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Molecular World Today and Tomorrow: Recent Trends in Biological Sciences 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 25649

Special Issue Editor

Special Issue Information

Dear Colleagues,

This Special Issue is supervised by Dr. Wajid Zaman and assisted by our Topical Advisory Panel Member Dr. Hakim Manghwar (Chinese Academy of Sciences).

Various molecular techniques based on omics (transcriptomics, proteomics, genomics) and phylogenetics have been applied in biological sciences. Molecular dynamics and approaches evolved over time into various quantitative tools that allow researchers from multiple disciplines to design different studies. The molecular-based techniques can be comprehensive and systematic, as they allow identification, resolve genetic differences, molecular docking, and prediction models of ecological niches and taxonomic ranks. Investigating genomics, proteomics, and phylogenetic techniques utilize a novel class of DNA elements such as microsatellites from mitochondria and chloroplast and retrotransposons, resulting in genetic variations using molecular data. Besides this, the advantages and limitations of molecular approaches have been well studied and acknowledged. The combination of molecular phylogenetic and omics techniques and expression and pathways analysis may greatly increase our capacity to understand and develop new molecular mechanisms and stress responses in biological systems. Furthermore, these techniques offer extensive opportunities for researchers to develop targeted therapy approaches and disease diagnoses using molecular data. It is necessary to evaluate and explore how data from diverse molecular techniques can be applied to different biological studies. The study and applications of molecular approaches hold significant potential for advancing genomics, proteomics, and phylogenetic techniques in biological sciences. 

Dr. Wajid Zaman
Guest Editor

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Keywords

  • molecular techniques
  • phylogenetics
  • transcriptomics
  • proteomics
  • genomics
  • biological sciences
  • gene expression

Published Papers (20 papers)

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16 pages, 2165 KiB  
Article
De Novo Assembly of the Genome of the Sea Urchin Paracentrotus lividus (Lamarck 1816)
Int. J. Mol. Sci. 2024, 25(3), 1685; https://doi.org/10.3390/ijms25031685 - 30 Jan 2024
Viewed by 405
Abstract
The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The [...] Read more.
The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans. Full article
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18 pages, 9861 KiB  
Article
Genome-Wide Analysis of MYB Genes in Primulina eburnea (Hance) and Identification of Members in Response to Drought Stress
Int. J. Mol. Sci. 2024, 25(1), 465; https://doi.org/10.3390/ijms25010465 - 29 Dec 2023
Viewed by 437
Abstract
Due to periodic water deficiency in karst environments, Primulina eburnea experiences sporadic drought stress in its habitat. Despite being one of the largest gene families and functionally diverse in terms of plant growth and development, MYB transcription factors in P. eburnea have not [...] Read more.
Due to periodic water deficiency in karst environments, Primulina eburnea experiences sporadic drought stress in its habitat. Despite being one of the largest gene families and functionally diverse in terms of plant growth and development, MYB transcription factors in P. eburnea have not been studied. Here, a total of 230 MYB genes were identified in P. eburnea, including 67 1R-MYB, 155 R2R3-MYB, six 3R-MYB, and two 4R-MYB genes. The R2R3-type PebMYB genes could be classified into 16 subgroups, while the remaining PebMYB genes (1R-MYB, 3R-MYB, and 4R-MYB genes) were divided into 10 subgroups. Notably, the results of the phylogenetic analysis were further supported by the motif and gene structure analysis, which showed that individuals in the same subgroup had comparable motif and structure organization. Additionally, gene duplication and synteny analyses were performed to better understand the evolution of PebMYB genes, and 291 pairs of segmental duplicated genes were found. Moreover, RNA-seq analysis revealed that the PebMYB genes could be divided into five groups based on their expression characteristics. Furthermore, 11 PebMYB genes that may be involved in drought stress response were identified through comparative analysis with Arabidopsis thaliana. Notably, seven of these genes (PebMYB3, PebMYB13, PebMYB17, PebMYB51, PebMYB142, PebMYB69, and PebMYB95) exhibited significant differences in expression between the control and drought stress treatments, suggesting that they may play important roles in drought stress response. These findings clarified the characteristics of the MYB gene family in P. eburnea, augmenting our comprehension of their potential roles in drought stress adaptation. Full article
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20 pages, 5613 KiB  
Article
Multi-Omics Analysis Reveals Intricate Gene Networks Involved in Female Development in Melon
Int. J. Mol. Sci. 2023, 24(23), 16905; https://doi.org/10.3390/ijms242316905 - 29 Nov 2023
Viewed by 491
Abstract
Sexual differentiation is an important developmental phenomenon in cucurbits that directly affects fruit yield. The natural existence of multiple flower types in melon offers an inclusive structure for studying the molecular basis of sexual differentiation. The current study aimed to identify and characterize [...] Read more.
