Computational approaches to characterize bacterial protein function and activity in their environments

Published: Jan. 1, 2024

In this thesis, I present three studies on novel improvements to the elucidation of gene and protein function in different systems; antimicrobial resistance, bacterial metabolic pathways, tagging. The focus these is improve functional inference their specific contexts, with overall expression that improvement annotation will be brought by advances multiple methods rather than a single approach. To understand microbial genomic contributors used an elastic net logistic regression model predict resistance (AMR) phenotypes for 24 antibiotics Escherichia coli isolates from veterinary animals. We compared fit performance models designed evaluate potential modes AMR genotype translation into phenotypes. Our results show considers presence individual genes total number set known confer was able accurately isolate average. concluded interpretable prediction can across host species accurately. revealed testable hypotheses about how mechanism may vary within same class animal hosts antibiotic. proteins contribute biological pathway, we binary phylogenetic profiling method fusions, definition function. A protein's profile indicates or absence similar organisms. our study, profiles created using fusion versus sequence similarity as measured MMseqs2, ultra-fast alignment tool. predicted participate pathway. demonstrated improved predictions over sequence-similarity method. then applied marine metagenome data identified new putative cross-organism generating future analysis. These emergent pathways are starting point characterizing microbiomes activity, essential step toward understanding communities. detection analysis vivo, piloted EpicTope, predicts optimal sites internally inserted epitope tags without disrupting Internal integration tag offers several important advantages external end tags; frameshift mutations isolated parallel tagging would otherwise disrupted have ends inaccessible surface upon folding. For target protein, integrated tertiary structure, secondary solvent accessibility, disordered binding regions, conservation score positions suitability insertion. empirically evaluated Smad5, downstream transcription factor TGF-βBMP signaling pathway zebrafish; performed preliminary computational assessment comparing EpicTope pathogenic non-frameshifting insertion mutations. internally-tagged Smad5 rescue zebrafish mutant embryos, while N- C-terminal tagged cannot. localized presumptive ventral-lateral region gastrula, correlating linearly phosphorylated region. showed simple algorithm error margins other state-of-the-art mutation predictors, despite not being explicit task. intend molecular biologists easily rank identify interest suitable internal tag, developing area research. available at https://github.com/FriedbergLab/EpicTope R package.

Language: Английский

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Host immunity alters successional ecology and stability of the microbiome in a C. elegans model

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: June 27, 2020

Abstract A growing body of data suggests that the microbiome a species can vary considerably from individual to individual, but reasons for this variation - and consequences ecology these communities – remain only partially explained. In mammals, emerging picture is metabolic state immune system status host affects composition microbiome, quantitative ecological studies are challenging perform in higher organisms. Here we show phenomena be quantitatively analyzed tractable nematode Caenorhabditis elegans . Mutants innate immunity, particular DAF-2/Insulin Growth Factor (IGF) pathway, shown contain differs wild type nematodes. We analyze underlying basis differences perspective community by comparing experimental observations predictions neutral sampling model conclude fundamental underlie observed composition. test hypothesis introducing minor perturbation colonization conditions, allowing us assess stability different strains. Our results altering immunity changes importance inter-species interactions within resulting emerge host-microbe ecology. Importance use demonstrate how genetic alter composition, diversity, changing processes shape communities. These provide insight into role genetics controlling host-associated microbiota, successional trajectories, response perturbation.

Language: Английский

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Learning from the unknown: exploring the range of bacterial functionality

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

Published: Nov. 29, 2022

ABSTRACT Determining the repertoire of a microbe’s molecular functions is central question in microbial biology. Modern techniques achieve this goal by comparing genetic material against reference databases functionally annotated genes/proteins or known taxonomic markers such as 16S rRNA. Here we describe novel approach to exploring bacterial functional repertoires without databases. Our Fusion scheme establishes relationships between bacteria and assigns organisms Fusion-taxa that differ from otherwise defined clades. Three key findings our work stand out. First, comparisons outperform marker genes assigning profiles are also better for task than other annotation schemes. Second, robust addition are, arguably, able capture environment-driven diversity. Finally, alignment-free nucleic acid-based Siamese Neural Network model, created using functions, enables finding shared functionality very distant, possibly structurally different, homologs. can thus help annotate further guide understanding communities.

Language: Английский

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Divergent patterns and assembly processes of soil fungal abundant and rare communities along an elevational gradient in subalpine areas of Southwest China

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

Published: Jan. 31, 2023

Abstract Aim Understanding the patterns and assembly processes of microbial communities along an elevational gradient remains largely debated. Methods We examined soil fungal abundant rare underlying drives across a wide elevation from 2100-3950 m (a. s. l.) Yulong Mountain Southwest China. Results found taxa were divergent in diversity, only α diversity followed humpback trend peaked at 2900 m, despite β significantly dependent on gradients. Soil showed significant elevation-decay relationship, with more dispersal limitation to than that taxa. Along gradients, sub-communities governed by combined effect both environmental factors (soil nitrogen potassium, temperature) limitation, whereas merely dominated stochastic (ecological drifts). Network modules analysis revealed higher functional redundancy this influence reinforced neutrality, hence impelled susceptible drift. Conclusion Our results suggested pattern process for emphasized communities’ assembly, especially low

Language: Английский

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Avaliação da microbiota do solo em resposta ao herbicida 2,4-D

Published: Sept. 12, 2019

também do gene nifH,

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