The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.

We have used differential RNA-seq (dRNA-seq) to characterise the transcriptomic architecture of S. Typhimurium SL1344, and its dependence on the bacterial alarmone, guanosine tetraphosphate (ppGpp) during late stationary phase, (LSP). Under LSP conditions we were able to identify the transcriptional...

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Main Authors: Vinoy K Ramachandran, Neil Shearer, Arthur Thompson
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2014-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC3963941?pdf=render
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spelling doaj-7b9a07703fc341f686c1f95acda77a742020-11-24T21:38:22ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0193e9269010.1371/journal.pone.0092690The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.Vinoy K RamachandranNeil ShearerArthur ThompsonWe have used differential RNA-seq (dRNA-seq) to characterise the transcriptomic architecture of S. Typhimurium SL1344, and its dependence on the bacterial alarmone, guanosine tetraphosphate (ppGpp) during late stationary phase, (LSP). Under LSP conditions we were able to identify the transcriptional start sites (TSSs) for 53% of the S. Typhimurium open reading frames (ORFs) and discovered 282 candidate non-coding RNAs (ncRNAs). The mapping of LSP TSSs enabled a detailed comparison with a previous dRNA-seq study of the early stationary phase (ESP) transcriptional architecture of S. Typhimurium SL1344 and its dependence on ppGpp. For the purposes of this study, LSP was defined as an aerobic LB culture grown to a later optical density reading (OD600 = 3.6) compared to ESP (OD600 = 2.3). The precise nucleotide positions of the majority of S. Typhimurium TSSs at LSP agreed closely with those identified at ESP. However, the identification of TSSs at different positions, or where additional or fewer TSSs were found at LSP compared to ESP enabled the genome-wide categorisation of growth phase dependent changes in promoter structure, the first time such an analysis has been done on this scale. Comparison of the ppGpp-dependency LSP and ESP TSSs for mRNAs and ncRNAs revealed a similar breadth of ppGpp-activation and repression. However, we note several ncRNAs previously shown to be involved in virulence were highly ppGpp-dependent at LSP. Finally, although SPI1 was expressed at ESP, we found SPI1 was not as highly expressed at LSP, instead we observed elevated expression of SPI2 encoded genes. We therefore also report an analysis of SPI2 transcriptional architecture at LSP resulting in localisation of SsrB binding sites and identification of a previously unreported SPI2 TSS. We also show that ppGpp is required for nearly all of SPI2 expression at LSP as well as for expression of SPI1 at ESP.http://europepmc.org/articles/PMC3963941?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Vinoy K Ramachandran
Neil Shearer
Arthur Thompson
spellingShingle Vinoy K Ramachandran
Neil Shearer
Arthur Thompson
The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.
PLoS ONE
author_facet Vinoy K Ramachandran
Neil Shearer
Arthur Thompson
author_sort Vinoy K Ramachandran
title The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.
title_short The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.
title_full The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.
title_fullStr The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.
title_full_unstemmed The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.
title_sort primary transcriptome of salmonella enterica serovar typhimurium and its dependence on ppgpp during late stationary phase.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2014-01-01
description We have used differential RNA-seq (dRNA-seq) to characterise the transcriptomic architecture of S. Typhimurium SL1344, and its dependence on the bacterial alarmone, guanosine tetraphosphate (ppGpp) during late stationary phase, (LSP). Under LSP conditions we were able to identify the transcriptional start sites (TSSs) for 53% of the S. Typhimurium open reading frames (ORFs) and discovered 282 candidate non-coding RNAs (ncRNAs). The mapping of LSP TSSs enabled a detailed comparison with a previous dRNA-seq study of the early stationary phase (ESP) transcriptional architecture of S. Typhimurium SL1344 and its dependence on ppGpp. For the purposes of this study, LSP was defined as an aerobic LB culture grown to a later optical density reading (OD600 = 3.6) compared to ESP (OD600 = 2.3). The precise nucleotide positions of the majority of S. Typhimurium TSSs at LSP agreed closely with those identified at ESP. However, the identification of TSSs at different positions, or where additional or fewer TSSs were found at LSP compared to ESP enabled the genome-wide categorisation of growth phase dependent changes in promoter structure, the first time such an analysis has been done on this scale. Comparison of the ppGpp-dependency LSP and ESP TSSs for mRNAs and ncRNAs revealed a similar breadth of ppGpp-activation and repression. However, we note several ncRNAs previously shown to be involved in virulence were highly ppGpp-dependent at LSP. Finally, although SPI1 was expressed at ESP, we found SPI1 was not as highly expressed at LSP, instead we observed elevated expression of SPI2 encoded genes. We therefore also report an analysis of SPI2 transcriptional architecture at LSP resulting in localisation of SsrB binding sites and identification of a previously unreported SPI2 TSS. We also show that ppGpp is required for nearly all of SPI2 expression at LSP as well as for expression of SPI1 at ESP.
url http://europepmc.org/articles/PMC3963941?pdf=render
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