Abstract
BackgroundBacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system.ResultsA total of 47, 15 and 11 putative sRNAs were predicted in M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively. A comparative genomic analysis revealed the presence of species or lineage specific sRNA candidates. Furthermore, the expression profile of some M. hyopneumoniae sRNAs was determined by a reverse transcription amplification approach, in three different culture conditions. All tested sRNAs were transcribed in at least one condition. A detailed investigation revealed a differential expression profile for two M. hyopneumoniae sRNAs in response to oxidative and heat shock stress conditions, suggesting that their expression is influenced by environmental signals. Moreover, we analyzed sRNA-mRNA hybrids and accessed putative target genes for the novel sRNA candidates. The majority of the sRNAs showed interaction with multiple target genes, some of which could be linked to pathogenesis and cell homeostasis activity.ConclusionThis study contributes to our knowledge of Mycoplasma sRNAs and their response to environmental changes. Furthermore, the mRNA target prediction provides a perspective for the characterization and comprehension of the function of the sRNA regulatory mechanisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3061-z) contains supplementary material, which is available to authorized users.
Highlights
Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes
SRNAs present in the intergenic regions (IGRs) were searched as the input file, since all regions marked as coding sequence (CDS) and known ncRNAs, such as ribosomal RNAs (rRNA), transfer RNAs (tRNA), RNase P and others, were masked
The Single Genome ncRNA Search (SIGRS) outputs associate with distinct regions, defined some of them as unique ncRNA candidates
Summary
Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system. In bacterial genomes the non-coding RNAs (ncRNA) identified were the ribosomal RNAs (rRNA) and transfer RNAs (tRNA), which are important components of the protein synthesis machinery [1,2,3]. Analyses of asRNAs and sRNAs targets have shown that these ncRNAs could alter the translation process or mRNA stability by target base pairing [3,4,5,6]. Non-coding RNA elements present in many bacterial genomes add a further complexity to the comprehension of bacterial gene regulation [7]. There are evidences that ncRNAs may regulate important processes, such as pathogenesis, iron metabolism, and quorum sensing [4, 11, 12]
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