In silico analysis of mitochondrial DNA genes: implication for conservation of Tor putitora (Hamilton, 1822)

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 2, 2025

Tor putitora is an endangered cyprinid fish constrained to cold water and also considered indicator of a healthy aquatic ecosystem. The present study aimed examine the haplotypic diversity, genetic variation population structure T. isolates using COI Cyt b gene sequences submitted in GenBank. Bioinformatic analysis was carried out 106 183 as well 2 reference genome sequences. Analysis reveals 18 85 haplotypes respectively. Mutation observed at 44 different sites 173 Haplotype 4 haplotype 37 were ancestral moderate diversity (0.630) low Nucleotide (0.00662) whereas has higher (0.804) (0.00582). Moreover, neutrality test such Tajima's D, Fu's Fs showed negative values both sequences, suggesting expansion attributed habitat destruction. So, comprehending variability within among crucial for conserving managing this species. Integration into conservation planning can enhance effectiveness breeding programs restoration efforts.

Language: Английский

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Identification of receptor-binding domains of Bacteroidales antibacterial pore-forming toxins

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

Published: Jan. 6, 2025

Abstract Bacteroidales are abundant Gram-negative bacteria present in the gut microbiota of most animals, including humans, where they carry out vital functions for host health. To thrive this competitive environment, use sophisticated weapons to outmatch competitors. Among these, BSAPs (Bacteroidales Secreted Antimicrobial Proteins) represent a novel class bactericidal pore-forming toxins that highly specific their receptor, typically targeting only single membrane protein or lipopolysaccharide. The molecular determinants conferring high selectivity remain unknown. In study, we therefore investigated model BSAP-1 and determined which its domains is involved providing receptor specificity. We clearly demonstrate recognition entirely driven by C-terminal domain (CTD) using combination vivo competition assays vitro binding studies. Specifically, show deletion CTD abrogates activity preventing binding, while grafting unrelated carrier proteins enables CTD-driven interaction with receptor. Building upon discovery, can be categorized according structure within same cluster likely target type Additionally, repurposed generate probes fluorescent labelling live cells. summary, our research demonstrates BSAP these engineered develop tools investigation biology.

Language: Английский

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Genome Sequence, Comparative Genome Analysis, and Expression Profiling of the Chitinase GH18 Gene Family in Cordyceps javanica Bd01

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 2031 - 2031

Published: Feb. 26, 2025

The fungus Cordyceps javanica is known for entomopathogenicity and effective in the control of various arthropods. Here, we aimed to reveal chitinase GH18 gene family expansion through high throughput sequencing genome C. strain Bd01 isolated from Xylotrechus quadripes larvae. was 34 Mb size with 9590 protein-coding genes. By comparative analysis, it found that genes expanded Bd01. phylogenetic analysis 27 genes, compared those four other species, revealed could be categorized into three distinct groups based on their conserved domains. Genes within same cluster exhibited shared protein motifs orthologous relationships. molecular mass these ranged 14.03 kDa 81.41 kDa, while theoretical isoelectric point (pI) values spanned 4.40 7.92. Most chitinases were characterized as extracellular, hydrophilic, thermostable proteins a negative charge. Additionally, they demonstrated favorable vivo half-life stability. A three-dimensional structural model further generated using SWISS-MODEL server. These findings establish robust genomic framework elucidating functional diversity, evolutionary conservation patterns, mechanistic contributions virulence-associated genetic determinants.

Language: Английский

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Factors affecting CRISPR-Cas defense against antibiotic resistance plasmids harbored byEnterococcus faecalislaboratory model strains and clinical isolates

