From gene to structure: Unraveling genomic dark matter in Ca. Accumulibacter DOI Creative Commons

Xiaojing Xie,

Xuhan Deng,

Liping Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 17, 2024

Abstract Candidatus Accumulibacter is a unique and pivotal genus of polyphosphate-accumulating organisms (PAOs) prevalent in wastewater treatment plants, plays mainstay roles the global phosphorus cycle. Whereas, efforts toward complete understanding their genetic metabolic characteristics are largely hindered by major limitations existing sequence-based annotation methods, leaving more than half protein-encoding genes unannotated. To address challenge, we developed comprehensive approach integrating pangenome analysis, gene-based protein structure function prediction, metatranscriptomic extending beyond constraints sequence-centric methodologies. The application to Ca . allowed establishment pan- proteome database, providing references for >200,000 proteins. Benchmarking on 28 genomes showed increases average coverage from 51% 83%. Genetic that had eluded exploration via conventional methods were unraveled. For instance, identification previously unknown phosphofructokinase gene suggests all Ca. encoded Embden-Meyerhof-Parnas pathway. A defined homolog phosphate-specific transport system accessory (PhoU) was actually an inorganic phosphate (Pit) protein, regulating Pit instead high-affinity (Pst), key emergence trait Accumulibacter. Additional lineage members found encoding denitrification pathways. This study offers readily usable transferable tool high-coverage reference databases diverse cultured uncultured bacteria, facilitating genomic dark matter bacterial domain. Synopsis integrated advanced unraveling applicable bacteria customerized database

Language: Английский

Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the Flaviviridae DOI Creative Commons
Peter Simmonds, Anamarija Butković, Joe Grove

et al.

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

Citations

0
A review of BioTree construction in the context of information fusion: Priors, methods, applications and trends DOI
Zelin Zang, Yongjie Xu,

Chenrui Duan

et al.

Information Fusion, Journal Year: 2025, Volume and Issue: unknown, P. 103108 - 103108

Published: March 1, 2025

Language: Английский

Citations

0
Conserved Local Structural Motifs in Glycoside Hydrolase Families Facilitate the Discovery of Functional Enzymes DOI

Yupeng Liang,

Yalan Zhao,

Zhongwei Yin

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: May 5, 2025

Glycoside hydrolases (GHs) are vital for natural glycoside biotransformation, especially in enhancing the pharmacological effects of products like ginsenosides. In this study, we collected 67 microbial-derived ginsenoside-hydrolyzing enzymes from nine GH families. Despite differences global structures, key residues surrounding substrate binding GH1 and GH3 exhibit conserved structural motifs. Leveraging these motifs, five genes Cellulosimicrobium were cloned, three (Cbgl496, Cbgl516, Cbgl766) characterized. Experimental results demonstrated that Cbgl766, Cbgl841 specifically catalyzed hydrolysis β(1-6) glycosidic bond C-20 sugar chain ginsenoside Rb1 to yield Rd. Cbgl496 selectively β(1-2) bonds oligosaccharide chains at C-3 position ginsenosides Rb1, Rb2, Rb3, Rc, thereby directionally producing minor Gy XVII, Compound O, Mx1, Mc1. Structural analysis 109,994 GH1/GH3 models AlphaFold database revealed across various organisms, emphasizing evolutionary conservation 3D structure catalytic core region despite sequence diversity. This study underscores importance local motifs GHs, offering insights functional enzyme screening understanding diversity industrial applications.

Language: Английский

Citations

0
Exploring the Structural Diversity and Evolution of the D1 Subunit of Photosystem II Using AlphaFold and Foldtree DOI Creative Commons
Tom Dongmin Kim,

Daniella Pretorius,

James W. Murray

et al.

Physiologia Plantarum, Journal Year: 2025, Volume and Issue: 177(3)

Published: May 1, 2025

ABSTRACT Although our knowledge of photosystem II has expanded to include time‐resolved atomic details, the diversity experimental structures enzyme remains limited. Recent advances in protein structure prediction with AlphaFold offer a promising approach fill this gap structural non‐model systems. This study used predict D1 protein, core subunit II, across broad range photosynthetic organisms. The produced high‐confidence structures, and alignment analyses highlighted conserved regions different groups, which were line high pLDDT scoring regions. In contrast, varying DE loop terminal appears correlate degrees flexibility or disorder. Subsequent phylogenetic analysis using Foldtree provided tree that is good agreement previous sequence‐based studies. Moreover, phylogeny supports parsimonious scenario far‐red INT evolved from an ancestral form G4 D1. work demonstrates potential molecular evolution photosynthesis.

Language: Английский

Citations

0
Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life DOI
Nathaniel J. Himmel, David Moi, Richard Benton

et al.

Current Biology, Journal Year: 2023, Volume and Issue: 33(22), P. 5023 - 5033.e4

Published: Oct. 31, 2023

Language: Английский

Citations

8
Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships DOI Creative Commons

Kimberly R. Sabsay,

Aartjan J.W. te Velthuis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 17, 2024

Abstract Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including influenza, Ebola and measles viruses. NSV genomes consist one or multiple single-stranded molecules that are encapsidated into more ribonucleoprotein (RNP) complexes. These RNPs viral RNA, a polymerase, many copies nucleoprotein (NP). Current evolutionary relationships within phylum based on alignment conserved RNA-directed polymerase (RdRp) domain amino acid sequences. However, RdRp domain-based phylogeny does not address whether NP, other core protein in genome, evolved along same trajectory several RdRp-NP pairs through convergent evolution segmented non-segmented architectures. Addressing how NP may help us better understand diversity. Since sequences too short to infer robust phylogenetic relationships, we here used experimentally-obtained AlphaFold 2.0-predicted structures probe can be estimated using Following flexible structure alignments modeled structures, find structural homology NPs reveals clusters consistent with RdRp-based clustering. In addition, were able assign for which currently missing available sequence. Both our NP-based deviate from current classification Naedrevirales , cluster NSVs analysis. Overall, results suggest genes largely similar trajectories even pieces genetic, protein-coding information potentially making metagenomic analyses valuable.

