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16 pages, 6565 KiB

Open AccessArticle

Endoribonuclease DNE1 Promotes Ethylene Response by Modulating EBF1/2 mRNA Processing in Arabidopsis

by Yan Yan, Hongwei Guo and Wenyang Li

Int. J. Mol. Sci. 2024, 25(4), 2138; https://doi.org/10.3390/ijms25042138 - 10 Feb 2024

Viewed by 857

Abstract

The gaseous phytohormone ethylene plays a crucial role in plant growth, development, and stress responses. In the ethylene signal transduction cascade, the F-box proteins EIN3-BINDING F-BOX 1 (EBF1) and EBF2 are identified as key negative regulators governing ethylene sensitivity. The translation and processing [...] Read more.

The gaseous phytohormone ethylene plays a crucial role in plant growth, development, and stress responses. In the ethylene signal transduction cascade, the F-box proteins EIN3-BINDING F-BOX 1 (EBF1) and EBF2 are identified as key negative regulators governing ethylene sensitivity. The translation and processing of EBF1/2 mRNAs are tightly controlled, and their 3′ untranslated regions (UTRs) are critical in these regulations. However, despite their significance, the exact mechanisms modulating the processing of EBF1/2 mRNAs remain poorly understood. In this work, we identified the gene DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1), which encodes an endoribonuclease and is induced by ethylene treatment, as a positive regulator of ethylene response. The loss of function mutant dne1-2 showed mild ethylene insensitivity, highlighting the importance of DNE1 in ethylene signaling. We also found that DNE1 colocalizes with ETHYLENE INSENSITIVE 2 (EIN2), the core factor manipulating the translation of EBF1/2, and targets the P-body in response to ethylene. Further analysis revealed that DNE1 negatively regulates the abundance of EBF1/2 mRNAs by recognizing and cleaving their 3′UTRs, and it also represses their translation. Moreover, the dne1 mutant displays hypersensitivity to 1,4-dithiothreitol (DTT)-induced ER stress and oxidative stress, indicating the function of DNE1 in stress responses. This study sheds light on the essential role of DNE1 as a modulator of ethylene signaling through regulation of EBF1/2 mRNA processing. Our findings contribute to the understanding of the intricate regulatory process of ethylene signaling and provide insights into the significance of ribonuclease in stress responses. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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22 pages, 4934 KiB

Open AccessArticle

Identification and Expression Analysis of the Nucleotidyl Transferase Protein (NTP) Family in Soybean (Glycine max) under Various Abiotic Stresses

by Liqing Kang, Changgen Li, Aokang Qin, Zehui Liu, Xuanyue Li, Liming Zeng, Hongyang Yu, Yihua Wang, Jianbo Song and Rongrong Chen

Int. J. Mol. Sci. 2024, 25(2), 1115; https://doi.org/10.3390/ijms25021115 - 17 Jan 2024

Viewed by 989

Abstract

Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3’ end of RNA. In plants, NTPs can regulate RNA stability by influencing 3’ end modifications, which in turn affect plant growth, development, stress responses, [...] Read more.

Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3’ end of RNA. In plants, NTPs can regulate RNA stability by influencing 3’ end modifications, which in turn affect plant growth, development, stress responses, and disease resistance. Although the functions of NTP family members have been extensively studied in Arabidopsis, rice, and maize, there is limited knowledge about NTP genes in soybeans. In this study, we identified 16 members of the NTP family in soybeans, including two subfamilies (G1 and G2) with distinct secondary structures, conserved motifs, and domain distributions at the protein level. Evolutionary analysis of genes in the NTP family across multiple species and gene collinearity analysis revealed a relatively conserved evolutionary pattern. Analysis of the tertiary structure of the proteins showed that NTPs have three conserved aspartic acids that bind together to form a possible active site. Tissue-specific expression analysis indicated that some NTP genes exhibit tissue-specific expression, likely due to their specific functions. Stress expression analysis showed significant differences in the expression levels of NTP genes under high salt, drought, and cold stress. Additionally, RNA-seq analysis of soybean plants subjected to salt and drought stress further confirmed the association of soybean NTP genes with abiotic stress responses. Subcellular localization experiments revealed that GmNTP2 and GmNTP14, which likely have similar functions to HESO1 and URT1, are located in the nucleus. These research findings provide a foundation for further investigations into the functions of NTP family genes in soybeans. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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18 pages, 30283 KiB

