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Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.

Vinay-Lara E, Hamilton JJ, Stahl B, Broadbent JR, Reed JL, Steele JL - PLoS ONE (2014)

Bottom Line: After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors.We conclude that the metabolic capabilities of the two networks are highly similar.The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

ABSTRACT
Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is strain dependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains for specific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotype relationships and to compare different organisms. To assist in the selection and development of strains with enhanced industrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate, were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined by evaluating ATP generating cycles, mass-and-charge-balances of reactions, and growth phenotypes. After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors. We conclude that the metabolic capabilities of the two networks are highly similar. The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes. The developed L. casei ATCC 334 and 12A metabolic models will enable better understanding of the physiology of these organisms and be valuable tools in the development and selection of strains with enhanced utility in a variety of industrial applications.

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Related in: MedlinePlus

Metabolic differences in the two L. casei strains.(A): Pathway for the synthesis of tetrahydrofolate (THF) from 5, 10-methylenetetrahydrofolate (5,10-CH2-THF) and its role in purine biosynthesis. This pathway is common to both strains. (B): Additional pathway for the conversion of 5,10-CH2-THF to THF active in the iLca12A_640 model. With the exception of the panthtothenate transporter, the reactions are found in both models. (A and B): Thick arrows indicate flux in both models. Double arrows represent flux in the iLca12A_640 model. The black ‘X’ indicates a gene deletion identified by CONGA lethal in iLca334_548 but not iLca12A_640, and gray arrows indicate inactive reactions arising from the deletion. The dashed arrow represents two separate steps. Reactions and metabolites corresponding to the given E.C. numbers and metabolite identifiers are given in the Supporting Material.
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pone-0110785-g003: Metabolic differences in the two L. casei strains.(A): Pathway for the synthesis of tetrahydrofolate (THF) from 5, 10-methylenetetrahydrofolate (5,10-CH2-THF) and its role in purine biosynthesis. This pathway is common to both strains. (B): Additional pathway for the conversion of 5,10-CH2-THF to THF active in the iLca12A_640 model. With the exception of the panthtothenate transporter, the reactions are found in both models. (A and B): Thick arrows indicate flux in both models. Double arrows represent flux in the iLca12A_640 model. The black ‘X’ indicates a gene deletion identified by CONGA lethal in iLca334_548 but not iLca12A_640, and gray arrows indicate inactive reactions arising from the deletion. The dashed arrow represents two separate steps. Reactions and metabolites corresponding to the given E.C. numbers and metabolite identifiers are given in the Supporting Material.

Mentions: Using CONGA we also identified one metabolic difference, in which deletion of the enzyme 5, 10-methylenetetrahydrofolate (5,10-CH2-THF) dehydrogenase (E.C. 1.5.1.5) is lethal only in the iLca334_548 model. This means that the iLca12A_640 model has a unique mechanism (shown in Figure 3) for recovering from this gene deletion. Briefly, 5,10-CH2-THF is a precursor to 10-formyltetrahydrofolate (10-CHO-THF) a cofactor involved in purine biosynthesis, an essential activity for cellular growth. The deletion of 5,10-CH2-THF dehydrogenase prevents the biosynthesis of THF in L. casei ATCC 334. Our model for L. casei 12A predicts that this deletion can be rescued by the actions of 5,10-CH2-THF:3-methyl-2-oxobutanoate (E.C. 2.1.2.11) and formate: THF ligase (E.C. 6.3.4.3), in which 5,10-CH2-THF is converted directly to THF, producing 2-dehydropantoate as a by-product. The reactions pantoate 2-oxidoreductase (E.C. 1.1.1.169) and pantothenate amidohydrolase (E.C. 3.5.1.22) convert 2-dehydropantoate to pantothenate, which can be secreted by a transporter unique to the iLca12A_640 model, or some pantothenate can also be used for CoA biosynthesis, important for biomass formation.


Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.

