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Phylogenetic analysis with prediction of cofactor or ligand binding for pseudomonas aeruginosa PAS and cache domains

Phylogenetic analysis with prediction of cofactor or ligand binding for pseudomonas aeruginosa PAS and cache domains
Phylogenetic analysis with prediction of cofactor or ligand binding for pseudomonas aeruginosa PAS and cache domains
PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.
2165-0497
Webb, Jeremy
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Hutchin, Andrew
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Cordery, Charlotte, Rose
1fe1f1a4-68f3-4528-a2c0-280d3f1e0f1f
Walsh, Martin A.
c51d771b-68b4-4c84-8906-650fc25bdad3
Tews, Ivo
9117fc5e-d01c-4f8d-a734-5b14d3eee8dd
Webb, Jeremy
ec0a5c4e-86cc-4ae9-b390-7298f5d65f8d
Hutchin, Andrew
5659cf31-f52e-451e-9cf0-4e786924d1ae
Cordery, Charlotte, Rose
1fe1f1a4-68f3-4528-a2c0-280d3f1e0f1f
Walsh, Martin A.
c51d771b-68b4-4c84-8906-650fc25bdad3
Tews, Ivo
9117fc5e-d01c-4f8d-a734-5b14d3eee8dd

Webb, Jeremy, Hutchin, Andrew, Cordery, Charlotte, Rose, Walsh, Martin A. and Tews, Ivo (2021) Phylogenetic analysis with prediction of cofactor or ligand binding for pseudomonas aeruginosa PAS and cache domains. Microbiology Spectrum, 9 (3). (doi:10.1128/spectrum.01026-21).

Record type: Article

Abstract

PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.

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Accepted/In Press date: 21 November 2021
Published date: 22 December 2021

Identifiers

Local EPrints ID: 454676
URI: http://eprints.soton.ac.uk/id/eprint/454676
ISSN: 2165-0497
PURE UUID: 00040f22-2f78-4cd4-a08e-495d7028d3fc
ORCID for Jeremy Webb: ORCID iD orcid.org/0000-0003-2068-8589
ORCID for Charlotte, Rose Cordery: ORCID iD orcid.org/0000-0003-2321-8144
ORCID for Ivo Tews: ORCID iD orcid.org/0000-0002-4704-1139

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Date deposited: 21 Feb 2022 17:31
Last modified: 17 Mar 2024 03:57

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Contributors

Author: Jeremy Webb ORCID iD
Author: Andrew Hutchin
Author: Martin A. Walsh
Author: Ivo Tews ORCID iD

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