title: Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum.
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 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.
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. stan.kwenda@fabi.up.ac.za.
authors.forename: Stanford
authors.initials: S
authors.lastname: Kwenda
authors.affiliation: Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia. gvy84@mail.ru.|Department of Botany and Plant Physiology, Kazan Federal University, Kazan, Russia. gvy84@mail.ru.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Gorshkov
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. ramesh.santu@gmail.com.
authors.forename: Aadi Moolam
authors.initials: AM
authors.lastname: Ramesh
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology (FABI), University of Pretoria, Pretoria, South Africa. sanushka.naidoo@up.ac.za.
authors.forename: Sanushka
authors.initials: S
authors.lastname: Naidoo
authors.affiliation: Genomics Research Institute, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa. enrico.rubagotti@gmail.com.
authors.forename: Enrico
authors.initials: E
authors.lastname: Rubagotti
authors.affiliation: Division of Plant Sciences, College of Life Sciences, University of Dundee (at The James Hutton Institute), Errol Road, Invergowrie, Dundee, DD25DA, Scotland, UK. Paul.Birch@hutton.ac.uk.
authors.forename: Paul R J
authors.initials: PR
authors.lastname: Birch
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. lucy.moleleki@up.ac.za.
authors.forename: Lucy N
authors.initials: LN
authors.lastname: Moleleki
mesh_terms: D015964:Gene Expression Regulation, Bacterial; D044043:Pectobacterium / Q000235:genetics* / Q000472:pathogenicity; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D010944:Plants / Q000235:genetics / Q000382:microbiology; D058727:RNA, Small Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D058727:RNA, Small Untranslated