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

Published: March 11, 2025

ABSTRACT Enterococcus faecalis is a Gram-positive bacterium and opportunistic pathogen that acquires resistance to wide range of antibiotics by horizontal gene transfer (HGT). The rapid increase multidrug-resistant (MDR) bacteria including MDR E. necessitates the development alternative therapies deeper understanding factors impact HGT. CRISPR-Cas systems provide sequence-specific defense against From previous studies, we know provides anti-plasmid during agar plate biofilm mating in murine intestine. Those studies were mainly conducted using laboratory model strains with single, CRISPR-targeted plasmid donor. typically possess multiple plasmids are diverse sequence may interact each other efficacy. Here, altered parameters our standard vitro conjugation assays assess efficacy, number genotype donor; as donor versus recent human isolates substrate utilized conjugation. We found pTEF2 pCF10, which not targeted recipient, enhance conjugative pTEF1 into both wild-type CRISPR-Cas-deficient (via deletion cas9 ) recipient cells. However, effect on much more pronounced, striking 6-log frequency when also present recipients deficient for (compared 4-log pCF10). identified Δ has structure thickness relative strain cultured plastic substrate, but equivalent growth biofilms widely used studies. Overall, this study insight about interplay between defense, opening avenues developing novel therapeutic strategies curb HGT among bacterial pathogens, highlighting additional mechanistic study. IMPORTANCE emergence bacteria, faecalis, limits treatment options therapeutics. In these circumstances, being explored field develop CRISPR-based antimicrobials. many cases efficacy only been assessed strains. More required investigate clinical isolates, those intended targets CRISPR demonstrated how harbored an can affect apparent strain. research important improved antimicrobials combat spread accumulation antibiotic determinants.

Language: Английский

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MAST Kinases’ Function and Regulation: Insights from Structural Modeling and Disease Mutations

Biomedicines, Journal Year: 2025, Volume and Issue: 13(4), P. 925 - 925

Published: April 9, 2025

Background/Objectives: The MAST kinases are ancient AGC associated with many human diseases, such as cancer, diabetes, and neurodevelopmental disorders. We set out to describe the origins diversification of from a structural bioinformatic perspective inform future research directions. Methods: investigated MAST-lineage using database sequence analysis. also estimate functional consequences disease point mutations on protein stability by integrating predictive algorithms AlphaFold. Results: Higher-order organisms often have multiple MASTs single MASTL kinase. proteins conserve an kinase domain, domain unknown function 1908 (DUF), PDZ binding domain. D. discoideum contains kinase-like that exhibit characteristic insertion within T-loop but do not DUF or domains. While is conserved in plants, not. four mammalian demonstrate tissue expression heterogeneity mRNA protein. MAST1-4 likely regulated 14-3-3 based interactome data silico predictions. Comparative ΔΔG estimation identified MAST1-L232P G522E destabilizing. Conclusions: conclude diverged primordial MAST, which operated both biological niches. number paralogs then expanded heterogeneous subfamily seen mammals all interaction. reported pathogenic primarily represent alterations post-translational modification topology Our report outlines computational basis for work regulation drug discovery.

Language: Английский

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Deep learning tools predict variants in disordered regions with lower sensitivity

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 12, 2025

The recent AI breakthrough of AlphaFold2 has revolutionized 3D protein structural modeling, proving crucial for design and variant effects prediction. However, intrinsically disordered regions-known their lack well-defined structure lower sequence conservation-often yield low-confidence models. latest Variant Effect Predictor (VEP), AlphaMissense, leverages models, achieving over 90% sensitivity specificity in predicting effects. the effectiveness tools variants regions, which account 30% human proteome, remains unclear. In this study, we found that pathogenicity regions is less accurate than ordered particularly mutations at first N-Methionine site. Investigations into efficacy effect predictors on (IDRs) indicated IDRs are predicted with gap between largest especially AlphaMissense VARITY. prevalence within coupled increasing repertoire biological functions they known to perform, necessitated an investigation state-of-the-art VEPs such regions. This analysis revealed consistently reduced differing prediction performance profile indicating new IDR-specific features paradigms needed accurately classify disease those

Language: Английский

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Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the Flaviviridae

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

Published: Jan. 18, 2025

Abstract The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse related to classical orthoflaviviruses pestiviruses but quite different genome lengths configurations, with hugely expanded host range that spans multiple animal phyla, molluscs, cnidarians stramenopiles,, plants. Grouping RNA-directed polymerase (RdRP) hallmark gene sequences flavivirus ‘flavi-like’ into four divergent clades lineages within them was congruent helicase phylogeny, PPHMM profile comparisons, comparison RdRP protein structure predicted by AlphFold2. These results support their classification the established order, Amarillovirales , in three families ( Flaviviridae, Pestiviridae Hepaciviridae ), 14 genera. This taxonomic framework informed evolutionary relationships provides stable reference from which major re-organisational events can be understood.