Sexual differentiation is an important developmental phenomenon in cucurbits that directly affects fruit yield. The natural existence of multiple flower types in melon offers an inclusive structure for studying the molecular basis of sexual differentiation. The current study aimed to identify and characterize the molecular network involved in sex determination and female development in melon. Male and female pools separated by the F2 segregated generation were used for sequencing. The comparative multi-omics data revealed 551 DAPs and 594 DEGs involved in multiple pathways of melon growth and development, and based on functional annotation and enrichment analysis, we summarized four biological process modules, including ethylene biosynthesis, flower organ development, plant hormone signaling, and ubiquitinated protein metabolism, that are related to female development. Furthermore, the detailed analysis of the female developmental regulatory pathway model of ethylene biosynthesis, signal transduction, and target gene regulation identified some important candidates that might have a crucial role in female development. Two CMTs ((cytosine-5)-methyltransferase), one AdoHS (adenosylhomocysteinase), four ACSs (1-aminocyclopropane-1-carboxylic acid synthase), three ACOs (ACC oxidase), two ARFs (auxin response factor), four ARPs (auxin-responsive protein), and six ERFs (Ethylene responsive factor) were identified based on various female developmental regulatory models. Our data offer new and valuable insights into female development and hold the potential to offer a deeper comprehension of sex differentiation mechanisms in melon. Full article
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8 pages, 732 KiB  
Communication
Physical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge
Int. J. Mol. Sci. 2023, 24(20), 15243; https://doi.org/10.3390/ijms242015243 - 17 Oct 2023
Viewed by 979
Abstract
Obtaining sufficient and high-quality genomic DNA from sludge samples is a fundamental issue of feasibility and comparability in genomic studies of microbial diversity. Commercial kits for soil are often used for the extraction of gDNA from sludge samples due to the lack of [...] Read more.
Obtaining sufficient and high-quality genomic DNA from sludge samples is a fundamental issue of feasibility and comparability in genomic studies of microbial diversity. Commercial kits for soil are often used for the extraction of gDNA from sludge samples due to the lack of specific kits. However, the evaluation of the performance of commercial kits for sludge DNA extraction is scarce and optimization of these methods to obtain a high quantity and quality of DNA is necessary, especially for downstream genomic sequencing. Sequential batch reactors (SBRs) loaded with lignocellulosic biomass are used for the synthesis of renewable resources such as levulinic acid (LA), adipic acid (AA), and polyhydroxyalkanoates (PHAs), and the biochemical synthesis of these compounds is conducted through the inoculation of microbes present in the residual activated sludge (AS) obtained from a municipal wastewater treatment plant. To characterize these microbes, the extraction of DNA from residual sewage sludge was conducted with three different commercial kits: Nucleospin® Soil from Macherey-Nagel, DNEasy® PowerSoil® from Qiagen, and E.Z.N.A.® Plant DNA Kit from Omega BIO-TEK. Nevertheless, to obtain the highest load and quality of DNA for next-generation sequencing (NGS) analysis, different pretreatments and different combinations of these pretreatments were used. The pretreatments considered were an ultrasonic bath and a temperature of 80 °C, together and separately with different incubation time periods of 30, 60, and 90 min. The results obtained suggest a significant improvement in the efficiency and quality of DNA extraction with the three commercial extraction kits when used together with the ultrasonic bath and 80 °C for 60 min. Here, we were able to prove that physical pretreatments are a viable alternative to chemical lysis for DNA extraction from complex samples such as sludge. Full article
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21 pages, 5506 KiB  
Article
Crystal Structure of DNA Replication Protein SsbA Complexed with the Anticancer Drug 5-Fluorouracil
Int. J. Mol. Sci. 2023, 24(19), 14899; https://doi.org/10.3390/ijms241914899 - 04 Oct 2023
Viewed by 951
Abstract
Single-stranded DNA-binding proteins (SSBs) play a crucial role in DNA metabolism by binding and stabilizing single-stranded DNA (ssDNA) intermediates. Through their multifaceted roles in DNA replication, recombination, repair, replication restart, and other cellular processes, SSB emerges as a central player in maintaining genomic [...] Read more.
