Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion
ABSTRACT Multipartite bacterial genome organization can confer advantages, including coordinated gene regulation and faster genome replication, but is challenging to maintain. Agrobacterium tumefaciens lineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmi...
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American Society for Microbiology
2025-06-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.01046-25 |
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| author | Ram Sanath-Kumar Arafat Rahman Zhongqing Ren Ian P. Reynolds Lauren Augusta Clay Fuqua Alexandra J. Weisberg Xindan Wang |
| author_facet | Ram Sanath-Kumar Arafat Rahman Zhongqing Ren Ian P. Reynolds Lauren Augusta Clay Fuqua Alexandra J. Weisberg Xindan Wang |
| author_sort | Ram Sanath-Kumar |
| collection | DOAJ |
| description | ABSTRACT Multipartite bacterial genome organization can confer advantages, including coordinated gene regulation and faster genome replication, but is challenging to maintain. Agrobacterium tumefaciens lineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the C58 lab model, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzed Agrobacterium natural isolates from the French Collection for Plant-Associated Bacteria and identified two strains distinct from C58 with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed that both replication origins remained active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres were essential. Importantly, the site-specific recombinase XerCD is required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains.IMPORTANCEMost bacterial genomes are monopartite with a single, circular chromosome. However, some species, like Agrobacterium tumefaciens, carry multiple chromosomes. Emergence of multipartite genomes is often related to adaptation to specific niches, including pathogenesis or symbiosis. Multipartite genomes confer certain advantages; however, maintaining this complex structure can present significant challenges. We previously reported a laboratory-propagated lineage of A. tumefaciens strain C58 in which the circular and linear chromosomes fused to form a single dicentric chromosome. Here we discovered two geographically separated environmental isolates of A. tumefaciens containing fused chromosomes with integration junctions different from the C58 fusion chromosome, revealing the constraints and diversification of this process. We found that balanced replication arm sizes and the repurposing of multimer resolution systems enable the survival and stable maintenance of dicentric chromosomes. These findings reveal how multipartite genomes function across different bacterial species and the role of genomic plasticity in bacterial genetic diversification. |
| format | Article |
| id | doaj-art-c390be6070d149c6a9f9d2e2271ccd66 |
| institution | Kabale University |
| issn | 2150-7511 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj-art-c390be6070d149c6a9f9d2e2271ccd662025-08-20T03:25:43ZengAmerican Society for MicrobiologymBio2150-75112025-06-0116610.1128/mbio.01046-25Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusionRam Sanath-Kumar0Arafat Rahman1Zhongqing Ren2Ian P. Reynolds3Lauren Augusta4Clay Fuqua5Alexandra J. Weisberg6Xindan Wang7Department of Biology, Indiana University, Bloomington, Indiana, USADepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USADepartment of Biology, Indiana University, Bloomington, Indiana, USADepartment of Biology, Indiana University, Bloomington, Indiana, USADepartment of Biology, Indiana University, Bloomington, Indiana, USADepartment of Biology, Indiana University, Bloomington, Indiana, USADepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USADepartment of Biology, Indiana University, Bloomington, Indiana, USAABSTRACT Multipartite bacterial genome organization can confer advantages, including coordinated gene regulation and faster genome replication, but is challenging to maintain. Agrobacterium tumefaciens lineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the C58 lab model, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzed Agrobacterium natural isolates from the French Collection for Plant-Associated Bacteria and identified two strains distinct from C58 with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed that both replication origins remained active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres were essential. Importantly, the site-specific recombinase XerCD is required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains.IMPORTANCEMost bacterial genomes are monopartite with a single, circular chromosome. However, some species, like Agrobacterium tumefaciens, carry multiple chromosomes. Emergence of multipartite genomes is often related to adaptation to specific niches, including pathogenesis or symbiosis. Multipartite genomes confer certain advantages; however, maintaining this complex structure can present significant challenges. We previously reported a laboratory-propagated lineage of A. tumefaciens strain C58 in which the circular and linear chromosomes fused to form a single dicentric chromosome. Here we discovered two geographically separated environmental isolates of A. tumefaciens containing fused chromosomes with integration junctions different from the C58 fusion chromosome, revealing the constraints and diversification of this process. We found that balanced replication arm sizes and the repurposing of multimer resolution systems enable the survival and stable maintenance of dicentric chromosomes. These findings reveal how multipartite genomes function across different bacterial species and the role of genomic plasticity in bacterial genetic diversification.https://journals.asm.org/doi/10.1128/mbio.01046-25Agrobacterium tumefacienschromosome fusionmultipartite genomeHi-Cnatural isolates |
| spellingShingle | Ram Sanath-Kumar Arafat Rahman Zhongqing Ren Ian P. Reynolds Lauren Augusta Clay Fuqua Alexandra J. Weisberg Xindan Wang Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion mBio Agrobacterium tumefaciens chromosome fusion multipartite genome Hi-C natural isolates |
| title | Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion |
| title_full | Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion |
| title_fullStr | Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion |
| title_full_unstemmed | Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion |
| title_short | Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion |
| title_sort | linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion |
| topic | Agrobacterium tumefaciens chromosome fusion multipartite genome Hi-C natural isolates |
| url | https://journals.asm.org/doi/10.1128/mbio.01046-25 |
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