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Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition.

Tajparast M, Frigon D - BMC Syst Biol (2015)

Bottom Line: The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA).Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected.PHA turned out to be the main storage pool of the mixture in R. jostii RHA1.

View Article: PubMed Central - PubMed

Affiliation: Microbial Community Engineering Laboratory, Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke Street West, Montreal, QC, H3A 0C3, Canada. mohammad.tajparast@mail.mcgill.ca.

ABSTRACT

Background: Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and triacylglycerols (TAG). Under nitrogen-limited (N-limited) condition, the level of storage increases as is commonly observed for other bacteria. The proportion of each storage compound changes with substrate, but it remains unclear what modelling approach should be adopted to predict the relative composition of the mixture of the storage compounds. We analyzed the growth of R. jostii RHA1 under N-limited conditions using a genome-scale metabolic modelling approach to determine which global metabolic objective function could be used for the prediction.

Results: The R. jostii RHA1 model (iMT1174) produced during this study contains 1,243 balanced metabolites, 1,935 unique reactions, and 1,174 open reading frames (ORFs). Seven objective functions used with flux balance analysis (FBA) were compared for their capacity to predict the mixture of storage compounds accumulated after the sudden onset of N-limitation. Predictive abilities were determined using a Bayesian approach. Experimental data on storage accumulation mixture (glycogen, polyhydroxyalkanoates, and triacylglycerols) were obtained for batch cultures grown on glucose or acetate. The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA). The FBA solutions for the non-limited growth conditions were simply constrained by the objective function of growth rate maximization. Measurement of central metabolic fluxes by (13)C-labelling experiments of amino acids further supported the application of the environmental MOMA principle in the context of changing environment. Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected.

Conclusions: The genome-scale metabolic model analysis of R. jostii RHA1 cultures suggested that the intracellular reaction flux profile immediately after the onset of N-limited condition are impacted by the values of the same fluxes during the period of non-limited growth. PHA turned out to be the main storage pool of the mixture in R. jostii RHA1.

No MeSH data available.


Related in: MedlinePlus

The conversion rates of storage, substrate, and oxygen, and the growth rate of R. jostii RHA1 on glucose (a and b) and acetate (c and d) in the non- and N-limited conditions. Panels a and c represent the conversion rates in the non-limited condition, while panels b and d show those in the N-limited condition. Note that the conversion rate of PHA is the sum of those of PHB and PHV
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Fig3: The conversion rates of storage, substrate, and oxygen, and the growth rate of R. jostii RHA1 on glucose (a and b) and acetate (c and d) in the non- and N-limited conditions. Panels a and c represent the conversion rates in the non-limited condition, while panels b and d show those in the N-limited condition. Note that the conversion rate of PHA is the sum of those of PHB and PHV

Mentions: Microbial activities in the non-limited and N-limited cultures were determined by monitoring the concentrations of several compounds over time: substrate (either glucose or acetate, concentrations determined by enzymatic assays and by chemical oxygen demand [COD]), NH4+, PO43−, glycogen, PHB, TAG. Additionally, the consumption rate of O2 was also monitored over time. Using these data, conversion rates were calculated. Considering the elemental and COD balances, the conversion rates were reconciled (i.e., adjusted for the balances to close) and their statistical consistency checked (i.e., tested for the presence of gross measurement errors) [21]. The measured conversion rates and the results of the reconciliation procedure are presented in Additional file 4. In these experiments, R. jostii RHA1 consumed acetate faster than glucose, and the specific substrate uptake rate during the N-limited phase was less than 14 % of the one in the non-limited phase (Fig. 3). During the N-limited phase, the glucose culture stored 58 % of the substrate COD consumed, with 74 % of it being stored as PHA and 23 % as TAG (Fig. 3). Finally, for the same culture phase, the acetate culture stored 48 % of the substrate COD consumed, with 78 % in the form of PHA and 20 % in the form of TAG.Fig. 3


Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition.

