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

Stanford Kwenda, Vladimir Gorshkov, Aadi Moolam Ramesh, Sanushka Naidoo, Enrico Rubagotti, Paul R J Birch, Lucy N. Moleleki (Lead / Corresponding author)

Research output: Contribution to journalArticle

8 Citations (Scopus)
21 Downloads (Pure)

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.

Original languageEnglish
Article number47
Number of pages15
JournalBMC Genomics
Volume17
DOIs
Publication statusPublished - 12 Jan 2016

Fingerprint

Pectobacterium
RNA
Starvation
Enterobacteriaceae
Computer Simulation

Keywords

  • 3' UTR
  • 5' UTR
  • in silico prediction
  • Pectobacterium atrosepticum
  • Riboswitches
  • Small RNAs
  • Strand-specific RNA-seq
  • Transcriptome

Cite this

Kwenda, Stanford ; Gorshkov, Vladimir ; Ramesh, Aadi Moolam ; Naidoo, Sanushka ; Rubagotti, Enrico ; Birch, Paul R J ; Moleleki, Lucy N. / Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. In: BMC Genomics. 2016 ; Vol. 17.
@article{6f8adc532fb14c638fc1ac1c7fd78608,
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.",
keywords = "3' UTR, 5' UTR, in silico prediction, Pectobacterium atrosepticum, Riboswitches, Small RNAs, Strand-specific RNA-seq, Transcriptome",
author = "Stanford Kwenda and Vladimir Gorshkov and Ramesh, {Aadi Moolam} and Sanushka Naidoo and Enrico Rubagotti and Birch, {Paul R J} and Moleleki, {Lucy N.}",
year = "2016",
month = "1",
day = "12",
doi = "10.1186/s12864-016-2376-0",
language = "English",
volume = "17",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "Springer Verlag",

}

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. / Kwenda, Stanford; Gorshkov, Vladimir; Ramesh, Aadi Moolam; Naidoo, Sanushka; Rubagotti, Enrico; Birch, Paul R J; Moleleki, Lucy N. (Lead / Corresponding author).

In: BMC Genomics, Vol. 17, 47, 12.01.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

AU - Kwenda, Stanford

AU - Gorshkov, Vladimir

AU - Ramesh, Aadi Moolam

AU - Naidoo, Sanushka

AU - Rubagotti, Enrico

AU - Birch, Paul R J

AU - Moleleki, Lucy N.

PY - 2016/1/12

Y1 - 2016/1/12

N2 - 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.

AB - 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.

KW - 3' UTR

KW - 5' UTR

KW - in silico prediction

KW - Pectobacterium atrosepticum

KW - Riboswitches

KW - Small RNAs

KW - Strand-specific RNA-seq

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=84953923815&partnerID=8YFLogxK

U2 - 10.1186/s12864-016-2376-0

DO - 10.1186/s12864-016-2376-0

M3 - Article

VL - 17

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 47

ER -