{
  "abstract": "The alternative sigma factor RpoS (σS) governs stress adaptation in many bacterial clades, yet how it coordinates stress responses with metabolic demands remains poorly understood. Thus, by integrating RNA-seq, ChIP-seq, and physiological and molecular assays, we redefined the RpoS regulon in Escherichia coli, expanding it to 667 genes and demonstrating that metabolic genes unexpectedly predominate over stress-response targets. RpoS directly drives a massive metabolic reprogramming event: it activates glycolytic and sugar transport genes while simultaneously repressing the trichloroacetic acid cycle and oxidative phosphorylation. This metabolic pivot is finely tuned by a novel RpoS-CRP-cAMP-Cra tripartite circuit to balance energy efficiency with survival during stationary phase. Furthermore, we provide a mechanistic framework for RpoS-mediated bidirectional regulation rooted in σS-factor competition, where transcriptional efficiency in the absence of RpoS dictates the regulatory mode: highly efficient promoters are repressed by RpoS displacement, whereas weak promoters are activated. This study advances our understanding of transcriptional precision during bacterial adaptation and offers an architectural blueprint for synthetic metabolic engineering.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University , Nanjing, Jiangsu 210003 ,",
    "Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University , Shenzhen, Guangdong 518060 ,",
    "School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, Pokfulam, SAR , Hong Kong 999077 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Wenbo Chen",
      "orcid": "0009-0007-6323-1913"
    },
    {
      "affs": [
        1
      ],
      "name": "Yong Feng"
    },
    {
      "affs": [
        1
      ],
      "name": "Lin Liu"
    },
    {
      "affs": [
        1
      ],
      "name": "Rao Ma"
    },
    {
      "affs": [
        2
      ],
      "name": "Antoine Danchin",
      "orcid": "0000-0002-6350-5001"
    },
    {
      "affs": [
        0
      ],
      "name": "Conghui You",
      "orcid": "0009-0003-1289-6422"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fzbtf1c1hcg1h.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag982",
  "fulltext_url": null,
  "id": "fzbtf1c1hcg1h",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag982/8915331",
  "language": null,
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1311|Bacterial Genetics and Biotechnology"
    ]
  ],
  "openalex": "W7221800971",
  "pdf_url": "https://academic.oup.com/nar/article-pdf/54/19/gkag982/71925367/gkag982.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-14",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/fzbtf1c1hcg1h.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag982",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag982/8915331"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Bacterial Genetics and Biotechnology",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "A tripartite RpoS-CRP-cAMP-Cra circuit orchestrates metabolic reprogramming during stress adaptation",
  "title_text": "A tripartite RpoS-CRP-cAMP-Cra circuit orchestrates metabolic reprogramming during stress adaptation",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:50Z",
  "url": "https://research.draconitic.com/paper/fzbtf1c1hcg1h",
  "venue": "Nucleic Acids Research",
  "versions": []
}