In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1

Abstract

Background: Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. Due to these properties this bacterium has great potential as a commercial inoculant for agriculture. The H. seropedicae SmR1 genome is completely sequenced and annotated but despite the availability of diverse structural and functional analysis of this genome, studies involving small non-coding RNAs (sRNAs) has not yet been done. We have conducted computational prediction and RNA-seq analysis to select and confirm the expression of sRNA genes in the H. seropedicae SmR1 genome, in the presence of two nitrogen independent sources and in presence of naringenin, a flavonoid secreted by some plants.Results: This approach resulted in a set of 117 sRNAs distributed in riboswitch, cis-encoded and transencoded categories and among them 20 have Rfam homologs. The housekeeping sRNAs tmRNA, ssrS and 4.5S were found and we observed that a large number of sRNAs are more expressed in the nitrate condition rather than the control condition and in the presence of naringenin. Some sRNAs expression were confirmed in vitro and this work contributes to better understand the post transcriptional regulation in this bacterium. Conclusions: H. seropedicae SmR1 express sRNAs in the presence of two nitrogen sources and/or in the presence of naringenin. The functions of most of these sRNAs remains unknown but their existence in this bacterium confirms the evidence that sRNAs are involved in many different cellular activities to adapt to nutritional and environmental changes.

Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution

“…Among the unique ncRNAs in the typical A. salmonicida J223, we identified a betaproteobacteria toxic small RNA (tsRNA). tsRNA was previously described in Burkholderia cenocepacia and Herbaspirillum seropedicae, and the evidence suggests that it could regulate gene expression by binding to the ribosome-binding sequence of the mRNA [96]. Other ncRNAs seem to be related to plasmid replication, such as RNAI (RF00106), an antisense repressor that regulates plasmid replication in ColE1 plasmids [97].…”