Annotation of Genes for RNA Degradosome Complex in Kytococcus sedentarius

Abstract

It has been reported that the microorganism responsible for causing pitted keratolysis is Kytococcus sedentarius. This aerobic, gram-positive bacterium secretes two serine proteases that lead to the formation of pitted keratolysis, and has also been known to produce natural antibiotics. Both of these observations generated interest in the investigation of its genome. The purpose of this study was to predict the proteins and enzymes that form the RNA degradosome complex in this bacterium. The function of RNA degradosome is to degrade mRNA to regulate gene expression in the cell. Gene annotation was performed by evaluating sequence homology, cellular localization, DNA coordinates of the open reading frame, domain prediction, enzymatic function, horizontal gene transfer and gene duplication and degradation. Using IMG-ACT, bioinformatics tools such as BLAST, TMHMM, Psortb, KEGG, MetaCyc, Pfam, Drawtree were used to functionally annotate the proteins. The analysis involved recognition of conserved domains across families and super-families by establishing homology amongst multiple sequences and assigning a function to the gene. The presence of pseudogenes and lateral gene transfer was verified by ascertaining the phylogenetic history of the genes and inspection of the gene neighborhood map. The presence of protein subunits belonging to different degradosome complexes was determined,and Kytococcus was observed to contain three enzymatic components to form a multi-protein complex for RNA degradosome complex type C: RNase E, ATP dependant helicase RecQ and Rho transcription terminating factor. Thus, it can be hypothesized that RNA degradosome complex type C is the predominant RNA degrading machinery for the microorganism.