Telomere protein arrays stall DNA loop extrusion by condensin DOI Creative Commons
Brian T. Analikwu, Alice Deshayes, Jaco van der Torre

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Окт. 29, 2023

Abstract DNA loop extrusion by SMC proteins is a key process underlying chromosomal organization. It unknown how extruders interact with telomeres where chromosome ends are covered dense array of tens neighboring DNA-binding proteins. Using complementary in vivo and vitro single-molecule approaches, we study the interaction between loop-extruding condensin arrays Rap1, double-stranded-DNA-binding telomeric protein Saccharomyces cerevisiae . We show that linear Rap1 can completely halt extrusion, blocking efficiency depends on length gap size In cells, found to act as contact insulators accumulate at their borders, direct implications for resolution dicentric chromosomes produced telomere fusions. Our findings DNA-bound efficiently proteins, which may impact wide range cellular processes from functions transcription repair.

Язык: Английский

Structural biology of SMC complexes across the tree of life DOI Creative Commons
Frank Bürmann, Jan Löwe

Current Opinion in Structural Biology, Год журнала: 2023, Номер 80, С. 102598 - 102598

Опубликована: Апрель 25, 2023

Structural maintenance of chromosomes (SMC) complexes guard and organize the three-dimensional structure chromosomal DNA across tree life. Many SMC functions can be explained by an inherent motor activity that extrudes large loops while move along their substrate. Here, we review recent structural insights into architecture conservation these molecular machines, interaction with DNA, conformational changes are linked to ATP hydrolysis cycle.

Язык: Английский

Процитировано

20
A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages DOI Creative Commons
Thomas Ipoutcha, Ratanachat Racharaks, Stefanie Huttelmaier

и другие.

Microbiology Spectrum, Год журнала: 2024, Номер 12(3)

Опубликована: Янв. 31, 2024

ABSTRACT The rise in the frequency of antibiotic resistance has made bacterial infections, specifically Pseudomonas aeruginosa , a cause for greater concern. Phage therapy is promising solution that uses naturally isolated phages to treat infections. Ecological limitations, which stipulate discrete host range and inevitable evolution resistance, may be overcome through better understanding phage biology utilization engineered phages. In this study, we developed synthetic approach construct tailed target clinically relevant strains . As proof concept, successfully cloned assembled JG024 DMS3 genomes yeast using transformation-associated recombination cloning rebooted these two different P. We identified factors affected reboot efficiency like species or presence antiviral defense systems strain. have extended method other observed enables are unable infect strain used reboot. This research represents critical step toward construction relevant, IMPORTANCE bacterium responsible severe infections common major complication cystic fibrosis. use antibiotics become increasingly difficult as more prevalent. an alternative already being some European countries, but its limited by narrow due receptor specificity, strain, possible emergence resistance. demonstrate significant expansion possibilities applications.

Язык: Английский

Процитировано

6
Loop extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex DOI
Biswajit Pradhan, Amar Deep,

Jessica König

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 17, 2024

Structural maintenance of chromosomes (SMC) protein complexes play pivotal roles in genome organization and across all domains life. In prokaryotes, SMC family Wadjet structurally resemble the widespread MukBEF genome-organizing but serve a defensive role by inhibiting plasmid transformation. We previously showed that specifically cleaves circular DNA; however, molecular mechanism underlying DNA substrate recognition remains unclear. Here, we use vitro single-molecule imaging to directly visualize loop extrusion cleavage Wadjet. find is symmetric extruder simultaneously reels from both sides growing this activity requires dimeric JetABC supercomplex containing two dimers JetC motor subunit. On surface-anchored DNAs, extrudes full length 44 kilobase pair plasmid, stalls, then DNA. Our findings reveal specific elimination plasmids Wadjet, establish as an evolutionarily conserved among kingdoms

Язык: Английский

Процитировано

6
Using Cupriavidus necator H16 to Provide a Roadmap for Increasing Electroporation Efficiency in Nonmodel Bacteria DOI Creative Commons
Matteo Vajente, Riccardo Clerici, Hendrik Ballerstedt

и другие.

ACS Synthetic Biology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 31, 2024

Bacteria are a treasure trove of metabolic reactions, but most industrial biotechnology applications rely on limited set established host organisms. In contrast, adopting nonmodel bacteria for the production various chemicals interest is often hampered by their genetic amenability coupled with low transformation efficiency. this study, we propose series steps that can be taken to increase electroporation efficiency in bacteria. As test strain, use Cupriavidus necator H16, lithoautotrophic bacterium has been engineered produce wide range products from CO2 and hydrogen. However, its hampers high-throughput engineering required develop C. into an industrially relevant organism. Thus, conjugation method choice introducing exogenous DNA, especially when large plasmids or suicide plasmids. We first species-independent technique based natively methylated DNA Golden Gate assembly one-pot cloning 70-fold. Second, bioinformatic tools were used predict defense systems restriction avoidance strategy was introduce obtain domesticated strain. The results discussed context

Язык: Английский

Процитировано

6
Loop-extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex DOI Creative Commons
Biswajit Pradhan, Amar Deep,

Jessica König

и другие.

