Novel type III effectors in Pseudomonas aeruginosa

MBio
David BursteinEhud Banin

Abstract

Pseudomonas aeruginosa is a Gram-negative, opportunistic pathogen that causes chronic and acute infections in immunocompromised patients. Most P. aeruginosa strains encode an active type III secretion system (T3SS), utilized by the bacteria to deliver effector proteins from the bacterial cell directly into the cytoplasm of the host cell. Four T3SS effectors have been discovered and extensively studied in P. aeruginosa: ExoT, ExoS, ExoU, and ExoY. This is especially intriguing in light of P. aeruginosa's ability to infect a wide range of hosts. We therefore hypothesized that additional T3SS effectors that have not yet been discovered are encoded in the genome of P. aeruginosa. Here, we applied a machine learning classification algorithm to identify novel P. aeruginosa effectors. In this approach, various types of data are integrated to differentiate effectors from the rest of the open reading frames of the bacterial genome. Due to the lack of a sufficient learning set of positive effectors, our machine learning algorithm integrated genomic information from another Pseudomonas species and utilized dozens of features accounting for various aspects of the effector coding genes and their products. Twelve top-ranking predictions were...Continue Reading

References

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Citations

Jan 26, 2016·Journal of Medicinal Chemistry·Stefanie WagnerAlexander Titz
Dec 5, 2015·Frontiers in Cellular and Infection Microbiology·Rafat ZrieqJohannes H Hegemann
Apr 24, 2019·Journal of Bacteriology·Emily A Williams McMackinTimothy L Yahr
Sep 10, 2020·Toxins·Salomé Sauvage, Julie Hardouin
Feb 15, 2021·Microbiological Research·Gertrudis Horna, Joaquim Ruiz
Nov 21, 2020·Nature Reviews. Microbiology·Elio RossiHelle Krogh Johansen
Apr 4, 2021·International Journal of Molecular Sciences·Irene Jurado-MartínSiobhán McClean

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Methods Mentioned

BETA
PCR

Software Mentioned

BLAST
Weka
R
AUCCalculator
PSI
HHpred

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