Article
Biology
Gemma L. M. Fisher, Jani R. Bolla, Karthik Rajasekar, Jarno Makela, Rachel Baker, Man Zhou, Josh P. Prince, Mathew Stracy, Carol Robinson, Lidia K. Arciszewska, David J. Sherratt
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
Brenna Conin, Ingrid Billault-Chaumartin, Hafez El Sayyed, Nicole Quenech'Du, Charlotte Cockram, Romain Koszul, Olivier Espeli
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)
Editorial Material
Biochemistry & Molecular Biology
Juraj Gregan
Summary: Understanding the spatial organization of genomes is crucial in cell biology, but distinguishing relationships between sister chromatids has been challenging due to limitations in sequencing-based techniques. Recent developments have provided insights into the organization of sister chromatids.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Rupesh Kumar, Soon Bahng, Kenneth J. Marians
Summary: The bacterial condensin MukB and the cellular chromosomal decatenase, topoisomerase IV interact and stimulate each other's activity in DNA condensation, while in stoichiometric complexes of the two enzymes they inhibit each other and provide a stable scaffold for chromosomal DNA condensation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Juechun Tang, Mark P. Brynildsen
Summary: Bacterial persisters, suspected culprits of recurrent infections, are rare phenotypic variants. The genomic cleavage strength of DNA gyrase is negatively correlated with fluoroquinolone (FQ) persister levels, indicating that FQs that better stabilize DNA gyrase in cleaved complexes with DNA will lead to lower levels of persistence.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Agnieszka Strzalka, Agnieszka Kois-Ostrowska, Magda Kedra, Tomasz Lebkowski, Grazyna Bieniarz, Marcin J. Szafran, Dagmara Jakimowicz
Summary: Bacterial chromosome topology is regulated by topoisomerases and nucleoid-associated proteins. Streptomyces bacteria utilize the topoisomerase I (TopA) and the HU homologue HupA to maintain chromosome organization and distribution, which is essential for hyphal growth and production of clinically important compounds.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Amar Deep, Yajie Gu, Yong-Qi Gao, Kaori M. Ego, Mark A. Herzik Jr, Huilin Zhou, Kevin D. Corbett
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.
Article
Biochemistry & Molecular Biology
Soon Bahng, Rupesh Kumar, Kenneth J. Marians
Summary: MukBEF, a protein complex similar to structural maintenance of chromosome, plays a role in bacterial condensation. It is found that MukBEF compacts DNA through an ATP hydrolysis-dependent DNA loop-extrusion reaction. Interaction between MukB and the ParC subunit of topoisomerase IV is necessary for proper chromosome condensation and segregation in Escherichia coli.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Microbiology
Dmitry Sutormin, Alina Galivondzhyan, Azamat Gafurov, Konstantin Severinov
Summary: Topoisomerase IV (Topo IV) is the primary decatenation enzyme in Escherichia coli, responsible for removing catenation links formed during DNA replication. Using a more sensitive Topo-Seq procedure, we identified thousands of Topo IV cleavage sites (TCSs) throughout the bacterial genome. The determined cleavage motif of Topo IV contained previously known cleavage determinants as well as some new positions. TCSs were found to be depleted in the Ter macrodomain, except for two exceptionally strong non-canonical cleavage sites near the dif-site.
FRONTIERS IN MICROBIOLOGY
(2023)
Editorial Material
Multidisciplinary Sciences
Itzhak Fishov, Sharanya Namboodiri
Summary: The type three secretion system (T3SS) is a membrane-anchored nano-machine used by pathogenic bacteria to inject effector proteins and control host cells. Recent research shows the colocalization of T3SS-encoding locus, its transcriptional activators, protein products, and the complete structure at the cell membrane, providing evidence for a mechanism called 'transertion'.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Zhen-Yu Wang, Yue Jiang, Yi-Qiao Shao, Heng-Fan Lu, Meng-Jun Lu, Xinan Jiao, Jing Wang, Qiu-Chun Li
Summary: This study investigates the prevalence and dissemination mechanism of ESBL-producing E. coli from healthy individuals in a community in Yangzhou, China. The study found nasal colonization of CTX-M-55-producing E. coli strains among healthy individuals in the community, indicating a potential risk of antimicrobial resistance dissemination through close contact or environmental transmission.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Debarshi Mitra, Shreerang Pande, Apratim Chatterji
Summary: The entropic repulsion between DNA ring polymers under confinement plays a crucial role in the spatial segregation of bacterial DNA before cell division. Additionally, the introduction of internal loops enhances this repulsion and induces entropy-driven spatial organization of polymer segments. By designing different polymer architectures and investigating their segregation under confinement, we identify the structures that lead to higher success rates of segregation and establish the mechanism behind the localization of specific polymer segments.