Single-stranded DNA-binding proteins (SSBs) play a crucial role in DNA metabolism by binding and stabilizing single-stranded DNA (ssDNA) intermediates. Through their multifaceted roles in DNA replication, recombination, repair, replication restart, and other cellular processes, SSB emerges as a central player in maintaining genomic integrity. These attributes collectively position SSBs as essential guardians of genomic integrity, establishing interactions with an array of distinct proteins. Unlike Escherichia coli, which contains only one type of SSB, some bacteria have two paralogous SSBs, referred to as SsbA and SsbB. In this study, we identified Staphylococcus aureus SsbA (SaSsbA) as a fresh addition to the roster of the anticancer drug 5-fluorouracil (5-FU) binding proteins, thereby expanding the ambit of the 5-FU interactome to encompass this DNA replication protein. To investigate the binding mode, we solved the complexed crystal structure with 5-FU at 2.3 Å (PDB ID 7YM1). The structure of glycerol-bound SaSsbA was also determined at 1.8 Å (PDB ID 8GW5). The interaction between 5-FU and SaSsbA was found to involve R18, P21, V52, F54, Q78, R80, E94, and V96. Based on the collective results from mutational and structural analyses, it became evident that SaSsbA’s mode of binding with 5-FU diverges from that of SaSsbB. This complexed structure also holds the potential to furnish valuable comprehension regarding how 5-FU might bind to and impede analogous proteins in humans, particularly within cancer-related signaling pathways. Leveraging the information furnished by the glycerol and 5-FU binding sites, the complexed structures of SaSsbA bring to the forefront the potential viability of several interactive residues as potential targets for therapeutic interventions aimed at curtailing SaSsbA activity. Acknowledging the capacity of microbiota to influence the host’s response to 5-FU, there emerges a pressing need for further research to revisit the roles that bacterial and human SSBs play in the realm of anticancer therapy. Full article
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24 pages, 11206 KiB  
Article
Paclitaxel and Caffeine–Taurine, New Colchicine Alternatives for Chromosomes Doubling in Maize Haploid Breeding
Int. J. Mol. Sci. 2023, 24(19), 14659; https://doi.org/10.3390/ijms241914659 - 28 Sep 2023
Viewed by 968
Abstract
The doubled haploid (DH) technology is employed worldwide in various crop-breeding programs, especially maize. Still, restoring tassel fertility is measured as one of the major restrictive factors in producing DH lines. Colchicine, nitrous oxide, oryzalin, and amiprophosmethyl are common chromosome-doubling agents that aid [...] Read more.
The doubled haploid (DH) technology is employed worldwide in various crop-breeding programs, especially maize. Still, restoring tassel fertility is measured as one of the major restrictive factors in producing DH lines. Colchicine, nitrous oxide, oryzalin, and amiprophosmethyl are common chromosome-doubling agents that aid in developing viable diploids (2n) from sterile haploids (n). Although colchicine is the most widely used polyploidy-inducing agent, it is highly toxic to mammals and plants. Therefore, there is a dire need to explore natural, non-toxic, or low-toxic cheaper and accessible substitutes with a higher survival and fertility rate. To the best of our knowledge, the advanced usage of human anticancer drugs “Paclitaxel (PTX)” and “Caffeine–Taurine (CAF–T)” for in vivo maize haploids doubling is being disclosed for the first time. These two antimitotic and antimicrotubular agents (PTX and CAF–T) were assessed under various treatment conditions compared to colchicine. As a result, the maximum actual doubling rates (ADR) for PTX versus colchicine in maize haploid seedlings were 42.1% (400 M, 16 h treatment) versus 31.9% (0.5 mM, 24 h treatment), respectively. In addition, the ADR in maize haploid seeds were CAF–T 20.0% (caffeine 2 g/L + taurine 12 g/L, 16 h), PTX 19.9% (100 μM, 24 h treatment), and colchicine 26.0% (2.0 mM, 8 h treatment). Moreover, the morphological and physiological by-effects in haploid plants by PTX were significantly lower than colchicine. Hence, PTX and CAF–T are better alternatives than the widely used traditional colchicine to improve chromosome-doubling in maize crop. Full article
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18 pages, 4890 KiB  
Article
The Change in Whole-Genome Methylation and Transcriptome Profile under Autophagy Defect and Nitrogen Starvation
Int. J. Mol. Sci. 2023, 24(18), 14047; https://doi.org/10.3390/ijms241814047 - 13 Sep 2023
Viewed by 798
Abstract
Through whole-genome bisulfite sequencing and RNA-seq, we determined the potential impact of autophagy in regulating DNA methylation in Arabidopsis, providing a solid foundation for further understanding the molecular mechanism of autophagy and how plants cope with nitrogen deficiency. A total of 335 [...] Read more.
