In-silico analysis of eukaryotic translation initiation factors (eIFs) in response to environmental stresses in rice ( O
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ORIGINAL ARTICLE
In-silico analysis of eukaryotic translation initiation factors (eIFs) in response to environmental stresses in rice (Oryza sativa) Abbas Saidi 1 & Zohreh Hajibarat 1 Received: 16 July 2019 / Accepted: 27 February 2020 # Institute of Molecular Biology, Slovak Academy of Sciences 2020
Abstract Eukaryotic translation initiation factors (eIFs) are one of the most important components in protein synthesis in plants. Most of eIFs genes are involved in growth processes like embryogenesis, flowering, and different stresses. In the present study, an in silico analysis of 17 rice eIFs genes was conducted in response to environmental stresses. Analysis of bioinformatics performed included gene network, chromosomal map, transcriptional factor binding sites (TFBs) analysis, and phylogenetic relationships among the eIF genes in rice. The transcription of a gene is mainly regulated by TFBs that are specifically bound by regulatory proteins called transcription factors (TFs). Analysis of bioinformatics databases was performed to identify TFBs in eIFs genes using Plant Promoter Analysis (PlantPAN). The analysis of network gene revealed that eIFs and transcription factors organized the major gene networks and are mainly expressed in nucleus, cytoplasm, mitochondria, and chloroplast. Co-expression analysis has shown that interacting proteins tend to have similar expression profiles and tend to be localized to the same or adjacent compartment. Several TFBs including AP2/ERF, WRKY, bZIP, bHLH, GATA, and NAC/NAM were identified in our analysis. We found a positive correlation between eIFs promoter regions of genes and presence of TFBs. This paper is the first report on in silico analysis of eIFs genes in O. sativa. In this paper, we will focus on analysis of initiation factors and their expressions under environmental stresses and different developmental stages using microarray data. Keywords eIFs . Transcriptional factor binding sites (TFBs) . Plant promoter analysis . Chromosomal map
Abbreviations TFBs Transcriptional Factor Binding Sites TFs Transcription Factors eIFs Eukaryotic Translation Initiation Factors DEGs Differential Gene Expression
Introduction In organisms, expression of genes is a complicated process activated at many steps such as transcription, post transcription, * Abbas Saidi [email protected] Zohreh Hajibarat [email protected] 1
Department of Plant Sciences & Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
structure and stability of mRNA, protein synthesis, and protein degradation. Protein translation is an important step during protein synthesis and plays a key role for all organisms such as allowing cellular adaptation under different stresses (Steitz 2008). Translation initiation stage is performed through a number of translation initiation factors (eIFs) (Dutt et al. 2015; Sharma et al. 2012). A better understanding of translation regulation can facilitate surveying mechanisms of gene expression or repression in plants (Merch
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