» Articles » PMID: 29547915

Bastion6: a Bioinformatics Approach for Accurate Prediction of Type VI Secreted Effectors

Overview
Journal Bioinformatics
Specialty Biology
Date 2018 Mar 17
PMID 29547915
Citations 50
Authors
Affiliations
Soon will be listed here.
Abstract

Motivation: Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data.

Results: We extracted a wide range of features from T6SE protein sequences and comprehensively analyzed the prediction performance of these features through unsupervised and supervised learning. By integrating these features, we subsequently developed a two-layer SVM-based ensemble model with fine-grain optimized parameters, to identify potential T6SEs. We further validated the predictive model using an independent dataset, which showed that the proposed model achieved an impressive performance in terms of ACC (0.943), F-value (0.946), MCC (0.892) and AUC (0.976). To demonstrate applicability, we employed this method to correctly identify two very recently validated T6SE proteins, which represent challenging prediction targets because they significantly differed from previously known T6SEs in terms of their sequence similarity and cellular function. Furthermore, a genome-wide prediction across 12 bacterial species, involving in total 54 212 protein sequences, was carried out to distinguish 94 putative T6SE candidates. We envisage both this information and our publicly accessible web server will facilitate future discoveries of novel T6SEs.

Availability And Implementation: http://bastion6.erc.monash.edu/.

Supplementary Information: Supplementary data are available at Bioinformatics online.

Citing Articles

sp. nov., a pathogen causing red stripe of sugarcane in Japan.

Sawada H, Shinohara H, Takashima Y, Naito K, Satou M Int J Syst Evol Microbiol. 2025; 75(2).

PMID: 39907557 PMC: 11797039. DOI: 10.1099/ijsem.0.006575.


Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction.

Peng Y, Wu J, Sun Y, Zhang Y, Wang Q, Shao S Nat Commun. 2025; 16(1):1299.

PMID: 39900608 PMC: 11791096. DOI: 10.1038/s41467-025-56526-1.


Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.

Bray A, Broberg C, Hudson A, Wu W, Nagpal R, Islam M Nat Commun. 2025; 16(1):940.

PMID: 39843522 PMC: 11754592. DOI: 10.1038/s41467-025-56309-8.


Genomic analysis of isolated from surface water and animal sources in Chile reveals new T6SS effector protein candidates.

Amaya F, Blondel C, Reyes-Mendez F, Rivera D, Moreno-Switt A, Toro M Front Microbiol. 2024; 15:1496223.

PMID: 39723139 PMC: 11669294. DOI: 10.3389/fmicb.2024.1496223.


T4Seeker: a hybrid model for type IV secretion effectors identification.

Li J, He S, Zhang J, Zhang F, Zou Q, Ni F BMC Biol. 2024; 22(1):259.

PMID: 39543674 PMC: 11566746. DOI: 10.1186/s12915-024-02064-z.


References
1.
Blondel C, Jimenez J, Contreras I, Santiviago C . Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes. BMC Genomics. 2009; 10:354. PMC: 2907695. DOI: 10.1186/1471-2164-10-354. View

2.
ANFINSEN C . The formation and stabilization of protein structure. Biochem J. 1972; 128(4):737-49. PMC: 1173893. DOI: 10.1042/bj1280737. View

3.
Murdoch S, Trunk K, English G, Fritsch M, Pourkarimi E, Coulthurst S . The opportunistic pathogen Serratia marcescens utilizes type VI secretion to target bacterial competitors. J Bacteriol. 2011; 193(21):6057-69. PMC: 3194891. DOI: 10.1128/JB.05671-11. View

4.
Zahiri J, Yaghoubi O, Mohammad-Noori M, Ebrahimpour R, Masoudi-Nejad A . PPIevo: protein-protein interaction prediction from PSSM based evolutionary information. Genomics. 2013; 102(4):237-42. DOI: 10.1016/j.ygeno.2013.05.006. View

5.
Altindis E, Dong T, Catalano C, Mekalanos J . Secretome analysis of Vibrio cholerae type VI secretion system reveals a new effector-immunity pair. mBio. 2015; 6(2):e00075. PMC: 4453574. DOI: 10.1128/mBio.00075-15. View