Novel function discovery through sequence and structural data mining

Lobb, Briallen; Doxey, Andrew C.

doi:10.1016/j.sbi.2016.05.017

Cited by 37 publications

(27 citation statements)

References 102 publications

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“…Given the extreme sequence diversity of the hypervariable region and its potential as a scaffold for surface-localized functions, we hypothesized that there are flagellins with novel functionality that can be predicted from available bacterial genomes. Here, by computational identification of unexpected domain fusions 18 , we report the discovery and experimental validation of a family of enzymatically active flagellins present in the genomes of 74 bacterial species including the pathogenic clostridia Clostridium haemolyticum , and strains of Clostridium novyi and Clostridium botulinum . We find that these flagellins harbor a catalytically active zinc-metallopeptidase domain that is localized to extracellular flagellar filaments, so resulting in flagella-embedded protease activity in structures of up to 10 µm.…”

Section: Introductionmentioning

confidence: 99%

Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella

et al. 2017

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Bacterial flagella are cell locomotion and occasional adhesion organelles composed primarily of the polymeric protein flagellin, but to date have not been associated with any enzymatic function. Here, we report the bioinformatics-driven discovery of a class of enzymatic flagellins that assemble to form proteolytically active flagella. Originating by a metallopeptidase insertion into the central flagellin hypervariable region, this flagellin family has expanded to at least 74 bacterial species. In the pathogen, Clostridium haemolyticum, metallopeptidase-containing flagellin (which we termed flagellinolysin) is the second most abundant protein in the flagella and is localized to the extracellular flagellar surface. Purified flagellar filaments and recombinant flagellin exhibit proteolytic activity, cleaving nearly 1000 different peptides. With ~ 20,000 flagellin copies per ~ 10-μm flagella this assembles the largest proteolytic complex known. Flagellum-mediated extracellular proteolysis expands our understanding of the functional plasticity of bacterial flagella, revealing this family as enzymatic biopolymers that mediate interactions with diverse peptide substrates.

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Section: Introductionmentioning

confidence: 99%

Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella

et al. 2017

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“…Once the structure of a protein is known, residues critical for stability, as well as its active sites can often be located, and targeted mutations can be introduced. Similar structures can be identified and used to infer about the studied protein . Similarly, resolution of protein complexes can provide valuable information concerning the interaction mechanisms of proteins, allowing for the improved characterization and manipulation of signaling pathways in the cell.…”

Section: Introductionmentioning

confidence: 99%

“…Similar structures can be identified and used to infer about the studied protein. 1 Similarly, resolution of protein complexes can provide valuable information concerning the interaction mechanisms of proteins, allowing for the improved characterization and manipulation of signaling pathways in the cell. Once the details of the interface are known, inhibitors and activators of the target proteins can be designed based on features of the binding interface.…”

Section: Introductionmentioning

confidence: 99%

FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility

et al. 2017

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CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites. These rounds have also provided us the opportunity to reassess the success criteria, to better reflect the quality of a peptide-protein complex model. Using all models submitted to CAPRI, we analyze the correlation between current classification criteria and the ability to retrieve critical interface features, such as hydrogen bonds and hotspots. We find that loosening the backbone (and ligand) RMSD threshold, together with a restriction on the side chain RMSD measure, allows us to improve the selection of high-accuracy models. We also suggest a new measure to assess interface hydrogen bond recovery, which is not assessed by the current CAPRI criteria. Finally, we find that surprisingly much can be learned from rather inaccurate models about binding hotspots, suggesting that the current status of peptide-protein docking methods, as reflected by the submitted CAPRI models, can already have a significant impact on our understanding of protein interactions. Proteins 2017; 85:445-462. © 2016 Wiley Periodicals, Inc.

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“…These characteristics suggest that FUnkFams are bona fide protein families, and the associations of specific FUnkFams with marine environments or body sites provide hints about protein function and ecology. This study therefore lays the groundwork for significant future work to (i) predict (e.g., via genome proximity and further metagenome profiling (Lobb and Doxey, 2016) or literature based similarity (Price and Arkin, 2017)) and (ii) experimentally validate (e.g., via biochemical and structural characterization (Gerlt et al, 2011)) the functions of FUnkFams and the unannotated protein domains they contain. Our approach can be flexibly extended to use other databases of gene families and sources of functional annotation, and it will be interesting to apply it to other protein catalogs as well as RNA genes.…”

Section: Figurementioning

confidence: 99%

A most wanted list of conserved protein families with no known domains

Wyman

Avila-Herrera

Nayfach

et al. 2017

Preprint

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The number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a “most wanted” list of genes to characterize.

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Novel function discovery through sequence and structural data mining

Cited by 37 publications

References 102 publications

Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella

Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella

FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility

A most wanted list of conserved protein families with no known domains

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