Enhanced annotations and features for comparing thousands of<i>Pseudomonas</i>genomes in the Pseudomonas genome database

Winsor, Geoffrey L.; Griffiths, Emma; Lo, Raymond; Dhillon, Bhavjinder K.; Shay, Julie A.; Brinkman, Fiona S. L.

doi:10.1093/nar/gkv1227

Cited by 951 publications

(1,130 citation statements)

References 46 publications

Supporting

Mentioning

1,106

Contrasting

Unclassified

Order By: Relevance

“…Homologs of the eatR (PA4021) gene and the PA4022-eat-eutBC operon are clustered in the genomes for many Pseudomonas spp., including common strains of P. putida, P. denitrificans, and P. fluorescens (57). This suggests that a variety of Pseudomonas strains use an EatR-RpoN mechanism for regulating ethanolamine catabolism.…”

Section: Discussionmentioning

confidence: 99%

Ethanolamine Catabolism in Pseudomonas aeruginosa PAO1 Is Regulated by the Enhancer-Binding Protein EatR (PA4021) and the Alternative Sigma Factor RpoN

et al. 2016

View full text Add to dashboard Cite

Although genes encoding enzymes and proteins related to ethanolamine catabolism are widely distributed in the genomes of Pseudomonas spp., ethanolamine catabolism has received little attention among this metabolically versatile group of bacteria. In an attempt to shed light on this subject, this study focused on defining the key regulatory factors that govern the expression of the central ethanolamine catabolic pathway in Pseudomonas aeruginosa PAO1. This pathway is encoded by the PA4022-eateutBC operon and consists of a transport protein (Eat), an ethanolamine-ammonia lyase (EutBC), and an acetaldehyde dehydrogenase (PA4022). EutBC is an essential enzyme in ethanolamine catabolism because it hydrolyzes this amino alcohol into ammonia and acetaldehyde. The acetaldehyde intermediate is then converted into acetate in a reaction catalyzed by acetaldehyde dehydrogenase. Using a combination of growth analyses and ␤-galactosidase fusions, the enhancer-binding protein PA4021 and the sigma factor RpoN were shown to be positive regulators of the PA4022-eat-eutBC operon in P. aeruginosa PAO1. PA4021 and RpoN were required for growth on ethanolamine, and both of these regulatory proteins were essential for induction of the PA4022-eat-eutBC operon. Unexpectedly, the results indicate that acetaldehyde (and not ethanolamine) serves as the inducer molecule that is sensed by PA4021 and leads to the transcriptional activation of the PA4022-eat-eutBC operon. Due to its regulatory role in ethanolamine catabolism, PA4021 was given the name EatR. Both EatR and its target genes are conserved in several other Pseudomonas spp., suggesting that these bacteria share a mechanism for regulating ethanolamine catabolism. IMPORTANCEThe results of this study provide a basis for understanding ethanolamine catabolism and its regulation in Pseudomonas aeruginosa PAO1. Interestingly, expression of the ethanolamine-catabolic genes in this bacterium was found to be under the control of a positive-feedback regulatory loop in a manner dependent on the transcriptional regulator PA4021, the sigma factor RpoN, and the metabolite acetaldehyde. Previously characterized regulators of ethanolamine catabolism are known to sense and respond directly to ethanolamine. In contrast, PA4021 (EatR) appears to monitor the intracellular levels of free acetaldehyde and responds through transcriptional activation of the ethanolamine-catabolic genes. This regulatory mechanism is unique and represents an alternative strategy used by bacteria to govern the acquisition of ethanolamine from their surroundings. E thanolamine serves as a source of carbon and nitrogen for a variety of bacteria, including members of the Enterobacteriaceae, Pseudomonadaceae, and Firmicutes (1-5). From studies mostly centered on Salmonella enterica subsp. enterica serovar Typhimurium and Escherichia coli, there is now a basic understanding of the catabolic steps involved in ethanolamine utilization. Extracellular ethanolamine enters the bacterial cell through simple diffusion or carrier-me...

show abstract

Section: Discussionmentioning

confidence: 99%

Ethanolamine Catabolism in Pseudomonas aeruginosa PAO1 Is Regulated by the Enhancer-Binding Protein EatR (PA4021) and the Alternative Sigma Factor RpoN

et al. 2016

View full text Add to dashboard Cite

show abstract

“…The data is compiled from the EcoCyc and Pseudomonas Genome database website [260,261]. *The value for protein sequence identity and similarity of E. coli and P. aeruginosa was obtained using CLUSTALW2 'pairwise sequence alignments'.…”

Section: Inner Membranementioning

confidence: 99%

Cell-wall recycling and synthesis in Escherichia coli and Pseudomonas aeruginosa – their role in the development of resistance

