scholarly journals Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops

2021 ◽  
Vol 22 (16) ◽  
pp. 8758
Author(s):  
Jishuai Huang ◽  
Qiannan Zhang ◽  
Yurong He ◽  
Wei Liu ◽  
Yanghong Xu ◽  
...  
Keyword(s):  
Gene Family ◽  
Profile Analysis ◽  
Binding Protein ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Limited Information ◽  
Protein Motifs ◽  
Biotic Stresses ◽  
Enhancer Binding Protein ◽  
Gene Structures

The GLABROUS1 enhancer-binding protein (GeBP) gene family encodes a typical transcription factor containing a noncanonical Leucine (Leu-)-zipper motif that plays an essential role in regulating plant growth and development, as well as responding to various stresses. However, limited information on the GeBP gene family is available in the case of the Gramineae crops. Here, 125 GeBP genes from nine Gramineae crops species were phylogenetically classified into four clades using bioinformatics analysis. Evolutionary analyses showed that whole genome duplication (WGD) and segmental duplication play important roles in the expansion of the GeBP gene family. The various gene structures and protein motifs revealed that the GeBP genes play diverse functions in plants. In addition, the expression profile analysis of the GeBP genes showed that 13 genes expressed in all tested organs and stages of development in rice, with especially high levels of expression in the leaf, palea, and lemma. Furthermore, the hormone- and metal-induced expression patterns showed that the expression levels of most genes were affected by various biotic stresses, implying that the GeBP genes had an important function in response to various biotic stresses. Furthermore, we confirmed that OsGeBP11 and OsGeBP12 were localized to the nucleus through transient expression in the rice protoplast, indicating that GeBPs function as transcription factors to regulate the expression of downstream genes. This study provides a comprehensive understanding of the origin and evolutionary history of the GeBP genes family in Gramineae, and will be helpful in a further functional characterization of the GeBP genes.

scholarly journals Genome-Wide Identification and Expression Profile Analysis of the Phospholipase C Gene Family in Wheat (Triticum aestivum L.)

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 885
Author(s):  
Xianguo Wang ◽  
Yang Liu ◽  
Zheng Li ◽  
Xiang Gao ◽  
Jian Dong ◽  
...  
Keyword(s):  
Gene Family ◽  
Phospholipase C ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Primary Root ◽  
In Silico Analysis ◽  
Triticum Aestivum L ◽  
Stress Conditions ◽  
Phosphatase Domain

Phospholipid-hydrolyzing enzymes include members of the phospholipase C (PLC) family that play important roles in regulating plant growth and responding to stress. In the present study, a systematic in silico analysis of the wheat PLC gene family revealed a total of 26 wheat PLC genes (TaPLCs). Phylogenetic and sequence alignment analyses divided the wheat PLC genes into 2 subfamilies, TaPI-PLC (containing the typical X, Y, and C2 domains) and TaNPC (containing a phosphatase domain). TaPLC expression patterns differed among tissues, organs, and under abiotic stress conditions. The transcript levels of 8 TaPLC genes were validated through qPCR analyses. Most of the TaPLC genes were sensitive to salt stress and were up-regulated rapidly, and some were sensitive to low temperatures and drought. Overexpression of TaPI-PLC1-2B significantly improved resistance to salt and drought stress in Arabidopsis, and the primary root of P1-OE was significantly longer than that of the wild type under stress conditions. Our results not only provide comprehensive information for understanding the PLC gene family in wheat, but can also provide a solid foundation for functional characterization of the wheat PLC gene family.

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 Genome-Wide Identification of the NHX Gene Family in Punica granatum L. and Their Expressional Patterns under Salt Stress

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 264
Author(s):  
Jianmei Dong ◽  
Cuiyu Liu ◽  
Yuying Wang ◽  
Yujie Zhao ◽  
Dapeng Ge ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Tertiary Structure ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Punica Granatum ◽  
Conserved Motifs ◽  
Cis Acting ◽  
Gene Structures ◽  
Punica Granatum L

Most cultivated lands are suffering from soil salinization, which is a global problem affecting agricultural development and economy. High NaCl concentrations in the soil result in the accumulation of toxic Cl− and Na+ in plants. Na+/H+ antiporter (NHX) can regulate Na+ compartmentalization or efflux to reduce Na+ toxicity. This study aims to identify the NHX genes in pomegranate (Punica granatum L.) from the genome sequences and investigate their expression patterns under different concentrations of NaCl stress. In this study, we used the sequences of PgNHXs to analyze the physicochemical properties, phylogenetic evolution, conserved motifs, gene structures, cis-acting elements, protein tertiary structure and expression pattern. A total of 10 PgNHX genes were identified, and divided into three clades. Conserved motifs and gene structures showed that most of them had an amiloride-binding site (FFI/LY/FLLPPI), except for the members of clade III. There were multiple cis-acting elements involved in abiotic stress in PgNHX genes. Additionally, protein-protein interaction network analysis suggested that PgNHXs might play crucial roles in keeping a balance of Na+ in cells. The qRT-PCR analysis suggested that PgNHXs had tissue-specific expressional patterns under salt stress. Overall, our findings indicated that the PgNHXs could play significant roles in response to salt stress. The theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in pomegranate.

