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<p>Bacterial genomes frequently harbor extrachromosomal replicons (ERs) that promote genome plasticity and adaptation, ranging from small plasmids to chromosome-scale replicons. In a few model organisms, including <i>Vibrio cholerae</i> and <i>Agrobacterium tumefaciens</i>, large ERs are coordinated with chromosome replication and cell-cycle organization by specific molecular mechanisms. Whether this applies broadly across bacteria remains unknown. Here, we analyzed more than 40,000 complete bacterial genomes to update the distribution of ERs across bacterial taxa. Their GC content converged toward that of the chromosome with increasing ER size, revealing a size-dependent trend toward chromosomal composition. Such large ERs were found as conserved genomic features in many distinct genera, consistent with independent acquisition and long-term maintenance. We selected representative strains from these lineages, spanning five taxonomic classes across three bacterial phyla, to investigate replication dynamics and spatial organization. Marker frequency analysis showed that these large ERs are maintained at the same copy number as the chromosome and often complete replication synchronously. Chromosome conformation capture further revealed frequent ER–chromosome contacts, including origin–origin interactions and extended contacts along replicated arms. Together, this exploratory study lays the groundwork for uncovering new mechanisms coordinating large-ER maintenance with the bacterial chromosome.</p>

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Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月2日

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  • Jakub Czarnecki,
  • Morgan Lamberioux,
  • Ole Skovgaard,
  • Amaury Bignaud,
  • Najwa Taib,
  • Théophile Niault,
  • Jasmin Ostermayer,
  • Pascale Bourhy,
  • Julia Bos,
  • Elvira Krakowska,
  • Dariusz Bartosik,
  • Romain Koszul,
  • Martial Marbouty,
  • Didier Mazel,
  • Marie-Eve Val

摘要

Bacterial genomes frequently harbor extrachromosomal replicons (ERs) that promote genome plasticity and adaptation, ranging from small plasmids to chromosome-scale replicons. In a few model organisms, including Vibrio cholerae and Agrobacterium tumefaciens, large ERs are coordinated with chromosome replication and cell-cycle organization by specific molecular mechanisms. Whether this applies broadly across bacteria remains unknown. Here, we analyzed more than 40,000 complete bacterial genomes to update the distribution of ERs across bacterial taxa. Their GC content converged toward that of the chromosome with increasing ER size, revealing a size-dependent trend toward chromosomal composition. Such large ERs were found as conserved genomic features in many distinct genera, consistent with independent acquisition and long-term maintenance. We selected representative strains from these lineages, spanning five taxonomic classes across three bacterial phyla, to investigate replication dynamics and spatial organization. Marker frequency analysis showed that these large ERs are maintained at the same copy number as the chromosome and often complete replication synchronously. Chromosome conformation capture further revealed frequent ER–chromosome contacts, including origin–origin interactions and extended contacts along replicated arms. Together, this exploratory study lays the groundwork for uncovering new mechanisms coordinating large-ER maintenance with the bacterial chromosome.