Through whole-genome bisulfite sequencing and RNA-seq, we determined the potential impact of autophagy in regulating DNA methylation in Arabidopsis, providing a solid foundation for further understanding the molecular mechanism of autophagy and how plants cope with nitrogen deficiency. A total of 335 notable differentially expressed genes (DEGs) were discovered in wild-type Arabidopsis (Col-0-N) and an autophagic mutant cultivated under nitrogen starvation (atg5-1-N). Among these, 142 DEGs were associated with hypomethylated regions (hypo-DMRs) and were upregulated. This suggests a correlation between DNA demethylation and the ability of Arabidopsis to cope with nitrogen deficiency. Examination of the hypo-DMR-linked upregulated DEGs indicated that the expression of MYB101, an ABA pathway regulator, may be regulated by DNA demethylation and the recruitment of transcription factors (TFs; ERF57, ERF105, ERF48, and ERF111), which may contribute to the growth arrest induced by abscisic acid (ABA). Additionally, we found that DNA methylation might impact the biosynthesis of salicylic acid (SA). The promoter region of ATGH3.12 (PBS3), a key enzyme in SA synthesis, was hypomethylated, combined with overexpression of PBS3 and its potential TF AT3G46070, suggesting that autophagy defects may lead to SA-activated senescence, depending on DNA demethylation. These findings suggest that DNA hypomethylation may impact the mechanism by which Arabidopsis autophagy mutants (atg5-1) respond to nitrogen deficiency, specifically in relation to ABA and SA regulation. Our evaluation of hormone levels verified that these two hormones are significantly enriched under nitrogen deficiency in atg5-1-N compared to Col-0-N. Full article
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23 pages, 4548 KiB  
Article
Analyzing the Antinociceptive Effect of Interleukin-31 in Mice
Int. J. Mol. Sci. 2023, 24(14), 11563; https://doi.org/10.3390/ijms241411563 - 17 Jul 2023
Cited by 1 | Viewed by 1075
Abstract
The theory that an itch inhibits pain has been refuted; however, previous research did not investigate this theory for an interleukin-31 (IL-31)-induced itch. Previously, we have found that morphine-induced antinociception was partially reduced in IL-31 receptor A (IL-31RA)-deficient (IL-31RAKI) mice, indicating that IL-31RA [...] Read more.
The theory that an itch inhibits pain has been refuted; however, previous research did not investigate this theory for an interleukin-31 (IL-31)-induced itch. Previously, we have found that morphine-induced antinociception was partially reduced in IL-31 receptor A (IL-31RA)-deficient (IL-31RAKI) mice, indicating that IL-31RA may play an important role in morphine-induced peripheral antinociception. In the present study, we evaluated the effect of IL-31-induced analgesia on a 2,4,6-trinitrochlorobenzene (TNCB)-sensitized mice using a hot-plate test. This test evaluated the antinociceptive activity of morphine and non-steroidal anti-inflammatory drugs (NSAIDs). Repeated pretreatment with IL-31 showed significant antinociceptive action. Furthermore, its combination with morphine, but not with NSAIDs, increased the analgesic action. In contrast, treatment with TNCB and capsaicin decreased antinociception. Moreover, TNCB increased IL-31RA expression in the dorsal root ganglia at 24 h, whereas capsaicin inhibited it. The comparative action of several analgesics on TNCB or capsaicin was evaluated using a hot-plate test, which revealed that the antinociceptive activity was decreased or disappeared in response to capsaicin-induced pain in IL-31RAKI mice. These results indicate that the analgesic action of IL-31 involves the peripheral nervous system, which affects sensory nerves. These results provide a basis for developing novel analgesics using this mechanism. Full article
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19 pages, 2377 KiB  
Article
A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors
Int. J. Mol. Sci. 2023, 24(14), 11515; https://doi.org/10.3390/ijms241411515 - 15 Jul 2023
Viewed by 1322
Abstract
Several molecular mechanisms of thalidomide embryopathy (TE) have been investigated, from anti-angiogenesis to oxidative stress to cereblon binding. Recently, it was discovered that thalidomide and its analogs, named immunomodulatory drugs (IMiDs), induced the degradation of C2H2 transcription factors (TFs). This mechanism might impact [...] Read more.
