Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

Winsor, Geoffrey L.; Rossum, Thea Van; Lo, Raymond; Khaira, Bhavjinder K.; Whiteside, Matthew D.; Hancock, Robert E. W.; Brinkman, Fiona S. L.

doi:10.1093/nar/gkn861

Cited by 230 publications

(280 citation statements)

References 33 publications

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“…The strongest evidence for PA0305 being an Ntn hydrolase is the presence of the conserved Ser 1 residue, the first residue of the b-subunit. The N-terminal amino acids 1-25 of PA0305 are predicted to compose a signal sequence peptide (LipoP v.1.0, Phobius, SignalP v.3.0 Hidden Markov Models) (Winsor et al, 2009), which is in line with the observation that most bacterial Ntn hydrolases are secreted. However, determination of the N-terminal sequence of the a-subunit purified from E. coli revealed that the signal peptide is not cleaved off from the a-subunit under the experimental conditions used, indicating that the protein may not be translocated to the periplasm in E. coli or that the E. coli signal peptidase is less capable of cleaving this sequence.…”

Section: Discussionsupporting

confidence: 66%

PA0305 of Pseudomonas aeruginosa is a quorum quenching acylhomoserine lactone acylase belonging to the Ntn hydrolase superfamily

et al. 2011

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The Pseudomonas aeruginosa PAO1 genome has at least two genes, pvdQ and quiP, encoding acylhomoserine lactone (AHL) acylases. Two additional genes, pa1893 and pa0305, have been predicted to encode penicillin acylase proteins, but have not been characterized. Initial studies on a pa0305 transposon insertion mutant suggested that the gene is not related to the AHL growth phenotype of P. aeruginosa. The close similarity (67 %) of pa0305 to HacB, an AHL acylase of Pseudomonas syringae, prompted us to investigate whether the PA0305 protein might also function as an AHL acylase. The pa0305 gene has been cloned and the protein (PA0305) has been overproduced, purified and subjected to functional characterization. Analysis of the purified protein showed that, like b-lactam acylases, PA0305 undergoes post-translational processing resulting in a-and b-subunits, with the catalytic serine as the first amino acid of the b-subunit, strongly suggesting that PA0305 is a member of the N-terminal nucleophile hydrolase superfamily. Using a biosensor assay, PA0305his was shown to degrade AHLs with acyl side chains ranging in length from 6 to 14 carbons. Kinetics studies using N-octanoyl-L-homoserine lactone (C 8 -HSL) and N-(3-oxo-dodecanoyl)-L-homoserine lactone (3-oxo-C 12 -HSL) as substrates showed that the enzyme has a robust activity towards these two AHLs, with apparent K cat /K m values of 0.14¾10 4 M "1 s "1 towards C 8 -HSL and 7.8¾10 4 M "1 s "1 towards 3-oxo-C 12 -HSL. Overexpression of the pa0305 gene in P. aeruginosa showed significant reductions in both accumulation of 3-oxo-C 12 -HSL and expression of virulence factors. A mutant P. aeruginosa strain with a deleted pa0305 gene showed a slightly increased capacity to kill Caenorhabditis elegans compared with the P. aeruginosa PAO1 wild-type strain and the PAO1 strain carrying a plasmid overexpressing pa0305. The harmful effects of the Dpa0305 strain on the animals were most visible at 5 days post-exposure and the mortality rate of the animals fed on the Dpa0305 strain was faster than for the animals fed on either the wild-type strain or the strain overexpressing pa0305. In conclusion, the pa0305 gene encodes an efficient acylase with activity towards longchain homoserine lactones, including 3-oxo-C 12 -HSL, the natural quorum sensing signal molecule in P. aeruginosa, and we propose to name this acylase HacB.

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Section: Discussionsupporting

confidence: 66%

PA0305 of Pseudomonas aeruginosa is a quorum quenching acylhomoserine lactone acylase belonging to the Ntn hydrolase superfamily

et al. 2011

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“…Protein Sequence Identification, Expression, and Purification-The NCBI reference sequence (NC_002516.2) for P. aeruginosa (strain PAO1) (46) contains a region gi͉110645304:2945264 -2945869 coding for a hypothetical protein PA2602 (NP_251292.1) (47). A BLAST search (48) of putative bacterial CDO sequence (YP_299237.1) from R. eutropha (strain JMP134) was performed using the SIB-BLAST network service and identified PA2602 as a CDO homologue (Fig.…”

Section: Methodsmentioning

confidence: 99%

The Cysteine Dioxygenase Homologue from Pseudomonas aeruginosa Is a 3-Mercaptopropionate Dioxygenase

Tchesnokov

Fellner

Siakkou

et al. 2015

Journal of Biological Chemistry

117

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Background: Thiol dioxygenation is catalyzed by enzymes specific for each substrate. Results: Kinetic, structural, and spectroscopic data describe an enzyme from P. aeruginosa that is a 3-mercaptopropionate dioxygenase with secondary cysteine dioxygenase activity. Conclusion: An arginine to glutamine switch and the absence of a cis-peptide bond correlate with substrate preference. Significance: Characterization of this enzyme deepens our understanding of substrate specificity in thiol dioxygenases.

