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Insights in bacterial genome folding

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Article Biochemistry & Molecular Biology

The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG

Manuela Weiss et al.

Summary: Cells face the constant risk of foreign DNA invasion, and bacteria have developed strategies similar to an innate immune system to defend against it. This study investigates the MksBEFG complex in Corynebacterium glutamicum, which degrades plasmid DNA. The structure of MksG reveals that it acts as a nuclease and has a binding site essential for DNA cleavage. The Mks system is regulated through the polar scaffold protein DivIVA and is activated when plasmids are introduced.

NUCLEIC ACIDS RESEARCH (2023)

Article Genetics & Heredity

A chromosomal loop anchor mediates bacterial genome organization

Gaurav Dugar et al.

Summary: A study reveals the existence of large nucleoprotein complexes formed by the transcription factor Rok in the bacterium Bacillus subtilis. These complexes can interact with each other over long distances and lead to the formation of chromosomal loops, spatially isolating large sections of DNA.

NATURE GENETICS (2022)

Article Multidisciplinary Sciences

Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens

Zhongqing Ren et al.

Summary: Bacterial species with multipartite genomes, such as Agrobacterium tumefaciens, have their circular and linear chromosomes interacting with each other, while plasmids do not show such interactions. There are also two types of interactions observed: clustering of replication origins and linear alignment of chromosome arms. Centromeric proteins are required for these interactions. The study provides a high-resolution view of the organization of multipartite genomes.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription

Bryan J. Visser et al.

Summary: DNA supercoiling is a key regulator of DNA metabolic processes, but a reliable genomic assay for supercoiling is lacking. In this study, a high-resolution method (Psora-seq) is presented to measure whole-genome supercoiling, and it is applied in Escherichia coli to observe a supercoiling landscape that is well correlated to transcription. The results indicate that transcription is the major determinant of chromosome supercoiling, while DNA replication also strongly influences supercoiling.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome

Brenna Conin et al.

Summary: In bacteria, the decatenation activity of topoisomerase IV plays a crucial role in chromosome replication and segregation. This study reveals that inactivation of topoisomerase IV leads to massive chromosome reorganization and increased contacts between nearby and distant loci. The roles of Topo III, MatP, and MukB in this process were also investigated.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage

Hon Wing Liu et al.

Summary: Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromo-some segregation and genome maintenance. Wadjet systems are derivative SMC complexes with roles in bacterial immunity against selfish DNA. JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. JetABCD complexes cleave circular DNA molecules regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase.

MOLECULAR CELL (2022)

Article Biochemistry & Molecular Biology

The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA

Amar Deep et al.

Summary: The Wadjet defense system protects the host against plasmid transformation by recognizing DNA topology. It forms a complex similar to the bacterial condensin complex MukBEF and has a novel nuclease subunit similar to a type II DNA topoisomerase. It uses DNA loop extrusion to sense the substrate's topology and cleaves plasmid DNA.

MOLECULAR CELL (2022)

Review Biochemistry & Molecular Biology

Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom

Haley M. Amemiya et al.

Summary: This article discusses the relationship between bacterial DNA organization and gene regulation, explores the similarity between bacterial chromatin and eukaryotic genome organization, and examines the role of nucleoid-associated proteins (NAPs) in regulating bacterial chromosomes. Through studying the regulatory roles of NAPs in several well-studied bacteria, a working definition and screening procedure for NAPs are proposed.

TRANSCRIPTION-AUSTIN (2021)

Article Biochemistry & Molecular Biology

XerD unloads bacterial SMC complexes at the replication terminus

Xheni Karaboja et al.

Summary: Through studying Bacillus subtilis, researchers have found that the XerD recombinase plays a key role in unloading SMC tethers at specific binding sites near the chromosome terminus. This study reveals that ParB and XerD homologs in different bacteria have similar functions in the loading and unloading of SMC complexes between the origin and terminus.

MOLECULAR CELL (2021)

Article Biochemistry & Molecular Biology

Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization

Charlotte Cockram et al.

Summary: This study developed a cost-effective Hi-C protocol for exploring chromosome conformations in prokaryotes and archaea. By validating and applying this method in different microorganisms, the research found that these euryarchaeota lack compartment-like structures and their genomes are mainly composed of self-interacting domains and chromatin loops.

MOLECULAR CELL (2021)

Article Multidisciplinary Sciences

Topoisomerase IV tracks behind the replication fork and the SeqA complex during DNA replication in Escherichia coli

Emily Helgesen et al.

Summary: TopoIV is a crucial bacterial enzyme that disentangles DNA and enables chromosome segregation. It localizes to the origin proximal side of the fork trailing protein and follows the movement pattern of replication machinery in the cell. Replication and segregation in bacteria are concurrent processes with a short time lag in between.

SCIENTIFIC REPORTS (2021)

Article Biochemistry & Molecular Biology

The coordinated replication of Vibrio cholerae's two chromosomes required the acquisition of a unique domain by the RctB initiator

Florian Fournes et al.

