Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model

Abstract

BackgroundThe halophilic bacterium Chromohalobacter salexigens is a natural producer of ectoines, compatible solutes with current and potential biotechnological applications. As production of ectoines is an osmoregulated process that draws away TCA intermediates, bacterial metabolism needs to be adapted to cope with salinity changes. To explore and use C. salexigens as cell factory for ectoine(s) production, a comprehensive knowledge at the systems level of its metabolism is essential. For this purpose, the construction of a robust and high-quality genome-based metabolic model of C. salexigens was approached.ResultsWe generated and validated a high quality genome-based C. salexigens metabolic model (iFP764). This comprised an exhaustive reconstruction process based on experimental information, analysis of genome sequence, manual re-annotation of metabolic genes, and in-depth refinement. The model included three compartments (periplasmic, cytoplasmic and external medium), and two salinity-specific biomass compositions, partially based on experimental results from C. salexigens. Using previous metabolic data as constraints, the metabolic model allowed us to simulate and analyse the metabolic osmoadaptation of C. salexigens under conditions for low and high production of ectoines. The iFP764 model was able to reproduce the major metabolic features of C. salexigens. Flux Balance Analysis (FBA) and Monte Carlo Random sampling analysis showed salinity-specific essential metabolic genes and different distribution of fluxes and variation in the patterns of correlation of reaction sets belonging to central C and N metabolism, in response to salinity. Some of them were related to bioenergetics or production of reducing equivalents, and probably related to demand for ectoines. Ectoines metabolic reactions were distributed according to its correlation in four modules. Interestingly, the four modules were independent both at low and high salinity conditions, as they did not correlate to each other, and they were not correlated with other subsystems.ConclusionsOur validated model is one of the most complete curated networks of halophilic bacteria. It is a powerful tool to simulate and explore C. salexigens metabolism at low and high salinity conditions, driving to low and high production of ectoines. In addition, it can be useful to optimize the metabolism of other halophilic bacteria for metabolite production.Electronic supplementary materialThe online version of this article (10.1186/s12934-017-0852-0) contains supplementary material, which is available to authorized users.

Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis

“…Hence, it is necessary to understand the interplay of the carbon and nitrogen supplies for the production of ectoines in greater detail [ 194 ]. Their synthesis burdens the assimilation of nitrogen via the glutamine synthetase pathway and central metabolic routes by recruiting TCA-cycle intermediates—in particular, oxaloacetate and acetyl-CoA [ 195 , 196 , 197 ]. Consequently, anaplerotic routes have to be engaged to replenish the TCA cycle for routine central carbon metabolism and at the same time an increased flux of metabolites into the ectoine/5-hydroxyectoine biosynthetic pathway has to be ensured.…”

Ectoine interaction with DNA: influence on ultraviolet radiation damage

“…1 These microorganisms achieve osmoadaptation to high external salt concentrations by the regulation of osmotic pressure via the accumulation of molar concentrations of ectoine. [2][3][4] In this context, an interesting property of ectoine is the compensating effect on water dynamics as opposed to that of sodium chloride. 5 Ectoine has a zwitterionic structure in the solid state 6 and in aqueous solution 7,8 at neutral pH.…”

“…Due to its versatile properties, ectoine is currently used in a multitude of biotechnological, cosmetic and medical applications. 2,3,[22][23][24][25] Most prominently, it is used in sunscreens, despite evidence from recent studies concerning its influence on UV irradiation of biological targets, showing Janus-faced behaviour. 17,20,[26][27][28] Bünger et al irradiated human keratinocytes with UV-A (340-400 nm).…”

The Genome-Scale Integrated Networks in Microorganisms

“…The results have provided important guidance for the in vivo experiments ( Hao et al, 2013 ). Recently, Piubeli et al (2018) constructed a GMN i FP764 of halophilic bacterium Chromohalobacter salexigens to explore the cell factory for producing ectoine. This model was constructed based on the experimental data, genome sequences and re-annotation of metabolic genes.…”

“…The salinity-specific essential genes and the patterns of correlated reactions in central carbon and nitrogen metabolisms response to the change of salinity were also simulated. The network is a useful tool to improve the production of ectoines with bacteria ( Piubeli et al, 2018 ).…”