24021715 - 15 Jan 2023
Cited by 2 | Viewed by 2235
Abstract
Two-Spotted Spider Mites (TSSMs, Tetranychus urticae Koch 1836 (Acari: Tetranychidae)) is one of the most important pests in many crop plants, and their feeding activity is based on sucking leaf cell contents. The purpose of this study was to evaluate the interaction between [...] Read more.
Two-Spotted Spider Mites (TSSMs, Tetranychus urticae Koch 1836 (Acari: Tetranychidae)) is one of the most important pests in many crop plants, and their feeding activity is based on sucking leaf cell contents. The purpose of this study was to evaluate the interaction between TSSMs and their host Lima bean (Phaseolus lunatus) by analyzing the metabolomics of leaf pigments and the transcriptomics of TSSM guanine production. We also used epifluorescence, confocal laser scanning, and transmission electron microscopies to study the morphology and structure of TSSMs and their excreta. Finally, we evaluated the potential photosynthetic ability of TSSMs and the activity and content of Ribulose-1,5-bisphosphate Carboxylase/Oxigenase (RubisCO). We found that TSSMs express several genes involved in guanine production, including Guanosine Monophosphate Synthetase (GMPS) and decoyinine (DCY), a potential inhibitor of GMPS, was found to reduce TSSMs proliferation in infested Lima bean leaves. Despite the presence of intact chloroplasts and chlorophyll in TSSMs, we demonstrate that TSSMs do not retain any photosynthetic activity. Our results show for the first time the transcriptomics of guanine production in TSSMs and provide new insight into the catabolic activity of TSSMs on leaf chlorophyll and carotenoids. Finally, we preliminary demonstrate that DCY has an acaricidal potential against TSSMs. Full article
Show Figures

Graphical abstract

18 pages, 1385 KiB  
Review
Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses
by Zhi-Fang Zuo, Hyo-Yeon Lee and Hong-Gyu Kang
Int. J. Mol. Sci. 2023, 24(2), 1419; https://doi.org/10.3390/ijms24021419 - 11 Jan 2023
Cited by 10 | Viewed by 3086
Abstract
Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed [...] Read more.
Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding. Full article
Show Figures

Figure 1

2022

Jump to: 2024, 2023, 2021, 2020, 2019

19 pages, 4655 KiB  
Article
Accumulation of Anthocyanins in Detached Leaves of Kalanchoë blossfeldiana: Relevance to the Effect of Methyl Jasmonate on This Process
by Marian Saniewski, Joanna Szablińska-Piernik, Agnieszka Marasek-Ciołakowska, Joanna Mitrus, Justyna Góraj-Koniarska, Lesław B. Lahuta, Wiesław Wiczkowski, Kensuke Miyamoto, Junichi Ueda and Marcin Horbowicz
Int. J. Mol. Sci. 2023, 24(1), 626; https://doi.org/10.3390/ijms24010626 - 30 Dec 2022
Cited by 4 | Viewed by 1665
Abstract
Accumulation of anthocyanins in detached leaves and in excised stems of Kalanchoë blossfeldiana kept under natural light conditions in the presence or absence of methyl jasmonate (JA-Me) was investigated. When the abaxial surface of detached leaves was held lower than the adaxial surface [...] Read more.
Accumulation of anthocyanins in detached leaves and in excised stems of Kalanchoë blossfeldiana kept under natural light conditions in the presence or absence of methyl jasmonate (JA-Me) was investigated. When the abaxial surface of detached leaves was held lower than the adaxial surface (the normal or natural position) under natural light conditions, anthocyanins were not accumulated on the abaxial side of the leaves. In contrast, when the adaxial surface of detached leaves was held lower than the abaxial surface (inverted position), anthocyanins were highly accumulated on the abaxial side of the leaves. These phenomena were independent of the growth stage of K. blossfeldiana as well as photoperiod. Application of JA-Me in lanolin paste significantly inhibited anthocyanin accumulation induced on the abaxial side of detached leaves held in an inverted position in a dose-dependent manner. Anthocyanin accumulation in the excised stem in response to natural light was also significantly inhibited by JA-Me in lanolin paste. Possible mechanisms of anthocyanin accumulation on the abaxial side of detached K. blossfeldiana leaves held in an inverted position under natural light conditions and the inhibitory effect of JA-Me on this process are described. The accompanying changes in the content of primary metabolites and histological analyses were also described. Full article
Show Figures

