Evolutionary constraints on RNA polymerase gene positioning in the genome of fast-growing bacteria

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Abstract
How gene order along chromosomes affects cellular homeostasis and genome evolution remains poorly understood. Bacterial chromosomes are organized along the replication origin (oriC)–terminus (ter) axis. The spatial arrangement of genes within this axis may influence cellular physiology, genome evolution, and transcriptional regulation. We tested the importance of the universally conserved rplKAJL-rpoBC locus, which encodes the β/β′ subunits of the sole bacterial RNA polymerase (RNAP), by relocating it to different genomic positions in the fast-growing pathogen Vibrio cholerae. Relocation close from locus native site was neutral but relocating it near either chromosomal terminus reduced exponential growth and competitive fitness specifically in nutrient-rich media. Marker-frequency analysis showed that distal positioning lowered locus copy number from ~3 to ~1 per cell, causing a 20%–25% depletion in cellular RNAP without altering its subcellular distribution. Introducing an additional oriC-proximal copy restored wild-type phenotypes, whereas two terminus copies rescued growth solely through increased dosage. Deleting the oriC-proximal RNAP genes reproduced all defects, identifying them as the primary drivers. Selection keeps RNAP genes close to oriC to harness replication-associated dosage increment during exponential growth, ensuring adequate transcription capacity for rapid proliferation. Gene order is a key but overlooked layer of bacterial genome evolution and ecological adaptation.
Funding Information
  • International Center for Genetic Engineering and Biotechnology (CRP/ARG18-06_EC)
  • Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (PICT-2017-0424)
  • Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (PICT-2018-0476)
  • Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (PICT-2020-SERIEA-00521)
  • UNSAM
  • ECOS-SUD France-Argentina Program ((A18ST06)
  • Institut National de la Santé et de la Recherche Médicale
  • Centre National de la Recherche Scientifique (CNRS-UMR 3525)
  • French National Research Agency (ANR-10-LABX62-IBEID)
  • Ministère de l’Enseignement Supérieur et de la Recherche (ANR-23-CE12-0005)
  • Gordon and Betty Moore Foundation (GBMF9319)
  • Allen Foundation

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