Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins

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

Published: July 3, 2024

Abstract Thirty to seventy percent of proteins in any given genome have no assigned function and been labeled as the protein “unknome”. This large knowledge gap prevents biological community from fully leveraging plethora genomic data that is now available. Machine-learning approaches are showing some promise propagating functional experimentally characterized correct set isofunctional orthologs. However, they largely fail predict enzymatic functions unseen training set, shown by dissecting predictions made for over 450 enzymes unknown model bacteria Escherichia coli uxgsing DeepECTransformer platform. Lessons these failures can help develop machine-learning methods assist domain experts making testable more members uncharacterized proteome. Article Summary Many genome, ranging 30 70%, lack an function. limits full use vast available data. Machine learning has transferring known similar ones, but fails novel not seen its Understanding guide development better make accurate proteins.

Language: Английский

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Genomic hotspots: localized chromosome gene expansions identify lineage-specific innovations as targets for functional biodiversity and predictions of stress resilience

Frontiers in Marine Science, Journal Year: 2024, Volume and Issue: 11

Published: Aug. 1, 2024

Functional and biodiversity genomics is essential for assessment monitoring of planetary health species-specific management in changing ecosystems. However, experimental knowledge gene functions limited to a few species, dependencies on distantly related models. Combined with unrecognized degrees lineage-specific family expansion, this means that traditional comparative methods are insufficient. Here, we introduce the concept hotspot, defined as innovations underlying evolution biology. We illustrate hotspots using molluscs having chromosome-scale genome assemblies focus heat-sensing TRPM channels species living environments extreme heat stress (e.g., high intertidal hydrothermal vent gastropods bivalves). Integrating family, orthogroup, domain-based genomic (local homolog expansions chromosomes), show conventional approaches overlook substantial amounts diversity due limitations distant homology detection. In contrast, local segmental duplications often recent, genetic reflecting emerging adaptions can be identified any genome. Revealed diversification highlights unique neural behavioral mechanisms could beneficial predicting species’ resilience stress. summary, identification their integration other types analyses illuminate evolutionary (neuro)genomic strategies do not depend from model organisms unbiasedly reveal evolutionarily recent adaptations. This strategy enables discoveries biological across prospective targets modeling, management, conservation.

Language: Английский

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Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota , and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.

mSystems, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 19, 2024

ABSTRACT The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of marine environment have been described; thus, little known about the physiology metabolism members lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to were sediments collected Xiaoshi Island Weihai, China, using an aerobic enrichment method. integrated results phylogenetic phenotypic characteristics supported that these represent one a genus, for which name Gaopeijia maritima gen. nov., sp. nov. proposed, as first representative taxa, Gaopeijiales ord. Gaopeijiaceae fam. class Longimicrobiia. was detected 22,884 out 95,549 amplicon data sets, mainly soil. highest mean relative abundances sponge (0.7%) sediment (0.35%), showing salt-related character. Most subgroups potentially belong rare biosphere. study could significantly increase abundance (from 0.37% 2.6%). Furthermore, metabolic capabilities inferred high-quality genomes/MAGs suggest group primarily performs chemoorganoheterotrophic with possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed strains. IMPORTANCE Despite rapid advances molecular sequencing technologies, obtaining pure cultures remains crucial research goal microbiology, it essential deeper understanding microbial metabolism. phylum. Currently, interesting group, all non-marine environments. Little Here we characterized strains, proposed new order within . global distribution, environmental preference, potential analyzed public data. Our work enriches resources available under-represented provides insights into physiological lineage ( ) through culturology omics.

Language: Английский

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Advances in the Use of Genomics as a Biomarker for Diabetic Nephropathy

Advances in Clinical Medicine, Journal Year: 2024, Volume and Issue: 14(12), P. 518 - 526

Published: Jan. 1, 2024

Language: Английский

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The swan genome and transcriptome: its not all black and white

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: May 3, 2022

ABSTRACT The Australian black swan ( Cygnus atratus ) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. relative geographic isolation may have resulted in a limited immune repertoire and increased susceptibility infectious disease, notably diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks mute olor ), extremely sensitive severe highly pathogenic avian influenza (HPAI). Understanding this impaired by absence any available genome transcriptome information. Here, we generate first chromosome-length annotated genomes data, all using long-read based pipelines generated for vertebrate species. We used these transcriptomes, show other wild waterfowl, swans lack expanded gene repertoire, key viral pattern-recognition receptor endothelial cells mount poorly controlled inflammatory response HPAI. also implicate genetic differences SLC45A2 swan. Together, data suggest system such should infection become established its native habitat survival would be significant peril.

Language: Английский

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