Kwenda, StanfordGorshkov, VladimirRamesh, Aadi MoolamNaidoo, SanushkaRubagotti, EnricoBirch, Paul R. J.Moleleki, Lucy N.2016-05-062016-05-062016-01-12Kwenda, S, Gorshkov, V, Ramesh, AM, Naidoo, S, Rubagotti E, Birch, PRJ & Moleleki, LN 2016, 'Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum', BMC Genomics, 17, art. #47, pp. 1-15.1471-216410.1186/s12864-016-2376-0http://hdl.handle.net/2263/52530Additional file 1: Table S1. Complete list of RNA-seq detected sRNAs (XLSX 19 kb)Additional file 2: Table S2. Predicted transcription start sites of RNA-seq detected sRNAs (XLSX 9114 kb)Additional file 3: Table S3. List of in silico predicted sRNAs using RITs from WebGester DB. S2A: Forward strand predictions. S2B: Complementary strand predictions (XLSX 30 kb)Additional file 4: Table S4. Combined list of predicted sRNA using SIPHT and RITs from WebGester DB. S3A: Matches of in silico predictions with SIPHT (forward strand) S3B: Matches of in silico predictions with SIPHT (complementary strand) (XLSX 15 kb)Additional file 5: Table S5. Conservation analysis in Soft Rot Enterobacteriaceae (XLSX 16 kb)Additional file 6: Table S6. Confirmation of RT-PCR amplicons by sequencing and BLASTn against respective sRNA sequences (XLSX 9 kb)Additional file 7: Table S7. Differentially expressed sRNA under nutrient-rich and starvation conditions (XLSX 19 kb)Additional file 8: Table S8. List of primers used for RT-PCR validation of novel sRNAs (DOCX 12 kb)Additional file 9: Table S9. List of primers used for RT-qPCR validation of RNA-seq expression data (DOCX 12 kb)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 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. RESULTS : In 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. 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.en© 2016 Kwenda et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.Strand-specific RNA-seqPectobacterium atrosepticumIn silico predictionTranscriptomeRiboswitches5′ UTR3′ UTRSmall RNAs (sRNAs)Soft Rot Enterobacteriaceae (SRE)Article