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Modelling microbial metabolic rewiring during growth in a complex medium

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ABSTRACT

Background: In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now.

Results: We used multi-step constraint-based metabolic modelling to simulate the growth in a complex medium over several time steps of the Antarctic model organism Pseudoalteromonas haloplanktis TAC125. As each of these phases is characterized by a specific set of amino acids to be used as carbon and energy source our modelling framework describes the major consequences of nutrients switching at the system level. The model predicts that a deep metabolic reprogramming might be required to achieve optimal biomass production in different stages of growth (different medium composition), with at least half of the cellular metabolic network involved (more than 50% of the metabolic genes). Additionally, we show that our modelling framework is able to capture metabolic functional association and/or common regulatory features of the genes embedded in our reconstruction (e.g. the presence of common regulatory motifs).

Results: Finally, to explore the possibility of a sub-optimal biomass objective function (i.e. that cells use resources in alternative metabolic processes at the expense of optimal growth) we have implemented a MOMA-based approach (called nutritional-MOMA) and compared the outcomes with those obtained with Flux Balance Analysis (FBA). Growth simulations under this scenario revealed the deep impact of choosing among alternative objective functions on the resulting predictions of fluxes distribution.

Conclusions: Here we provide a time-resolved, systems-level scheme of PhTAC125 metabolic re-wiring as a consequence of carbon source switching in a nutritionally complex medium. Our analyses suggest the presence of a potential efficient metabolic reprogramming machinery to continuously and promptly adapt to this nutritionally changing environment, consistent with adaptation to fast growth in a fairly, but probably inconstant and highly competitive, environment. Also, we show i) how functional partnership and co-regulation features can be predicted by integrating multi-step constraint-based metabolic modelling with fed-batch growth data and ii) that performing simulations under a sub-optimal objective function may lead to different flux distributions in respect to canonical FBA.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3311-0) contains supplementary material, which is available to authorized users.

No MeSH data available.


Changes in the central metabolism of PhTAC125. a. The number of active (flux-carrying) reactions for five major pathways across all the time points is shown. b. A simplified representation of the interconnections in the central metabolism of PhTAC125. Dashed lines indicate the presence of more than one reaction between the connected compounds. Modified from [39]
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Fig2: Changes in the central metabolism of PhTAC125. a. The number of active (flux-carrying) reactions for five major pathways across all the time points is shown. b. A simplified representation of the interconnections in the central metabolism of PhTAC125. Dashed lines indicate the presence of more than one reaction between the connected compounds. Modified from [39]

Mentions: Not all PhTAC125 metabolic pathways are impacted by this switching of nutrients in the same manner, according to our simulations. Figure 2a shows the hypothetical number of flux-carrying reactions for five pathways, i.e. TCA cycle, Lys biosynthesis, Glu metabolism, Val, Leu and Ile biosynthesis and degradation (a complete overview is presented Additional file 2). TCA cycle, for example, displays and increasing trend in the number of flux-carrying reactions according to our modelling framework; this is consistent with the exhaustion of amino acids (Asp, Asn and Glu) whose degradation provides important TCA cycle intermediates, i.e. oxaloacetate, fumarate and 2-oxo-glutarate and, consequently, with the necessity to activate those reactions leading to the biosynthesis of such compounds. Conversely, Lys and Glu metabolic routes display an overall constant trend (Fig. 2a), with a similar number of active reactions across the different simulated growth phases. This is in line with i) the necessity to use (part) of the lysine biosynthetic route to synthesize diaminopimelic acid, an essential component of bacterial cell wall (see below) and ii) with the importance of Glu metabolism for PhTAC125 (see below and [14]). Finally, Val, Leu and Ile biosynthesis and degradation pathways display an opposite trend one another (Fig. 2a). Intuitively, this reflects the necessity to synthesize these molecules in the first part of the growth phase (when they are not used from the medium) and the necessity to catabolise them once PhTAC125 is using those amino acids as carbon sources, respectively.Fig. 2