Tajparast M, Frigon D - BMC Syst Biol (2015)

The conversion rates of storage, substrate, and oxygen, and the growth rate of R. jostii RHA1 on glucose (a and b) and acetate (c and d) in the non- and N-limited conditions. Panels a and c represent the conversion rates in the non-limited condition, while panels b and d show those in the N-limited condition. Note that the conversion rate of PHA is the sum of those of PHB and PHV
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4528721&req=5

Fig3: The conversion rates of storage, substrate, and oxygen, and the growth rate of R. jostii RHA1 on glucose (a and b) and acetate (c and d) in the non- and N-limited conditions. Panels a and c represent the conversion rates in the non-limited condition, while panels b and d show those in the N-limited condition. Note that the conversion rate of PHA is the sum of those of PHB and PHV
Mentions: Microbial activities in the non-limited and N-limited cultures were determined by monitoring the concentrations of several compounds over time: substrate (either glucose or acetate, concentrations determined by enzymatic assays and by chemical oxygen demand [COD]), NH4+, PO43−, glycogen, PHB, TAG. Additionally, the consumption rate of O2 was also monitored over time. Using these data, conversion rates were calculated. Considering the elemental and COD balances, the conversion rates were reconciled (i.e., adjusted for the balances to close) and their statistical consistency checked (i.e., tested for the presence of gross measurement errors) [21]. The measured conversion rates and the results of the reconciliation procedure are presented in Additional file 4. In these experiments, R. jostii RHA1 consumed acetate faster than glucose, and the specific substrate uptake rate during the N-limited phase was less than 14 % of the one in the non-limited phase (Fig. 3). During the N-limited phase, the glucose culture stored 58 % of the substrate COD consumed, with 74 % of it being stored as PHA and 23 % as TAG (Fig. 3). Finally, for the same culture phase, the acetate culture stored 48 % of the substrate COD consumed, with 78 % in the form of PHA and 20 % in the form of TAG.Fig. 3

Bottom Line: The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA).Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected.PHA turned out to be the main storage pool of the mixture in R. jostii RHA1.

View Article: PubMed Central - PubMed

Affiliation: Microbial Community Engineering Laboratory, Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke Street West, Montreal, QC, H3A 0C3, Canada. mohammad.tajparast@mail.mcgill.ca.

ABSTRACT

Background: Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and triacylglycerols (TAG). Under nitrogen-limited (N-limited) condition, the level of storage increases as is commonly observed for other bacteria. The proportion of each storage compound changes with substrate, but it remains unclear what modelling approach should be adopted to predict the relative composition of the mixture of the storage compounds. We analyzed the growth of R. jostii RHA1 under N-limited conditions using a genome-scale metabolic modelling approach to determine which global metabolic objective function could be used for the prediction.

Results: The R. jostii RHA1 model (iMT1174) produced during this study contains 1,243 balanced metabolites, 1,935 unique reactions, and 1,174 open reading frames (ORFs). Seven objective functions used with flux balance analysis (FBA) were compared for their capacity to predict the mixture of storage compounds accumulated after the sudden onset of N-limitation. Predictive abilities were determined using a Bayesian approach. Experimental data on storage accumulation mixture (glycogen, polyhydroxyalkanoates, and triacylglycerols) were obtained for batch cultures grown on glucose or acetate. The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA). The FBA solutions for the non-limited growth conditions were simply constrained by the objective function of growth rate maximization. Measurement of central metabolic fluxes by (13)C-labelling experiments of amino acids further supported the application of the environmental MOMA principle in the context of changing environment. Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected.

Conclusions: The genome-scale metabolic model analysis of R. jostii RHA1 cultures suggested that the intracellular reaction flux profile immediately after the onset of N-limited condition are impacted by the values of the same fluxes during the period of non-limited growth. PHA turned out to be the main storage pool of the mixture in R. jostii RHA1.

No MeSH data available.


Related in: MedlinePlus