Modelling microbial metabolic rewiring during growth in a complex medium

Abstract

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

Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments

“…In a previous work 26 , we have simulated the growth of PhTAC125 in a nutritionally complex environment (peptone) and derived the overall metabolic reprogramming occurring during growth in a rich undefined medium using constraintbased metabolic modelling (i.e., flux balance analysis, FBA) (Supplementary Note 4). We observed a good correlation between the measured changes in the expression of AA gene regulons and the predicted changes in metabolic fluxes of their encoded reactions using FBA (Pearson's product-moment correlation = 0.89, p value = 0.019).…”

“…Using constraint-based metabolic modelling we attempted to provide a systems level scheme of PhTAC125 metabolic re-wiring as a consequence of carbon source switching in such a nutritionally complex medium. Our simulations highlighted an efficient reprogramming of PhTAC125 metabolic machinery to quickly adapt to a nutritionally unstable environment, compatible with adaptation to fast growth in a highly competitive environment 26 .…”

“…Their metabolism is pivotal for the maintenance and the correct balance of oceanic biogeochemical cycles as they are central to the so-called microbial loop, i.e., the trophic pathway of the marine food web responsible for the microbial assimilation of dissolved organic matter, by transforming phytoplankton-derived organic matter and fuelling the entire ocean biogeochemical nutrient cycle. In this regard, the metabolism of Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a heterotrophic marine bacterium isolated from Antarctica, has recently gained a certain attention due to its potential biotechnological exploitation 22 , its capability to synthesize anti-biofilm compounds 23 , the necessity to set up efficient culture conditions 24,25 and the metabolic reprogramming during growth in complex environments 26 . In particular, the analysis of its growth phenotype in an amino acid rich medium has shown the presence of metabolic switches among different groups of amino acids 25 , although nothing could be said about the molecular mechanisms underlying such phenotype and the possible regulation involved.…”

High cell density cultivation of Escherichia coli DH5α in shake flasks with a new formulated medium

“…NH 4 Cl was not detrimental to biomass formation and growth rates. Collectively, a semidefined formulated medium could increase optical density of E. coli DH5α beyond that of LB Lennox and Tryptic Soy Broth, and may find use in cultivation of cells for applied microbiology research.…”

Activation Studies of the γ-Carbonic Anhydrases from the Antarctic Marine Bacteria Pseudoalteromonas haloplanktis and Colwellia psychrerythraea with Amino Acids and Amines

“…Pseudoalteromonas haloplanktis and Colwellia psychrerythraea are bacteria adapted to live in the extreme conditions of the Antarctic Ocean. These marine heterotrophic bacteria are thought to rely on simplified metabolic strategies which evolved in order to overcome thermodynamic constraints connected toliving at low temperatures and in the dark for prolonged periods during the Antarctic winter [1,2,3,4,5,6,7]. Thus, these two bacteria are considered model organisms for studying metabolic processes and, more generally, strategies used for adaptation to harsh environmental conditions typical of the Antarctic region, which may also provide interesting insights for potential biotechnological or biomedical applications of enzymes encoded in their genomes [1,2,5].…”