Characterization of WRKY transcription factors in Solanum lycopersicum reveals collinearity and their expression patterns under cold treatment

2015 ◽  
Vol 464 (3) ◽  
pp. 962-968 ◽  
Author(s):  
Lin Chen ◽  
Yang Yang ◽  
Can Liu ◽  
Yanyan Zheng ◽  
Mingshuang Xu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Solanum Lycopersicum ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Wrky Transcription Factors

scholarly journals Identification and Characterization of the Grape WRKY Family

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Ying Zhang ◽  
Jian can Feng
Keyword(s):  
Transcription Factors ◽  
Pathogenic Bacteria ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Structural Features ◽  
Functional Identification ◽  
Wrky Transcription Factors ◽  
Genes Expression ◽  
Wrky Proteins

WRKY transcription factors have functions in plant growth and development and in response to biotic and abiotic stresses. Many studies have focused on functional identification of WRKY transcription factors, but little is known about the molecular phylogeny or global expression patterns of the complete WRKY family. In this study, we identified 80 WRKY proteins encoded in the grape genome. Based on the structural features of these proteins, the grapeWRKYgenes were classified into three groups (groups 1–3). Analysis ofWRKYgenes expression profiles indicated that 28WRKYgenes were differentially expressed in response to biotic stress caused by grape whiterot and/or salicylic acid (SA). In that 16WRKYgenes upregulated both by whiterot pathogenic bacteria and SA. The results indicated that 16 WRKY proteins participated in SA-dependent defense signal pathway. This study provides a basis for cloning genes with specific functions from grape.

scholarly journals Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Peng Di ◽  
Ping Wang ◽  
Min Yan ◽  
Peng Han ◽  
Xinyi Huang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Panax Ginseng ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Wrky Transcription Factors ◽  
Drought Treatment ◽  
Ginsenoside Biosynthesis ◽  
Genome Wide

Abstract Background Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported. Results In this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside. Conclusions This work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis.

Analysis of WRKY transcription factors and characterization of two Botrytis cinerea-responsive LrWRKY genes from Lilium regale

2018 ◽  
Vol 127 ◽  
pp. 525-536 ◽  
Author(s):  
Qi Cui ◽  
Xiao Yan ◽  
Xue Gao ◽  
Dong-mei Zhang ◽  
Heng-bin He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Botrytis Cinerea ◽  
Wrky Transcription Factors ◽  
Lilium Regale

Genome-wide investigation of WRKY transcription factors in sweet osmanthus and their potential regulation of aroma synthesis

2019 ◽  
Vol 40 (4) ◽  
pp. 557-572 ◽  
Author(s):  
Wenjie Ding ◽  
Qixia Ouyang ◽  
Yuli Li ◽  
Tingting Shi ◽  
Ling Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Volatile Compounds ◽  
Floral Scent ◽  
Expression Patterns ◽  
Ornamental Plants ◽  
Gas Chromatography Mass Spectrometry ◽  
Wrky Transcription Factors ◽  
Specific Expression ◽  
Zinc Cluster ◽  
Terpene Synthesis

Abstract WRKY transcription factors, one of the largest transcription factor families, play important roles in regulating the synthesis of secondary metabolites. In sweet osmanthus (Osmanthus fragrans), the monoterpenes have been demonstrated as the most important volatile compounds, and the W-box, which is the cognate binding site of WRKY transcription factors, could be identified in most of the terpene-synthesis-related genes’ promoters. However, the role of the WRKY family in terpene synthesis in sweet osmanthus has rarely been examined. In this study, 154 WRKY genes with conserved WRKY domain were identified and classified into three groups. The group II was further divided into five subgroups, and almost all members of IId contained a plant zinc cluster domain. Eight OfWRKYs (OfWRKY7/19/36/38/42/84/95/139) were screened from 20 OfWRKYs for their flower-specific expression patterns in different tissues. Simultaneously, the expression patterns of OfWRKYs and emission patterns of volatile compounds during the flowering process were determined and gas chromatography-mass spectrometry results showed that monoterpenes, such as linalool and ocimene, accounted for the highest proportion, contributing to the floral scent of sweet osmanthus in two cultivars. In addition, correlation analysis revealed the expression patterns of OfWRKYs (OfWRKY7/19/36/139) were each correlated with distinct monoterpenes (linalool, linalool derivatives, ocimene and ocimene derivatives). Subcellular localization analysis showed that p35S::GFP–OfWRKY7/38/95/139 were localized in the nucleus and OfWRKY139 had very strong transactivation activity. Collectively, the results indicated potential roles of OfWRKY139 and OfWRKYs with plant zinc cluster domain in regulating synthesis of aromatic compounds in sweet osmanthus, laying the foundation for use of OfWRKYs to improve the aroma of ornamental plants.

