@article {142319, title = {Chromosome organization shapes replisome dynamics in Caulobacter crescentus.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Apr 24}, pages = {3460}, abstract = {

DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial species, driving the hypothesis that a physical linker may tether them together. However, replisome splitting has also been reported in many of the same species, leaving the principles behind replisome organization a long-standing puzzle. Here, by tracking the replisome β-clamp subunit in live Caulobacter crescentus, we find that rapid DNA segregation can give rise to a second focus which resembles a replisome, but does not replicate DNA. Sister replisomes can remain colocalized, or split apart to travel along DNA separately upon disruption of chromosome inter-arm alignment. Furthermore, chromosome arm-specific replication-transcription conflicts differentially modify replication speed on the two arms, facilitate the decoupling of the two replisomes. With these observations, we conclude that the dynamic chromosome organization flexibly shapes the organization of sister replisomes, and we outline principles which can help to reconcile previously conflicting models of replisome architecture.

}, keywords = {Bacterial Proteins, Caulobacter crescentus, Chromosome Segregation, Chromosomes, Bacterial, DNA Replication, DNA, Bacterial}, issn = {2041-1723}, doi = {10.1038/s41467-024-47849-6}, author = {Zhang, Chen and Joseph, Asha Mary and Casini, Laurent and Collier, Justine and Badrinarayanan, Anjana and Manley, Suliana} } @article {906, title = {Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid.}, journal = {Soft Matter}, volume = {11}, year = {2015}, month = {2015 Mar 7}, pages = {1677-87}, abstract = {

Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework combining solely these two ingredients, in order to characterize their joint effects. Specifically, we study a simple polymer physics computational model with weak ubiquitous short-ranged self attraction and stronger sparse bridging interactions. Combining theoretical arguments and simulations, we study the general phenomenology of polymer collapse induced by these dual contributions, in the case of regularly spaced bridging. Our results distinguish a regime of classical Flory-like coil-globule collapse dictated by the interplay of excluded volume and attractive energy and a switch-like collapse where bridging interactions compete with entropy loss terms from the looped arms of a star-like rosette. Additionally, we show that bridging can induce stable compartmentalized domains. In these configurations, different "cores" of bridging proteins are kept separated by star-like polymer loops in an entropically favorable multi-domain configuration, with a mechanism that parallels micellar polysoaps. Such compartmentalized domains are stable, and do not need any intra-specific interactions driving their segregation. Domains can be stable also in the presence of uniform attraction, as long as the uniform collapse is above its theta point.

}, keywords = {Chromosomes, Bacterial, Escherichia coli, Models, Chemical, Polymers}, issn = {1744-6848}, doi = {10.1039/c4sm02434f}, author = {Scolari, Vittore F and Cosentino Lagomarsino, Marco} } @article {905, title = {The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli.}, journal = {Nucleic Acids Res}, volume = {43}, year = {2015}, month = {2015 Jan}, pages = {295-308}, abstract = {

The gene expression state of exponentially growing Escherichia coli cells is manifested by high expression of essential and growth-associated genes and low levels of stress-related and horizontally acquired genes. An important player in maintaining this homeostasis is the H-NS-StpA gene silencing system. A Δhns-stpA deletion mutant results in high expression of otherwise-silent horizontally acquired genes, many located in the terminus-half of the chromosome, and an indirect downregulation of many highly expressed genes. The Δhns-stpA double mutant displays slow growth. Using laboratory evolution we address the evolutionary strategies that E. coli would adopt to redress this gene expression imbalance. We show that two global gene regulatory mutations-(i) point mutations inactivating the stress-responsive sigma factor RpoS or σ38 and (ii) an amplification of \~{}40\% of the chromosome centred around the origin of replication-converge in partially reversing the global gene expression imbalance caused by Δhns-stpA. Transcriptome data of these mutants further show a three-way link amongst the global gene regulatory networks of H-NS and σ38, as well as chromosome architecture. Increasing gene expression around the terminus of replication results in a decrease in the expression of genes around the origin and vice versa; this appears to be a persistent phenomenon observed as an association across \~{}300 publicly-available gene expression data sets for E. coli. These global suppressor effects are transient and rapidly give way to more specific mutations, whose roles in reversing the growth defect of H-NS mutations remain to be understood.

}, keywords = {Chromosomes, Bacterial, Directed Molecular Evolution, DNA-Binding Proteins, DNA-Directed RNA Polymerases, Escherichia coli, Escherichia coli Proteins, Gene Deletion, Gene Expression Regulation, Bacterial, Gene Silencing, Genome, Bacterial, Molecular Chaperones, Sigma Factor, Stress, Physiological, Transcription, Genetic}, issn = {1362-4962}, doi = {10.1093/nar/gku1229}, author = {Srinivasan, Rajalakshmi and Scolari, Vittore Ferdinando and Lagomarsino, Marco Cosentino and Seshasayee, Aswin Sai Narain} }