A global virome of methanogenic archaea highlights novel diversity and adaptations to the gut environment

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 9, 2023

Abstract Mobile genetic elements (MGEs), especially viruses, have a major impact on microbial communities. Methanogenic archaea play key environmental and economical roles, being the main producers of methane -a potent greenhouse gas an energy source. They are widespread in diverse anoxic artificial natural environments, including animal gut microbiomes. However, their viruses remain vastly unknown. Here, we carried out global investigation MGEs 3436 genomes metagenome-assembled covering all known diversity methanogens using newly assembled CRISPR database consisting 60,000 spacers methanogens, most extensive collection to date. We obtained 248 high-quality (pro)viral 63 plasmid sequences assigned hosts belonging nine orders methanogenic archaea, first Methanonatronarchaeales, Methanocellales Methanoliparales archaea. found novel arrays ‘ Ca. Methanomassiliicoccus intestinalis’ Methanomethylophilus’ with targeting small ssDNA Smacoviridae, supporting extending hypothesis interaction between smacoviruses associated Methanomassiliicoccales. Gene network analysis shows that encompass unique interconnected MGE repertoire, viral families head-tailed Caudoviricetes , but also icosahedral archaeal-specific pleomorphic, spherical, spindle (pro)viruses. reveal well-delineated modules for virus-host interaction, genome replication virion assembly, rich repertoire defense counter-defense systems suggesting highly dynamic complex interactions MGEs. identify potential conjugation composed VirB4, VirB5 VirB6 proteins encoded plasmids (pro)viruses Methanosarcinales, report Euryarchaeota. identified 15 new infecting Methanobacteriales, prominent microbiome. These encode large protein domains recognizing cleaving pseudomurein entry egress, convergent adaptation bacterial archaeal presence cell wall. Finally, highlight enrichment glycan-binding (immunoglobulin-like (Ig-like)/Flg_new) diversity-generating retroelements (DGRs) from gut-associated role host environments remarkable convergence phages bacteria. Our work represents important step toward characterization vast better understanding regulating communities globally development much-needed tools.

Language: Английский

---

3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors

Journal of Cheminformatics, Journal Year: 2023, Volume and Issue: 15(1)

Published: Aug. 28, 2023

Abstract Proteochemometric (PCM) modelling is a powerful computational drug discovery tool used in bioactivity prediction of potential candidates relying on both chemical and protein information. In PCM features are computed to describe small molecules proteins, which directly impact the quality predictive models. State-of-the-art descriptors, however, calculated from sequence neglect dynamic nature proteins. This can be computationally simulated with molecular dynamics (MD). Here, novel 3D descriptors (3DDPDs) were designed applied tasks As test case, publicly available G protein-coupled receptor (GPCR) MD data GPCRmd was used. GPCRs membrane-bound activated by hormones neurotransmitters, constitute an important target family for discovery. exist different conformational states that allow transmission diverse signals modified ligand interactions, among other factors. To translate MD-encoded two types 3DDPDs considered: one-hot encoded residue-specific (rs) embedding-like protein-specific (ps) 3DDPDs. The developed calculating distributions trajectory coordinates partial charges, applying dimensionality reduction, subsequently condensing them into vectors per residue or protein, respectively. benchmarked several against state-of-the-art non-dynamic descriptors. Our rs- ps3DDPDs outperformed regression using temporal split showed comparable performance random all classification tasks. Combinations did not result increased performance. Finally, power capture fluctuations mutant explored. results presented here show including information machine learning tasks, specifically prediction, open opportunities applications discovery, oncology.

Language: Английский

---

Realities of the consortium approach in Science: Sustainable enzymatic production of C1 chemicals from carbon dioxide

RSC Sustainability, Journal Year: 2024, Volume and Issue: 2(11), P. 3264 - 3275

Published: Jan. 1, 2024

This perspective reflects on the implementation of a multidisciplinary consortium project combining biological, chemical and computational sciences to discover develop new enzymes for carbon dioxide fixation.

Language: Английский

---

Massive expansion of the pig gut virome based on global metagenomic mining

npj Biofilms and Microbiomes, Journal Year: 2024, Volume and Issue: 10(1)

Published: Aug. 29, 2024

The pig gut virome plays a vital role in the microbial ecosystem of pigs. However, comprehensive understanding their diversity and reference database for are currently lacking. To address this gap, we established Pig Virome Database (PVD) that comprised 5,566,804 viral contig sequences from 4650 publicly available metagenomic samples using pipeline designated "metav". By clustering sequences, identified 48,299 operational taxonomic units (vOTUs) genomes at least medium quality, which 92.83% were not found existing major databases. majority vOTUs as Caudoviricetes (72.21%). PVD contained total 2,362,631 protein-coding genes across above medium-quality can be used to explore functional potential virome. These findings highlight extensive viruses provide pivotal dataset forthcoming research concerning

Language: Английский

---

Methanobrevibacter smithii cell variants in human physiology and pathology: a review

Heliyon, Journal Year: 2024, Volume and Issue: unknown, P. e36742 - e36742

Published: Sept. 1, 2024

---