Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. (December 2016)

• Record Type: Journal Article
• Authors: Kwenda, Stanford; Gorshkov, Vladimir; Ramesh, Aadi; Naidoo, Sanushka; Rubagotti, Enrico; Birch, Paul; Moleleki, Lucy
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 15
• Publication Date: 2016-12
• Subjects: Small RNAs -- Strand-specific RNA-seq -- Pectobacterium atrosepticum -- in silico prediction -- Transcriptome -- Riboswitches -- 5′ UTR -- 3′ UTR; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2376-0
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Small 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 RotEnterobacteriaceae (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. Results In the study reported herein, by using strand-specific RNA-seq analysis andin silico sRNA predictions, we describe the sRNA pool ofPectobacterium 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 bacteriumin silico . Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs inP. 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 theP. atrosepticum genome. Conclusions Since 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.