scholarly journals What functional genomics has taught us about transcriptional regulation in malaria parasites

2019 ◽  
Vol 18 (5) ◽  
pp. 290-301 ◽  
Author(s):  
Christa G Toenhake ◽  
Richárd Bártfai
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Life Cycle ◽  
Functional Genomics ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Complex Life Cycle ◽  
Malaria Parasites ◽  
Gene Regulatory

Abstract Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights into the interplay between epigenetic, transcriptional and post-transcriptional mechanisms. Recently, considerable progress has been made in identifying sequence-specific transcription factors and DNA-encoded regulatory elements. Here, we review the insights obtained from these efforts including the characterization of core promoters, the involvement of sequence-specific transcription factors in life cycle progression and the mapping of gene regulatory elements. Furthermore, we discuss recent developments in the field of functional genomics and how they might contribute to further characterization of this complex gene regulatory network.

scholarly journals Characterization of Citrus WRKY transcription factors and their responses to phytohormones and abiotic stresses

2018 ◽  
Vol 62 (1) ◽  
pp. 33-44 ◽  
Author(s):  
V. Vives-Peris ◽  
D. Marmaneu ◽  
A. Gomez-Cadenas ◽  
R. M. Perez-Clemente
Keyword(s):  
Transcription Factors ◽  
Abiotic Stresses ◽  
Wrky Transcription Factors

scholarly journals Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Zhao ◽  
Yonghui Liu ◽  
Lin Li ◽  
Haijun Meng ◽  
Ying Yang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Developmental Stage ◽  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Regulatory Elements

Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.

scholarly journals Identification and Characterization of Tomato SWI3-Like Proteins: Overexpression of SlSWIC Increases the Leaf Size in Transgenic Arabidopsis

2019 ◽  
Vol 20 (20) ◽  
pp. 5121 ◽  
Author(s):  
Zhongyi Zhao ◽  
Tao Li ◽  
Xiuling Peng ◽  
Keqiang Wu ◽  
Songguang Yang
Keyword(s):  
Chromatin Remodeling ◽  
Transgenic Arabidopsis ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Leaf Size ◽  
Localization Analysis ◽  
Chromatin Remodeling Complexes ◽  
Mating Type Switching ◽  
Identification And Characterization

As the subunits of the SWI/SNF (mating-type switching (SWI) and sucrose nonfermenting (SNF)) chromatin-remodeling complexes (CRCs), Swi3-like proteins are crucial to chromatin remodeling in yeast and human. Growing evidence indicate that AtSWI3s are also essential for development and response to hormones in Arabidopsis. Nevertheless, the biological functions of Swi3-like proteins in tomato (Solanum lycopersicum) have not been investigated. Here we identified four Swi3-like proteins from tomato, namely SlSWI3A, SlSWI3B, SlSWI3C, and SlSWI3D. Subcellular localization analysis revealed that all SlSWI3s are localized in the nucleus. The expression patterns showed that all SlSWI3s are ubiquitously expressed in all tissues and organs, and SlSWI3A and SlSWI3B can be induced by cold treatment. In addition, we found that SlSWI3B can form homodimers with itself and heterodimers with SlSWI3A and SlSWI3C. SlSWI3B can also interact with SlRIN and SlCHR8, two proteins involved in tomato reproductive development. Overexpression of SlSWI3C increased the leaf size in transgenic Arabidopsis with increased expression of GROWTH REGULATING FACTORs, such as GRF3, GRF5, and GRF6. Taken together, our results indicate that SlSWI3s may play important roles in tomato growth and development.

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