Dataset Information

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

ABSTRACT: 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-?m 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.So far no enzymatic activity has been attributed to flagellin, the major component of bacterial flagella. Here the authors use bioinformatic analysis and identify a metallopeptidase insertion in flagellins from 74 bacterial species and show that recombinant flagellin and flagellar filaments have proteolytic activity.

SUBMITTER: Eckhard U

PROVIDER: S-EPMC5595980 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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

Eckhard Ulrich U Bandukwala Hina H Mansfield Michael J MJ Marino Giada G Cheng Jiujun J Wallace Iain I Holyoak Todd T Charles Trevor C TC Austin John J Overall Christopher M CM Doxey Andrew C AC

Nature communications 20170912 1

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. I ...[more]

PMID: 28900095

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Project description:Protein function prediction has been the most worked upon and the most challenging problem for computational biologists. The vast majority of known proteins have yet not been characterised experimentally, and there is significant gap between their structures and functions. New un-annotated sequences are being added to the public protein databases (e.g. UniprotKB) at an enormous pace [1]. Such proteins with unknown functions might play key role in the metabolism, growth and development regulation. Thus, if functions of unknown proteins left undiscovered, researchers may skip important information(s). Based on their sequence, structure, evolutionary history, and their association with other proteins, tools of computational biology can provide insights into the function of proteins [2]. For proteins with well characterised close relatives, it is trivial to infer function. Orphan proteins without discernible sequence relatives present a greater challenge [3]. Here the task of experimental characterisation is blind and becomes unwieldy. It is highly unlikely that all known proteins will ever be completely experimentally characterised [4]. Thus, there is an emergent need to develop fast and accurate computational approaches to fulfil this requirement. Towards this end, we prepared a dataset for protein function prediction by extracting protein sequences and annotations of reviewed prokaryotic proteins (total count 323,719 as accessed on date March 10, 2019) belonging to 9 bacterial phyla Actinobacteria, Bacteroidetes, Chlamydiae, Cyanobacteria, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes and Tenericutes. Corresponding to the most frequent 1739 Gene Ontology (Molecular Function) terms, samples were filtered, and 171,212 proteins were retrieved for feature generation. The Dataset was generated by calculating the sequence, sub-sequence, physiochemical, annotation-based features for each 171,212 reviewed proteins using method in [10]. These features constitute a total of 9890 attributes for each sequence of protein along with 1739 Gene Ontology terms. Each protein sequence is assigned one or more of 1739 Gene Ontology (Molecular Function) term as its target label. The Dataset contains the Entry and Entry name of each sequence corresponding to UniprotKB Database. This dataset being huge in size (171,212 samples X 9890 features, 1739 classes with multiple values) and equipped with enough number of positive and negative samples of each 1739 class, is good for testing efficiency of any upcoming deep learning models [5]. We divided the full dataset of 171,212 reviewed proteins in the ratio 3:1 to form Train/Test dataset 1; train dataset with 128,409 samples and test dataset with 42,803 samples to facilitate training of a deep learning model. The train and test datasets are stratified to contain good proportion of each 1739 classes. We then prepared a dataset 2 of pathogenic unreviewed proteins of the 9 bacterial phyla each with 9890 features same as train/train dataset of reviewed proteins but without target labels in order to predict their functions using deep learning model proposed in [5].

Dataset Information

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

Publications

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

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