Role of Proteins in the Formation of Melanoidins during Coffee Roasting

The objective of the study was to investigate structural changes in the protein-rich, high-molecular-weight fraction of coffee during roasting and their contribution to the melanoidin formation in the course of the Maillard reaction. For this purpose, high- and low-molecular-weight fractions of one raw and five coffee beans with an increased roasting degree were analyzed in terms of general (color, molecular weight, functionality, elemental composition) and specific parameters (amino acid composition, Maillard reaction products). It could be demonstrated that the high -molecular-weight fraction undergoes significant changes during roasting, where proteins appear to play an important role in melanoidin formation due to their diverse nucleophilic side chains. Modification of the amino acid side chains with known Maillard reaction products (MRPs) occurs in the early stages of roasting and decreases rapidly as color development progresses. The decrease suggests that MRPs are involved in further reactions and thus extend the functionality of the amino acid side chains, opening further possibilities for protein modification. Overall, the large number of reaction pathways leads to the formation of a well-mixed, continuous melanoidin spectrum covering a wide range of molecular masses. In this process, cross-linking and fragmentation reactions oppose each other, leading to an approximation of the molecular weight.

Dehazing redox homeostasis to foster purple bacteria biotechnology

Purple non-sulfur bacteria (PNSB) show great potential for environmental and industrial biotechnology, producing microbial protein, biohydrogen, polyhydroxyalkanoates (PHAs), pigments, etc. When grown photoheterotrophically, the carbon source is typically more reduced than the PNSB biomass, which leads to a redox imbalance. To mitigate the excess of electrons, PNSB can exhibit several 'electron sinking' strategies, such as CO₂ fixation, N₂ fixation, and H₂ and PHA production. The lack of a comprehensive (over)view of these redox strategies is hindering the implementation of PNSB for biotechnology applications. This review aims to present the state of the art of redox homeostasis in phototrophically grown PNSB, presenting known and theoretically expected strategies, and discussing them from stoichiometric, thermodynamic, metabolic, and economic points of view.

Analysis of the Involvement of the Isoleucine Biosynthesis Pathway in Photoheterotrophic Metabolism of Rhodospirillum rubrum

Purple non-sulfur bacteria (PNSB) are recognized as a highly versatile group of bacteria that assimilate a broad range of carbon sources. Growing heterotrophically, PNSB such as Rhodospirillum rubrum (Rs. rubrum) generate reduced equivalents that are used for biomass production. However, under photoheterotrophic conditions, more reduced electron carriers than required to produce biomass are generated. The excess of reduced equivalents still needs to be oxidized for the metabolism to optimally operate. These metabolic reactions are known as electron sinks. Most PNSB rely on the CO2-fixing Calvin cycle and H2 production to oxidize these reduced equivalents. In addition to these well-described electron sinks, the involvement of some pathways, such as polyhydroxyalkanoate (PHA) biosynthesis, in redox poise is still controversial and requires further studies. Among them, isoleucine biosynthesis has been recently highlighted as one of these potential pathways. Here, we explore the role of isoleucine biosynthesis in Rs. rubrum. Our results demonstrate that the isoleucine content is higher under illuminated conditions and that submitting Rs. rubrum to light stress further increases this phenomenon. Moreover, we explore the production of (p)ppGpp in Rs. rubrum and its potential link with light stress. We further demonstrate that a fully functional isoleucine biosynthesis pathway could be an important feature for the onset of Rs. rubrum growth under photoheterotrophic conditions even in the presence of an exogenous isoleucine source. Altogether, our data suggest that isoleucine biosynthesis could play a key role in redox homeostasis.

Enhancing in silico strain design predictions through next generation metabolic modeling approaches

The reconstruction and analysis of metabolic models has garnered increasing attention due to the multitude of applications in which these have proven to be practical. The growing number of generated metabolic models has been accompanied by an exponentially expanding arsenal of tools used to analyze them. In this work, we discussed the biological relevance of a number of promising modeling frameworks, focusing on the questions and hypotheses each method is equipped to address. To this end, we critically analyzed the steady-state modeling approaches focusing on resource allocation and incorporation of thermodynamic considerations which produce promising results and aid in the generation and experimental validation of numerous predictions. For smaller networks involving more complex regulation, we addressed kinetic modeling techniques which show encouraging results in addressing questions outside the scope of steady-state modeling. Finally, we discussed the potential application of the discussed frameworks within the field of strain design. Adoption of such methodologies is believed to significantly enhance the accuracy of in silico predictions and hence decrease the number of design-build-test cycles required.