Modelling microbial metabolic rewiring during growth in a complex medium
Changes in the central metabolism of PhTAC125. a. The number of active (flux-carrying) reactions for five major pathways across all the time points is shown. b. A simplified representation of the interconnections in the central metabolism of PhTAC125. Dashed lines indicate the presence of more than one reaction between the connected compounds. Modified from [39]
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5121958&req=5

Fig2: Changes in the central metabolism of PhTAC125. a. The number of active (flux-carrying) reactions for five major pathways across all the time points is shown. b. A simplified representation of the interconnections in the central metabolism of PhTAC125. Dashed lines indicate the presence of more than one reaction between the connected compounds. Modified from [39]
Mentions: Not all PhTAC125 metabolic pathways are impacted by this switching of nutrients in the same manner, according to our simulations. Figure 2a shows the hypothetical number of flux-carrying reactions for five pathways, i.e. TCA cycle, Lys biosynthesis, Glu metabolism, Val, Leu and Ile biosynthesis and degradation (a complete overview is presented Additional file 2). TCA cycle, for example, displays and increasing trend in the number of flux-carrying reactions according to our modelling framework; this is consistent with the exhaustion of amino acids (Asp, Asn and Glu) whose degradation provides important TCA cycle intermediates, i.e. oxaloacetate, fumarate and 2-oxo-glutarate and, consequently, with the necessity to activate those reactions leading to the biosynthesis of such compounds. Conversely, Lys and Glu metabolic routes display an overall constant trend (Fig. 2a), with a similar number of active reactions across the different simulated growth phases. This is in line with i) the necessity to use (part) of the lysine biosynthetic route to synthesize diaminopimelic acid, an essential component of bacterial cell wall (see below) and ii) with the importance of Glu metabolism for PhTAC125 (see below and [14]). Finally, Val, Leu and Ile biosynthesis and degradation pathways display an opposite trend one another (Fig. 2a). Intuitively, this reflects the necessity to synthesize these molecules in the first part of the growth phase (when they are not used from the medium) and the necessity to catabolise them once PhTAC125 is using those amino acids as carbon sources, respectively.Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Background: In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now.

Results: We used multi-step constraint-based metabolic modelling to simulate the growth in a complex medium over several time steps of the Antarctic model organism Pseudoalteromonas haloplanktis TAC125. As each of these phases is characterized by a specific set of amino acids to be used as carbon and energy source our modelling framework describes the major consequences of nutrients switching at the system level. The model predicts that a deep metabolic reprogramming might be required to achieve optimal biomass production in different stages of growth (different medium composition), with at least half of the cellular metabolic network involved (more than 50% of the metabolic genes). Additionally, we show that our modelling framework is able to capture metabolic functional association and/or common regulatory features of the genes embedded in our reconstruction (e.g. the presence of common regulatory motifs).

Results: Finally, to explore the possibility of a sub-optimal biomass objective function (i.e. that cells use resources in alternative metabolic processes at the expense of optimal growth) we have implemented a MOMA-based approach (called nutritional-MOMA) and compared the outcomes with those obtained with Flux Balance Analysis (FBA). Growth simulations under this scenario revealed the deep impact of choosing among alternative objective functions on the resulting predictions of fluxes distribution.

Conclusions: Here we provide a time-resolved, systems-level scheme of PhTAC125 metabolic re-wiring as a consequence of carbon source switching in a nutritionally complex medium. Our analyses suggest the presence of a potential efficient metabolic reprogramming machinery to continuously and promptly adapt to this nutritionally changing environment, consistent with adaptation to fast growth in a fairly, but probably inconstant and highly competitive, environment. Also, we show i) how functional partnership and co-regulation features can be predicted by integrating multi-step constraint-based metabolic modelling with fed-batch growth data and ii) that performing simulations under a sub-optimal objective function may lead to different flux distributions in respect to canonical FBA.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3311-0) contains supplementary material, which is available to authorized users.

No MeSH data available.