scholarly journals A tuber mustard AP2/ERF transcription factor gene, BjABR1, functioning in abscisic acid and abiotic stress responses, and evolutionary trajectory of the ABR1 homologous genes in Brassica species

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6071 ◽  
Author(s):  
Liuxin Xiang ◽  
Chao Liu ◽  
Jingzhi Luo ◽  
Lin He ◽  
Yushan Deng ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abscisic Acid ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Sequence Similarity ◽  
Amino Acid Sequence Similarity ◽  
Genome Database ◽  
Homologous Genes ◽  
High Amino Acid ◽  
Tuber Mustard

The AP2/ERF superfamily of transcription factors is one of the largest transcription factor families in plants and plays an important role in plant development processes and stress responses. In this study, BjABR1, an AP2/ERF superfamily gene, from tuber mustard (Brassica juncea var. tumida Tsen et Lee), sharing high amino acid sequence similarity with the AtABR1 (Arabidopsis thaliana AP2-like abscisic acid repressor 1) gene, were performed functional research, and the ABR1 homologous genes in Brassica species were identified and performed phylogenetic analysis. The promoter sequence of BjABR1 contained many phytohormone- and stress-related cis-elements; ABA (abscisic acid) and abiotic stresses can induce BjABR1 expression in tuber mustard; overexpression of BjABR1 in Arabidopsis can alleviate plant sensitivity to ABA and salt and osmotic stresses, and the alleviation may be due to changes in stress/ABA-induced gene expression. These results indicated that BjABR1 functions in ABA and abiotic stress responses. By BLAST searches against the genome database of five Brassica species (three diploids, B. rapa, B. nigra, and B. oleracea, and two allotetraploid, B. juncea and B. napus) using the protein sequence of AtABR1, 3, 3, 3, 6, and 5 ABR1 homologous genes in B. nigra, B. rapa, B. oleracea, B. juncea, and B. napus were identified, respectively, and they shared high sequence similarity. By sequence analysis, annotation mistakes of the protein-coding regions of two ABR1 homologous genes, GSBRNA2T00134741001 and BjuB007684, were found and corrected. Then, the evolution analysis of these ABR1 homologous genes showed that the ancestor of the three diploid species had three ABR1 homologous genes and each diploid inherited all the three genes from their ancestor; then, allotetraploid B. juncea inherited all the six genes from B. rapa and B. nigra with no gene lost, while allotetraploid B. napus inherited all the three genes from B. oleracea and two genes from B. rapa with one gene lost, indicating that ABR1 homologous genes possessed greater hereditary conservation in Brassica species. The ABR1 homologous genes between B. rapa and B. oleracea shared much higher sequence similarity compared to that of B. nigra in diploid species, indicating that ABR1 homologous genes in B. nigra had experienced more rapid evolution, and B. rapa and B. oleracea may share closer relationship compared to B. nigra. Moreover, the spatial and temporal expression analysis of six ABR1 homologous genes of tuber mustard showed that they possessed different expression models. These results imply that ABR1 homologous genes are important to Brassica plants, and they may possess similar function in ABA and abiotic stress responses but play a role in different tissues and growing stages of plant. This study will provide the foundation to the functional research of ABR1 homologous genes in the Brassica species and help to reveal and understand the evolution mechanisms of Brassica species.

scholarly journals Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

2020 ◽  
Author(s):  
Yue Liu ◽  
Nannan Liu ◽  
Xiong Deng ◽  
Dongmiao Liu ◽  
Mengfei Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Positive Selection ◽  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Genome Database ◽  
Genome Wide Analysis ◽  
Dof Transcription Factor ◽  
Genome Wide

Abstract Background: DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Using the recently released wheat genome database (Results: Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions: The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

scholarly journals pH-dependent regulation of the multi-subunit cation/proton antiporter Pha1 system from Sinorhizobium meliloti

Microbiology ◽  
2009 ◽  
Vol 155 (8) ◽  
pp. 2750-2756 ◽  
Author(s):  
Toshio Yamaguchi ◽  
Fuminori Tsutsumi ◽  
Péter Putnoky ◽  
Masahiro Fukuhara ◽  
Tatsunosuke Nakamura
Keyword(s):  
Sinorhizobium Meliloti ◽  
Sequence Similarity ◽  
Plant Root ◽  
Functional Expression ◽  
Amino Acid Sequence Similarity ◽  
Ph Optimum ◽  
Cation Selectivity ◽  
High Amino Acid ◽  
Alkaline Conditions ◽  
Ph Dependent

The pha1 gene cluster (pha1A′-G) of Sinorhizobium meliloti has previously been characterized as a necessary component for proper invasion into plant root tissue. It has been suggested to encode a multi-subunit K+/H+ antiporter, since mutations in the pha1 region rendered S. meliloti cells sensitive to K+ and alkali, and because there is high amino acid sequence similarity to previously characterized multi-subunit cation/H+ antiporters (Mrp antiporters). However, the detailed transport properties of the Pha1 system are yet to be determined. Interestingly, most of the Mrp antiporters are highly selective for Na+, unlike the Pha1 system. Here, we report the functional expression of the Pha1 system in Escherichia coli and the measurement of cation/H+ antiport activity. We showed that the Pha1 system is indeed a K+/H+ antiporter with a pH optimum under mildly alkaline conditions. Moreover, we found that the Pha1 system can transport Na+; this was unexpected based on previous phenotypic analyses of pha1 mutants. Furthermore, we demonstrated that the cation selectivity of the Pha1 system was altered when the pH was lowered from the optimum. The downregulation of Na+/H+ and K+/H+ antiport activities upon acidic shift appeared to occur via different processes, which might indicate the presence of distinct mechanisms for the regulation of the K+/H+ and Na+/H+ antiport activities of the Pha1 system.