Figure 1

26 pages, 3502 KiB  
Article
A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)
by Julia C. Hooker, Nour Nissan, Doris Luckert, Martin Charette, Gerardo Zapata, François Lefebvre, Ramona M. Mohr, Ketema A. Daba, Thomas D. Warkentin, Mehri Hadinezhad, Brent Barlow, Anfu Hou, Ashkan Golshani, Elroy R. Cober and Bahram Samanfar
Int. J. Mol. Sci. 2023, 24(1), 222; https://doi.org/10.3390/ijms24010222 - 23 Dec 2022
Cited by 2 | Viewed by 2162
Abstract
Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help [...] Read more.
Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018–2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars. Full article
Show Figures

Figure 1

17 pages, 5988 KiB  
Article
Study on ZmRPN10 Regulating Leaf Angle in Maize by RNA-Seq
by Xiangzhuo Ji, Bingbing Jin, Zelong Zhuang, Fangguo Chang, Fang Wang and Yunling Peng
Int. J. Mol. Sci. 2023, 24(1), 189; https://doi.org/10.3390/ijms24010189 - 22 Dec 2022
Cited by 2 | Viewed by 1676
Abstract
Ubiquitin/proteasome-mediated proteolysis (UPP) plays a crucial role in almost all aspects of plant growth and development, proteasome subunit RPN10 mediates ubiquitination substrate recognition in the UPP process. The recognition pathway of ubiquitinated UPP substrate is different in different species, which indicates that the [...] Read more.
Ubiquitin/proteasome-mediated proteolysis (UPP) plays a crucial role in almost all aspects of plant growth and development, proteasome subunit RPN10 mediates ubiquitination substrate recognition in the UPP process. The recognition pathway of ubiquitinated UPP substrate is different in different species, which indicates that the mechanism and function of RPN10 are different in different species. However, the homologous ZmRPN10 in maize has not been studied. In this study, the changing of leaf angle and gene expression in leaves in maize wild-type B73 and mutant rpn10 under exogenous brassinosteroids (BRs) were investigated. The regulation effect of BR on the leaf angle of rpn10 was significantly stronger than that of B73. Transcriptome analysis showed that among the differentially expressed genes, CRE1, A-ARR and SnRK2 were significantly up-regulated, and PP2C, BRI1 AUX/IAA, JAZ and MYC2 were significantly down-regulated. This study revealed the regulation mechanism of ZmRPN10 on maize leaf angle and provided a promising gene resource for maize breeding. Full article
Show Figures

Figure 1

20 pages, 4936 KiB  
Article
GA-Mediated Disruption of RGA/BZR1 Complex Requires HSP90 to Promote Hypocotyl Elongation
by Panagiota Konstantinia Plitsi, Despina Samakovli, Loukia Roka, Aggeliki Rampou, Konstantinos Panagiotopoulos, Konstantinos Koudounas, Ioannis Isaioglou, Kosmas Haralampidis, Stamatis Rigas, Polydefkis Hatzopoulos and Dimitra Milioni
Int. J. Mol. Sci. 2023, 24(1), 88; https://doi.org/10.3390/ijms24010088 - 21 Dec 2022
Cited by 2 | Viewed by 1991
Abstract
Circuitries of signaling pathways integrate distinct hormonal and environmental signals, and influence development in plants. While a crosstalk between brassinosteroid (BR) and gibberellin (GA) signaling pathways has recently been established, little is known about other components engaged in the integration of the two [...] Read more.
Circuitries of signaling pathways integrate distinct hormonal and environmental signals, and influence development in plants. While a crosstalk between brassinosteroid (BR) and gibberellin (GA) signaling pathways has recently been established, little is known about other components engaged in the integration of the two pathways. Here, we provide supporting evidence for the role of HSP90 (HEAT SHOCK PROTEIN 90) in regulating the interplay of the GA and BR signaling pathways to control hypocotyl elongation of etiolated seedlings in Arabidopsis. Both pharmacological and genetic depletion of HSP90 alter the expression of GA biosynthesis and catabolism genes. Major components of the GA pathway, like RGA (REPRESSOR of ga1–3) and GAI (GA-INSENSITIVE) DELLA proteins, have been identified as physically interacting with HSP90. Interestingly, GA-promoted DELLA degradation depends on the ATPase activity of HSP90, and inhibition of HSP90 function stabilizes the DELLA/BZR1 (BRASSINAZOLE-RESISTANT 1) complex, modifying the expression of downstream transcriptional targets. Our results collectively reveal that HSP90, through physical interactions with DELLA proteins and BZR1, modulates DELLA abundance and regulates the expression of BZR1-dependent transcriptional targets to promote plant growth. Full article
Show Figures