scholarly journals Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1848
Author(s):  
Meimei Hu ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Patterns ◽  
Protein Structures ◽  
Evolutionary Process ◽  
Orthologous Gene ◽  
Evolutionary Relationships ◽  
Protein Motifs ◽  
Gene Pairs ◽  
Gene Structures

SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

scholarly journals Genome-Wide Identification and Characterization of SQUAMOSA—Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina

Biomolecules ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 66 ◽  
Author(s):  
Ren-Fang Zeng ◽  
Jing-Jing Zhou ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Floral Induction ◽  
Binding Protein ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Specific Expression ◽  
Water Deficits ◽  
Citrus Clementina ◽  
Squamosa Promoter Binding Protein ◽  
Gene Structures

SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron–exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis.

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 Gene Expression of CCAAT/Enhancer-Binding Protein .DELTA. Mediated by Autoregulation Is Repressed by Related Gene Family Proteins.

2000 ◽  
Vol 23 (12) ◽  
pp. 1424-1429 ◽  
Author(s):  
Atsuhiro TANABE ◽  
Chizumi KUMAHARA ◽  
Shigehiro OSADA ◽  
Tsutomu NISHIHARA ◽  
Masayoshi IMAGAWA
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Binding Protein ◽  
Related Gene ◽  
Enhancer Binding Protein ◽  
Ccaat Enhancer Binding Protein

Identification of MdDof genes in apple and analysis of their response to biotic or abiotic stress

2018 ◽  
Vol 45 (5) ◽  
pp. 528 ◽  
Author(s):  
Qing Yang ◽  
Qiuju Chen ◽  
Yuandi Zhu ◽  
Tianzhong Li
Keyword(s):  
Abiotic Stress ◽  
Zinc Finger ◽  
Flower Development ◽  
Higher Plants ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Biological Processes ◽  
Protein Motifs ◽  
Gene Structures ◽  
Dof Transcription Factors

As a classic plant-specific transcription factor family – the Dof domain proteins – are involved in a variety of biological processes in organisms ranging from unicellular Chlamydomonas to higher plants. However, there are limited reports of MdDof (Malus domestica Borkh. DNA-binding One Zinc Finger) domain proteins in fruit trees, especially in apple. In this study we identified 54 putative Dof transcription factors in the apple genome. We analysed the gene structures, protein motifs, and chromosome locations of each of the MdDof genes. Next, we characterised all 54 MdDofs their expression patterns under different abiotic and biotic stress conditions. It was found that MdDof6,26 not only played an important role in the biotic/abiotic stress but may also be involved in many molecular functions. Further, both in flower development and pollen tube growth it was found that the relative expression of MdDof24 increased rapidly, also with gene ontology analysis it was indicated that MdDof24 was involved in the chemical reaction and flower development pathways. Taken together, our results provide useful clues as to the function of MdDof genes in apple and serve as a reference for studies of Dof zinc finger genes in other plants.

Identification and expression analysis of E2 ubiquitin-conjugating enzymes in cucumber

2021 ◽  
Author(s):  
Wei Lai ◽  
Zhaoyang Hu ◽  
Chuxia Zhu ◽  
Yingui Yang ◽  
Shiqiang Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Biological Processes ◽  
Protein Ubiquitination ◽  
Genome Wide ◽  
Conjugating Enzymes ◽  
Gene Structures ◽  
Ubiquitin Conjugating Enzymes ◽  
Genome Wide Survey

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

Genome-wide characterization and expression profiling of the MAPKKK genes in Gossypium arboreum L.

Genome ◽  
2019 ◽  
Vol 62 (9) ◽  
pp. 609-622 ◽  
Author(s):  
Weidong Zhu ◽  
Wei Tan ◽  
Qiulin Li ◽  
Xiugui Chen ◽  
Junjuan Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Mitogen Activated Protein Kinase ◽  
Gossypium Arboreum ◽  
Developmental Processes ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stresses

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are important components of MAPK cascades, which have different functions during developmental processes and stress responses. To date, there has been no systematic investigation of this gene family in the diploid cotton Gossypium arboreum L. In this study, a genome-wide survey was performed that identified 78 MAPKKK genes in G. arboreum. Phylogenetic analysis classified these genes into three subgroups: 14 belonged to ZIK, 20 to MEKK, and 44 to Raf. Chromosome location, phylogeny, and the conserved protein motifs of the MAPKKK gene family in G. arboreum were analyzed. The MAPKKK genes had a scattered genomic distribution across 13 chromosomes. The members in the same subfamily shared similar conserved motifs. The MAPKKK expression patterns were analyzed in mature leaves, stems, roots, and at different ovule developmental stages, as well as under salt and drought stresses. Transcriptome analysis showed that 76 MAPKKK genes had different transcript accumulation patterns in the tested tissues and 38 MAPKKK genes were differentially expressed in response to salt and drought stresses. These results lay the foundation for understanding the complex mechanisms behind MAPKKK-mediated developmental processes and abiotic stress-signaling transduction pathways in cotton.

Sign in / Sign up

Export Citation Format

Share Document