scholarly journals Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses

2016 ◽  
Vol 7 ◽  
Author(s):  
Jérôme Grimplet ◽  
Patricia Agudelo-Romero ◽  
Rita T. Teixeira ◽  
Jose M. Martinez-Zapater ◽  
Ana M. Fortes
Keyword(s):  
Functional Analysis ◽  
Gene Family ◽  
Stress Responses ◽  
Gras Gene

scholarly journals Genome-Wide Identification, Evolutionary Analysis, and Stress Responses of the GRAS Gene Family in Castor Beans

2016 ◽  
Vol 17 (7) ◽  
pp. 1004 ◽  
Author(s):  
Wei Xu ◽  
Zexi Chen ◽  
Naeem Ahmed ◽  
Bing Han ◽  
Qinghua Cui ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
Gras Gene

scholarly journals Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mengyuan Wei ◽  
Aili Liu ◽  
Yujuan Zhang ◽  
Yong Zhou ◽  
Donghua Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Genome Wide ◽  
Gene Structures ◽  
Relationship Of ◽  
Zip Genes

Abstract Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

scholarly journals Lighting the way: advances in transcriptional regulation and integrative crosstalk of melatonin biosynthetic enzymes in cassava

2020 ◽  
Author(s):  
Yunxie Wei ◽  
Yujing Bai ◽  
Xiao Cheng ◽  
Russel J Reiter ◽  
Xiaojian Yin ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Transcriptional Regulation ◽  
Signaling Pathways ◽  
Stress Responses ◽  
Protein Complex ◽  
Recent Progress ◽  
Biosynthetic Enzymes ◽  
Dual Roles ◽  
Melatonin Synthesis

Abstract The role of melatonin biosynthetic enzymes has been well studied. However, the transcriptional regulation of melatonin biosynthetic enzymes and their integrative crosstalk with other signaling pathways remain elusive. Here, we summarize recent progress in the functional analysis of melatonin biosynthetic enzymes and the major sites of melatonin synthesis in plants. We focus on the dual roles of melatonin biosynthetic enzymes in melatonin biosynthesis and in the crosstalk between melatonin and autophagy, antioxidant signaling, and stress responses in cassava. We highlight the transcriptional regulation and integrative protein complex of melatonin biosynthetic enzymes, and then raise the challenge of uncovering their precise regulation and crosstalk.

scholarly journals Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10811
Author(s):  
Yanfeng Liu ◽  
Wei Wang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Epigenetic Modification ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
High Rate ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
And Function ◽  
Gras Gene

GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.

scholarly journals Genome-Wide Analysis Elucidates the Role of CONSTANS-like Genes in Stress Responses of Cotton

2018 ◽  
Vol 19 (9) ◽  
pp. 2658 ◽  
Author(s):  
Wenqiang Qin ◽  
Ya Yu ◽  
Yuying Jin ◽  
Xindong Wang ◽  
Ji Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Purifying Selection ◽  
Phylogenetic Tree Analysis ◽  
Group Iii ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Drought And Salt Stress

The CONSTANS (CO)-like gene family has been well studied for its role in the regulation of plant flowering time. However, their role remains poorly understood in cotton. To better understand the possible roles of CO-like in cotton, we performed a comprehensive genome-wide analysis of CO-like genes in cotton. Phylogenetic tree analysis showed that CO-like genes naturally clustered into three groups. Segmental duplication and whole genome duplication (WGD), which occurred before polyploidy, were important contributors to its expansion within the At (“t” indicates tetraploid) and Dt subgenomes, particularly in Group III. Long-terminal repeat retroelements were identified as the main transposable elements accompanying 18 genes. The genotype of GhCOL12_Dt displayed low diversity; it was a candidate involved in domestication. Selection pressure analyses indicated that relaxed purifying selection might have provided the main impetus during the evolution of CO-like genes in upland cotton. In addition, the high expression in the torus and calycle indicated that CO-like genes might affect flowering. The genes from Group II, and those from Group III involved in segmental duplication or WGD, might play important roles in response to drought and salt stress. Overall, this comprehensive genome-wide study of the CO-like gene family would facilitate further detailed studies in cotton.

scholarly journals Arabidopsis NDL-AGB1 modules Play Role in Abiotic Stress and Hormonal Responses Along with Their Specific Functions

2019 ◽  
Vol 20 (19) ◽  
pp. 4736 ◽  
Author(s):  
Arpana Katiyar ◽  
Yashwanti Mudgil
Keyword(s):  
Gene Family ◽  
G Protein ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Specific Expression ◽  
Hormonal Responses

Arabidopsis N-MYC Downregulated Like Proteins (NDLs) are interacting partners of G-Protein core components. Animal homologs of the gene family N-myc downstream regulated gene (NDRG) has been found to be induced during hypoxia, DNA damage, in presence of reducing agent, increased intracellular calcium level and in response to metal ions like nickel and cobalt, which indicates the involvement of the gene family during stress responses. Arabidopsis NDL gene family contains three homologs NDL1, NDL2 and NDL3 which share up to 75% identity at protein level. Previous studies on NDL proteins involved detailed characterization of the role of NDL1; roles of other two members were also established in root and shoot development using miRNA knockdown approach. Role of entire family in development has been established but specific functions of NDL2 and NDL3 if any are still unknown. Our in-silico analysis of NDLs promoters reveled that all three members share some common and some specific transcription factors (TFs) binding sites, hinting towards their common as well as specific functions. Based on promoter elements characteristics, present study was designed to carry out comparative analysis of the Arabidopsis NDL family during different stages of plant development, under various abiotic stresses and plant hormonal responses, in order to find out their specific and combined roles in plant growth and development. Developmental analysis using GUS fusion revealed specific localization/expression during different stages of development for all three family members. Stress analysis after treatment with various hormonal and abiotic stresses showed stress and tissue-specific differential expression patterns for all three NDL members. All three NDL members were collectively showed role in dehydration stress along with specific responses to various treatments. Their specific expression patterns were affected by presence of interacting partner the Arabidopsis heterotrimeric G-protein β subunit 1 (AGB1). The present study will improve our understanding of the possible molecular mechanisms of action of the independent NDL–AGB1 modules during stress and hormonal responses. These findings also suggest potential use of this knowledge for crop improvement.

Functional Analysis and the Role of Members of SGT Gene Family of Withania somnifera

2016 ◽  
pp. 1-14
Author(s):  
Pratibha Misra ◽  
Gaurav Singh ◽  
Manoj K Mishra ◽  
Vibha Pandey ◽  
Syed Saema
Keyword(s):  
Functional Analysis ◽  
Gene Family ◽  
Withania Somnifera
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