Summary: Vibrio cholerae, the pathogenic bacterium responsible for cholera, possesses two chromosomes and utilizes the molecule RctB to regulate the coordinated replication process. The study reveals that the crtS site on Chr1 plays a crucial role in controlling the initiation of Chr2 replication, with the extreme C-terminal tail of RctB also being essential for this process. This unique domain in RctB, conserved in all Vibrio species, is likely responsible for the coordinated replication of both chromosomes.

NUCLEIC ACIDS RESEARCH (2021)

Article Microbiology

Cargo Genes of Tn7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

Sean Benler et al.

Summary: A computational approach was used to identify the boundaries of 6,549 Tn7-like transposons and reveal their roles as conduits of genes between phylogenetically distant hosts. Comparative analysis showed significant enrichment of mobile genetic elements, defense systems, and antibiotic resistance genes among the cargo genes. Unexpectedly, genes encoding metabolic enzymes were also found in the cargo genes carried by these transposons.
Article Biology

Competitive binding of MatP and topoisomerase IV to the MukB hinge domain

Gemma L. M. Fisher et al.

Summary: Research indicates that there is competitive binding between the Structural Maintenance of Chromosomes (SMC) complex MukBEF, MatP, and ParC, serving as a means of globally regulating the activity of MukBEF-topoisomerase IV in space and time.
Article Biochemistry & Molecular Biology

DNA-loop-extruding SMC complexes can traverse one another in vivo

Hugo B. Brandao et al.

Summary: Hi-C analyses and 3D polymer simulations on engineered Bacillus subtilis strains reveal that SMC complex encounters on the same DNA are resolved via bypassing in vivo. Over 20 engineered strains show a variety of chromosome folding patterns, which require SMC complexes to bypass each other in vivo. This bypassing activity enables SMC complexes to avoid traffic jams while spatially organizing the genome.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Review Biochemistry & Molecular Biology

The regulation of DNA supercoiling across evolution

Alexandre Duprey et al.

Summary: DNA supercoiling is a crucial factor in controlling cellular processes, with similarities and differences across different domains of life. Topoisomerases play a key role in mediating changes in DNA supercoiling.

PROTEIN SCIENCE (2021)

Article Cell Biology

Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions

Leonid Mirny et al.

Cold Spring Harbor Perspectives in Biology (2021)

Article Multidisciplinary Sciences

Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation

Virginia S. Lioy et al.

Summary: The linear chromosome structure of Streptomyces bacteria is linked to genetic compartmentalization, and the onset of metabolic differentiation involves rearrangement of chromosome architecture.

NATURE COMMUNICATIONS (2021)

Article Biology

High-resolution, genome-wide mapping of positive supercoiling in chromosomes

Monica S. Guo et al.

Summary: The GapR-seq method allows high-resolution mapping of positive supercoiling in genomes, revealing its widespread presence, association with transcription, and enrichment between certain genes. This approach provides new insights into chromosome structure and organization that are not accessible with existing methods like Hi-C.
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Organization of the Escherichia coli Chromosome by a MukBEF Axial Core

Jarno Makela et al.

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Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress

Joanna Holowka et al.

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High-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts

Elena Espinosa et al.

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RNA polymerases as moving barriers to condensin loop extrusion

Hugo B. Brandao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Topoisomerase III Acts at the Replication Fork To Remove Precatenanes

Chong M. Lee et al.

JOURNAL OF BACTERIOLOGY (2019)

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Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

Virginia S. Lioy et al.

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Systematic discovery of antiphage defense systems in the microbial pangenome

Shany Doron et al.

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Xer Site Specific Recombination: Double and Single Recombinase Systems

Fabio Castillo et al.

FRONTIERS IN MICROBIOLOGY (2017)

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Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries

Tung B. K. Le et al.

EMBO JOURNAL (2016)

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MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation

Sophie Nolivos et al.

NATURE COMMUNICATIONS (2016)

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Bacterial partition complexes segregate within the volume of the nucleoid

Antoine Le Gall et al.

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Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid

Mathew Stracy et al.

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Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells

Jay K. Fisher et al.

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The MukB-ParC Interaction Affects the Intramolecular, Not Intermolecular, Activities of Topoisomerase IV

Ryo Hayama et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2013)

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High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

Tung B. K. Le et al.

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Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions

Nastaran Hadizadeh Yazdi et al.

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Physical manipulation of the Escherichia coli chromosome reveals its soft nature

James Pelletier et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

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The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Mark A. Umbarger et al.

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A new family of bacterial condensins

Zoya M. Petrushenko et al.

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Modulation of Escherichia coli sister chromosome cohesion by topoisomerase IV

Xindan Wang et al.

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Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

Nicolas Blot et al.

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DNA reshaping by MukB - Right-handed knotting, left-handed supercoiling

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Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

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SeqA protein stimulates the relaxing and decatenating activities of topoisomerase IV

SH Kang et al.

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