Bioinformatics
Samira Mohammadi
Abstract
60 kDa heat shock proteins (HSP60s) also known as chaperonin (cpn60) play an important role in plant growth and stress response. In this study, 32 HSP60 genes were identified in the soybean genome through bioinformatics tools, which are distributed on 14 chromosomes. Most of these proteins are hydrophilic, ...
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60 kDa heat shock proteins (HSP60s) also known as chaperonin (cpn60) play an important role in plant growth and stress response. In this study, 32 HSP60 genes were identified in the soybean genome through bioinformatics tools, which are distributed on 14 chromosomes. Most of these proteins are hydrophilic, acidic, and unstable with a high aliphatic index The evolutionary tree divided HSP60 proteins of soybean, Arabidopsis, and rice into three main groups based on their cellular location. The proteins of different subgroups have highly conserved gene structure, conserved motifs, intron phase, and three-dimensional structure, which can indicate their functional similarities in different subgroups. Several cis-regulatory elements responsive to stresses, growth and hormones were found in the promoter of GmHSP60 genes, that indicate their role in plant growth and response to environmental stresses. Gene ontology (GO) analysis predicted that GmHSP60 genes were responsible for protein folding and refolding in an ATP-dependent manner in response to various stresses. Analysis of the transcriptome pattern (RNA-seq) showed that most of the GmHSP60 genes had high expression in response to salt, drought, cold, heat, submergence, and nutrient deficiency stresses, which indicates their role in improving soybean tolerance to abiotic stresses. Overall, these findings provide useful information to better understand the function of GmHSP60 genes in soybean and facilitate the way for the utilization of chaperonin family genes for achieving plant tolerance against abiotic stresses.
Bioinformatics
Seyyed Hamidreza Hashemi-petroudi; Samira Mohammadi; Esmaeil Bakhshandeh; Markus Kuhlmann
Abstract
From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. ...
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From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. Based on the unique structure of the PP2C domain, 34 AlPP2C genes were discovered and classified into ten evolutionary branches based on homology with Arabidopsis thaliana. According to exon-intron structural analyses, they possessed a wide range of exon counts. AlPP2Cs shared similar motif organization in the same evolutionary branches based on motif distribution. The motifs ABRE, MBS, DRE, STRE, and LTR, which are related with stress, were discovered in the promoter region of the AlPP2C. AlPP2Cs displayed varied expression patterns in leaf and root tissues in response to salt stress and recovery conditions, according to transcriptome analyses. The AlPP2C4 gene is only expressed in the root tissues. These results expand our understanding of the PP2C gene family and provide valuable information for future research on PP2Cs molecular function and biological processes studies.
Bioinformatics
Samira Mohammadi; Ghorbanali Nematzadeh; Hamid Najafi Zarini; Seyyed Hamidreza Hashemi-petroudi
Abstract
MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target ...
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MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target NAC genes. In the present study, 68 putative NAC domain-encoding genes (NACs) were identified in Aeluropus littoralis, a halophyte plant of family Poaceae. Among the AlNAC genes identified, 4 were predicted putative targets for regulation by miR164. The high conservation of miR164 recognition sites in AlNAC genes indicates the essential role of target sites in the normal function of these genes as transcription factors. Expression profile of AlNAC1L.1 candidate gene in response to salt and drought stresses and ABA phytohormone in leaf, stem and root tissues was analyzed by RT-qPCR. The results showed that AlNAC1L.1 gene down-regulated in all tissues at 6 hours after applying stresses. Among the treatments, 600 mM NaCl treatment reduced AlNAC1L.1 expression in leaf, stem and root tissues to about -217, -26 and -9 folds, respectively. Therefore, the AlNAC1L.1 which is ortholog of known Oryza miR164-targeted NAC gene OMTN6, may play negative regulatory role in response to salt, drought and ABA treatments. These results indicated that function of some NAC proteins might be conserved among species. Collectively, these findings provided a useful resource for further analysis of the interactions between NAC genes and their intricate regulation by miR164 in response to abiotic stresses.
Bioinformatics
Seyyed Hamidreza Hashemi-petroudi; Samira Mohammadi
Abstract
Salt stress is one of the abiotic stresses limiting plant growth and development. The ethylene response factor (ERF) is one of the transcription factor family that involved in plant development and responses to biotic and abiotic stresses. Regarding to importance role of genes belonging to ERF gene family ...
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Salt stress is one of the abiotic stresses limiting plant growth and development. The ethylene response factor (ERF) is one of the transcription factor family that involved in plant development and responses to biotic and abiotic stresses. Regarding to importance role of genes belonging to ERF gene family in plant responses to salt stress, identification of these genes in the Aeluropus littoralis, halophyte plant, was considered in this study. In total, 36 non-redundant ERF genes were identified in A. littoralis genome. The phylogenetic tree classified the AlERF gene family into six distinct groups (B1 to B6) based on hemology with the Araboidopsis thaliana. Gene structure analysis revealed that AlERF genes contained zero to two introns. Domain search and conserved motif analyses in AlERF protein sequences determined that 2 motifs (1 and 2) out of the identified 10 motifs participate in the AP2/ERF domain structure. Based on transcriptome data and heatmap diagram, AlERF6.3 gene was expressed more in root tissue under salinity stress, and the least expression level was observed in AlERF6.7 gene in leaf tissue under recovery conditions. The different expression patterns of genes in leaf and root tissues under salt stress suggested different regulatory mechanisms in the gene expression. The results of this study, as the first report on the ERF gene family in A. littoralis, provides basic information for further studies of the functional characteristics of AlERF genes.
