Genome-wide identification, in silico characterization and expression analysis of the RNA helicase gene family in chickpea (C. arietinum L.)

Abstract

The RNA helicases are an important class of enzymes which are known to influence almost every aspect of RNA metabolism. The majority of RNA helicases belong to the SF2 (superfamily 2) superfamily, members of which are further categorized into three separate subfamilies i.e., the DEAD, DEAH and DExD/H-box subfamilies. In chickpea, these RNA helicases have not been characterized until now. A genome-wide analysis across the chickpea genome led to the identification of a total of 150 RNA helicase genes which included 50 DEAD, 33 DEAH and 67 DExD/H-box genes. These were distributed across all the eight chromosomes, with highest number on chromosome 4 (26) and least on chromosome 8 (8). Gene duplication analysis resulted in identification of 15 paralogous gene pairs with Ka/Ks values < 1, indicating towards the genes being under purifying selection during the course of evolution. The promoter regions of the RNA helicase genes were enriched in cis-acting elements like the light and ABA-responsive elements. The drought responsiveness of the genes was analysed by studying the expression profiles of few of these genes, in two different genotypes, the cultivated variety ICC 8261 (kabuli, C. arietinum) and the wild accession ILWC 292 (C. reticulatum), through qRT-PCR. These genotypes were selected based on their drought responsiveness in a field experiment, where it was observed that the percentage (%) reduction in relative water content (RWC) and membrane stability index (MSI) for the drought stressed plants after withholding water for 24 days, over the control or well-watered plants, was least for both the genotypes. The genes CaDEAD50 and CaDExD/H66 were identified as drought-responsive RNA helicase genes in chickpea. The protein encoded by the CaDExD/H66 gene shares a high degree of homology with one of the CLSY (CLASSY) proteins of A. thaliana. We hypothesize that this gene could possibly be involved in regulation of DNA methylation levels in chickpea by regulating siRNA production, in conjunction with other proteins like the Argonaute, RNA dependent RNA polymerases and Dicer-like proteins.

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system

“…Our findings of hyperosmotic MYC TF mRNA elevation and the presence of multiple MYC CREs (E-boxes) in IMPA1.1 suggests that combinatorial transcriptional regulation involving NFAT5 and MYC controls the hyperosmotic induction of tilapia IMPA1.1 . To enable functional analyses of the role of MYC and its interaction with NFAT5 for osmoregulatory target gene transactivation this study generated multiple poly- and mono-clonal myca ko tilapia cell lines that can be used in combination with reporter assays 56 , 57 , molecular and cellular phenotyping 58 – 60 , and other approaches 61 , 62 to comprehensively characterize the role of MYC for teleost osmoregulation.…”