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

Carriel, Diego; Garcia, Pierre; Castelli, Florence; Lamourette, Patricia; Fenaille, François; Brochier-Armanet, Céline; Elsen, Sylvie; Gutsche, Irina

doi:10.1093/gbe/evy228

Cited by 9 publications

(22 citation statements)

References 85 publications

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“…S1 ). This corresponds to the canonical organization of the wing-containing LAOdc superfamily 26 . Based on sequence comparison, LdcF proteins appear more similar to Escherichia coli LdcI (52.65% identity) and LdcC (48.18%) than to Pseudomonas aeruginosa LdcA (36.44%), E. coli AdcI (33.03%), E. coli OdcI (30.34%) and E. coli OdcC (27.28%).…”

Section: Resultsmentioning

confidence: 84%

“…The tree is a cladogram, meaning that the length of the branches has no evolutionary significance. The cladogram is rooted according to Carriel et al 26 . The colour of leaves corresponds to the LdcI, LdcC, AdcI, OdcC, OdcI, and LdcA subfamilies 26 .…”

Section: Resultsmentioning

confidence: 99%

“…The cladogram is rooted according to Carriel et al 26 . The colour of leaves corresponds to the LdcI, LdcC, AdcI, OdcC, OdcI, and LdcA subfamilies 26 . The group corresponding to Francisellaceae sequences (referred as to LdcF) is indicated in pink.…”

Section: Resultsmentioning

confidence: 99%

“…As polycations, polyamines bind negatively charged macromolecules such as DNA, proteins and phospholipids 28 , 29 , thereby contributing to a remarkable diversity of processes such as DNA replication, gene expression, protein synthesis, stress and antibiotic resistance, siderophore synthesis, biofilm formation and virulence 30 . In this work, we investigate the genetic environment of Francisella ldcF and the evolutionary relationships of LdcF with the other superfamily members in the light of a recent exhaustive phylogenetic analysis of proteobacterial LAOdcs 26 . We determine its crystal structure and identify specific structural elements which distinguish LdcF from E. coli LdcI, the most thoroughly-studied Ldc.…”

Section: Introductionmentioning

confidence: 99%

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Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Félix

Siebert

Ducassou

et al. 2021

Sci Rep

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Francisella tularensis is one of the most virulent pathogenic bacteria causing the acute human respiratory disease tularemia. While the mechanisms underlying F. tularensis pathogenesis are largely unknown, previous studies have shown that a F. novicida transposon mutant with insertions in a gene coding for a putative lysine decarboxylase was attenuated in mouse spleen, suggesting a possible role of its protein product as a virulence factor. Therefore, we set out to structurally and functionally characterize the F. novicida lysine decarboxylase, which we termed LdcF. Here, we investigate the genetic environment of ldcF as well as its evolutionary relationships with other basic AAT-fold amino acid decarboxylase superfamily members, known as key actors in bacterial adaptative stress response and polyamine biosynthesis. We determine the crystal structure of LdcF and compare it with the most thoroughly studied lysine decarboxylase, E. coli LdcI. We analyze the influence of ldcF deletion on bacterial growth under different stress conditions in dedicated growth media, as well as in infected macrophages, and demonstrate its involvement in oxidative stress resistance. Finally, our mass spectrometry-based quantitative proteomic analysis enables identification of 80 proteins with expression levels significantly affected by ldcF deletion, including several DNA repair proteins potentially involved in the diminished capacity of the F. novicida mutant to deal with oxidative stress. Taken together, we uncover an important role of LdcF in F. novicida survival in host cells through participation in oxidative stress response, thereby singling out this previously uncharacterized protein as a potential drug target.

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Section: Resultsmentioning

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Félix

Siebert

Ducassou

et al. 2021

Sci Rep

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“…The knock-out ΔacoR and Δaco mutants were generated in the P. aeruginosa PA2600 strain via allelic exchange thanks to suicide plasmids pEXG2ΔacoR and pEXG2Δaco constructed as described previously (21,22). Gentamicin (Euromedex) was used at final concentrations of 50µg/ml.…”

Section: Bacterial Strainsmentioning

confidence: 99%

Trophic cooperation promotes bacterial survival ofStaphylococcus aureusandPseudomonas aeruginosa

