scholarly journals Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response

2021 ◽  
Vol 12 ◽  
Author(s):  
Hemeng Wang ◽  
Jin-Gui Chen ◽  
Ying Chang
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Gene Family ◽  
Interaction Analysis ◽  
Populus Trichocarpa ◽  
Functional Characterization ◽  
Woody Species ◽  
Hormone Treatment ◽  
Mature Stage ◽  
Systematic Analysis

Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis, and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis-acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.

scholarly journals In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8539 ◽  
Author(s):  
Kang Zhang ◽  
Lu Yu ◽  
Xi Pang ◽  
Hongzhe Cao ◽  
Helong Si ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Gene Family ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Hormone Treatment ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Biotic Stresses

Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses.

scholarly journals Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

2019 ◽  
Vol 20 (22) ◽  
pp. 5796
Author(s):  
Qianqian Zhou ◽  
Qingchang Li ◽  
Peng Li ◽  
Songtao Zhang ◽  
Che Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Physiological Stress ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Hormone Treatment ◽  
Nicotiana Sylvestris ◽  
Regulatory Elements ◽  
Evolutionary Analysis ◽  
Comprehensive Overview ◽  
Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

scholarly journals Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate PtFBH Genes Involved in the Flowering Process of Populus trichocarpa

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1439
Author(s):  
Yang Ye ◽  
Haodong Xin ◽  
Xiting Gu ◽  
Jianwen Ma ◽  
Lingli Li
Keyword(s):  
Gene Family ◽  
Growth And Development ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Interaction Network ◽  
Systematic Analysis ◽  
Protein Motifs ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Flowering Process

As one of the largest TF families+ in plants, the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. FLOWERING BHLH (FBH) encodes a bHLH-type transcriptional factor related to the flowering process. Poplar is a model woody plant as well as an important economic tree species with a small genome. However, the characteristics of the bHLHs and FBHs gene family in the newest version of Populustrichocarpa genome have not been analyzed yet. We identified 233 PtbHLHs and 10 PtFBHs in the newest version genome, and PtbHLHs were classified into 21 groups with FBH subfamily occupying one, supported by phylogenetic analysis, exon–intron patterns, and conserved protein motifs. These PtHLHs were distributed on 19 chromosomes unevenly and expressed in nucleus mainly. Gene duplication and synteny analysis have indicated that the PtbHLHs gene family has undergone strong purification selection during the evolution process. The cis-elements analysis has suggested that PtbHLHs may be related to the growth and development. Conserved residues of FBHs among Arabidopsis and poplar were also identified. Expression of 227 PtHLH genes (6 unmatched, 13 no expressed) showed diverse patterns in different tissues, implying their multiple functions. Protein–protein interaction network prediction and expression patterns in three states of the flowering process (Flowers-Dormant, Flowers-Expanding and Flowers-Expanded) suggested that some members of PtbHLH and PtFBH family may be involved in the flowering process. Our comprehensive and systematic analysis can provide some valuable clues and basic reference toward further investigations on physiological and molecular functions of PtbHLHs.

Identification of the ASR gene family from Brachypodium distachyon and functional characterization of BdASR1 in response to drought stress

2016 ◽  
Vol 35 (6) ◽  
pp. 1221-1234 ◽  
Author(s):  
Lianzhe Wang ◽  
Wei Hu ◽  
Jialu Feng ◽  
Xiaoyue Yang ◽  
Quanjun Huang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gene Family ◽  
Brachypodium Distachyon ◽  
Functional Characterization ◽  
Asr Gene

scholarly journals Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 59
Author(s):  
Elsa-Herminia Quezada ◽  
Gabriel-Xicoténcatl García ◽  
Manoj-Kumar Arthikala ◽  
Govindappa Melappa ◽  
Miguel Lara ◽  
...  
Keyword(s):  
Gene Family ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Arbuscular Mycorrhizal ◽  
Comprehensive Analysis ◽  
Biological Processes ◽  
Kinase Gene ◽  
Systematic Analysis ◽  
Rhizobial Symbiosis

