Molecular characterization of lysR-lysXE, gcdR-gcdHG and amaR-amaAB operons for lysine export and catabolism: a comprehensive lysine catabolic network in Pseudomonas aeruginosa PAO1

Indurthi, Sai Madhuri; Chou, Han-Ting; Lu, Chung‐Dar

doi:10.1099/mic.0.000277

Cited by 11 publications

(14 citation statements)

References 27 publications

(37 reference statements)

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“…In this organism exhibiting tightly interconnected lysine and arginine catabolism networks ( Chou et al. 2010 ; Madhuri Indurthi et al. 2016 ), the PA1818 gene was identified as a part of the ArgR regulon upon growth on excess arginine, but was surprisingly found to code for a lysine decarboxylase, and not for an arginine decarboxylase as one would have logically supposed, and was therefore called ldcA ( Chou et al.…”

Section: Resultsmentioning

confidence: 99%

A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Carriel

Garcia

Castelli

et al. 2018

Genome Biology and Evolution

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Polyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by pyridoxal-5-phosphate-dependent amino acid decarboxylases referred to as Lysine-Arginine-Ornithine decarboxylases (LAOdcs). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancient nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria. We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral in Betaproteobacteria and Pseudomonadaceae. We analyzed the expression of LdcA from Pseudomonas aeruginosa, and uncovered its role, intimately linked to cadaverine (Cad) production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines—Cad, putrescine (Put), and spermidine (Spd)—in P. aeruginosa by demonstrating the link between their intracellular level, as well as the capacity of Put and Spd to complement the growth phenotype of the ldcA mutant.

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Section: Resultsmentioning

confidence: 99%

A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Carriel

Garcia

Castelli

et al. 2018

Genome Biology and Evolution

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“…Genomic contexts of csiR and gcdR homologs and prediction of P. putida binding sites Work in Pseudomonas aeruginosa has characterized the GcdR regulation of ketogenic glutarate metabolism, and shown that the binding site is conserved across multiple bacterial species 17 . While binding sites for CsiR in E. coli have been identified, whether there is a conserved binding site for homologs across bacterial species has yet to be investigated 18 .…”

Section: Resultsmentioning

confidence: 99%

“…The P. aeruginosa GcdR was demonstrated to be a positive regulator of the gcdHG operon, with a binding site that was conserved in P. putida KT2440 among other Pseudomonas strains 17 . While other strains of P. aeruginosa have csiD homologs, the type strain PA01 does not.…”

Section: Discussionmentioning

confidence: 99%

Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors

Thompson

Cruz-Morales

Krishna

et al. 2019

Preprint

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A significant bottleneck in synthetic biology involves screening the large genetically encoded libraries enabled by the latest technologies for desirable phenotypes such as chemical production. However, transcription factor based biosensors can be leveraged to screen thousands of genetic designs for optimal chemical production in engineered microbes. In this study we characterize two glutarate sensing transcription factors (CsiR and GcdR) from Pseudomonas putida. The genomic contexts of csiR homologs were analyzed and DNA binding sites were bioinformatically predicted. Both CsiR and GcdR were purified and shown to bind upstream of their coding sequencing in vitro. CsiR was shown to dissociate from DNA in vitro when exogenous glutarate was added confirming it acts as a genetic repressor. Both transcription factors and cognate promoters were then cloned into broad host range vectors to create two glutarate biosensors. Their respective sensing performance features were characterized, and more sensitive derivatives of the GcdR biosensor were created by manipulating the expression of the transcription factor. Sensor vectors were then reintroduced into P. putida and were evaluated for their ability to respond to glutarate as well as various lysine metabolites. Additionally, we developed a novel mathematical approach to describe the usable range of detection for genetically encoded biosensors which may be broadly useful to future efforts to better characterize biosensor performance.

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“…To our knowledge, the only publication describing a member of the LdcA subfamily concerns P. aeruginosa , a highly versatile bacterium that efficiently grows on arginine but not on lysine (Fothergill & Guest, 1977, Rahman & Clarke, 1980). In this organism exhibiting tightly interconnected lysine and arginine catabolism networks (Chou et al , 2010, Madhuri Indurthi et al , 2016), the PA1818 gene was identified as a part of the ArgR regulon upon growth on excess arginine, but was surprisingly found to code for a lysine decarboxylase, and not for an arginine decarboxylase as one would have logically supposed, and therefore called ldcA (Chou et al ., 2010, Madhuri Indurthi et al , 2016). P. aeruginosa is a major cause of gram-negative infections, especially in patients with compromised and weakened immune system.…”

Section: Resultsmentioning

confidence: 99%

Identification of a novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative:Pseudomonas aeruginosaLdcA

Carriel-Lopez¹,

Garcia²,

Castelli³

et al. 2018

Preprint

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SummaryPolyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by PLP-dependent amino acid decarboxylases referred to as LAOdcs (Lysine-Arginine-Ornithine decarboxylases). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancestral nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria. We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral in Betaproteobacteria and Pseudomortadaceae {Gammaproteobacteria). We analyzed the expression of LdcA from Pseudomonas aeruginosa, and uncovered its role, intimately linked to cadaverine production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines - cadaverine, putrescine and spermidine - in P. aeruginosa by demonstrating the link between their intracellular level, as well as the capacity of putrescine and spermidine to complement the growth phenotype of the IdcA mutant.

show abstract

Molecular characterization of lysR-lysXE, gcdR-gcdHG and amaR-amaAB operons for lysine export and catabolism: a comprehensive lysine catabolic network in Pseudomonas aeruginosa PAO1

Cited by 11 publications

References 27 publications

A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors

Identification of a novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative:Pseudomonas aeruginosaLdcA

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