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| Status |
Public on Sep 17, 2016 |
| Title |
Genome-Wide Transcriptional Profiling of Salmonella Typhimurium Epiphytically Colonizing Tomato Points to Anaerobic Respiration, and Nitrosative and Oxidative Stress Responses |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Foodborne illness from contaminated fresh produce has increased over the past decade, with the enteric human pathogen Salmonella enterica being frequently implicated in foodborne illness outbreaks associated with tomato consumption. Our previous work demonstrated that Salmonella responds to tomato cultivar differences, but knowledge of the underlying genetic responses is limited. To identify the mechanisms permitting this human pathogen-plant commodity association, a genome-wide transcriptomic analysis of Salmonella on tomato shoots and roots was conducted using an RNA-seq approach. Expression signal for 4,556 out of 4,745 annotated chromosomal and plasmid genes was obtained, indicating >96% coverage of the whole S. Typhimurium transcriptome. Identified key signals of differential expression related to cellular processes preserving viability while dealing with multiple biotic stresses and limited nutrient availability, compared to growth in nutrient-rich medium. Data suggest that sulfur metabolism, anaerobic respiration, nitrosative and oxidative stress tolerance and biofilm formation may be crucial functions for Salmonella survival on tomato. Some effector protein genes from pathogenicity island-2 were expressed, though their function in this niche is largely unknown. A large proportion of up-regulated genes remain uncharacterized, pointing to as yet undescribed strategies that allow enteric pathogens to associate with plants during transit in the environment to herbivorous hosts.
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| Overall design |
mRNA profiles of Salmonella Typhimurium while epiphytically colonizing tomato plants were generated by RNA-seq, in triplicate, using Illumina HiSeq 100bp-PE.
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| Contributor(s) |
Han S, Ferelli AM, Lin S, Micallef SA |
| Citation(s) |
33024855 |
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| Submission date |
Sep 18, 2015 |
| Last update date |
Oct 13, 2020 |
| Contact name |
Sanghyun Han |
| E-mail(s) |
h.sanghyun@gmail.com
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| Organization name |
RDA-NAAS
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| Street address |
166 Nong-Saeng-Myung-Ro
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| City |
Wan-Ju-Goon |
| ZIP/Postal code |
55365 |
| Country |
South Korea |
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| Platforms (1) |
| GPL20934 |
Illumina HiSeq 1000 (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA296349 |
| SRA |
SRP063839 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE73192_SampleSheet.csv.gz |
233 b |
(ftp)(http) |
CSV |
| GSE73192_cds_chromosome_exp.diff.gz |
426.6 Kb |
(ftp)(http) |
DIFF |
| GSE73192_cds_plasmid_exp.diff.gz |
8.4 Kb |
(ftp)(http) |
DIFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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