Receptor-like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Cysteine (C)-rich receptor-like kinases (CRKs) are an important class of RLK that play vital roles in disease resistance and cell death in plants. Genome-wide analyses of CRK genes have been carried out in Arabidopsis and rice, while functional characterization of some CRKs has been carried out in wheat and tomato in addition to Arabidopsis. A comprehensive analysis of the CRK gene family in leguminous crops has not yet been conducted, and our understanding of their roles in symbiosis is rather limited. Here, we report the comprehensive analysis of the Phaseolus CRK gene family, including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, transcript expression profiles, and in silico promoter analysis. Forty-six CRK homologs were identified and phylogenetically clustered into five groups. Expression analysis suggests that PvCRK genes are differentially expressed in both vegetative and reproductive tissues. Further, transcriptomic analysis revealed that shared and unique CRK genes were upregulated during arbuscular mycorrhizal and rhizobial symbiosis. Overall, the systematic analysis of the PvCRK gene family provides valuable information for further studies on the biological roles of CRKs in various Phaseolus tissues during diverse biological processes, including Phaseolus-mycorrhiza/rhizobia symbiosis.

scholarly journals Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar

2021 ◽  
Author(s):  
Nan Chao ◽  
Qi Qi ◽  
Xue-Chun Wang ◽  
Shuang Li ◽  
Xiang-Ning Jiang ◽  
...  
Keyword(s):  
Gene Family ◽  
Biochemical Characterization ◽  
Populus Trichocarpa ◽  
Phylogenetic Analyses ◽  
Lignin Biosynthesis ◽  
Phenylpropanoid Pathway ◽  
Biochemical Properties ◽  
Phylogenetic Groups ◽  
Systematic Analysis ◽  
A Genome

Abstract Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed systematic analysis of CSE gene family in poplar and investigated the possible roles of CSEs and CSE-like genes in Populus. We performed a genome-wide analysis of the CSE family, including functional and phylogenetic analyses of CSE and CSE-like genes using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12 might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of Populus tomentosa (Popto) CSE1, -2 and -12 showed that PoptoCSE1 and -2 kept CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression pattern and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides systematic understanding of this novel gene family and suggests the CSE function in monolignol biosynthesis in Populus.

scholarly journals Phylogeny and gene expression of the complete NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Triticum aestivum

2020 ◽  
Vol 71 (15) ◽  
pp. 4531-4546
Author(s):  
Huadun Wang ◽  
Yongfang Wan ◽  
Peter Buchner ◽  
Robert King ◽  
Hongxiang Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Expression Profiles ◽  
Peptide Transporter ◽  
Specific Gene ◽  
Rna Seq ◽  
Systematic Analysis ◽  
Whole Wheat ◽  
Transporter Family ◽  
Systematic Identification

Abstract NPF genes encode membrane transporters involved in the transport of a large variety of substrates including nitrate and peptides. The NPF gene family has been described for many plants, but the whole NPF gene family for wheat has not been completely identified. The release of the wheat reference genome has enabled the identification of the entire wheat NPF gene family. A systematic analysis of the whole wheat NPF gene family was performed, including responses of specific gene expression to development and nitrogen supply. A total of 331 NPF genes (113 homoeologous groups) have been identified in wheat. The chromosomal location of the NPF genes is unevenly distributed, with predominant occurrence in the long arms of the chromosomes. The phylogenetic analysis indicated that wheat NPF genes are closely clustered with Arabidopsis, Brachypodium, and rice orthologues, and subdivided into eight subfamilies. The expression profiles of wheat NPF genes were examined using RNA-seq data, and a subset of 44 NPF genes (homoeologous groups) with contrasting expression responses to nitrogen and/or development in different tissues were identified. The systematic identification of gene composition, chromosomal locations, evolutionary relationships, and expression profiles contributes to a better understanding of the roles of the wheat NPF genes and lays the foundation for further functional analysis in wheat.

Sign in / Sign up

Export Citation Format

Share Document