Several molecular mechanisms of thalidomide embryopathy (TE) have been investigated, from anti-angiogenesis to oxidative stress to cereblon binding. Recently, it was discovered that thalidomide and its analogs, named immunomodulatory drugs (IMiDs), induced the degradation of C2H2 transcription factors (TFs). This mechanism might impact the strict transcriptional regulation of the developing embryo. Hence, this study aims to evaluate the TFs altered by IMiDs, prioritizing the ones associated with embryogenesis through transcriptome and systems biology-allied analyses. This study comprises only the experimental data accessed through bioinformatics databases. First, proteins and genes reported in the literature as altered/affected by the IMiDs were annotated. A protein systems biology network was evaluated. TFs beta-catenin (CTNNB1) and SP1 play more central roles: beta-catenin is an essential protein in the network, while SP1 is a putative C2H2 candidate for IMiD-induced degradation. Separately, the differential expressions of the annotated genes were analyzed through 23 publicly available transcriptomes, presenting 8624 differentially expressed genes (2947 in two or more datasets). Seventeen C2H2 TFs were identified as related to embryonic development but not studied for IMiD exposure; these TFs are potential IMiDs degradation neosubstrates. This is the first study to suggest an integration of IMiD molecular mechanisms through C2H2 TF degradation. Full article
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24 pages, 4692 KiB  
Article
Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation
Int. J. Mol. Sci. 2023, 24(13), 10431; https://doi.org/10.3390/ijms241310431 - 21 Jun 2023
Cited by 1 | Viewed by 1656
Abstract
Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in [...] Read more.
Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms. Full article
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19 pages, 8989 KiB  
Article
Omics Analysis Unveils the Pathway Involved in the Anthocyanin Biosynthesis in Tomato Seedling and Fruits
Int. J. Mol. Sci. 2023, 24(10), 8690; https://doi.org/10.3390/ijms24108690 - 12 May 2023
Cited by 1 | Viewed by 1190
Abstract
The purple tomato variety ‘Indigo Rose’ (InR) is favored due to its bright appearance, abundant anthocyanins and outstanding antioxidant capacity. SlHY5 is associated with anthocyanin biosynthesis in ‘Indigo Rose’ plants. However, residual anthocyanins still present in Slhy5 seedlings and fruit peel indicated there [...] Read more.
The purple tomato variety ‘Indigo Rose’ (InR) is favored due to its bright appearance, abundant anthocyanins and outstanding antioxidant capacity. SlHY5 is associated with anthocyanin biosynthesis in ‘Indigo Rose’ plants. However, residual anthocyanins still present in Slhy5 seedlings and fruit peel indicated there was an anthocyanin induction pathway that is independent of HY5 in plants. The molecular mechanism of anthocyanins formation in ‘Indigo Rose’ and Slhy5 mutants is unclear. In this study, we performed omics analysis to clarify the regulatory network underlying anthocyanin biosynthesis in seedling and fruit peel of ‘Indigo Rose’ and Slhy5 mutant. Results showed that the total amount of anthocyanins in both seedling and fruit of InR was significantly higher than those in the Slhy5 mutant, and most genes associated with anthocyanin biosynthesis exhibited higher expression levels in InR, suggesting that SlHY5 play pivotal roles in flavonoid biosynthesis both in tomato seedlings and fruit. Yeast two-hybrid (Y2H) results revealed that SlBBX24 physically interacts with SlAN2-like and SlAN2, while SlWRKY44 could interact with SlAN11 protein. Unexpectedly, both SlPIF1 and SlPIF3 were found to interact with SlBBX24, SlAN1 and SlJAF13 by yeast two-hybrid assay. Suppression of SlBBX24 by virus-induced gene silencing (VIGS) retarded the purple coloration of the fruit peel, indicating an important role of SlBBX24 in the regulation of anthocyanin accumulation. These results deepen the understanding of purple color formation in tomato seedlings and fruits in an HY5-dependent or independent manner via excavating the genes involved in anthocyanin biosynthesis based on omics analysis. Full article
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14 pages, 11336 KiB  
Article
GmTCP and GmNLP Underlying Nodulation Character in Soybean Depending on Nitrogen
Int. J. Mol. Sci. 2023, 24(9), 7750; https://doi.org/10.3390/ijms24097750 - 24 Apr 2023
Viewed by 1203
Abstract
Soybean is a cereal crop with high protein and oil content which serves as the main source of plant-based protein and oil for human consumption. The symbiotic relationship between legumes and rhizobia contributes significantly to soybean yield and quality, but the underlying molecular [...] Read more.
