Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 119; no. 6; p. 1
• Main Authors: Ren, Zhongqing, Liao, Qin, Karaboja, Xheni, Barton, Ian S, Schantz, Eli G, Mejia-Santana, Adrian, Fuqua, Clay, Wang, Xindan
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 08.02.2022
• Subjects: Agrobacterium tumefaciens; Agrobacterium tumefaciens - genetics; Bacterial Proteins - genetics; Biological Sciences; Cell cycle; Cell Cycle - genetics; Chromosomes; Chromosomes, Bacterial; Clustering; Conformation; Fluorescence; Fluorescence microscopy; Genome, Bacterial; Genomes; Maintenance; Origins; Plasmids; Replication origins; Replicon; Agrobacterium tumefaciens; ChIP-seq; SMC; ParB; Hi-C
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2115854119

Bacterial species from diverse phyla contain multiple replicons, yet how these multipartite genomes are organized and segregated during the cell cycle remains poorly understood. has a 2.8-Mb circular chromosome (Ch1), a 2.1-Mb linear chromosome (Ch2), and two large plasmids (pAt and pTi). We used this alpha proteobacterium as a model to investigate the global organization and temporal segregation of a multipartite genome. Using chromosome conformation capture assays, we demonstrate that both the circular and the linear chromosomes, but neither of the plasmids, have their left and right arms juxtaposed from their origins to their termini, generating interarm interactions that require the broadly conserved structural maintenance of chromosomes complex. Moreover, our study revealed two types of interreplicon interactions: " clustering" in which the replication origins of all four replicons interact, and "Ch1-Ch2 alignment" in which the arms of Ch1 and Ch2 interact linearly along their lengths. We show that the centromeric proteins (ParB1 for Ch1 and RepB for Ch2) are required for both types of interreplicon contacts. Finally, using fluorescence microscopy, we validated the clustering of the origins and observed their frequent colocalization during segregation. Altogether, our findings provide a high-resolution view of the conformation of a multipartite genome. We hypothesize that intercentromeric contacts promote the organization and maintenance of diverse replicons.