PREDICTION OF NON-CODING RNA OF THE FIRST GENOME SEQUENCED Proteus mirabilis ISOLATED FROM TRACHEAL SECRETION

Proteus spp. bacteria are mostly known as opportunistic human pathogens Among the species of this genus, the most prevalent in infections in humans is Proteus mirabilis, a bacilli Gram-negative bacterium of Enterobacteriaceae family. P. mirabilis is an important pathogen frequently associated with nosocomial infection around the world. It is also observed that the size of the genome varies from 3.0377 to 5.0252 Mb. The Proteus mirabilis LBUEL-H11 strain was isolated from tracheal secretion of a hospitalized inpatient admitted to the University Hospital of the State University of Londrina in South of Brazil. This strain had its genome completely sequenced recently by our group. It presents a genome size of 4,534,929 bp. The computational approach is considered one of the most efficient method for locating non-coding RNA (ncRNA). A ncRNA is any RNA molecule that is not translated into protein and the term small RNA (sRNA) is still used for bacteria. In this work, we used the websites RNAspace (http://rnaspace.org) and Rfam (http://rfam.org), with the objective of to evaluate in silico prediction and annotation of non-coding RNAs in Proteus mirabilis LBUEL-H11 (GenBank acession QGGA01000000). The RNAspace is a platform which aims at providing an integrated environment for ncRNA prediction. The Rfam database is an annotated, open access database containing information about ncRNA families and other structured RNA elements. With the results generated by RNAspace, we send to Rfam and were obtained sixteen RNAs described, being that twelve were characterized (Alpha_RBS, HIV-1_SD, Parecho_CRE, RRE, SNORD17, bantam, rli, snR82, snoZ107_R87, snoZ247, sxy and yybP-ykoY) and four were not characterized (tRNA_Bacteria, Pseudomonas_sRNA_P9, CRISPR_RNA_direct_repeat_element, istR_Hfq_binding). About RNAs characterized in Rfam database, it was possible to observe non-coding RNAs present in some bacteria as Listeria monocytogenes, Haemophilus influenzae, Escherichia coli and Bacillus subtilis. There are no reports in the literature regarding the characterization and targets of ncRNA in P. mirabilis. But bacteria have several virulence factors that can be regulated by small non-coding RNAs. In conclusion, in silico analysis of Proteus mirabilis LBUEL-H11 strain, found sixteen RNAs described however, these molecules are only predicted. So these results are just a prediction, it is necessary to perform in vitro experimental validation as well as the search for the targets and understanding of its regulatory functions.