Soybean is a cereal crop with high protein and oil content which serves as the main source of plant-based protein and oil for human consumption. The symbiotic relationship between legumes and rhizobia contributes significantly to soybean yield and quality, but the underlying molecular mechanisms remain poorly understood, hindering efforts to improve soybean productivity. In this study, we conducted a transcriptome analysis and identified 22 differentially expressed genes (DEGs) from nodule-related quantitative trait loci (QTL) located in chromosomes 12 and 19. Subsequently, we performed functional characterisation and haplotype analysis to identify key candidate genes among the 22 DEGs that are responsive to nitrate. Our findings identified GmTCP (TEOSINTE-BRANCHED1/CYCLOIDEA/PCF) and GmNLP (NIN-LIKE PROTEIN) as the key candidate genes that regulate the soybean nodule phenotype in response to nitrogen concentration. We conducted homologous gene mutant analysis in Arabidopsis thaliana, which revealed that the homologous genes of GmTCP and GmNLP play a vital role in regulating root development in response to nitrogen concentration. We further performed overexpression and gene knockout of GmTCP and GmNLP through hairy root transformation in soybeans and analysed the effects of GmTCP and GmNLP on nodulation under different nitrogen concentrations using transgenic lines. Overexpressing GmTCP and GmNLP resulted in significant differences in soybean hairy root nodulation phenotypes, such as nodule number (NN) and nodule dry weight (NDW), under varying nitrate conditions. Our results demonstrate that GmTCP and GmNLP are involved in regulating soybean nodulation in response to nitrogen concentration, providing new insights into the mechanism of soybean symbiosis establishment underlying different nitrogen concentrations. Full article
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10 pages, 1800 KiB  
Article
First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing
Int. J. Mol. Sci. 2023, 24(8), 7311; https://doi.org/10.3390/ijms24087311 - 15 Apr 2023
Viewed by 1649
Abstract
Root-lesion nematodes (genus Pratylenchus) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to Pratylenchus genus is scarcely available. Here, we report the [...] Read more.
Root-lesion nematodes (genus Pratylenchus) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to Pratylenchus genus is scarcely available. Here, we report the draft genome assembly of Pratylenchus scribneri generated on the PacBio Sequel IIe System using the ultra-low DNA input HiFi sequencing workflow. The final assembly created using 500 nematodes consisted of 276 decontaminated contigs, with an average contig N50 of 1.72 Mb and an assembled draft genome size of 227.24 Mb consisting of 51,146 predicted protein sequences. The benchmarking universal single-copy ortholog (BUSCO) analysis with 3131 nematode BUSCO groups indicated that 65.4% of the BUSCOs were complete, whereas 24.0%, 41.4%, and 1.8% were single-copy, duplicated, and fragmented, respectively, and 32.8% were missing. The outputs from GenomeScope2 and Smudgeplots converged towards a diploid genome for P. scribneri. The data provided here will facilitate future studies on host plant-nematode interactions and crop protection at the molecular level. Full article
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19 pages, 5675 KiB  
Article
Systematical Characterization of the AT-Hook Gene Family in Juglans regia L. and the Functional Analysis of the JrAHL2 in Flower Induction and Hypocotyl Elongation
Int. J. Mol. Sci. 2023, 24(8), 7244; https://doi.org/10.3390/ijms24087244 - 14 Apr 2023
Viewed by 1098
Abstract
AT-hook motif nuclear localization (AHL) proteins play essential roles in various plant biological processes. Yet, a comprehensive understanding of AHL transcription factors in walnut (Juglans regia L.) is missing. In this study, 37 AHL gene family members were first identified in the [...] Read more.
AT-hook motif nuclear localization (AHL) proteins play essential roles in various plant biological processes. Yet, a comprehensive understanding of AHL transcription factors in walnut (Juglans regia L.) is missing. In this study, 37 AHL gene family members were first identified in the walnut genome. Based on the evolutionary analysis, JrAHL genes were grouped into two clades, and their expansion may occur due to segmental duplication. The stress-responsive nature and driving of developmental activities of JrAHL genes were revealed by cis-acting elements and transcriptomic data, respectively. Tissue-specific expression analysis showed that JrAHLs had a profound transcription in flower and shoot tip, JrAHL2 in particular. Subcellular localization showed that JrAHL2 is anchored to the nucleus. Overexpression of JrAHL2 in Arabidopsis adversely affected hypocotyl elongation and delayed flowering. Our study, for the first time, presented a detailed analysis of JrAHL genes in walnut and provided theoretical knowledge for future genetic breeding programs. Full article
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16 pages, 8859 KiB  
Article
Identification and Characterization of PRE Genes in Moso Bamboo (Phyllostachys edulis)
Int. J. Mol. Sci. 2023, 24(8), 6886; https://doi.org/10.3390/ijms24086886 - 07 Apr 2023
Cited by 1 | Viewed by 1182
Abstract
Basic helix–loop–helix (bHLH)/HLH transcription factors are involved in various aspects of the growth and development of plants. Here, we identified four HLH genes, PePRE1-4, in moso bamboo plants that are homologous to Arabidopsis PRE genes. In bamboo seedlings, PePRE1/3 were [...] Read more.
