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| Status |
Public on Jan 26, 2016 |
| Title |
Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum |
| Organism |
Pectobacterium atrosepticum SCRI1043 |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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 the adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. 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 response. 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: 63 sRNAs were differentially expressed with 57 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST (e-value < 0.001) showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. A large number of these sRNAs is starvation-induced, suggesting their role in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.
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| Overall design |
sRNA profiles from P. atrosepticum SCRI1043 cells existing under growth-promoting and starvation conditions were generated using Strand-specific RNA sequencing
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| Contributor(s) |
Kwenda S, Gorshkov V, Rubagotti E, Birch P, Moleleki LN |
| Citation(s) |
26753530, 28081189 |
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| Submission date |
May 05, 2015 |
| Last update date |
Sep 12, 2019 |
| Contact name |
Stanford Kwenda |
| E-mail(s) |
[email protected]
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| Organization name |
University of Pretoria
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| Department |
Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)
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| Lab |
9-5 New Agricultural Building
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| Street address |
Lunnon Road, Hilcrest
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| City |
Pretoria |
| State/province |
Gauteng |
| ZIP/Postal code |
0028 |
| Country |
South Africa |
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| Platforms (1) |
| GPL20147 |
Illumina HiSeq 2000 (Pectobacterium atrosepticum SCRI1043) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA283104 |
| SRA |
SRP058005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68547_Table_S5_sRNA_differential_expression_analysis_revsd-1.xlsx |
14.4 Kb |
(ftp)(http) |
XLSX |
| GSE68547_sRNA_countsList.tab.gz |
2.2 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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