Kiwa rescues RecBCD for anti-phage activity DOI Creative Commons
Zhiying Zhang,

Thomas C. Todeschini,

Yi Wu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 26, 2023

Bacteria and archaea deploy diverse, sophisticated defence systems to counter virus infection, yet many immunity mechanisms remain poorly understood. Here, we characterise the Kiwa system as a membrane-associated supercomplex that senses changes in membrane induced by phage infection plasmid conjugation. This supercomplex, comprising KwaA tetramers bound KwaB dimers, its basic repeating unit, detects structural stress via KwaA, activating KwaB, which binds ejected DNA through DUF4868 domain, stalling replication forks thus disrupting late transcription. We show phage-encoded mimic protein Gam, inhibits RecBCD, also targets recognition. However, Gam binding one precludes inhibition of other. These findings reveal distinct mechanism bacterial immune coordination, where sensing disruptions inhibitor partitioning enhance protection against phages plasmids.

Language: Английский

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact? DOI Creative Commons
Armen Y. Mulkidjanian, Daria V. Dibrova, A. Yu. Bychkov

et al.

Life, Journal Year: 2025, Volume and Issue: 15(3), P. 399 - 399

Published: March 4, 2025

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor potassium alkali cofactor, which implies their abundance in the habitats of first organisms. Intriguingly, lunar rocks contain a hundred times less ten than Earth’s crust; Moon is also depleted other moderately volatile elements (MVEs). Current theories impact formation attribute this depletion to MVEs still being gaseous state when hot post-impact disk contracted separated from nascent Moon. then fell out onto juvenile protocrust; zinc, most metal, precipitated last, just after potassium. According our calculations, top layer protocrust must have contained up 1019 kg metallic powerful reductant. venting geothermal fluids through MVE-fallout layer, rich radioactive potassium, both capable reducing carbon dioxide dinitrogen, yielded plethora organic molecules released with vapor. In pools vapor condensate, RNA-like may emerged pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, polymerizable molecules.

Language: Английский

Citations

0
A telomere-to-telomere genome assembly of Chinese grain sorghum 654 DOI Creative Commons
Fulin Wang, Jiandong Bao, Heng Zhang

et al.

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: March 19, 2025

The grain sorghum inbred line 654 serves as a parent for numerous Chinese commercial hybrids and recombinant lines (RILs), which have played pivotal role in the cloning of several agronomically important traits. In this study, we present telomere-to-telomere (T2T) genome assembly (728.81 Mb) using PacBio HiFi, ultra-long Oxford Nanopore Technology, Hi-C sequencing data. T2T has high integrity (contains all 10 centromeres 20 telomeres without any gaps), contiguity (contig N90: 52.02 Mb), completeness (98.33% BUSCO completeness, 98.88% k-mer LAI 24.38), extremely low base error (3.37 × 10-7, QV: 64.72). A total 62.34% sequences were identified repetitive, rest region contained 44,399 protein-coding genes, 30,245 functionally annotated. gap-free enables full picture potential translational genomics, provides highest resolution genetic map future studies on evolution, structure variation, control agronomic traits breeding.

Language: Английский

Citations

0
Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera DOI Creative Commons
Fatmah O. Sefrji, Aala A. Abulfaraj, Fatimah Alshehrei

et al.

Functional & Integrative Genomics, Journal Year: 2025, Volume and Issue: 25(1)

Published: April 7, 2025

Language: Английский

Citations

0
Bakta Web – rapid and standardized genome annotation on scalable infrastructures DOI Creative Commons
Sebastian Beyvers, Lukas Jelonek, Alexander Goesmann

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: unknown

Published: April 24, 2025

Abstract The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, usage software interpretation result files in various formats might be challenging pose technical barriers. Here, we present recent updates on web server, a user-friendly interface conducting visualizing annotations using without requiring expertise or local computing resources. Key features include interactive visualizations through circular plots, linear browsers, searchable data tables facilitating complex results. server generates standard bioinformatics outputs (GFF3, GenBank, EMBL) annotates diverse genomic features, including coding sequences, non-coding RNAs, small open reading frames (sORFs), many more. development an auto-scaling cloud-native architecture improved database integration led to substantially faster processing times higher throughputs. system supports FAIR principles extensive cross-reference links external databases, RefSeq, UniRef, Gene Ontology. Also, novel have been implemented foster sharing collaborative freely available at https://bakta.computational.bio.