Language: Английский

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The DUF506 Gene Family in Triticum aestivum: Genome-Wide Identification and Expression Profiling Under Salt Stress

Agronomy, Journal Year: 2025, Volume and Issue: 15(2), P. 281 - 281

Published: Jan. 23, 2025

As a subfamily of the PD-(D/E)XK nuclease superfamily, DUF506 family shows great potential in abiotic stress responding higher plant, yet its clues structure, evolution and functions remain largely unexplored due to their distant phylogenetic relationship with other families, especially Triticum aestivum. In this study, 26 T. aestivum genes (TaDUF506) were identified from genome-wide level through bioinformatic techniques. Phylogenetic structural analyses revealed that TaDUF506 exhibit conserved motif gene structure patterns intra-phylogenetic clusters but display significant divergence inter-clusters. Gene duplication identification showed whole-genome event (WGD) was primary driver expansion, while Ka/Ks analysis indicated whole experienced purifying selection generally. ontology protein-protein interaction prediction suggested plays role transcription regulation nucleotide-excision Promoter highlighted an enrichment hormone-responsive elements linked salt TaDUF1.3-3D TaDUF5.1-3A, expression demonstrated upregulation under stress, suggesting roles responses. Altogether, our study advances understanding plant structural, evolutional functional aspects, thereby provides foundation for development salt-tolerant wheat varieties.

Language: Английский

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Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers in metazoans

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

Published: Jan. 31, 2025

ABSTRACT Branched actin networks nucleated by the Arp2/3 complex play critical roles in various cellular processes, from cell migration to intracellular transport. However, when activated WISH/DIP/SPIN90 family proteins, nucleates linear filaments. Unexpectedly, we found that human SPIN90 is a dimer can nucleate bidirectional To understand basis for this, determined 3 Å resolution structure of SPIN90-Arp2/3 nucleating Our shows dimerises via 3-helix bundle and interacts with two complexes. Each molecule binds both complexes promote their activation. analysis demonstrates single filament nucleation mechanistically more like branch formation than previously appreciated. The dimerisation domain orthologues conserved metazoans, suggesting this mode common strategy generate anti-parallel

Language: Английский

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Genomic and Transcriptomic Characterization of Carbohydrate-Active Enzymes in the Anaerobic Fungus Neocallimastix cameroonii var. constans

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

Published: Jan. 30, 2025

Abstract Anaerobic gut fungi effectively degrade lignocellulose in the guts of large herbivores, but there remains a limited number isolated, publicly available, and sequenced strains that impede our understanding role anaerobic within microbial communities. We isolated characterized new fungal isolate, Neocallimastix cameroonii var. constans, providing transcriptomic genomic its ability to diverse carbohydrates. This strain was stably cultivated for multiple years vitro among members an initial enrichment community derived from goat feces, it demonstrated pair with other members, namely archaeal methanogens produce methane lignocellulose. Genomic analysis revealed higher predicted carbohydrate-active enzymes encoded N. constans genome compared most fungi. The enzyme profile this isolate contained 660 glycoside hydrolases, 160 carbohydrate esterases, 194 glycosyltrasferases, 85 polysaccharide lyases. Differential gene expression showed upregulation thousands genes (including enzymes) when grown on (reed canary grass) less complex substrates, such as cellulose (filter paper), cellobiose, glucose. AlphaFold used predict functions transcriptionally active yet poorly annotated genes, revealing feruloyl esterases likely play important degradation by combination strain’s characterization, omics-informed structural prediction, robustness co-culture make well-suited platform conduct future investigations into bioprocessing discovery.

Language: Английский

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