Camus

Briaud

Bastien

et al. 2020

Preprint

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In the context of infection, Pseudomonas aeruginosa and Staphylococcus aureus are frequently coisolated, particularly in cystic fibrosis (CF) patients. Within lungs, the two pathogens exhibit a range of competitive and coexisting interactions. In the present study, we explored the impact of S. aureus on the physiology of P. aeruginosa in the context of coexistence. Transcriptomic analyses showed that S. aureus significantly and specifically affects the expression of numerous genes involved in P. aeruginosa carbon and amino acid metabolism. In particular, 65% of the strains presented considerable overexpression of the genes involved in the acetoin catabolic (aco) pathway. We demonstrated that acetoin is (i) produced by clinical S. aureus strains, (ii) detected in sputa from CF patients, and (iii) involved in P. aeruginosa's aco system induction. Furthermore, acetoin is catabolized by P. aeruginosa, a metabolic process that improves the survival of both pathogens by providing a new carbon source for P. aeruginosa and avoiding the toxic accumulation of acetoin on S. aureus. Due to its beneficial effects on both bacteria, acetoin catabolism could testify to the establishment of trophic cooperation between S. aureus and P. aeruginosa in the CF lung environment, thus promoting their persistence. Figure 5: Monitoring of P. aeruginosa growth (A) and acetoin concentration (B) in minimal medium supplemented with acetoin. P. aeruginosa PA2600 WT, ΔacoR and Δaco strains were grown in M63 medium and 1.5mM acetoin was added every 2 hours, indicated by black arrows. A. Cultures were plated on TSA each 2 hours to count bacteria. Points represent the mean bacterial concentration ± SEM from three independent experiments. B. Acetoin was quantified from the supernatant each hour. Points represent the mean acetoin concentration ± SEM from three independent experiments. 9 Figure 6: Monitoring of S. aureus survival (A), P. aeruginosa survival (B) and acetoin concentration (C) during long-term co-culture. S. aureus SA2599 was cultivated in the presence of P. aeruginosa PA2600 WT, ΔacoR and Δaco during 5 days. Cultures were plated at J0, J3 and J5 on MSA and cetrimide to count S. aureus and P. aeruginosa respectively and acetoin was quantified from supernatant. A, B. Survival rate was estimated by dividing the bacterial concentration in co-culture by bacterial concentration in monoculture for each bacterium. Bars represent the mean survival rate + SEM from five independent experiments. *Padj<0.05, ****Padj<0.0001 one-way ANOVA with Dunnett correction (WT vs. condition). C. Acetoin concentration was normalized to S. aureus counts. Bars represent the median acetoin concentration per 10 6 S. aureus ± 95% CI from five independent experiments. *Padj<0.05, **Padj<0.01, Kruskal-Wallis with Dunn's correction.

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Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis

Liang

Hanfrey

et al. 2021

Journal of Biological Chemistry

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Polyamines are fundamental molecules of life, and their deep evolutionary history is reflected in extensive biosynthetic diversification. The polyamines putrescine, agmatine, and cadaverine are produced by pyridoxal 5′-phosphate-dependent L-ornithine, L-arginine, and L-lysine decarboxylases (ODC, ADC, LDC), respectively, from both the alanine racemase (AR) and aspartate aminotransferase (AAT) folds. Two homologous forms of AAT-fold decarboxylase are present in bacteria: an ancestral form and a derived, acid-inducible extended form containing an N-terminal fusion to the receiver-like domain of a bacterial response regulator. Only ADC was known from the ancestral form and limited to the Firmicutes phylum, whereas extended forms of ADC, ODC, and LDC are present in Proteobacteria and Firmicutes. Here, we report the discovery of ancestral form ODC, LDC, and bifunctional O/LDC and extend the phylogenetic diversity of functionally characterized ancestral ADC, ODC, and LDC to include phyla Fusobacteria, Caldiserica, Nitrospirae, and Euryarchaeota. Using purified recombinant enzymes, we show that these ancestral forms have a nascent ability to decarboxylate kinetically less preferred amino acid substrates with low efficiency, and that product inhibition primarily affects preferred substrates. We also note a correlation between the presence of ancestral ODC and ornithine/arginine auxotrophy and link this with a known symbiotic dependence on exogenous ornithine produced by species using the arginine deiminase system. Finally, we show that ADC, ODC, and LDC activities emerged independently, in parallel, in the homologous AAT-fold ancestral and extended forms. The emergence of the same ODC, ADC, and LDC activities in the nonhomologous AR-fold suggests that polyamine biosynthesis may be inevitable.

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

Cited by 9 publications

References 85 publications

Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Trophic cooperation promotes bacterial survival ofStaphylococcus aureusandPseudomonas aeruginosa

Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis

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