Molecular Cell, Год журнала: 2024, Номер unknown

Опубликована: Дек. 1, 2024

Structural maintenance of chromosomes (SMC) complexes play pivotal roles in genome organization and across all domains life. In prokaryotes, SMC-family Wadjet structurally resemble the widespread MukBEF but serve a defensive role by inhibiting plasmid transformation. We previously showed that specifically cleaves DNA; however, molecular mechanism underlying recognition remains unclear. Here, we use vitro single-molecule imaging to directly visualize DNA loop extrusion cleavage Wadjet. find is symmetric extruder simultaneously reels from both sides this activity requires dimeric JetABC supercomplex. On surface-anchored DNAs, extrudes full length 44-kb-pair plasmid, stalls, DNA. Our findings reveal specific elimination plasmids establish as an evolutionarily conserved among SMC kingdoms

Язык: Английский

Процитировано

6
SMC-based immunity against extrachromosomal DNA elements DOI Creative Commons
Hon Wing Liu, Florian Roisné-Hamelin, Stephan Gruber

и другие.

Biochemical Society Transactions, Год журнала: 2023, Номер 51(4), С. 1571 - 1583

Опубликована: Авг. 16, 2023

SMC and SMC-like complexes promote chromosome folding genome maintenance in all domains of life. Recently, they were also recognized as factors cellular immunity against foreign DNA. In bacteria archaea, Wadjet Lamassu are anti-plasmid/phage defence systems, while Smc5/6 Rad50 play a role anti-viral humans. This raises an intriguing paradox — how can the same, or closely related, on one hand secure integrity chromosomal DNA, other recognize restrict extrachromosomal DNA? this minireview, we will briefly describe latest understanding each these including speculations principles SMC(-like) function may explain systems linear circular forms invading

Язык: Английский

Процитировано

13
Genome engineering of the human gut microbiome DOI Creative Commons

Linggang Zheng,

Juntao Shen,

Ruiyue Chen

и другие.

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2024, Номер 51(5), С. 479 - 491

Опубликована: Янв. 12, 2024

The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To deepen our comprehension control of the molecular mechanisms orchestrating intricate interplay between commensal bacteria exploration genome engineering for microbes is promising frontier. Nevertheless, complexities diversities inherent in microbiome pose substantial challenges to development effective tools microbes. In this comprehensive review, we provide an overview current progress bacteria, whether executed vitro or situ. A specific focus directed towards advancements prospects cargo DNA delivery high-throughput techniques. Additionally, elucidate immense potential methods understanding engineer microorganisms enhance health.

Язык: Английский

Процитировано

5
Insights in bacterial genome folding DOI Creative Commons

Fares Osam Yáñez-Cuna,

Romain Koszul

Current Opinion in Structural Biology, Год журнала: 2023, Номер 82, С. 102679 - 102679

Опубликована: Авг. 19, 2023

Chromosomes in all domains of life are well-defined structural entities with complex hierarchical organization. The regulation this organization and its functional interplay gene expression or other chromosome metabolic processes such as repair, replication, segregation is actively investigated a variety species, including prokaryotes. Bacterial chromosomes typically gene-dense few non-coding sequences organized into the nucleoid, membrane-less compartment composed DNA, RNA, proteins (nucleoid-associated NAPs). continuous improvement imaging genomic methods has put these Mb-long molecules at reach, allowing to disambiguate some their highly dynamic properties intertwined features. Here we review discuss recent advances field bacterial

Язык: Английский

Процитировано

11
Nucleic acid recognition during prokaryotic immunity DOI Creative Commons
Christian F. Baca, Luciano A. Marraffini

Molecular Cell, Год журнала: 2025, Номер 85(2), С. 309 - 322

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0
A unified model for cohesin function in sisterchromatid cohesion and chromatin loop formation DOI Creative Commons
Frank Uhlmann

Molecular Cell, Год журнала: 2025, Номер 85(6), С. 1058 - 1071

Опубликована: Март 1, 2025

The ring-shaped cohesin complex topologically entraps two DNAs to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape by forming DNA loops, which it is thought achieve using an in vitro-observed loop extrusion mechanism. However, recent studies revealed that loop-extrusion-deficient retains its ability form suggesting a divergence of vitro and vivo formation. Instead extrusion, we examine whether forms loops mechanism akin cohesion establishment: sequential topological capture DNAs. We explore similarities differences between "loop capture" extrusion" model, how they compare at explaining experimental observations, future approaches can delineate their possible respective contributions. extend our DNA-DNA model for function related structural maintenance chromosomes (SMC) family members, condensin, Smc5-Smc6 complex, bacterial SMC complexes.

Язык: Английский

Процитировано

0