For the most part, these sRNAs affect target genes in a negative fashion by binding to the region surrounding the start codon and ribosome binding site, but can act through base pairing in a region far upstream, and occasionally affect translation positively (for review see [ 1]).
This suggests that these sRNAs affect functions that are not required under the conditions tested or that additional sRNAs with redundant functions may exist.
It has been shown that sRNAs affect mRNA degradation and translation and modulate protein activity [ 14, 16].
This finding has functional importance since most sRNAs bind through the proximal site.
Thus, again very strong positive and negative expression correlations were only observed for sRNAs from certain sRNA clusters, while most sRNAs originating from the same sRNA clusters were only slightly positively correlated with each other.
We determined the sRNA sequences in our V. parahaemolyticus strains and found that most sRNAs were highly conserved (Additional file 2: Table S2).
Thus, although strong expression correlations, either positive or negative, were observed between specific sRNAs and their mother gene, the expression levels of most sRNAs were not correlated with their mother genes, suggesting independent transcription of sRNAs and mRNAs.
We primarily employed recommended default settings to identify most sRNA features.
Transcript levels for most sRNA sizes were obviously decreased in the 25 DAP samples.
For all samples except HAE and TAE, most sRNA sequences were clustered into miRNA sequences.
