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Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism.

Vital-Lopez FG, Reifman J, Wallqvist A - PLoS Comput. Biol. (2015)

Bottom Line: Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules.Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants.Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm metabolism.

View Article: PubMed Central - PubMed

Affiliation: Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America.

ABSTRACT
A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm metabolism. Our simulation results showed that plausible, non-intuitive explanations of difficult-to-interpret experimental observations could be generated by integrating genome-scale kinetic models with gene expression profiles.

No MeSH data available.


Related in: MedlinePlus

Dysregulation of secondary metabolites related to biofilm formation by inhibition of anthranilate degradation.(A) Sketch of the metabolic pathways involved in anthranilate and chorismate metabolism. Metabolite names written in red were predicted to increase when the reactions marked with a red x, which correspond to the low biofilm producers identified by Costaglioli et al. [11], were inhibited. (B) Correlation of the gene expression intensity of genes associated with anthranilate- and chorismate-derived secondary metabolites, psl and pel genes, with the genes of the kynurenine pathway.
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pcbi.1004452.g004: Dysregulation of secondary metabolites related to biofilm formation by inhibition of anthranilate degradation.(A) Sketch of the metabolic pathways involved in anthranilate and chorismate metabolism. Metabolite names written in red were predicted to increase when the reactions marked with a red x, which correspond to the low biofilm producers identified by Costaglioli et al. [11], were inhibited. (B) Correlation of the gene expression intensity of genes associated with anthranilate- and chorismate-derived secondary metabolites, psl and pel genes, with the genes of the kynurenine pathway.

Mentions: Anthranilate is a key node in a complex pathway for the synthesis of several important secondary metabolites for P. aeruginosa physiology derived from chorismate and tryptophan (Fig 4A). In simulations of the mutants that reduced biofilm formation in the study by Costaglioli et al. [11], concentrations of 19 metabolites changed by a factor of two or more in at least one mutant (S11 Table). Of the altered metabolites, only tryptophan, formylkynurenine, and kynurenine appeared in the set of metabolites with increased concentration in the low biofilm producers (these mutants were used in the computation of the sets of metabolites associated with the biofilm-reducing and biofilm-increasing reactions). Formylkynurenine and kynurenine are intermediate metabolites in the conversion of tryptophan to anthranilate through the kynurenine pathway, and kynurenine is known to be an inducer of the genes (kynABU) in this pathway [38]. Notably, the expression of kynABU correlated with the expression of genes downstream of anthranilate and chorismate, as well as with psl genes, but had a negative correlation with the pel genes in the dataset for P. aeruginosa biofilms (Fig 4B). Thus, we hypothesized that kynurenine accumulation led to up-regulation of kynABU and increased flux to anthranilate, which could not be degraded and, therefore, it was diverted to the synthesis of other metabolites, such as PQS, pyocyanine, and hydroxyphenazine, altering the normal development of the biofilm. This hypothesis is supported in part by a study by Oglesby et al. [39], who demonstrated the link between the regulation of anthranilate degradation genes (antABC) and the synthesis of PQS by showing that the expression of antABC affected the production of PQS, and that overexpression of pqsR (a quorum-sensing regulator co-induced by PQS) inhibited antABC expression.


Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism.

Vital-Lopez FG, Reifman J, Wallqvist A - PLoS Comput. Biol. (2015)

Dysregulation of secondary metabolites related to biofilm formation by inhibition of anthranilate degradation.(A) Sketch of the metabolic pathways involved in anthranilate and chorismate metabolism. Metabolite names written in red were predicted to increase when the reactions marked with a red x, which correspond to the low biofilm producers identified by Costaglioli et al. [11], were inhibited. (B) Correlation of the gene expression intensity of genes associated with anthranilate- and chorismate-derived secondary metabolites, psl and pel genes, with the genes of the kynurenine pathway.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4592021&req=5

pcbi.1004452.g004: Dysregulation of secondary metabolites related to biofilm formation by inhibition of anthranilate degradation.(A) Sketch of the metabolic pathways involved in anthranilate and chorismate metabolism. Metabolite names written in red were predicted to increase when the reactions marked with a red x, which correspond to the low biofilm producers identified by Costaglioli et al. [11], were inhibited. (B) Correlation of the gene expression intensity of genes associated with anthranilate- and chorismate-derived secondary metabolites, psl and pel genes, with the genes of the kynurenine pathway.
Mentions: Anthranilate is a key node in a complex pathway for the synthesis of several important secondary metabolites for P. aeruginosa physiology derived from chorismate and tryptophan (Fig 4A). In simulations of the mutants that reduced biofilm formation in the study by Costaglioli et al. [11], concentrations of 19 metabolites changed by a factor of two or more in at least one mutant (S11 Table). Of the altered metabolites, only tryptophan, formylkynurenine, and kynurenine appeared in the set of metabolites with increased concentration in the low biofilm producers (these mutants were used in the computation of the sets of metabolites associated with the biofilm-reducing and biofilm-increasing reactions). Formylkynurenine and kynurenine are intermediate metabolites in the conversion of tryptophan to anthranilate through the kynurenine pathway, and kynurenine is known to be an inducer of the genes (kynABU) in this pathway [38]. Notably, the expression of kynABU correlated with the expression of genes downstream of anthranilate and chorismate, as well as with psl genes, but had a negative correlation with the pel genes in the dataset for P. aeruginosa biofilms (Fig 4B). Thus, we hypothesized that kynurenine accumulation led to up-regulation of kynABU and increased flux to anthranilate, which could not be degraded and, therefore, it was diverted to the synthesis of other metabolites, such as PQS, pyocyanine, and hydroxyphenazine, altering the normal development of the biofilm. This hypothesis is supported in part by a study by Oglesby et al. [39], who demonstrated the link between the regulation of anthranilate degradation genes (antABC) and the synthesis of PQS by showing that the expression of antABC affected the production of PQS, and that overexpression of pqsR (a quorum-sensing regulator co-induced by PQS) inhibited antABC expression.

Bottom Line: Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules.Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants.Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm metabolism.

View Article: PubMed Central - PubMed

Affiliation: Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America.

ABSTRACT
A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm metabolism. Our simulation results showed that plausible, non-intuitive explanations of difficult-to-interpret experimental observations could be generated by integrating genome-scale kinetic models with gene expression profiles.

No MeSH data available.


Related in: MedlinePlus