Vinay-Lara E, Hamilton JJ, Stahl B, Broadbent JR, Reed JL, Steele JL - PLoS ONE (2014)

Metabolic differences in the two L. casei strains.(A): Pathway for the synthesis of tetrahydrofolate (THF) from 5, 10-methylenetetrahydrofolate (5,10-CH2-THF) and its role in purine biosynthesis. This pathway is common to both strains. (B): Additional pathway for the conversion of 5,10-CH2-THF to THF active in the iLca12A_640 model. With the exception of the panthtothenate transporter, the reactions are found in both models. (A and B): Thick arrows indicate flux in both models. Double arrows represent flux in the iLca12A_640 model. The black ‘X’ indicates a gene deletion identified by CONGA lethal in iLca334_548 but not iLca12A_640, and gray arrows indicate inactive reactions arising from the deletion. The dashed arrow represents two separate steps. Reactions and metabolites corresponding to the given E.C. numbers and metabolite identifiers are given in the Supporting Material.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231531&req=5

pone-0110785-g003: Metabolic differences in the two L. casei strains.(A): Pathway for the synthesis of tetrahydrofolate (THF) from 5, 10-methylenetetrahydrofolate (5,10-CH2-THF) and its role in purine biosynthesis. This pathway is common to both strains. (B): Additional pathway for the conversion of 5,10-CH2-THF to THF active in the iLca12A_640 model. With the exception of the panthtothenate transporter, the reactions are found in both models. (A and B): Thick arrows indicate flux in both models. Double arrows represent flux in the iLca12A_640 model. The black ‘X’ indicates a gene deletion identified by CONGA lethal in iLca334_548 but not iLca12A_640, and gray arrows indicate inactive reactions arising from the deletion. The dashed arrow represents two separate steps. Reactions and metabolites corresponding to the given E.C. numbers and metabolite identifiers are given in the Supporting Material.
Mentions: Using CONGA we also identified one metabolic difference, in which deletion of the enzyme 5, 10-methylenetetrahydrofolate (5,10-CH2-THF) dehydrogenase (E.C. 1.5.1.5) is lethal only in the iLca334_548 model. This means that the iLca12A_640 model has a unique mechanism (shown in Figure 3) for recovering from this gene deletion. Briefly, 5,10-CH2-THF is a precursor to 10-formyltetrahydrofolate (10-CHO-THF) a cofactor involved in purine biosynthesis, an essential activity for cellular growth. The deletion of 5,10-CH2-THF dehydrogenase prevents the biosynthesis of THF in L. casei ATCC 334. Our model for L. casei 12A predicts that this deletion can be rescued by the actions of 5,10-CH2-THF:3-methyl-2-oxobutanoate (E.C. 2.1.2.11) and formate: THF ligase (E.C. 6.3.4.3), in which 5,10-CH2-THF is converted directly to THF, producing 2-dehydropantoate as a by-product. The reactions pantoate 2-oxidoreductase (E.C. 1.1.1.169) and pantothenate amidohydrolase (E.C. 3.5.1.22) convert 2-dehydropantoate to pantothenate, which can be secreted by a transporter unique to the iLca12A_640 model, or some pantothenate can also be used for CoA biosynthesis, important for biomass formation.

Bottom Line: After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors.We conclude that the metabolic capabilities of the two networks are highly similar.The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

ABSTRACT
Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is strain dependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains for specific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotype relationships and to compare different organisms. To assist in the selection and development of strains with enhanced industrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate, were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined by evaluating ATP generating cycles, mass-and-charge-balances of reactions, and growth phenotypes. After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors. We conclude that the metabolic capabilities of the two networks are highly similar. The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes. The developed L. casei ATCC 334 and 12A metabolic models will enable better understanding of the physiology of these organisms and be valuable tools in the development and selection of strains with enhanced utility in a variety of industrial applications.

Show MeSH
Related in: MedlinePlus