Figure 1

17 pages, 2454 KiB  
Review
The Plant Fatty Acyl Reductases
by Xuanhao Zhang, Yi Liu, Asma Ayaz, Huayan Zhao and Shiyou Lü
Int. J. Mol. Sci. 2022, 23(24), 16156; https://doi.org/10.3390/ijms232416156 - 18 Dec 2022
Cited by 8 | Viewed by 2302
Abstract
Fatty acyl reductase (FAR) is a crucial enzyme that catalyzes the NADPH-dependent reduction of fatty acyl-CoA or acyl-ACP substrates to primary fatty alcohols, which in turn acts as intermediate metabolites or metabolic end products to participate in the formation of plant extracellular lipid [...] Read more.
Fatty acyl reductase (FAR) is a crucial enzyme that catalyzes the NADPH-dependent reduction of fatty acyl-CoA or acyl-ACP substrates to primary fatty alcohols, which in turn acts as intermediate metabolites or metabolic end products to participate in the formation of plant extracellular lipid protective barriers (e.g., cuticular wax, sporopollenin, suberin, and taproot wax). FARs are widely present across plant evolution processes and play conserved roles during lipid synthesis. In this review, we provide a comprehensive view of FAR family enzymes, including phylogenetic analysis, conserved structural domains, substrate specificity, subcellular localization, tissue-specific expression patterns, their varied functions in lipid biosynthesis, and the regulation mechanism of FAR activity. Finally, we pose several questions to be addressed, such as the roles of FARs in tryphine, the interactions between transcription factors (TFs) and FARs in various environments, and the identification of post-transcriptional, translational, and post-translational regulators. Full article
Show Figures

Figure 1

27 pages, 1090 KiB  
Review
The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites’ Biosynthesis
by Mohammad Murtaza Alami, Zhen Ouyang, Yipeng Zhang, Shaohua Shu, Guozheng Yang, Zhinan Mei and Xuekui Wang
Int. J. Mol. Sci. 2022, 23(24), 15932; https://doi.org/10.3390/ijms232415932 - 14 Dec 2022
Cited by 16 | Viewed by 4634
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of [...] Read more.
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine. Full article
Show Figures

Figure 1

13 pages, 1258 KiB  
Article
Application of the NanoString nCounter System as an Alternative Method to Investigate Molecular Mechanisms Involved in Host Plant Responses to Plasmodiophora brassicae
by Qinqin Zhou, Leonardo Galindo-González, Sheau-Fang Hwang and Stephen E. Strelkov
Int. J. Mol. Sci. 2022, 23(24), 15581; https://doi.org/10.3390/ijms232415581 - 8 Dec 2022
Viewed by 1994
Abstract
Clubroot, caused by the soilborne pathogen Plasmodiophora brassicae, is an important disease of canola (Brassica napus) and other crucifers. The recent application of RNA sequencing (RNA-seq) technologies to study P. brassicae–host interactions has generated large amounts of gene expression [...] Read more.
Clubroot, caused by the soilborne pathogen Plasmodiophora brassicae, is an important disease of canola (Brassica napus) and other crucifers. The recent application of RNA sequencing (RNA-seq) technologies to study P. brassicae–host interactions has generated large amounts of gene expression data, improving knowledge of the molecular mechanisms of pathogenesis and host resistance. Quantitative PCR (qPCR) analysis has been widely applied to examine the expression of a limited number of genes and to validate the results of RNA-seq studies, but may not be ideal for analyzing larger suites of target genes or increased sample numbers. Moreover, the need for intermediate steps such as cDNA synthesis may introduce variability that could affect the accuracy of the data generated by qPCR. Here, we report the validation of gene expression data from a previous RNA-seq study of clubroot using the NanoString nCounter System, which achieves efficient gene expression quantification in a fast and simple manner. We first confirm the robustness of the NanoString system by comparing the results with those generated by qPCR and RNA-seq and then discuss the importance of some candidate genes for resistance or susceptibility to P. brassicae in the host. The results show that the expression of genes measured using NanoString have a high correlation with the values obtained using the other two technologies, with R > 0.90 and p < 0.01, and the same expression patterns for most genes. The three methods (qPCR, RNA-seq, and NanoString) were also compared in terms of laboratory procedures, time, and cost. We propose that the NanoString nCounter System is a robust, sensitive, highly reproducible, and simple technology for gene expression analysis. NanoString could become a common alternative to qPCR to validate RNA-seq data or to create panels of genes for use as markers of resistance/susceptibility when plants are challenged with different P. brassicae pathotypes. Full article
Show Figures

