In silico identification and expression analysis of MscS like gene family in rice

Abstract

Mechanosensitive channels are membrane proteins that open and shut in response to mechanical forces produced by osmotic pressure, sound, touch and gravity. These channels are involved in multiple physiological functions including hypoosmotic pressure, pain, hearing, blood pressure and cell volume regulation. In plants, these channels play a major role in proprioception, gravity sensing and maintenance of plastid shape and size. In the present study, we identified the mechanosensitive channel of small conductance like (MscS) homologue gene family in rice and analyzed their structure, phylogenetic relationship, localization and expression pattern. Five MscS like genes of rice (OsMSL) were found to be distributed on four chromosomes and clustered into two major groups. Subcellular localization predictions of the OsMSL family revealed their localization to plasma membrane, plastid envelope and mitochondria. The predicted gene structure, bonafide conserved signature motif, domain and the presence of transmembrane regions in each OsMSL strongly supported their identity as members of MscS-like gene family. Furthermore, in silico expression analysis of OsMSL genes revealed differential regulation patterns in tissue specific and abiotic stress libraries. These findings indicate that the in silico approach used here successfully identified in a genome-wide context MscS like gene family in rice, and further suggest the functional importance of MscS-like genes in rice.

Genome-wide analysis of mechanosensitive channel of small conductance (MscS)-like gene family in common bean

“…Conserved motif PF(X12-16)GXV(X20-21)PN(X9)N was identified at C-terminal for the TM domain in Class I MSL in common bean (PvMSL1, PvMSL2, PvMSL3 and PvMSL4). Class I proteins align relatively closely to E. coli MsSC and their C-terminal TM domains (Pivetti et al, 2003;Saddhe and Kumar, 2015). Proteins in Class II showed the presence of consensus sequence F(X3)P(X3)GD(X10-14)V(X20-21)PN(X7)IXNXXR at the C-terminal TM domain in P. vulgaris (PvMSL5, PvMSL6, PvMSL7, PvMSL8 and PvMSL9) ( Figure 1B).…”

“…Generally, the number of MSL genes distribution in dicotyledons is nearly double than in monocotyledons, possibly due to the higher rate of genome duplication events in the former. In Arabidopsis, Saddhe and Kumar (2015) attributed this to four different major genome duplication events over 100 to 200 million years ago. Moreover, the number of MSL genes in P. vulgaris is not associated with the size of the genome itself.…”

“…In agreement with a previous analysis by Pivetti et al (2003), the conserved motif includes most C-terminal TM domain and surrounding sequence in E. coli. Generally, members of MscS family have good conservation throughout the TM3 helix (Pivetti et al, 2003;Miller et al, 2003;Saddhe and Kumar, 2015).…”

“…The MaximumLikelihood (ML) phylogenetic tree divided MSL genes into two classes (Figures 3 and 4), supported by bootstrap values and the occurrence of conserved protein motifs ( Figure 4A and B). In Arabidopsis and rice, two classes, I and II, have been classified (Haswell and Meyerowitz, 2006;Saddhe and Kumar, 2015) and the corresponding groups in common bean are labeled in Figures 3 and 4A. The Class I and II common bean contains four and five PvMSL genes, respectively, according to the classification in Arabidopsis.…”

“…MS ion channels were characterized in Arabidopsis thaliana and Oriza sativa model plants (Haswell and Meyerowitz, 2006;Saddhe and Kumar, 2015). In Arabidopsis and rice, ten and five MscS homologs, respectively, were identified and classified into two main classes, Class I and Class II.…”