Language: Английский

Citations

2
Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps DOI Creative Commons
Yingchun Han, Yongyi Peng,

Jiaxue Peng

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 24, 2024

Reductive dehalogenation is crucial for halogen cycling and environmental remediation, yet its ecological role incompletely understood, especially in deep-sea environments. To address this gap, we investigated the diversity of reductive dehalogenases (RDases) ecophysiology organohalide reducers cold seeps, which are environments rich halogenated compounds. Through genome-resolved metagenomic analysis 165 global seep sediment samples, identified four types RDases, namely prototypical respiratory, transmembrane cytosolic one novel clade. These RDases encoded by physiologically diverse microbes across archaeal 36 bacterial phyla, significantly broadening known reducers. Halogen geochemistry, metatranscriptomic data, metabolomic profiling confirm that organohalides occur at as high 18 mg/g these sediments actively reduced microorganisms. This process tightly linked to other biogeochemical cycles, including carbon, hydrogen, nitrogen, sulfur, trace elements. from seeps have N-terminal structures different gene groups, dehalogenase genes mostly functionally constrained conserved. Altogether, findings suggest a central rather than supplemental environments, mediated numerous enzymes.

Language: Английский

Citations

2
An ancient lysozyme in placozoans DOI Open Access
Henry Berndt,

Igor Duarte,

Urska Repnik

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 6, 2024

Lysozymes are an essential part of nutrition and antibacterial immunity in metazoans, executing the breakdown bacterial cell walls via hydrolysis peptidoglycan. Although various lysozymes have been reported for several bilaterian phyla, origin metazoan remains elusive as they seem to be lacking non-bilaterian animals. In this study, we investigated a putative goose-type lysozyme (PLys, glycoside hydrolase family 23, GH23) placozoan Trichoplax sp. H2 which localized gland cells ventral epithelium. N-terminal conserved GH23 domain, PLys contains non-conserved cysteine-rich domain. We could show truncation domain maturation process drastic increase enzymatic activity at cost stability using recombinantly expressed physiological proteoforms PLys. Phylogenetic analysis from all domains life revealed monophyletic radiation Based on structural comparisons their distribution animal tree life, g-type appear originated horizontal gene transfer event bacteria early pre-bilaterian ancestor. then retained expanded many including Porifera, Cnidaria, Placozoa chordates, acting key component arsenal since evolution.

Language: Английский

Citations

2
Reticulate Evolution: Detection and Utility in the Phylogenomics Era DOI Open Access

Saelin Bjornson,

Heroen Verbruggen, Nathan S. Upham

et al.

Published: May 14, 2024

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Non-vertical modes evolution—such as hybridization/introgression horizontal gene transfer—deviate from a strictly bifurcating tree model, causing non-treelike patterns. Here, we present brief overview phylogenomic workflow for inferring organismal histories compare methods detecting evolution. We discuss how timing coalescent events help disentangle introgression incomplete lineage sorting transfer determine relative speciation events. In doing so, identify pitfalls certain to extend their utility across Life. Workflows, methods, future directions discussed herein underscore need embrace evolutionary patterns rates events, providing clearer life’s history.

Language: Английский

Citations

1
Cold seeps are hotspots of deep-sea nitrogen-loss driven by microorganisms across 21 phyla DOI Creative Commons
Qiuyun Jiang, Lei Cao, Yingchun Han

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 6, 2024

Abstract Nitrogen bioavailability, governed by the balance of fixation and loss processes, is a key factor regulating oceanic productivity, ecosystem functions, global biogeochemical cycles. The nitrogen-loss organisms—denitrifiers anaerobic ammonium-oxidizing (anammox) bacteria—are not well understood in marine seafloor environments, especially deep-sea cold seeps. In this study, we combined geochemical measurements, 15 N stable isotope tracer analysis, metagenomics, metatranscriptomics, three-dimensional protein structural simulations to investigate diversity denitrifying anammox microbial communities their roles these habitats. Geochemical evidence from 301 sediment samples shows significantly higher rates seeps compared typical sediments, with an estimated annual nitrogen 6.16 Tg surface sediments. Examination total 147 million non-redundant genes reveals high prevalence active expression genes, including nitrous-oxide reductase (NosZ; 6.88 per or GPM on average), nitric oxide dismutase (Nod; 1.29 GPM), hydrazine synthase (HzsA; 3.35 GPM) Analysis 3,164 metagenome-assembled genomes habitat has expanded known reducers six phyla oxide-dismutating organisms one phylum two new orders, while ten host bacteria going beyond Planctomycetota . These microbes show diverse adaptations complex gene cluster arrangements that potentially enable survival harsh conditions findings suggest seeps, despite low temperatures, are significant, previously underestimated hotspots loss, contribute substantially cycle.

Language: Английский

Citations

1