High-Resolution 3D Genome Map of Brucella Chromosomes in Exponential and Stationary Phases

Huang, Yong-Fang; Liu, Lin; Wang, Fei; Yuan, Xinwei; Chen, Huanchun; Liu, Zhengfei

doi:10.1128/spectrum.04290-22

Cited by 6 publications

(3 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, the G+C content of CID boundaries is significantly lower than the interior ( Fig. S3 ), which has also been reported in other species (46,47), suggesting a potential role of AT-rich DNA sequences in CID boundary formation. In view of the biased base composition of the CID boundary, we use the MEME software to search for conserved sequences (motifs) at these boundaries.…”

Section: Resultssupporting

confidence: 80%

Spatial chromosome organization and adaptation of the radiation-resistant extremophileDeinococcus radiodurans

Qiu,

Zhang,

Gao

et al. 2023

Preprint

View full text Add to dashboard Cite

Radiation-resistantDeinococcus radioduransis an extremophilic microorganism capable of withstanding high levels of ionizing radiation and chemical mutagens. It possesses remarkable DNA repair capability and serves as a model organism for studying stress resistance mechanism. However, our understanding on the spatial chromosome organization of this species remains limited. In this study, we employed chromosome conformation capture (3C) technology to determine the 3D genome structure ofD. radioduransand to further investigate the changes of chromosome conformation induced by ultraviolet (UV) irradiation. We observed that UV irradiation reduced short-range chromosome interactions, and smaller chromosomal interaction domains (CIDs) merged to form larger CIDs. Integrating transcriptomic data analysis, we found that the majority of upregulated differentially expressed genes were significantly enriched near specific CID boundaries. Specially, we comprehensively elucidated that the nucleoid-associated protein Dr_ebfC may serve as a global regulator for gene expression by altering chromosome structure, thereby influencing the physiological state of the bacterium. Overall, our study revealed the chromosome conformations ofD. radioduransunder different conditions, and offered valuable insights into the molecular responses of this extremophile to environmental stresses.

show abstract

Section: Resultssupporting

confidence: 80%

Spatial chromosome organization and adaptation of the radiation-resistant extremophileDeinococcus radiodurans

Qiu,

Zhang,

Gao

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…In Agrobacterium tumefaciens , the origins of the four replicons are clustered together, which regulates DNA replication and drives the maintenance of this multipartite genome [ 41 , 42 ]. Similarly, the two origins of Brucella melitensis chromosomes also showed frequent interactions [ 43 ]. In Vibrio cholerae , the origin of Chromosome 2 (Ch2) interacts with the crtS region on Chromosome 1 (Ch1) for replication control, and the terminus regions of Ch1 and Ch2 interact for coordinated replication termination and terminus segregation [ 40 , 44 ].…”

Section: Introductionmentioning

confidence: 99%

Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi

et al. 2023

View full text Add to dashboard Cite

Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/Smc. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that Smc and the Smc-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.

show abstract

“…In Agrobacterium tumefaciens , the origins of the four replicons are clustered together, which regulates the replication and drives the maintenance of this multipartite genome [41, 42]. Similarly, the two origins of Brucella melitensis chromosomes also showed frequent interactions [43]. In Vibrio cholerae , the origin of Chromosome 2 (Ch2) interacts with the crtS region on Chromosome 1 (Ch1) for replication control, and the terminus region of Ch1 and Ch2 are interacting for coordinated replication termination and terminus segregation [40, 44].…”

Section: Introductionmentioning

confidence: 99%

Organization and replicon interactions within the highly segmented genome ofBorrelia burgdorferi

Ren

Takacs

Brandão

et al. 2023

Preprint

View full text Add to dashboard Cite

Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/SMC. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that SMC and the SMC-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.

show abstract

High-Resolution 3D Genome Map of Brucella Chromosomes in Exponential and Stationary Phases

Cited by 6 publications

References 58 publications

Spatial chromosome organization and adaptation of the radiation-resistant extremophileDeinococcus radiodurans

Spatial chromosome organization and adaptation of the radiation-resistant extremophileDeinococcus radiodurans

Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi

Organization and replicon interactions within the highly segmented genome ofBorrelia burgdorferi

Contact Info

Product

Resources

About