Figure 1

18 pages, 3032 KiB  
Article
Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia
by Monika Ślipiko, Kamil Myszczyński, Katarzyna Buczkowska, Alina Bączkiewicz and Jakub Sawicki
Int. J. Mol. Sci. 2022, 23(24), 15570; https://doi.org/10.3390/ijms232415570 - 8 Dec 2022
Cited by 8 | Viewed by 1677
Abstract
Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the [...] Read more.
Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be ‘the Holy Grail’; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species. Full article
Show Figures

Figure 1

21 pages, 6679 KiB  
Article
Cross-Talk between Transcriptome Analysis and Dynamic Changes of Carbohydrates Identifies Stage-Specific Genes during the Flower Bud Differentiation Process of Chinese Cherry (Prunus pseudocerasus L.)
by Chunqiong Shang, Xuejiao Cao, Tian Tian, Qiandong Hou, Zhuang Wen, Guang Qiao and Xiaopeng Wen
Int. J. Mol. Sci. 2022, 23(24), 15562; https://doi.org/10.3390/ijms232415562 - 8 Dec 2022
Cited by 3 | Viewed by 1479
Abstract
Flower bud differentiation is crucial to reproductive success in plants. In the present study, RNA-Seq and nutrients quantification were used to identify the stage-specific genes for flower bud differentiation with buds which characterize the marked change during flower bud formation from a widely [...] Read more.
Flower bud differentiation is crucial to reproductive success in plants. In the present study, RNA-Seq and nutrients quantification were used to identify the stage-specific genes for flower bud differentiation with buds which characterize the marked change during flower bud formation from a widely grown Chinese cherry (Prunus pseudocerasus L.) cultivar ‘Manaohong’. A KEGG enrichment analysis revealed that the sugar metabolism pathways dynamically changed. The gradually decreasing trend in the contents of total sugar, soluble sugar and protein implies that the differentiation was an energy-consuming process. Changes in the contents of D-glucose and sorbitol were conformed with the gene expression trends of bglX and SORD, respectively, which at least partially reflects a key role of the two substances in the transition from physiological to morphological differentiation. Further, the WRKY and SBP families were also significantly differentially expressed during the vegetative-to-reproductive transition. In addition, floral meristem identity genes, e.g., AP1, AP3, PI, AGL6, SEP1, LFY, and UFO demonstrate involvement in the specification of the petal and stamen primordia, and FPF1 might promote the onset of morphological differentiation. Conclusively, the available evidence justifies the involvement of sugar metabolism in the flower bud differentiation of Chinese cherry, and the uncovered candidate genes are beneficial to further elucidate flower bud differentiation in cherries. Full article
Show Figures

