Analysis of differentially expressed genes in abiotic stress response and their role in signal transduction pathways

PROTOPLASMA ◽  
2013 ◽  
Vol 251 (1) ◽  
pp. 81-91 ◽  
Author(s):  
Sanchita ◽  
Sunita Singh Dhawan ◽  
Ashok Sharma
Keyword(s):  
Signal Transduction ◽  
Abiotic Stress ◽  
Stress Response ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Signal Transduction Pathways ◽  
Abiotic Stress Response

scholarly journals Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuanda Lv ◽  
Fengqin Hu ◽  
Yongfeng Zhou ◽  
Feilong Wu ◽  
Brandon S. Gaut
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Transposable Elements ◽  
Rna Sequencing ◽  
Sequence Similarity ◽  
Long Terminal Repeat Retrotransposons ◽  
Differentially Expressed ◽  
Abiotic Stress Response ◽  
Total Rna ◽  
Non Coding Rnas

Abstract Background Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.

scholarly journals The Raf-like kinase ILK1 and the high affinity K+ transporter HAK5 are required for Innate Immunity and Abiotic Stress Response

2016 ◽  
pp. pp.00035.2016 ◽  
Author(s):  
Elizabeth Kalinda Brauer ◽  
Nagib Ahsan ◽  
Renee Dale ◽  
Naohiro Kato ◽  
Alison E Coluccio ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Abiotic Stress ◽  
Stress Response ◽  
Abiotic Stress Response ◽  
High Affinity

scholarly journals A unique Ni2+ -dependent and methylglyoxal-inducible rice glyoxalase I possesses a single active site and functions in abiotic stress response

2014 ◽  
Vol 78 (6) ◽  
pp. 951-963 ◽  
Author(s):  
Ananda Mustafiz ◽  
Ajit Ghosh ◽  
Amit K. Tripathi ◽  
Charanpreet Kaur ◽  
Akshay K. Ganguly ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Active Site ◽  
Glyoxalase I ◽  
Abiotic Stress Response

scholarly journals CV-containing vesicle budding from chloroplast inner envelope membrane is mediated by clathrin but inhibited by GAPC

2021 ◽  
Author(s):  
Ting Pan ◽  
Yangxuan Liu ◽  
Chengcheng Ling ◽  
Yuying Tang ◽  
Wei Tang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Abiotic Stress ◽  
Water Stress ◽  
Stress Response ◽  
Eukaryotic Cells ◽  
Envelope Membrane ◽  
Vesicle Budding ◽  
Cargo Transport ◽  
Membrane Defects ◽  
Inner Envelope

AbstractClathrin-mediated vesicular formation and trafficking are highly conserved in eukaryotic cells and are responsible for molecular cargo transport and signal transduction among organelles. It remains largely unknown whether clathrin-coated vesicles can be generated from chloroplasts. CHLOROPLAST VESICULATION (CV)-containing vesicles (CVVs) generate from chloroplasts and mediate chloroplast degradation under abiotic stress. In this study, we showed that CV interacted with the clathrin heavy chain (CHC) and induced vesicle budding from the chloroplast inner envelope membrane. Defects on CHC2 and the dynamin-encoding DRP1A gene affected CVV budding and releasing from chloroplast. CHC2 is also required for CV-induced chloroplast degradation and hypersensitivity to water stress. Moreover, GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPC) interacts with CV and impairs the CV-CHC2 interaction. GAPC1 overexpression inhibited CV-mediated chloroplast degradation and hypersensitivity to water stress. CV silencing alleviated the hypersensitivity of gapc1gapc2 plant to water stress. Together, our work revealed a pathway of clathrin-assisted CVV budding from the chloroplast inner envelope membrane, which mediated the stress-induced chloroplast degradation and stress response.

scholarly journals The DUB family in Populus: identification, characterization, evolution and expression patterns

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenqing Zheng ◽  
Liang Du
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Structure ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Foliar Spray ◽  
Regulatory Elements ◽  
Limited Information ◽  
Abiotic Stress Response

Abstract Background The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. Results In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. Conclusions The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.

Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response

2004 ◽  
Vol 9 (5) ◽  
pp. 244-252 ◽  
Author(s):  
Wangxia Wang ◽  
Basia Vinocur ◽  
Oded Shoseyov ◽  
Arie Altman
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Molecular Chaperones ◽  
Abiotic Stress Response ◽  
Shock Proteins

Recent understanding on molecular mechanisms of plant abiotic stress response and tolerance.

2021 ◽  
pp. 1-23
Author(s):  
Geoffrey Onaga ◽  
Kerstin Wydra
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Abiotic Stresses ◽  
Crop Production ◽  
Molecular Mechanisms ◽  
Abiotic Stress Response ◽  
Molecular Components ◽  
Plant Abiotic Stress

Abstract This chapter provides an overview of the recent significant perspectives on molecules involved in response and tolerance to drought and salinity, the 2 major abiotic stresses affecting crop production, and highlights major molecular components identified in major cereals.

Phytohormone transporters during abiotic stress response

2021 ◽  
pp. 235-260
Author(s):  
Varucha Misra ◽  
A.K. Mall ◽  
M. Iqbal R. Khan ◽  
Mohammad Israil Ansari
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Abiotic Stress Response
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