Dhar

Kumari

Balasubramanian

et al. 2018

Journal of Medical Microbiology

View full text Add to dashboard Cite

The bacterial cell-wall that forms a protective layer over the inner membrane is called the murein sacculus -a tightly crosslinked peptidoglycan mesh unique to bacteria. Cell-wall synthesis and recycling are critical cellular processes essential for cell growth, elongation and division. Both de novo synthesis and recycling involve an array of enzymes across all cellular compartments, namely the outer membrane, periplasm, inner membrane and cytoplasm. Due to the exclusivity of peptidoglycan in the bacterial cell-wall, these players are the target of choice for many antibacterial agents. Our current understanding of cell-wall biochemistry and biogenesis in Gram-negative organisms stems mostly from studies of Escherichia coli. An incomplete knowledge on these processes exists for the opportunistic Gram-negative pathogen, Pseudomonas aeruginosa. In this review, cell-wall synthesis and recycling in the various cellular compartments are compared and contrasted between E. coli and P. aeruginosa. Despite the fact that there is a remarkable similarity of these processes between the two bacterial species, crucial differences alter their resistance to b-lactams, fluoroquinolones and aminoglycosides. One of the common mediators underlying resistance is the amp system whose mechanism of action is closely associated with the cell-wall recycling pathway. The activation of amp genes results in expression of AmpC blactamase through its cognate regulator AmpR which further regulates multi-drug resistance. In addition, other cell-wall recycling enzymes also contribute to antibiotic resistance. This comprehensive summary of the information should spawn new ideas on how to effectively target cell-wall processes to combat the growing resistance to existing antibiotics.

show abstract

“…In the proposed pathway for Hyp catabolism, L-Hyp is first converted into D-Hyp by epimerization. While LhpA has been reported as the Hyp epimerase (Watanabe et al, 2014), LhpK was annotated as proline racemase (Winsor et al, 2016). As shown in Fig.…”

Section: Effects Of Lhpr Lhpa and Lhpk Mutations On Promoter Activationmentioning

confidence: 99%

Molecular characterization of LhpR in control of hydroxyproline catabolism and transport in Pseudomonas aeruginosa PAO1

2016

Microbiology

View full text Add to dashboard Cite

Utilization of hydroxy-L-proline (L-Hyp) in Pseudomonas aeruginosa requires conversion of L-Hyp to D-Hyp followed by the D-Hyp dehydrogenase pathway; however, the molecular mechanism in control of L-Hyp catabolism and transport was not clear. DNA microarray analysis revealed twelve genes in two adjacent loci that were induced by exogenous L-Hyp and D-Hyp. The first locus includes lhpABFE encoding a Hyp epimerase (LhpA) and D-Hyp dehydrogenase (LhpBEF), while the second locus codes for a putative ABC transporter (LhpPMNO), a protein of unknown function (LhpH), Hyp/Pro racemase (LhpK) and two enzymes in L-Hyp catabolism (LhpC and LhpG). Proximal to these two loci, lhpR encodes a transcriptional regulator of the AraC family. The importance of these genes on L-Hyp catabolism was supported by growth phenotype analysis on knockout mutants. Induction of the lhpA and lhpP promoters by exogenous L-Hyp and D-Hyp was demonstrated by the measurement of b-galactosidase activities from promoter-lacZ fusions in PAO1, and no induction could be detected in the DlhpR mutant. Induction of the lhpA promoter by D-Hyp was completely abolished in the lhpA lhpK double mutant devoid of two epimerases, while the induction effect of L-Hyp remained unchanged. The purified His-tagged LhpR binds specifically to the lhp promoter regions, and formation of nucleoprotein complexes is affected by the presence of L-Hyp but not D-Hyp. Putative LhpR binding sites were deduced from serial deletions and comparative genomic sequence analysis. In summary, expression of lhp genes for Hyp catabolism and uptake requires the transcriptional activator LhpR and L-Hyp as the signalling compound.

show abstract

Enhanced annotations and features for comparing thousands ofPseudomonasgenomes in the Pseudomonas genome database

Cited by 951 publications

References 46 publications

Ethanolamine Catabolism in Pseudomonas aeruginosa PAO1 Is Regulated by the Enhancer-Binding Protein EatR (PA4021) and the Alternative Sigma Factor RpoN

Ethanolamine Catabolism in Pseudomonas aeruginosa PAO1 Is Regulated by the Enhancer-Binding Protein EatR (PA4021) and the Alternative Sigma Factor RpoN

Cell-wall recycling and synthesis in Escherichia coli and Pseudomonas aeruginosa – their role in the development of resistance

Molecular characterization of LhpR in control of hydroxyproline catabolism and transport in Pseudomonas aeruginosa PAO1

Contact Info

Product

Resources

About