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Cited by 306Bacterial Genetics and BiotechnologyBiochemical and Molecular ResearchMicrobial Metabolic Engineering and Bioproduction

Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis

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Eymann, Christine, Homuth, Georg, Scharf, Christian, Hecker, Michael·2002·Journal of Bacteriology
DOI 10.1128/jb.184.9.2500-2520.2002PMC PMC134987
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Abstract

The stringent response in Bacillus subtilis was characterized by using proteome and transcriptome approaches. Comparison of protein synthesis patterns of wild-type and relA mutant cells cultivated under conditions which provoke the stringent response revealed significant differences. According to their altered synthesis patterns in response to dl-norvaline, proteins were assigned to four distinct classes: (i) negative stringent control, i.e., strongly decreased protein synthesis in the wild type but not in the relA mutant (e.g., r-proteins); (ii) positive stringent control, i.e., induction of protein synthesis in the wild type only (e.g., YvyD and LeuD); (iii) proteins that were induced independently of RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA (e.g., glycolytic enzymes). Transcriptome studies based on DNA macroarray techniques were used to complement the proteome data, resulting in comparable induction and repression patterns of almost all corresponding genes. However, a comparison of both approaches revealed that only a subset of RelA-dependent genes or proteins was detectable by proteomics, demonstrating that the transcriptome approach allows a more comprehensive global gene expression profile analysis. The present study presents the first comprehensive description of the stringent response of a bacterial species and an almost complete map of protein-encoding genes affected by (p)ppGpp. The negative stringent control concerns reactions typical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.). Negatively controlled unknown y-genes may also code for proteins with a specific function during growth and reproduction (e.g., YlaG). On the other hand, many genes are induced in a RelA-dependent manner, including genes coding for already-known and as-yet-unknown proteins. A passive model is preferred to explain this positive control relying on the redistribution of the RNA polymerase under the influence of (p)ppGpp.

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  • In B. subtilis, ylbN has been observed to be downregulated by the stringent response.

    “Previously, in B. subtilis,77ylbN has been observed to be downregulated by the stringent response (for example, by the alarmone metabolite ppGpp that is synthesized by a gene present in JCVI-syn3A relA/041478), whereby a cell reduces its growth activity to conserve energy often by decreasing the generation of ribosomes.79”

    From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [78]

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Authors
Eymann, C., Homuth, G., Scharf, C., & Hecker, M.
Affiliations
Universität Greifswald (DE)
Corresponding author
Hecker, Michael
ORCID
Venue
Journal of Bacteriology
Publisher
American Society for Microbiology
Published
2002-05
Volume
184
Issue
9
Pages
2500-2520
ISSN
  • 0021-9193 (ISSN-L)
  • 1098-5530
DOI
10.1128/jb.184.9.2500-2520.2002
PMC
PMC134987
OpenAlex
W2161630640
Cited by
306
References
96
Citations by year
2026: 10 · 2025: 8 · 2024: 3 · 2023: 5 · 2022: 5 · 2021: 6 · 2020: 16 · 2019: 2 · 2018: 9 · 2017: 12 · 2016: 5 · 2015: 9 · 2014: 12 · 2013: 7 · 2012: 12
FWCI
12.77
Type
journal article
Language
en
Open access
Licence
journals.asm.org/non-commercial-tdm-license (tdm)
Locations
  • Journal of Bacteriology (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Fonds der Chemischen Industrie
  • Deutsche Forschungsgemeinschaft
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Molecular Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords
stringent response, Bacillus subtilis, RelA, (p)ppGpp, protein synthesis regulation, transcriptome, proteome, gene expression profiling, ribosome biogenesis, glycolytic enzymes
MeSH terms
Bacillus subtilis, Bacterial Proteins, Guanosine Tetraphosphate, Ligases, RNA, Messenger, Transcription, Genetic, Protein Biosynthesis, Valine, Electrophoresis, Gel, Two-Dimensional, Gene Expression, Gene Expression Regulation, Bacterial, DNA, Complementary, Regulon, Oligonucleotide Array Sequence Analysis, Proteome

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