A fast comparative genome browser for diverse bacteria and archaea

Price, Morgan N.; Arkin, Adam P.

doi:10.1101/2023.08.23.554478

Cited by 4 publications

(3 citation statements)

References 46 publications

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“…A recently developed tool of particularly exciting functionality is fast.genomics , a tool built within the suite of PaperBLAST ( Fig. 8 ) [ 56 ] and that uses the genomes of MicrobesOnline. This tool is one of very few that pairs the power of a sequence-based search in tandem with the inferential value of clustering analysis for pairs of distinct protein families ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families

Reed,

Denise,

Hourihan

et al. 2024

Microbial Genomics

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Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3) family, we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most information published on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighbourhood information were reviewed for their versatility and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.

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Section: Resultsmentioning

confidence: 99%

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families

Reed,

Denise,

Hourihan

et al. 2024

Microbial Genomics

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show abstract

“…Previous structural characterization and genome context analysis predicts DUF364 has a role in heavy-metal chelation (23). In organisms that encode DUF364 homologs, its presence is conserved next to molybdate uptake genes (16). We hypothesize it could have a role in chelating molybdate for biosynthesis of the molybdate cofactor (FeMoCo) required for nitrogen fixation.…”

Section: Panel A)mentioning

confidence: 85%

“…Both homologs contain the zinc CxC binding motif and conserved ADP biding residues. Additionally, the presence of both CooC domains is conserved across 340 representative genomes from different genera (16). Of the 340 genomes with both CooC homologs, 50 appear to be co-transcribed as they occur on the same strand and are within 5 kb of each other.…”

Section: Identification Of Genes Important For Autotrophic Growthmentioning

confidence: 99%

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

Day,

Carlson,

Fonseca

et al. 2024

Preprint

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Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly-barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that M. maripaludis can utilize additional nitrogen sources including L-glutamine, D-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP, group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale dataset that can be used as a resource to further understand gene function and metabolism in the archaeal domain.

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Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families

Reed

Denise

Hourihan

et al. 2023

Preprint

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Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on any specific member of that said family. This step is often performed only superficially or partially by experimentalists as the most common approaches and tools to pursue this objective are far from optimal. Using a previously gathered dataset of 284 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3), we evaluated the productivity of different databases and search tools, and devised a workflow that can be used by experimentalists to capture the most information in less time. To complement this workflow, web-based platforms allowing for the exploration of member distributions for several protein families across sequenced genomes or for the capture of gene neighborhood information were reviewed for their versatility, completeness and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.

show abstract

A fast comparative genome browser for diverse bacteria and archaea

Cited by 4 publications

References 46 publications

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families

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