Figure 1

20 pages, 2689 KiB  
Review
Cis-Regulation by NACs: A Promising Frontier in Wheat Crop Improvement
by Adnan Iqbal, Joanna Bocian, Amir Hameed, Waclaw Orczyk and Anna Nadolska-Orczyk
Int. J. Mol. Sci. 2022, 23(23), 15431; https://doi.org/10.3390/ijms232315431 - 6 Dec 2022
Cited by 6 | Viewed by 2041
Abstract
Crop traits are controlled by multiple genes; however, the complex spatio-temporal transcriptional behavior of genes cannot be fully understood without comprehending the role of transcription factors (TFs) and the underlying mechanisms of the binding interactions of their cis-regulatory elements. NAC belongs to [...] Read more.
Crop traits are controlled by multiple genes; however, the complex spatio-temporal transcriptional behavior of genes cannot be fully understood without comprehending the role of transcription factors (TFs) and the underlying mechanisms of the binding interactions of their cis-regulatory elements. NAC belongs to one of the largest families of plant-specific TFs and has been associated with the regulation of many traits. This review provides insight into the cis-regulation of genes by wheat NACs (TaNACs) for the improvement in yield-related traits, including phytohormonal homeostasis, leaf senescence, seed traits improvement, root modulation, and biotic and abiotic stresses in wheat and other cereals. We also discussed the current potential, knowledge gaps, and prospects of TaNACs. Full article
Show Figures

Figure 1

10 pages, 1316 KiB  
Article
Comprehensive Analysis of Copy Number Variations on Glycoside Hydrolase 45 Genes among Different Bursaphelenchus xylophilus Strains
by Xiaolei Ding, Ruiwen Zhao, Yonglin Dai, Yue Zhang, Sixi Lin and Jianren Ye
Int. J. Mol. Sci. 2022, 23(23), 15323; https://doi.org/10.3390/ijms232315323 - 5 Dec 2022
Cited by 1 | Viewed by 1379
Abstract
Bursaphelenchus xylophilus is considered the most dangerous quarantine pest in China. It causes enormous economic and ecological losses in many countries from Asia and Europe. The glycoside hydrolase 45 gene family has been demonstrated in early studies to contribute to the cell wall [...] Read more.
Bursaphelenchus xylophilus is considered the most dangerous quarantine pest in China. It causes enormous economic and ecological losses in many countries from Asia and Europe. The glycoside hydrolase 45 gene family has been demonstrated in early studies to contribute to the cell wall degradation ability of B. xylophilus during its infection. However, the copy number variation (CNV) of the GH45 gene and its association with B. xylophilus pathogenicity were not fully elucidated. In this study, we found that the GH45 gene with two copies is the most predominant type among 259 B. xylophilus strains collected from China and Japan. Additionally, 18 strains are identified as GH45 genes with a single copy, and only two strains are verified to have three copies. Subsequent expression analysis and inoculation test suggest that the copy numbers of the GH45 gene are correlated with gene expression as well as the B. xylophilus pathogenicity. B. xylophilus strains with more copies of the GH45 gene usually exhibit more abundant expression and cause more severe wilt symptoms on pine trees. The aforementioned results indicated the potential regulatory effects of CNV in B. xylophilus and provided novel information to better understand the molecular pathogenesis of this devastating pest. Full article
Show Figures