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“…The presence of the T443G SNP in FS and its absence in SBW25 was confirmed by Sanger sequencing (Macrogen). Analyses of regions upstream and downstream of fuzY, including the identification of orthologous genes in Pseudomonas species, were performed using Artemis 14.0.0 (Rutherford et al 2000) and the Generic Genome Browser (GBrowse) version 2.37 (Stein et al 2002) within the Pseudomonas Genome Database (Winsor et al 2009).…”

Section: Sequencing and Sequence Analysismentioning

confidence: 99%

Adaptive Divergence in Experimental Populations ofPseudomonas fluorescens. V. Insight into the Niche Specialist Fuzzy Spreader Compels Revision of the ModelPseudomonasRadiation

2013

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Pseudomonas fluorescens is a model for the study of adaptive radiation. When propagated in a spatially structured environment, the bacterium rapidly diversifies into a range of niche specialist genotypes. Here we present a genetic dissection and phenotypic characterization of the fuzzy spreader (FS) morphotype-a type that arises repeatedly during the course of the P. fluorescens radiation and appears to colonize the bottom of static broth microcosms. The causal mutation is located within gene fuzY (pflu0478)-the fourth gene of the five-gene fuzVWXYZ operon. fuzY encodes a b-glycosyltransferase that is predicted to modify lipopolysaccharide (LPS) O antigens. The effect of the mutation is to cause cell flocculation. Analysis of 92 independent FS genotypes showed each to have arisen as the result of a loss-of-function mutation in fuzY, although different mutations have subtly different phenotypic and fitness effects. Mutations within fuzY were previously shown to suppress the phenotype of mat-forming wrinkly spreader (WS) types. This prompted a reinvestigation of FS niche preference. Time-lapse photography showed that FS colonizes the meniscus of broth microcosms, forming cellular rafts that, being too flimsy to form a mat, collapse to the vial bottom and then repeatably reform only to collapse. This led to a reassessment of the ecology of the P. fluorescens radiation. Finally, we show that ecological interactions between the three dominant emergent types (smooth, WS, and FS), combined with the interdependence of FS and WS on fuzY, can, at least in part, underpin an evolutionary arms race with bacteriophage SBW25F2, to which mutation in fuzY confers resistance.A DAPTIVE radiation-the rapid emergence of phenotypic and ecological diversity within an expanding lineage-is among the most striking of evolutionary phenomena (Darwin 1859;Lack 1947;Dobzhansky 1951;Simpson 1953;Schluter 2000;Kassen 2009;Losos 2010). Fueled by competition and facilitated by ecological opportunity, successive radiations have shaped much of life's diversity. Of central importance are the phenotypic innovations that fashion the fit between organism and environment (Schluter 2000).Understanding the nature of these innovations and the pathways by which they emerge and rise to prominenceoften in parallel across estranged populations experiencing similar environments-is a central issue (Colosimo et al. 2005;Bantinaki et al. 2007;Conte et al. 2012). How mutational processes generate the variation presented to selection (McDonald et al. 2009;Braendle et al. 2010), how genetic architecture underpinning extant phenotypes determines the capacity of lineages to generate new and adaptive phenotypes (Poole et al. 2003;Wagner and Zhang 2011), and how ecological factors drive phenotypic divergence (Schluter 2009) are questions of seminal interest.The relative simplicity of microbial systems, their capacity for rapid evolutionary change, and advances in technology that enable detailed genotypic traceability offer a unique opportunity to log moment-by-...

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Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

Cited by 230 publications

References 33 publications

PA0305 of Pseudomonas aeruginosa is a quorum quenching acylhomoserine lactone acylase belonging to the Ntn hydrolase superfamily

PA0305 of Pseudomonas aeruginosa is a quorum quenching acylhomoserine lactone acylase belonging to the Ntn hydrolase superfamily

The Cysteine Dioxygenase Homologue from Pseudomonas aeruginosa Is a 3-Mercaptopropionate Dioxygenase

Adaptive Divergence in Experimental Populations ofPseudomonas fluorescens. V. Insight into the Niche Specialist Fuzzy Spreader Compels Revision of the ModelPseudomonasRadiation

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