ReviewJournal of bacteriology2009
Discovering functional novelty in metagenomes: examples from light-mediated processes.
Review in Journal of bacteriology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
24 citing papers in PubMed, 62 citations in OpenAlex.
- Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective.International journal of molecular sciences · 2021Review
- Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life.mSphere · 2019Article
- Physical methods for studying flavoprotein photoreceptors.Methods in enzymology · 2019Article
- Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes.Scientific reports · 2018Article
- Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes.Frontiers in microbiology · 2018Article
- Functional and structural characterization of a novel putative cysteine protease cell wall-modifying multi-domain enzyme selected from a microbial metagenome.Scientific reports · 2016Article
- Web Resources for Metagenomics Studies.Genomics, proteomics & bioinformatics · 2015Review
- Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters.Frontiers in microbiology · 2015Article
- Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater.BMC microbiology · 2014Article
- Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.BMC genomics · 2014Article
- From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World.Plants (Basel, Switzerland) · 2014Review
- A Statistical Approach to Correcting Cross-Annotations in a Metagenomic Functional Profile Generated by Short Reads.Journal of biometrics & biostatistics · 2014Article
- Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.Ecology and evolution · 2013Article
- Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.Genome biology and evolution · 2013Article
- Away from darkness: a review on the effects of solar radiation on heterotrophic bacterioplankton activity.Frontiers in microbiology · 2013Article
- Gene prediction in metagenomic fragments based on the SVM algorithm.BMC bioinformatics · 2013Article
- Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea.PeerJ · 2013Article
- Article
- Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134.Applied and environmental microbiology · 2011Article
- Orthology prediction methods: a quality assessment using curated protein families.BioEssays : news and reviews in molecular, cellular and developmental biology · 2011Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The emerging coverage of diverse habitats by metagenomic shotgun data opens new avenues of discovering functional novelty using computational tools. Here, we apply three different concepts for predicting novel functions within light-mediated microbial pathways in five diverse environments. Using phylogenetic approaches, we discovered two novel deep-branching subfamilies of photolyases (involved in light-mediated repair) distributed abundantly in high-UV environments. Using neighborhood approaches, we were able to assign seven novel functional partners in luciferase synthesis, nitrogen metabolism, and quorum sensing to BLUF domain-containing proteins (involved in light sensing). Finally, by domain analysis, for RcaE proteins (involved in chromatic adaptation), we predict 16 novel domain architectures that indicate novel functionalities in habitats with little or no light. Quantification of protein abundance in the various environments supports our findings that bacteria utilize light for sensing, repair, and adaptation far more widely than previously thought. While the discoveries illustrate the opportunities in function discovery, we also discuss the immense conceptual and practical challenges that come along with this new type of data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.