Global analysis of sRNA target genes in Mycoplasma hyopneumoniae

Abstract

BackgroundSmall RNAs (sRNAs) are noncoding molecules that regulate different cellular activities in several bacteria. The role of sRNAs in gene expression regulation is poorly characterized in the etiological agent of porcine enzootic pneumonia Mycoplasma hyopneumoniae. We performed a global analysis of the sRNAs, sRNA target genes and regulatory elements previously identified in their genome and analyzed the expression of some sRNAs and their target genes by quantitative RT-PCR (qPCR) in three different culture conditions.ResultsSeven of the 145 sRNA target genes are organized as monocistronic genes (mCs) while the other 138 sRNA target genes are organized into transcriptional units (TU). The identification of transcriptional regulatory elements (promoter motif, DNA repeat sequence or intrinsic terminator) was verified in 116 of the 145 sRNA target genes. Moreover, the 29 sRNA target genes without regulatory elements revealed the presence of at least one regulatory element in the boundaries of the TU or in other internal genes of the TU. We verified that 16 sRNAs showed differential expression, seven in heat shock condition and 14 in oxidative stress condition. Analysis of the differential expression of the sRNA target genes showed that the tested sRNAs possibly regulate gene expression. The sRNA target genes were up- or down-regulated possibly in response to sRNA only under oxidative stress condition. Moreover, the sRNA target genes are involved in diverse processes of the cell, some of which could be linked to transcription processes and cell homeostasis.ConclusionOur results indicate that bacterial sRNAs could regulate a number of targets with various outcomes, and different correlations between the levels of sRNA transcripts and their target gene mRNAs were found, which suggest that the regulation of gene expression via sRNAs may play an important role in mycoplasma.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5136-5) contains supplementary material, which is available to authorized users.

Bioinformatic and experimental methods to identify and validate bacterial RNA-human RNA interactions

“…Short non-coding RNAs are regulatory molecules that are able to modulate gene expression via base pairing with a potential target transcript 14. Eukaryotic short non-coding RNAs often take the form of microRNAs (miRNA) which are processed from miRNA genes,15 while in bacteria, short non-coding RNAs are called small RNAs (sRNAs) and are generally derived from intergenic regions 1617. tRNA fragments are considered a type of sRNA,1819 and are found in bacterial EVs 9.…”

“…14 Eukaryotic short non-coding RNAs often take the form of microRNAs (miRNA) which are processed from miRNA genes, 15 while in bacteria, short non-coding RNAs are called small RNAs (sRNAs) and are generally derived from intergenic regions. 16 17 tRNA fragments are considered a type of sRNA, 18 19 and are found in bacterial EVs. 9 Additionally, both rRNA and tRNA fragments have been implicated in inducing apoptosis in human cells.…”

Small noncoding RNA sRNA0426 is involved in regulating biofilm formation in Streptococcus mutans

“…And the most stable predicted binding sites between the biofilm-associated mRNAs and sRNA0426 are not limited in the seed sequence. Therefore, the seed sequence of sRNA0426 might serve an important role for sRNA0426, but the association between it and the function of sRNA0426 in S. mutants on biofilm formation is needed to be further verified (Fritsch, Siqueira, & Schrank, 2018).…”