Basic helix–loop–helix (bHLH)/HLH transcription factors are involved in various aspects of the growth and development of plants. Here, we identified four HLH genes, PePRE1-4, in moso bamboo plants that are homologous to Arabidopsis PRE genes. In bamboo seedlings, PePRE1/3 were found to be highly expressed in the internode and lamina joint by using quantitative RT-PCR analysis. In the elongating internode of bamboo shoots, PePRE genes are expressed at higher levels in the basal segment than in the mature top segment. Overexpression of PePREs (PePREs-OX) in Arabidopsis showed longer petioles and hypocotyls, as well as earlier flowering. PePRE1 overexpression restored the phenotype due to the deficiency of AtPRE genes caused by artificial micro-RNA. PePRE1-OX plants showed hypersensitivity to propiconazole treatment compared with the wild type. In addition, PePRE1/3 but not PePRE2/4 proteins accumulated as punctate structures in the cytosol, which was disrupted by the vesicle recycling inhibitor brefeldin A (BFA). PePRE genes have a positive function in the internode elongation of moso bamboo shoots, and overexpression of PePREs genes promotes flowering and growth in Arabidopsis. Our findings provided new insights about the fast-growing mechanism of bamboo shoots and the application of PRE genes from bamboo. Full article
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17 pages, 3748 KiB  
Article
Morphological and Physio-Chemical Responses to PEG-Induced Water Stress in Vanilla planifolia and V. pompona Hybrids
Int. J. Mol. Sci. 2023, 24(5), 4690; https://doi.org/10.3390/ijms24054690 - 28 Feb 2023
Viewed by 1646
Abstract
Vanilla planifolia is an orchid of cultural and economic value. However, its cultivation in many tropical countries is threatened by water stress. In contrast, V. pompona is a species that is tolerant of prolonged periods of drought. Due to the need for plants’ [...] Read more.
Vanilla planifolia is an orchid of cultural and economic value. However, its cultivation in many tropical countries is threatened by water stress. In contrast, V. pompona is a species that is tolerant of prolonged periods of drought. Due to the need for plants’ resistant to water stress, the use of hybrids of these two species is considered. Therefore, the objective of this study was to evaluate the morphological and physio-chemical responses of in vitro vanilla seedlings of the parental genotype V. planifolia, and the hybrids V. planifolia × V. pompona and V. pompona × V. planifolia, which were then exposed over five weeks to polyethylene glycol-induced water stress (−0.49 mPa). Stem and root length, relative growth rate, number of leaves and roots, stomatal conductance, specific leaf area, and leaf water content were determined. Metabolites potentially associated with the response to water stress were identified in leaves, through untargeted and targeted metabolomics. Both hybrids exhibited a smaller decrease in the morphophysiological responses compared to V. planifolia and exhibited an enrichment of metabolites such as carbohydrates, amino acids, purines, phenols, and organic acids. Hybrids of these two species are considered as a potential alternative to the traditional cultivation of vanilla to face drought in a global warming scenario. Full article
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Review

Jump to: Research, Other

31 pages, 2714 KiB  
Review
Mesenchymal Stem Cells and Exosomes: A Novel Therapeutic Approach for Corneal Diseases
Int. J. Mol. Sci. 2023, 24(13), 10917; https://doi.org/10.3390/ijms241310917 - 30 Jun 2023
Cited by 4 | Viewed by 1803
Abstract
The cornea, with its delicate structure, is vulnerable to damage from physical, chemical, and genetic factors. Corneal transplantation, including penetrating and lamellar keratoplasties, can restore the functions of the cornea in cases of severe damage. However, the process of corneal transplantation presents considerable [...] Read more.