Language: Английский

Citations

0
BASys2: a next-generation bacterial genome annotation system DOI Creative Commons

Jenna Poelzer,

Scott Han,

Sukanta Saha

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Originally released in 2005, BASys (Bacterial Annotation System) was one of the first web servers to support online bacterial genome annotation and interactive genomic display. Over past 20 years, technologies algorithms have advanced considerably. To keep current with these advances changing needs microbial genomics, we developed BASys2 System 2.0). represents a significant upgrade BASys, offering much more rapid (up 8000× faster) far complete (2× as many data fields) significantly improved visualization capabilities. More specifically, reduces time from 24 h little 10 s through fast genome-matching novel transfer strategy. Accepting either FASTA or FASTQ files, is able generate up 62 fields per gene/protein, leveraging over 30 bioinformatics tools different databases. Among unique features its extensive for whole metabolome structural proteome generation. BASys2's new viewer allows rapid, dynamic maps options display/hide multiple concentric tracks, show/remove color-coded legends, manipulate map, select/view individual gene metabolite annotations. Available server, desktop application, locally installable Docker image, researchers achieve unprecedented depth easily upload, download, display rich genome/metabolome The server freely accessible at https://basys2.ca.

Language: Английский

Citations

0
The architecture, assembly, and evolution of a complex flagellar motor DOI Creative Commons

Xueyin Feng,

Shoichi Tachiyama, Jing He

et al.

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

Published: Feb. 19, 2025

Summary Bacterial flagella drive motility in many species, likely including the last bacterial common ancestor 1,2 . Knowledge of flagellar assembly and function has mainly come from studies Escherichia coli Salmonella enterica , which have simple motors 3–7 However, most flagellated bacteria possess complex with unique, species-specific adaptations whose mechanisms evolution remain largely unexplored 8–10 Here, we deploy a multidisciplinary approach to build near-complete model motor Campylobacter jejuni revealing its remarkable complexity architecture composition. We identify an E-ring around MS-ring, periplasmic cage two distinctive conformations, intricate interaction network between cage. These scaffolds play critical roles stabilizing regulating 17 torque-generating stator complexes for optimal motility. In-depth evolutionary analyses uncover ancient origin prevalence species domain Bacteria as well unique exaptation type IV pili components PilMNOPQF ancestral phylum Campylobacterota Collectively, our reveal novel shed light on modern species.

Language: Английский

Citations

0
The 2025 Nucleic Acids Research database issue and the online molecular biology database collection DOI Creative Commons
Daniel J. Rigden, Xosé M. Fernández

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D1 - D9

Published: Dec. 10, 2024

The 2025 Nucleic Acids Research database issue contains 185 papers spanning biology and related areas. Seventy three new databases are covered, while resources previously described in the account for 101 update articles. Databases most recently published elsewhere a further 11 papers. acid include EXPRESSO multi-omics of 3D genome structure (this issue's chosen Breakthrough Resource Article) NAIRDB Fourier transform infrared data. New protein predictions human isoforms at ASpdb viral proteins BFVD. UniProt, Pfam InterPro have all provided updates: metabolism signalling covered by descriptions STRING, KEGG CAZy, updated microbe-oriented Enterobase, VFDB PHI-base. Biomedical research is supported, among others, ClinVar, PubChem DrugMAP. Genomics-related Ensembl, UCSC Genome Browser dbSNP. plant cover Solanaceae (SolR) Asteraceae (AMIR) families an from NCBI Taxonomy also features. Database Issue freely available on website (https://academic.oup.com/nar). At NAR online Molecular Biology Collection (http://www.oxfordjournals.org/nar/database/c/), 932 entries been reviewed last year, 74 added 226 discontinued URLs eliminated bringing current total to 2236 databases.

Language: Английский

Citations

2
Kiwa rescues RecBCD for anti-phage activity DOI Creative Commons
Zhiying Zhang,

Thomas C. Todeschini,

Yi Wu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 26, 2023

Bacteria and archaea deploy diverse, sophisticated defence systems to counter virus infection, yet many immunity mechanisms remain poorly understood. Here, we characterise the Kiwa system as a membrane-associated supercomplex that senses changes in membrane induced by phage infection plasmid conjugation. This supercomplex, comprising KwaA tetramers bound KwaB dimers, its basic repeating unit, detects structural stress via KwaA, activating KwaB, which binds ejected DNA through DUF4868 domain, stalling replication forks thus disrupting late transcription. We show phage-encoded mimic protein Gam, inhibits RecBCD, also targets recognition. However, Gam binding one precludes inhibition of other. These findings reveal distinct mechanism bacterial immune coordination, where sensing disruptions inhibitor partitioning enhance protection against phages plasmids.

Language: Английский

Citations

4