Article
Physics, Fluids & Plasmas
James M. Polson, Qinxin Zhu
Summary: Highly confined polymers in narrow channels experience strong entropic forces that may drive them apart. Studies show that different polymer lengths result in different segregation behaviors, with specific separation regimes observed.
Article
Microbiology
Ashok R. Nayak, Pradip K. Singh, Jinlei Zhao, Montserrat Samso, Michael S. Donnenberg
Summary: Type 4 pili are important surface appendages on bacteria and archaea that can extend and retract with great force. This study presents the detailed structure of an enzyme that converts chemical energy to mechanical energy in a human pathogen, revealing a mechanism of action not previously seen in enzymes that power type 4 pilus extension.
Article
Multidisciplinary Sciences
Jarno Makela, Stephan Uphoff, David J. Sherratt
Summary: This study elucidates the crucial role of Structural maintenance of chromosomes (SMC) complexes in chromosome organization and genetic material inheritance, with a focus on the essential functions of MukBEF and MatP in maintaining chromosome orientation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Fernando H. Ramirez-Guadiana, Alexander J. Meeske, Xindan Wang, Christopher D. A. Rodrigues, David Z. Rudner
MOLECULAR MICROBIOLOGY
(2017)
Article
Multidisciplinary Sciences
Xindan Wang, Hugo B. Brandao, Tung B. K. Le, Michael T. Laub, David Z. Rudner
Article
Genetics & Heredity
Ting Pang, Xindan Wang, Hoong Chuin Lim, Thomas G. Bernhardt, David Z. Rudner
Article
Biochemistry & Molecular Biology
Xindan Wang, Anna C. Hughes, Hugo B. Brandao, Benjamin Walker, Carrie Lierz, Jared C. Cochran, Martha G. Oakley, Andrew C. Kruse, David Z. Rudner
Article
Multidisciplinary Sciences
Hugo B. Brandao, Payel Paul, Aafke A. van den Berg, David Z. Rudner, Xindan Wang, Leonid A. Mirny
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Genetics & Heredity
Yannick R. Brunet, Xindan Wang, David Z. Rudner
Article
Biochemistry & Molecular Biology
Xheni Karaboja, Zhongqing Ren, Hugo B. Brandao, Payel Paul, David Z. Rudner, Xindan Wang
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.
Article
Multidisciplinary Sciences
Chun-Kai Yang, Des R. Kashyap, Dominik A. Kowalczyk, David Z. Rudner, Xindan Wang, Dipika Gupta, Roman Dziarski
Summary: The research demonstrates that mammalian PGRPs or PGLYRPs kill bacteria through various mechanisms. Mutants in key genes in Bacillus subtilis or Escherichia coli exhibit higher survival rates following PGLYRP4 treatment, with corresponding weaker depletion of thiols.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Hugo B. Brandao, Zhongqing Ren, Xheni Karaboja, Leonid A. Mirny, Xindan Wang
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)
Article
Microbiology
Genevieve S. Dobihal, Josue Flores-Kim, Ian J. Roney, Xindan Wang, David Z. Rudner
Summary: The WaIR-WalK signaling system is crucial for the homeostatic control of cell wall hydrolases in Bacillus subtilis.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Multidisciplinary Sciences
Zhongqing Ren, Qin Liao, Xheni Karaboja, Ian S. Barton, Eli G. Schantz, Adrian Mejia-Santana, Clay Fuqua, Xindan Wang
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
Microbiology
Xheni Karaboja, Xindan Wang
Summary: Nucleoid-associated proteins (NAPs) play crucial roles in structuring bacterial genomes and various DNA transactions. While NAPs are generally nonessential, the HU homolog HBsu is essential for cell viability in Bacillus subtilis. This study demonstrates that HBsu is required for the initiation of DNA replication, likely by promoting origin melting by DnaA, as well as another unknown essential function.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Microbiology
Zhongqing Ren, Qin Liao, Ian S. Barton, Emma E. Wiesler, Clay Fuqua, Xindan Wang
Summary: This study provides evidence that centromeric clustering, mediated by centromeric proteins, plays a crucial role in maintaining the stability of multipartite genomes. Disruption of centromere clustering results in the loss of replicons.
Article
Microbiology
Sandra Sanchez, Elizabeth Snider, Xindan Wang, Daniel B. Kearns
Summary: Using TnSeq, researchers identified new genes involved in swarming motility of Bacillus subtilis. The study confirmed the known genes required for flagellar biosynthesis and regulators that promote swarming, and also discovered additional genes that enhance swarming. The results demonstrate the power of TnSeq for genetic analysis of nonessential processes and provide insights into the mechanism of swarming in B. subtilis.
JOURNAL OF BACTERIOLOGY
(2022)
Meeting Abstract
Biophysics
Hugo Brandao, Xindan Wang, David Rudner, Leonid Mirny
BIOPHYSICAL JOURNAL
(2017)