Open AccessArticle

Genome-Wide Analysis of Sweet Potato Ammonium Transporter (AMT): Influence on Nitrogen Utilization, Storage Root Development and Yield

by Ya-Yi Meng, Ning Wang, Hai-Yan Zhang, Ran Xu and Cheng-Cheng Si

Int. J. Mol. Sci. 2023, 24(24), 17424; https://doi.org/10.3390/ijms242417424 - 13 Dec 2023

Viewed by 813

Abstract

Ammonium, as a major inorganic source of nitrogen (N) for sweet potato N utilization and growth, is specifically transported by ammonium transporters (AMTs). However, the activities of AMT family members in sweet potatoes have not been analyzed. In the present study, [...] Read more.

Ammonium, as a major inorganic source of nitrogen (N) for sweet potato N utilization and growth, is specifically transported by ammonium transporters (AMTs). However, the activities of AMT family members in sweet potatoes have not been analyzed. In the present study, the sweet potato cultivar ‘Pushu 32’, which is planted in a large area in China, was used in field experiments at the Agricultural Base of Hainan University (20°06′ N, 110°33′ E) in 2021, and Sanya Nanfan Research Institute of Hainan University (18°30′ N, 109°60′ E) in 2022. Four N levels were tested: 0, 60, 120, and 180 kg ha⁻¹. The results are as follows. Twelve IbAMT genes were identified in the sweet potato genome, which were classified into three distinct subgroups based on phylogeny; the same subgroup genes had similar properties and structures. IbAMT1.3 and IbAMT1.5 were mostly expressed in the storage roots under N deficiency. Compared with the NN and HN groups, IbAMT1.3 and IbAMT1.5 expressions, N content in storage roots, N uptake efficiency at the canopy closure, N fertilization contribution rates, number of storage roots per plant, storage root weight, and yield were all increased in the MN group. Furthermore, there was a significant positive correlation between the expressions of IbAMT1.3 and IbAMT1.5 with N content in the storage roots of sweet potato. In a word, IbAMT1.3 and IbAMT1.5 may regulate N utilization, affect the development of the storage root. and determine the yield of sweet potato. The results provide valuable insights into the AMT gene family’s role in the use of N and effects on storage root development and yield in sweet potatoes. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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37 pages, 20027 KiB

Open AccessArticle

Analysis of Raffinose Synthase Gene Family in Bread Wheat and Identification of Drought Resistance and Salt Tolerance Function of TaRS15-3B

by Jiagui Guo, Yan Yang, Tingting Wang, Yizhen Wang, Xin Zhang, Donghong Min and Xiaohong Zhang

Int. J. Mol. Sci. 2023, 24(13), 11185; https://doi.org/10.3390/ijms241311185 - 6 Jul 2023

Viewed by 1408

Abstract

Raffinose synthase (RS) plays a crucial role in plant growth and development, as well as in responses to biotic stresses and abiotic stresses, yet few studies have been conducted on its role in bread wheat. Therefore, in this study we screened and identified [...] Read more.

Raffinose synthase (RS) plays a crucial role in plant growth and development, as well as in responses to biotic stresses and abiotic stresses, yet few studies have been conducted on its role in bread wheat. Therefore, in this study we screened and identified a family of bread wheat raffinose synthase genes based on bread wheat genome information and analyzed their physicochemical properties, phylogenetic evolutionary relationships, conserved structural domains, promoter cis-acting elements, and expression patterns. The BSMV-induced silencing of TaRS15-3B resulted in the bread wheat seedlings being susceptible to drought and salt stress and reduced the expression levels of stress-related and ROS-scavenging genes in bread wheat plants. This further affected the ability of bread wheat to cope with drought and salt stress. In conclusion, this study revealed that the RS gene family in bread wheat plays an important role in plant response to abiotic stresses and that the TaRS15-3B gene can improve the tolerance of transgenic bread wheat to drought and salt stresses, provide directions for the study of other RS gene families in bread wheat, and supply candidate genes for use in molecular breeding of bread wheat for stress resistance. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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13 pages, 1754 KiB

Open AccessArticle

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

by Raisa Kulyan, Lidiia Samarina, Ruset Shkhalakhova, Alexandr Kuleshov, Yulia Ukhatova, Olga Antonova, Natalia Koninskaya, Alexandra Matskiv, Valentina Malyarovskaya and Alexey Ryndin

Int. J. Mol. Sci. 2023, 24(9), 8276; https://doi.org/10.3390/ijms24098276 - 5 May 2023

Cited by 3 | Viewed by 1469

Abstract

Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification [...] Read more.

Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification of valuable accessions. In this study, the efficiency of 36 SCoT markers and 60 InDel markers were evaluated as part of the broad citrus collection of the Western Caucasus. The interspecific and intraspecific genetic diversity and genetic structures were analyzed for 172 accessions, including 31 species and sets of the locally derived cultivars. Single markers, such as SCoT18 (0.84), SCoT20 (0.93), SCoT23 (0.87), SCoT31 (0.88), SCoT36 (0.87) и LG 1-4 (0.94), LG 4-3 (0.86), LG 7-11 (0.98), and LG 8-10 (0.83), showed a high discriminating power, indicating the good applicability of these markers to assess intraspecific diversity of the genus Citrus. Overall, SCoT markers showed a higher level of polymorphism than InDel markers. According to analysis of population structure, SCoT and InDel markers showed K = 9 and K = 5 genetic clusters, respectively. The lowest levels of genetic admixtures and diversity were observed among the locally derived satsumas and lemons. The highest level of genetic admixtures was observed in the lime group. Phylogenetic relationships indicated a high level of interspecific genetic diversity but a low level of intraspecific diversity in locally derived satsumas and lemons. The results provide new insight into the origin of citrus germplasms and their distribution in colder regions. Furthermore, they are important for implementing conservation measures, controlling genetic erosion, developing breeding strategies, and improving breeding efficiency. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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19 pages, 4346 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of the Trehalose-6-Phosphate Synthetase Gene Family in Chinese Cabbage (Brassica rapa) and Plasmodiophora brassicae during Their Interaction

by Liyan Kong, Jiaxiu Liu, Wenjun Zhang, Xiaonan Li, Yuting Zhang, Xueyu Chen, Zongxiang Zhan and Zhongyun Piao

Int. J. Mol. Sci. 2023, 24(2), 929; https://doi.org/10.3390/ijms24020929 - 4 Jan 2023

Cited by 3 | Viewed by 1512

Abstract

Trehalose is a nonreducing disaccharide that is widely distributed in various organisms. Trehalose-6-phosphate synthase (TPS) is a critical enzyme responsible for the biosynthesis of trehalose, which serves important functions in growth and development, defense, and stress resistance. Although previous studies have found that [...] Read more.

Trehalose is a nonreducing disaccharide that is widely distributed in various organisms. Trehalose-6-phosphate synthase (TPS) is a critical enzyme responsible for the biosynthesis of trehalose, which serves important functions in growth and development, defense, and stress resistance. Although previous studies have found that the clubroot pathogen Plasmodiophora brassicae can lead to the accumulation of trehalose in infected Arabidopsis organs, it has been proposed that much of the accumulated trehalose is derived from the pathogen. At present, there is very little evidence to verify this view. In this study, a comprehensive analysis of the TPS gene family was conducted in Brassica rapa and Plasmodiophora brassicae. A total of 14 Brassica rapa TPS genes (BrTPSs) and 3 P. brassicae TPS genes (PbTPSs) were identified, and the evolutionary characteristics, functional classification, and expression patterns were analyzed. Fourteen BrTPS genes were classified into two distinct classes according to phylogeny and gene structure. Three PbTPSs showed no significant differences in gene structure and protein conserved motifs. However, evolutionary analysis showed that the PbTPS2 gene failed to cluster with PbTPS1 and PbTPS3. Furthermore, cis-acting elements related to growth and development, defense and stress responsiveness, and hormone responsiveness were predicted in the promoter region of the BrTPS genes. Expression analysis of most BrTPS genes at five stages after P. brassicae interaction found no significant induction. Instead, the expression of the PbTPS genes of P. brassicae was upregulated, which was consistent with the period of trehalose accumulation. This study deepens our understanding of the function and evolution of BrTPSs and PbTPSs. Simultaneously, clarifying the biosynthesis of trehalose in the interaction between Brassica rapa and P. brassicae is also of great significance. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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17 pages, 3847 KiB