The cornea, with its delicate structure, is vulnerable to damage from physical, chemical, and genetic factors. Corneal transplantation, including penetrating and lamellar keratoplasties, can restore the functions of the cornea in cases of severe damage. However, the process of corneal transplantation presents considerable obstacles, including a shortage of available donors, the risk of severe graft rejection, and potentially life-threatening complications. Over the past few decades, mesenchymal stem cell (MSC) therapy has become a novel alternative approach to corneal regeneration. Numerous studies have demonstrated the potential of MSCs to differentiate into different corneal cell types, such as keratocytes, epithelial cells, and endothelial cells. MSCs are considered a suitable candidate for corneal regeneration because of their promising therapeutic perspective and beneficial properties. MSCs compromise unique immunomodulation, anti-angiogenesis, and anti-inflammatory properties and secrete various growth factors, thus promoting corneal reconstruction. These effects in corneal engineering are mediated by MSCs differentiating into different lineages and paracrine action via exosomes. Early studies have proven the roles of MSC-derived exosomes in corneal regeneration by reducing inflammation, inhibiting neovascularization, and angiogenesis, and by promoting cell proliferation. This review highlights the contribution of MSCs and MSC-derived exosomes, their current usage status to overcome corneal disease, and their potential to restore different corneal layers as novel therapeutic agents. It also discusses feasible future possibilities, applications, challenges, and opportunities for future research in this field. Full article
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15 pages, 1680 KiB  
Review
The Role of Increased Expression of Sirtuin 6 in the Prevention of Premature Aging Pathomechanisms
Int. J. Mol. Sci. 2023, 24(11), 9655; https://doi.org/10.3390/ijms24119655 - 02 Jun 2023
Cited by 2 | Viewed by 2634
Abstract
Sirtuins, in mammals, are a group of seven enzymes (SIRT1–SIRT7) involved in the post-translational modification of proteins—they are considered longevity proteins. SIRT6, classified as class IV, is located on the cell nucleus; however, its action is also connected with other regions, e.g., mitochondria [...] Read more.
Sirtuins, in mammals, are a group of seven enzymes (SIRT1–SIRT7) involved in the post-translational modification of proteins—they are considered longevity proteins. SIRT6, classified as class IV, is located on the cell nucleus; however, its action is also connected with other regions, e.g., mitochondria and cytoplasm. It affects many molecular pathways involved in aging: telomere maintenance, DNA repair, inflammatory processes or glycolysis. A literature search for keywords or phrases was carried out in PubMed and further searches were carried out on the ClinicalTrials.gov website. The role of SIRT6 in both premature and chronological aging has been pointed out. SIRT6 is involved in the regulation of homeostasis—an increase in the protein’s activity has been noted in calorie-restriction diets and with significant weight loss, among others. Expression of this protein is also elevated in people who regularly exercise. SIRT6 has been shown to have different effects on inflammation, depending on the cells involved. The protein is considered a factor in phenotypic attachment and the migratory responses of macrophages, thus accelerating the process of wound healing. Furthermore, exogenous substances will affect the expression level of SIRT6: resveratrol, sirtinol, flavonoids, cyanidin, quercetin and others. This study discusses the importance of the role of SIRT6 in aging, metabolic activity, inflammation, the wound healing process and physical activity. Full article
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19 pages, 1945 KiB  
Review
Multi-Faceted Role of Luteolin in Cancer Metastasis: EMT, Angiogenesis, ECM Degradation and Apoptosis
Int. J. Mol. Sci. 2023, 24(10), 8824; https://doi.org/10.3390/ijms24108824 - 16 May 2023
Cited by 8 | Viewed by 1344
Abstract
Luteolin (3′,4′,5,7-tetrahydroxyflavone), a member of the flavonoid family derived from plants and fruits, shows a wide range of biomedical applications. In fact, due to its anti-inflammatory, antioxidant and immunomodulatory activities, Asian medicine has been using luteolin for centuries to treat several human diseases, [...] Read more.
Luteolin (3′,4′,5,7-tetrahydroxyflavone), a member of the flavonoid family derived from plants and fruits, shows a wide range of biomedical applications. In fact, due to its anti-inflammatory, antioxidant and immunomodulatory activities, Asian medicine has been using luteolin for centuries to treat several human diseases, including arthritis, rheumatism, hypertension, neurodegenerative disorders and various infections. Of note, luteolin displays many anti-cancer/anti-metastatic properties. Thus, the purpose of this review consists in highlighting the relevant mechanisms by which luteolin inhibits tumor progression in metastasis, i.e., affecting epithelial-mesenchymal transition (EMT), repressing angiogenesis and lysis of extracellular matrix (ECM), as well as inducing apoptosis. Full article
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Other

Jump to: Research, Review

13 pages, 5074 KiB  
Brief Report
Marine Bacterioplankton Community Dynamics and Potentially Pathogenic Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding
Int. J. Mol. Sci. 2023, 24(17), 13561; https://doi.org/10.3390/ijms241713561 - 01 Sep 2023
Cited by 2 | Viewed by 780
Abstract
Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December [...] Read more.
Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance. Full article
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