In-silico detection and characterization of non-coding RNAs from the non-fermenting gram-negative bacilli Shewanella and Acinetobacter

GISELA PARMECIANO DI NOTO; SAREDA T.J. SCHRAMM; MATÍAS SACCOMANO; TOMÁS DEL GESSO; DANIELA CENTRÓN; MARÍA SOLEDAD RAMÍREZ; CECILIA QUIROGA

Congreso; ISCB Latinamerica 2016; 2016

Non-coding RNAs (ncRNAs) are key elements involved in several cellular processes. In bacteria,they can participate in the regulation of the response to environmental signals and metabolicpathways or in the protection of the host from exogenous material. The aim of this work was toidentify ncRNAs in the non-fermenting gram-negative bacilli Shewanella spp. and Acinetobacter spp.isolated from different niches using an in-silico approach and to analyze the secondary structure ofessential regulatory elements. Prediction of ncRNAs in 2 Shewanella and 2 Acinetobacter genomeswas done using 8 RNA families from the Rfam v.12.0 database as queries and run in the Infernalsoftware. We used a cut-off e-value > -5. We detected 258 candidates in the clinical strainShewanella sp. Sh95, 31 in the environmental strain S. frigidimarina Ag06-30, 33 in A. baumanniiA118, and 48 in Acinetobacter spp. A47. Most candidates were conserved in each genus. Wefocused on three ncRNAs i) mini-ykkC from strain Sh95, associated to quaternary ammoniumresistance determinants, ii) JumpStart, found in both Shewanella strains and involved in theregulation of capsule biogenesis; and iii) traJ-II, related to mobile genetic elements in Shewanellaand Acinetobacter. Analysis of the secondary structures using the Mfold software revealed that keyresidues were conserved, which suggests that these RNAs maintained their functionality. Ouranalysis allowed us to identify unique regulatory RNAs in Shewanella spp. and Acinetobacter spp.with the potential to regulate virulence factors,