Figure 1

19 pages, 4207 KiB  
Article
Enhancing the Expression of the OsF3H Gene in Oryza sativa Leads to the Regulation of Multiple Biosynthetic Pathways and Transcriptomic Changes That Influence Insect Resistance
by Rahmatullah Jan, Sajjad Asaf, Lubna, Saleem Asif, Eun-Gyeong Kim, Yoon-Hee Jang, Nari Kim, Ahmed Al-Harrasi, Gang-Seob Lee and Kyung-Min Kim
Int. J. Mol. Sci. 2022, 23(23), 15308; https://doi.org/10.3390/ijms232315308 - 4 Dec 2022
Cited by 2 | Viewed by 1920
Abstract
The white-backed planthopper (WBPH) is a major pest of rice crops and causes severe loss of yield. We previously developed the WBPH-resistant rice cultivar “OxF3H” by overexpressing the OsF3H gene. Although there was a higher accumulation of the flavonoids kaempferol (Kr) [...] Read more.
The white-backed planthopper (WBPH) is a major pest of rice crops and causes severe loss of yield. We previously developed the WBPH-resistant rice cultivar “OxF3H” by overexpressing the OsF3H gene. Although there was a higher accumulation of the flavonoids kaempferol (Kr) and quercetin (Qu) as well as salicylic acid (SA) in OxF3H transgenic (OsF3H or Trans) plants compared to the wild type (WT), it is still unclear how OsF3H overexpression affects these WBPH resistant-related changes in gene expression in OxF3H plants. In this study, we analyze RNA-seq data from OxF3H and WT at several points (0 h, 3 h, 12 h, and 24 h) after WBPH infection to explain how overall changes in gene expression happen in these two cultivars. RT-qPCR further validated a number of the genes. Results revealed that the highest number of DEGs (4735) between the two genotypes was detected after 24 h of infection. Interestingly, it was found that several of the DEGs between the WT and OsF3H under control conditions were also differentially expressed in OsF3H in response to WBPH infestation. These results indicate that significant differences in gene expression between the “OxF3H” and “WT” exist as the infection time increases. Many of these DEGs were related to oxidoreductase activity, response to stress, salicylic acid biosynthesis, metabolic process, defense response to pathogen, cellular response to toxic substance, and regulation of hormone levels. Moreover, genes involved in salicylic acid (SA) and ethylene (Et) biosynthesis were upregulated in OxF3H plants, while jasmonic acid (JA), brassinosteroid (Br), and abscisic acid (ABA) signaling pathways were found downregulated in OxF3H plants during WBPH infestation. Interestingly, many DEGs related to pathogenesis, such as OsPR1, OsPR1b, OsNPR1, OsNPR3, and OsNPR5, were found to be significantly upregulated in OxF3H plants. Additionally, genes related to the MAPKs pathway and about 30 WRKY genes involved in different pathways were upregulated in OxF3H plants after WBPH infestation. This suggests that overexpression of the OxF3H gene leads to multiple transcriptomic changes and impacts plant hormones and pathogenic-related and secondary-metabolites-related genes, enhancing the plant’s resistance to WBPH infestation. Full article
Show Figures

Figure 1

18 pages, 2639 KiB  
Article
Diacylglycerol Acyltransferase 3(DGAT3) Is Responsible for the Biosynthesis of Unsaturated Fatty Acids in Vegetative Organs of Paeonia rockii
by Longyan Han, Yuhui Zhai, Yumeng Wang, Xiangrui Shi, Yanfeng Xu, Shuguang Gao, Man Zhang, Jianrang Luo and Qingyu Zhang
Int. J. Mol. Sci. 2022, 23(22), 14390; https://doi.org/10.3390/ijms232214390 - 19 Nov 2022
Cited by 4 | Viewed by 2012
Abstract
‘Diacylglycerol acyltransferase (DGAT)’ acts as a key rate-limiting enzyme that catalyzes the final step of the de novo biosynthesis of triacylglycerol (TAG). The study was to characterize the function of the DGAT3 gene in Paeonia rockii, which is known for its accumulation [...] Read more.
‘Diacylglycerol acyltransferase (DGAT)’ acts as a key rate-limiting enzyme that catalyzes the final step of the de novo biosynthesis of triacylglycerol (TAG). The study was to characterize the function of the DGAT3 gene in Paeonia rockii, which is known for its accumulation of high levels of unsaturated fatty acids (UFAs). We identified a DGAT3 gene which encodes a soluble protein that is located within the chloroplasts of P. rockii. Functional complementarity experiments in yeast demonstrated that PrDGAT3 restored TAG synthesis. Linoleic acid (LA, C18:2) and α-linolenic acid (ALA, C18:3) are essential unsaturated fatty acids that cannot be synthesized by the human body. Through the yeast lipotoxicity test, we found that the yeast cell density was largely increased by adding exogenous LA and, especially, ALA to the yeast medium. Further ectopic transient overexpression in Nicotiana benthamiana leaf tissue and stable overexpression in Arabidopsis thaliana indicated that PrDGAT3 significantly enhanced the accumulation of the TAG and UFAs. In contrast, we observed a significant decrease in the total fatty acid content and in several major fatty acids in PrDGAT3-silenced tree peony leaves. Overall, PrDGAT3 is important in catalyzing TAG synthesis, with a substrate preference for UFAs, especially LA and ALA. These results suggest that PrDGAT3 may have practical applications in improving plant lipid nutrition and increasing oil production in plants. Full article
Show Figures

Figure 1