Dataset Information

Periscope Proteins are variable-length regulators of bacterial cell surface interactions.

ABSTRACT: Changes at the cell surface enable bacteria to survive in dynamic environments, such as diverse niches of the human host. Here, we reveal "Periscope Proteins" as a widespread mechanism of bacterial surface alteration mediated through protein length variation. Tandem arrays of highly similar folded domains can form an elongated rod-like structure; thus, variation in the number of domains determines how far an N-terminal host ligand binding domain projects from the cell surface. Supported by newly available long-read genome sequencing data, we propose that this class could contain over 50 distinct proteins, including those implicated in host colonization and biofilm formation by human pathogens. In large multidomain proteins, sequence divergence between adjacent domains appears to reduce interdomain misfolding. Periscope Proteins break this "rule," suggesting that their length variability plays an important role in regulating bacterial interactions with host surfaces, other bacteria, and the immune system.

SUBMITTER: Whelan F

PROVIDER: S-EPMC8201768 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Periscope Proteins are variable-length regulators of bacterial cell surface interactions.

Whelan Fiona F Lafita Aleix A Gilburt James J Dégut Clément C Griffiths Samuel C SC Jenkins Huw T HT St John Alexander N AN Paci Emanuele E Moir James W B JWB Plevin Michael J MJ Baumann Christoph G CG Bateman Alex A Potts Jennifer R JR

Proceedings of the National Academy of Sciences of the United States of America 20210601 23

Changes at the cell surface enable bacteria to survive in dynamic environments, such as diverse niches of the human host. Here, we reveal "Periscope Proteins" as a widespread mechanism of bacterial surface alteration mediated through protein length variation. Tandem arrays of highly similar folded domains can form an elongated rod-like structure; thus, variation in the number of domains determines how far an N-terminal host ligand binding domain projects from the cell surface. Supported by newly ...[more]

PMID: 34074781

Similar Datasets

Project description:Cells detect changes of external environments or communicate with each other through proteins on their surfaces. These cell surface proteins form a complicated network of interactions in order to fulfill their functions. The interactions between cell surface proteins are highly dynamic and thus challenging to detect using traditional experimental techniques. Here we tackle this challenge by a computational framework. The primary focus of the framework is to develop new tools to identify interactions between domains in immunoglobulin (Ig) fold, which is the most abundant domain family in cell surface proteins. These interactions could be formed between ligands and receptors from different cells, or between proteins on the same cell surface. In practice, we collected all structural data of Ig domain interactions and transformed them into an interface fragment pair library. A high dimensional profile can be then constructed from the library for a given pair of query protein sequences. Multiple machine learning models were used to read this profile, so that the probability of interaction between the query proteins can be predicted. We tested our models to an experimentally derived dataset which contains 564 cell surface proteins in human. The cross-validation results show that we can achieve higher than 70% accuracy in identifying the PPIs within this dataset. We then applied this method to a group of 46 cell surface proteins in C elegans. We screened every possible interaction between these proteins. Many interactions recognized by our machine learning classifiers have been experimentally confirmed in the literatures. In conclusion, our computational platform serves a useful tool to help identifying potential new interactions between cell surface proteins in addition to current state-of-the-art experimental techniques. The tool is freely accessible for use by the scientific community. Moreover, the general framework of the machine learning classification can also be extended to study interactions of proteins in other domain superfamilies.

Dataset Information

Periscope Proteins are variable-length regulators of bacterial cell surface interactions.

Publications

Periscope Proteins are variable-length regulators of bacterial cell surface interactions.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets