ArticleBMC genomics2012
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 34 citations in OpenAlex.
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- σFrontiers in microbiology · 2021Article
- Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria.Bio-protocol · 2020Article
- Survival of the Fittest: The Relationship of (p)ppGpp With Bacterial Virulence.Frontiers in microbiology · 2020Review
- Guanosine tetraphosphate relieves the negative regulation of Salmonella pathogenicity island-2 gene transcription exerted by the AT-rich ssrA discriminator region.Scientific reports · 2018Article
- The Stringent Response-Regulated sRNA Transcriptome ofFrontiers in cellular and infection microbiology · 2018Article
- Genome-wide primary transcriptome analysis of HScientific reports · 2017Article
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- Bacterial antisense RNAs are mainly the product of transcriptional noise.Science advances · 2016Article
- Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells.BMC genomics · 2015Article
- Article
- TSSAR: TSS annotation regime for dRNA-seq data.BMC bioinformatics · 2014Article
- Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella.PloS one · 2014Article
- The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase.PloS one · 2014Article
- The RNA chaperone Hfq impacts growth, metabolism and production of virulence factors in Yersinia enterocolitica.PloS one · 2014Article
- S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA.RNA (New York, N.Y.) · 2013Article
- Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria.BMC genomics · 2013Article
- Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.Molecular bioSystems · 2013Article
- A connecter-like factor, CacA, links RssB/RpoS and the CpxR/CpxA two-component system in Salmonella.BMC microbiology · 2012Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundInvasion of intestinal epithelial cells by Salmonella enterica serovar Typhimurium (S. Typhimurium) requires expression of the extracellular virulence gene expression programme (ST(EX)), activation of which is dependent on the signalling molecule guanosine tetraphosphate (ppGpp). Recently, next-generation transcriptomics (RNA-seq) has revealed the unexpected complexity of bacterial transcriptomes and in this report we use differential RNA sequencing (dRNA-seq) to define the high-resolution transcriptomic architecture of wild-type S. Typhimurium and a ppGpp null strain under growth conditions which model ST(EX). In doing so we show that ppGpp plays a much wider role in regulating the S. Typhimurium ST(EX) primary transcriptome than previously recognised.
resultsHere we report the precise mapping of transcriptional start sites (TSSs) for 78% of the S. Typhimurium open reading frames (ORFs). The TSS mapping enabled a genome-wide promoter analysis resulting in the prediction of 169 alternative sigma factor binding sites, and the prediction of the structure of 625 operons. We also report the discovery of 55 new candidate small RNAs (sRNAs) and 302 candidate antisense RNAs (asRNAs). We discovered 32 ppGpp-dependent alternative TSSs and determined the extent and level of ppGpp-dependent coding and non-coding transcription. We found that 34% and 20% of coding and non-coding RNA transcription respectively was ppGpp-dependent under these growth conditions, adding a further dimension to the role of this remarkable small regulatory molecule in enabling rapid adaptation to the infective environment.
conclusionsThe transcriptional architecture of S. Typhimurium and finer definition of the key role ppGpp plays in regulating Salmonella coding and non-coding transcription should promote the understanding of gene regulation in this important food borne pathogen and act as a resource for future research.
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