Amyloid-like DNA bridging: a new mode of DNA shaping

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(5)

Published: Feb. 27, 2025

Abstract All organisms depend on specific proteins to compact and organize their genomes. In eukaryotes, histones fulfil this role, while bacterial chromosomes are shaped by nucleoid-associated (NAPs). Among its pleiotropic functions, the NAP Hfq plays a pivotal role in genome organization. study, we characterized structure of C-terminal extension Hfq, which mediates chromosomal compaction, DNA-bound state. Using an integrative approach that combined transmission electron microscopy, neutron scattering, site-directed mutagenesis, molecular modeling, identified amyloid module formed region Hfq. This uniquely bridges compacts six DNA molecules, marking first documented instance with DNA-bridging properties. Our findings redefine functional landscape amyloids, linking them architecture gene regulation. result suggests amyloid–DNA interactions may represent conserved mechanism across biological systems, profound implications for understanding organization regulation expression both prokaryotes eukaryotes.

Language: Английский

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Chromosome segregation in Escherichia coli involves DNA binding by the MinC-MinD complex

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

Abstract The Escherichia coli Min system, composed of the proteins MinC, MinD, and MinE, is crucial for directing septum formation at mid-cell. MinD has also been implicated in chromosome segregation due to its non-sequence-specific DNA binding ability. Here, we demonstrate that MinCD complex, rather than alone, primary driver Min-mediated MinE regulates transient nature this interaction. We further reveal a critical function linker connecting MinC’s N- C-terminal domains both FtsZ polymerization inhibition. E. strains expressing MinC variants from native locus exhibit defects. defects are more pronounced where nucleoid-associated protein HU endogenously tagged with GFP. These findings reinforce involvement system highlight previously unrecognized role linker.

Language: Английский

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Bright antimicrobial surfaces based on Schottky interfaces: from light illumination to bacterial charging

Smart Materials in Medicine, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

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Nucleolar origins: challenging perspectives on evolution and function

Open Biology, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

The nucleolus, once considered a mere ‘ribosome factory’, is now recognized as dynamic hub influencing nearly every aspect of cellular life, from genome organization to stress response and ageing. Despite being hallmark eukaryotic cells, recent discoveries reveal that even prokaryotes exhibit nucleolus-like structures, hinting at ancient origins for nucleolar functions. This review explores the evolutionary journey tracing its roots back early life examining structural functional diversity across domains. We highlight key proteins play vital roles not only in ribosome production but also regulating cell cycle, DNA repair stress, linking activity directly health disease. Dysfunctions processes are implicated cancer, ribosomopathies neurodegenerative disorders, positioning nucleolus critical target innovative therapeutic strategies. As advanced imaging molecular techniques unlock deeper insights into both canonical mysterious non-canonical roles, stands model how microenvironments can evolve meet complex biological demands. By addressing open questions surrounding evolution diverse functions, ideas presented here aim contribute ongoing discussion, challenging traditional paradigms suggesting new avenues uncovering fundamental principles drive life.

Language: Английский

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DNA Transactions in Bacteria and Membranes: A Place for the Hfq Protein?

Membranes, Journal Year: 2025, Volume and Issue: 15(4), P. 103 - 103

Published: April 1, 2025

DNA metabolism consists of crucial processes occurring in all living cells. These include various transactions, such as replication, genetic recombination, transposition, mutagenesis, and repair. While it was initially assumed that these might occur the cytoplasm prokaryotic cells, subsequent reports indicated importance cell membrane transactions. Furthermore, newly identified factors play significant roles regulating DNA-related cellular processes. One factor is Hfq protein, originally discovered an RNA chaperone but later shown to be involved several molecular mechanisms. transactions interaction with membrane. Recent studies have suggested plays a role regulation recombination. In this narrative review, we will focus on membranes discuss potential Hfq-mediated Escherichia coli, where protein best characterized. Special attention given affinity small for both membranes, which help explain some findings from recent experiments.

Language: Английский

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UV induces codirectional replication–transcription conflicts and an alternative DnaA-dependent replication origin in the rnhA B mutants of Escherichia coli

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: April 10, 2025

Abstract The rnhAB mutants of Escherichia coli lacking both RNase H enzymes are unexpectedly UV-sensitive, being unable to restore normal levels post-UV replication. Examining patterns chromosomal replication in the after UV could identify problem sites. We show that rnhA (B) mutant initiates at three distinct oriK areas origin macrodomain, none them coinciding with oriC proper, dominant some 400 kb away. Interestingly, initiation switches DnaA-dependent closest and continues from there until growth pattern is restored, like single mutants. However, double mutant, forks initiated new have difficulty reaching terminus, major stalling sites rrn operons. In recBC mutants, additionally deficient linear DNA degradation/repair, cannot traverse origin-distal ribosomal RNA operons, rrnG rrnH, showing restoration disintegrated essential for mutant. contrast, rpoB* which transcription complexes unstable, UV-resistant resumes even faster than WT cells, indicating suffer UV-induced replication–transcription conflicts.

Language: Английский

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Effect of base methylation on binding and mobility of bacterial protein Hfq on double-stranded DNA

Lab on a Chip, Journal Year: 2024, Volume and Issue: 24(22), P. 5137 - 5144

Published: Jan. 1, 2024

Regulation of protein mobility is a fundamental aspect cellular processes. In this study, we examined the impact DNA methylation on diffusion nucleoid associated Hfq. This one most abundant proteins that shapes bacterial chromosome and involved in several aspects nucleic acid metabolism. Fluorescence microscopy was employed to monitor movement Hfq along double-stranded DNA, which stretched due confinement within nanofluidic channel. The significantly influenced by methylation. Our results underscore importance epigenetic modifications governing such as Increased levels result enhanced binding affinity, turn slows down DNA. reported control has potential implications for mechanisms target search processes dynamic modelling chromosome.

Language: Английский

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2024: A “nucleoid space” odyssey featuring H‐NS

BioEssays, Journal Year: 2024, Volume and Issue: 46(11)

Published: Sept. 26, 2024

Abstract The three‐dimensional architecture of the bacterial chromosome is intertwined with genome processes such as transcription and replication. Conspicuously so, that structure permits accurate prediction active processes. Although appreciation this interplay has developed rapidly in past two decades, our understanding subject still its infancy, research primarily focusing on how process regulates regulated by structure. Here, we summarize latest developments field a focus between Escherichia coli ( E. ) mediated H‐NS—a model nucleoid structuring protein. We describe organization chromosomes at global local scales dependent transcription, Finally, take note studies highlight limited knowledge structure‐function relationships chromosome, point out tracks will improve insight topic.

Language: Английский

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Kinetic Features of Degradation of R-Loops by RNase H1 from Escherichia coli

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(22), P. 12263 - 12263

Published: Nov. 15, 2024

R-loops can act as replication fork barriers, creating transcription-replication collisions and inducing stress by arresting DNA synthesis, thereby possibly causing aberrant processing the formation of strand breaks. RNase H1 (RH1) is one enzymes that participates in R-loop degradation cleaving RNA within a hybrid RNA-DNA duplex. In this study, kinetic features interaction RH1 from

Language: Английский

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