Open AccessArticle

A YSK-Type Dehydrin from Nicotiana tabacum Enhanced Copper Tolerance in Escherichia coli

by Jinran Dai, Lirou Shen, Jin Zhou, Xinyu Liu and Suiyun Chen

Int. J. Mol. Sci. 2022, 23(23), 15162; https://doi.org/10.3390/ijms232315162 - 2 Dec 2022

Viewed by 1131

Abstract

Copper is an essential micronutrient for the maintenance of normal cell function but is toxic in excess. Dehydrins are group two late embryogenesis abundant proteins, which facilitate plant survival in harsh environmental conditions. Here, a YSK-type dehydrin, NtDhn17, was cloned from Nicotiana [...] Read more.

Copper is an essential micronutrient for the maintenance of normal cell function but is toxic in excess. Dehydrins are group two late embryogenesis abundant proteins, which facilitate plant survival in harsh environmental conditions. Here, a YSK-type dehydrin, NtDhn17, was cloned from Nicotiana tabacum under copper toxicity and characterized using a heterologous expression system and in vitro or in vivo experiments and exhibited characteristics of intrinsic disorder during in vitro analyses. Heterologous expression of NtDHN17 enhanced the tolerance of E. coli to various metals, osmotic, and oxidative stress. NtDHN17 showed no Cu²⁺-binding properties in vivo or in vitro, indicating that metal ion binding is not universal among dehydrins. In vitro and in vivo experiments suggested that NtDHN17 behaved as a potent anti-aggregation agent providing strong protection to aggregated proteins induced by excess copper ions, an effect dependent on the K-segment but not on the Y- or S-segments. In summary, the protective role of NtDHN17 towards E. coli under conditions of copper toxicity may be related to anti-aggregation ability rather than its acting as an ion scavenger, which might be a valuable target for the genetic improvement of resistance to heavy metal stresses in plants. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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Review

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18 pages, 1175 KiB

Open AccessReview

Environmental Stimuli: A Major Challenge during Grain Filling in Cereals

by Zhenning Teng, Yinke Chen, Shuan Meng, Meijuan Duan, Jianhua Zhang and Nenghui Ye

Int. J. Mol. Sci. 2023, 24(3), 2255; https://doi.org/10.3390/ijms24032255 - 23 Jan 2023

Cited by 13 | Viewed by 3201

Abstract

Light, temperature, water, and fertilizer are arguably the most important environmental factors regulating crop growth and productivity. Environmental stimuli, including low light, extreme temperatures, and water stresses caused by climate change, affect crop growth and production and pose a growing threat to sustainable [...] Read more.

Light, temperature, water, and fertilizer are arguably the most important environmental factors regulating crop growth and productivity. Environmental stimuli, including low light, extreme temperatures, and water stresses caused by climate change, affect crop growth and production and pose a growing threat to sustainable agriculture. Furthermore, soil salinity is another major environmental constraint affecting crop growth and threatening global food security. The grain filling stage is the final stage of growth and is also the most important stage in cereals, directly determining the grain weight and final yield. However, the grain filling process is extremely vulnerable to different environmental stimuli, especially for inferior spikelets. Given the importance of grain filling in cereals and the deterioration of environmental problems, understanding environmental stimuli and their effects on grain filling constitutes a major focus of crop research. In recent years, significant advances made in this field have led to a good description of the intricate mechanisms by which different environmental stimuli regulate grain filling, as well as approaches to adapt cereals to changing climate conditions and to give them better grain filling. In this review, the current environmental stimuli, their dose–response effect on grain filling, and the physiological and molecular mechanisms involved are discussed. Furthermore, what we can do to help cereal crops adapt to environmental stimuli is elaborated. Overall, we call for future research to delve deeper into the gene function-related research and the commercialization of gene-edited crops. Meanwhile, smart agriculture is the development trend of the future agriculture under environmental stimuli. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: From Gene to the Fields 2.0)

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