Abstract
BackgroundSmall RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood.ResultsIn the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome.ConclusionsSince many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2376-0) contains supplementary material, which is available to authorized users.
Highlights
Small RNAs have emerged as important regulatory molecules and have been studied in several bacteria
We demonstrated the efficiency of ssRNAseq in detecting sRNAs and determining the sRNA expression levels in response to specific bacterial growth conditions
Most of the identified sRNAs in P. atrosepticum are conserved within the soft rot enterobacteria (SRE) species suggesting their importance in physiological responses for the Soft Rot Enterobacteriaceae (SRE) species
Summary
Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. SRNAs play essential regulatory roles in diverse processes including metabolic reactions, stress response, biofilm formation and pathogenesis [3]. The importance of small RNAs (sRNAs) in bacterial gene expression regulation is broadly appreciated [1, 2]. They act as either activators or repressors of proteins and mRNAs. The length of most of the bacterial sRNAs ranges between 50 and 300 but can reach up to 500 nucleotides [4]. Trans-acting sRNAs typically regulate mRNAs encoded at different genomic locations on the chromosome in response to changes in environmental conditions [1].
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