Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

BMC Genomics

Research Article

Sanushka Naidoo¹  Stanford Kwenda²  Aadi Moolam Ramesh²  Lucy N. Moleleki²  Paul R. J. Birch³  Enrico Rubagotti⁴  Vladimir Gorshkov⁵ 

[1] Department of Genetics, Forestry and Agricultural Biotechnology (FABI), University of Pretoria, Pretoria, South Africa;Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa;Division of Plant Sciences, College of Life Sciences, University of Dundee (at The James Hutton Institute), Errol Road, Invergowrie, DD25DA, Dundee, Scotland, UK;Genomics Research Institute, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa;Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia;Department of Botany and Plant Physiology, Kazan Federal University, Kazan, Russia;

关键词: Small RNAs;    Strand-specific RNA-seq;    Pectobacterium atrosepticum;    in silico;    Transcriptome;    Riboswitches;    5′ UTR;    3′ UTR;   

DOI  :  10.1186/s12864-016-2376-0

 received in 2015-09-03, accepted in 2016-01-06,  发布年份 2016

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Kwenda et al. 2016