Analysis of the NAC transcription factor gene family in citrus reveals a novel member involved in multiple abiotic stress responses

2011 ◽  
Vol 7 (6) ◽  
pp. 1123-1134 ◽  
Author(s):  
Tahise M. de Oliveira ◽  
Luciana C. Cidade ◽  
Abelmon S. Gesteira ◽  
Maurício A. Coelho Filho ◽  
Walter S. Soares Filho ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Nac Transcription Factor ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Transcription Factor Gene Family

scholarly journals Inhibition of mitogen-activated protein kinase by a Drosophila dual-specific phosphatase

2000 ◽  
Vol 349 (3) ◽  
pp. 821-828 ◽  
Author(s):  
Won-Jae LEE ◽  
Sun-Hong KIM ◽  
Yong-Sik KIM ◽  
Sung-Jun HAN ◽  
Ki-Sook PARK ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Expressed Sequence Tag ◽  
Mapk Pathway ◽  
Sequence Similarity ◽  
Mitogen Activated Protein Kinase ◽  
Amino Acid Sequence Similarity ◽  
Calculated Molecular Mass ◽  
High Amino Acid ◽  
Mitogen Activated Protein

The Drosophila extracellular signal-regulated kinase (DERK) mitogen-activated protein kinase (MAPK) is involved in the regulation of multiple differentiation and developmental processes. Tight control of MAPK activity is critical for normal cell behaviour. We identified a novel Drosophila MAPK phosphatase (DMKP) cDNA from the expressed-sequence-tag database and characterized it. Analysis of the nucleotide sequence revealed an open reading frame encoding the 203-amino acid protein, with a calculated molecular mass of 23kDa, which has a high amino acid sequence similarity with ‘VH1-like’dual-specific phosphatases at the broad region near the catalytic sites. The expression of DMKP mRNA occurs from the late larval stages to adulthood in Drosophila development. The recombinant DMKP protein produced in yeast retained its phosphatase activity. When expressed in Schneider cells, DMKP dose-dependently inhibited DERK and Drosophila c-Jun N-terminal kinase activities with high selectivity towards DERK. However, DMKP did not have any affect on Drosophila p38 activity. When DMKP was expressed in yeast, it down-regulated the fus1-lacZ trans-reporter gene of the pheromone MAPK pathway without any significant effect on the high-osmolarity-glycerol-response pathway.

scholarly journals Association of transcription factor WRKY56 gene from Populus simonii × P. nigra with salt tolerance in Arabidopsis thaliana

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7291 ◽  
Author(s):  
Lei Wang ◽  
Wenjing Yao ◽  
Yao Sun ◽  
Jiying Wang ◽  
Tingbo Jiang
Keyword(s):  
Transcription Factor ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Germination Rate ◽  
Wrky Transcription Factor ◽  
Biotic And Abiotic Stress ◽  
Populus Simonii ◽  
Reading Frame

The WRKY transcription factor family is one of the largest groups of transcription factor in plants, playing important roles in growth, development, and biotic and abiotic stress responses. Many WRKY genes have been cloned from a variety of plant species and their functions have been analyzed. However, the studies on WRKY transcription factors in tree species under abiotic stress are still not well characterized. To understand the effects of the WRKY gene in response to abiotic stress, mRNA abundances of 102 WRKY genes in Populus simonii × P. nigra were identified by RNA sequencing under normal and salt stress conditions. The expression of 23 WRKY genes varied remarkably, in a tissue-specific manner, under salt stress. Since the WRKY56 was one of the genes significantly induced by NaCl treatment, its cDNA fragment containing an open reading frame from P. simonii × P. nigra was then cloned and transferred into Arabidopsis using the floral dip method. Under salt stress, the transgenic Arabidopsis over-expressed the WRKY56 gene, showing an increase in fresh weight, germination rate, proline content, and peroxidase and superoxide dismutase activity, when compared with the wild type. In contrast, transgenic Arabidopsis displayed a decrease in malondialdehyde content under salt stress. Overall, these results indicated that the WRKY56 gene played an important role in regulating salt tolerance in transgenic Arabidopsis.

scholarly journals Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

2020 ◽  
Author(s):  
Yue Liu ◽  
Nannan Liu ◽  
Xiong Deng ◽  
Dongmiao Liu ◽  
Mengfei Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Positive Selection ◽  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Acid Sites ◽  
Genome Wide Analysis ◽  
Dof Transcription Factor ◽  
Genome Wide

Abstract Background: DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results: Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions: The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

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