Reductive tricarboxylic acid cycle enzymes and reductive amino acid synthesis pathways contribute to electron balance in a Rhodospirillum rubrum Calvin-cycle mutant

Purple non-sulfur bacteria (PNSB) use light for energy and organic substrates for carbon and electrons when growing photoheterotrophically. This lifestyle generates more reduced electron carriers than are required for biosynthesis, even during consumption of some of the most oxidized organic substrates like malate and fumarate. Reduced electron carriers not used in biosynthesis must still be oxidized for photoheterotrophic growth to occur. Diverse PNSB commonly rely on the CO₂-fixing Calvin cycle to oxidize reduced electron carriers. Some PNSB also produce H₂ or reduce terminal electron acceptors as alternatives to the Calvin cycle. Rhodospirillum rubrum Calvin-cycle mutants defy this trend by growing phototrophically on malate or fumarate without H₂ production or access to terminal electron acceptors. We used ¹³C-tracer experiments to examine how a Rs. rubrum Calvin-cycle mutant maintains electron balance under such conditions. We detected the reversal of some tricarboxylic acid cycle enzymes, carrying reductive flux from malate or fumarate to αKG. This pathway and the reductive synthesis of αKG-derived amino acids are likely important for electron balance, as supplementing the growth medium with αKG-derived amino acids prevented Rs. rubrum Calvin-cycle-mutant growth unless a terminal electron acceptor was provided. Flux estimates also suggested that the Calvin-cycle mutant preferentially synthesized isoleucine using the reductive threonine-dependent pathway instead of the less-reductive citramalate-dependent pathway. Collectively, our results suggest that alternative biosynthetic pathways can contribute to electron balance within the constraints of a relatively constant biomass composition.

Photoheterotrophic Assimilation of Valerate and Associated Polyhydroxyalkanoate Production by Rhodospirillum rubrum

Purple nonsulfur bacteria are increasingly recognized for industrial applications in bioplastics, pigment, and biomass production. In order to optimize the yield of future biotechnological processes, the assimilation of different carbon sources by Rhodospirillum rubrum has to be understood. As they are released from several fermentation processes, volatile fatty acids (VFAs) represent a promising carbon source in the development of circular industrial applications. To obtain an exhaustive characterization of the photoheterotrophic metabolism of R. rubrum in the presence of valerate, we combined phenotypic, proteomic, and genomic approaches. We obtained evidence that valerate is cleaved into acetyl coenzyme A (acetyl-CoA) and propionyl-CoA and depends on the presence of bicarbonate ions. Genomic and enzyme inhibition data showed that a functional methylmalonyl-CoA pathway is essential. Our proteomic data showed that the photoheterotrophic assimilation of valerate induces an intracellular redox stress which is accompanied by an increased abundance of phasins (the main proteins present in polyhydroxyalkanoate [PHA] granules). Finally, we observed a significant increase in the production of the copolymer P(HB-co-HV), accounting for a very high (>80%) percentage of HV monomer. Moreover, an increase in the PHA content was obtained when bicarbonate ions were progressively added to the medium. The experimental conditions used in this study suggest that the redox imbalance is responsible for PHA production. These findings also reinforce the idea that purple nonsulfur bacteria are suitable for PHA production through a strategy other than the well-known feast-and-famine process.IMPORTANCE The use and the littering of plastics represent major issues that humanity has to face. Polyhydroxyalkanoates (PHAs) are good candidates for the replacement of oil-based plastics, as they exhibit comparable physicochemical properties but are biobased and biodegradable. However, the current industrial production of PHAs is curbed by the production costs, which are mainly linked to the carbon source. Volatile fatty acids issued from the fermentation processes constitute interesting carbon sources, since they are inexpensive and readily available. Among them, valerate is gaining interest regarding the ability of many bacteria to produce a copolymer of PHAs. Here, we describe the photoheterotrophic assimilation of valerate by Rhodospirillum rubrum, a purple nonsulfur bacterium mainly known for its metabolic versatility. Using a knowledge-based optimization process, we present a new strategy for the improvement of PHA production, paving the way for the use of R. rubrum in industrial processes.

Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

Kinetic models are critical to predict the dynamic behaviour of metabolic networks. Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting their parameters. Recent modelling frameworks promise new ways to overcome this obstacle while retaining predictive capabilities. In this review, we present an overview of the relevant mathematical frameworks for kinetic formulation, construction and analysis. Starting with kinetic formalisms, we next review statistical methods for parameter inference, as well as recent computational frameworks applied to the construction and analysis of kinetic models. Finally, we discuss opportunities and limitations hindering the development of larger kinetic reconstructions.

Altered residues in key proteins influence the expression and activity of the nitrogenase complex in an adaptive CO2 fixation-deficient mutant strain of Rhodobacter sphaeroides

Previously, the RubisCO-compromised spontaneous adaptive Rhodobacter sphaeroides mutant, strain 16PHC, was shown to derepress the expression of genes that encode the nitrogenase complex under normal repressive conditions. As a result of this adaptation, the active nitrogenase complex restored redox balance, thus allowing strain 16PHC to grow under photoheterotrophic conditions in the absence of an exogenous electron acceptor. A combination of whole genome pyrosequencing and whole genome microarray analyses was employed to identify possible loci responsible for the observed phenotype. Mutations were found in two genes, glnA and nifA, whose products are involved in the regulatory cascade that controls nitrogenase complex gene expression. In addition, a nucleotide reversion within the nifK gene, which encodes a subunit of the nitrogenase complex, was also identified. Subsequent genetic, physiological and biochemical studies revealed alterations that led to derepression of the synthesis of an active nitrogenase complex in strain 16PHC.

Metabolic ensemble modeling for strain engineers

Previous mathematical modeling efforts have made significant contributions to the development of systems biology for predicting biological behavior quantitatively. However, dynamic metabolic model construction remains challenging due to uncertainties in mechanistic structures and parameters. In addition, parameter estimation and model validation often require designated experiments conducted only for purpose of modeling. Such difficulties have hampered the progress of modeling in biology and biotechnology. To circumvent these problems, ensemble approaches have been used to account for uncertainties in model structure and parameters. Specifically, this review focuses on approaches that utilize readily available fermentation data for parameter screening and model validation. Time course data for metabolite measurements, if available, can further calibrate the model. The basis for this approach is explained in non-mathematical terms accessible to experimentalists. Information gained from such an approach has been shown to be useful in designing Escherichia coli strains for metabolic engineering and synthetic biology.

iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

BACKGROUND

Rhodobacter sphaeroides is one of the best studied purple non-sulfur photosynthetic bacteria and serves as an excellent model for the study of photosynthesis and the metabolic capabilities of this and related facultative organisms. The ability of R. sphaeroides to produce hydrogen (H₂), polyhydroxybutyrate (PHB) or other hydrocarbons, as well as its ability to utilize atmospheric carbon dioxide (CO₂) as a carbon source under defined conditions, make it an excellent candidate for use in a wide variety of biotechnological applications. A genome-level understanding of its metabolic capabilities should help realize this biotechnological potential.

RESULTS

Here we present a genome-scale metabolic network model for R. sphaeroides strain 2.4.1, designated iRsp1095, consisting of 1,095 genes, 796 metabolites and 1158 reactions, including R. sphaeroides-specific biomass reactions developed in this study. Constraint-based analysis showed that iRsp1095 agreed well with experimental observations when modeling growth under respiratory and phototrophic conditions. Genes essential for phototrophic growth were predicted by single gene deletion analysis. During pathway-level analyses of R. sphaeroides metabolism, an alternative route for CO₂ assimilation was identified. Evaluation of photoheterotrophic H2 production using iRsp1095 indicated that maximal yield would be obtained from growing cells, with this predicted maximum ~50% higher than that observed experimentally from wild type cells. Competing pathways that might prevent the achievement of this theoretical maximum were identified to guide future genetic studies.

CONCLUSIONS

iRsp1095 provides a robust framework for future metabolic engineering efforts to optimize the solar- and nutrient-powered production of biofuels and other valuable products by R. sphaeroides and closely related organisms.

Coassimilation of organic substrates via the autotrophic 3-hydroxypropionate bi-cycle in Chloroflexus aurantiacus

Chloroflexus aurantiacus is a facultative autotrophic green nonsulfur bacterium that grows phototrophically in thermal springs and forms microbial mats with cyanobacteria. Cyanobacteria produce glycolate during the day (photorespiration) and excrete fermentation products at night. C. aurantiacus uses the 3-hydroxypropionate bi-cycle for autotrophic carbon fixation. This pathway was thought to be also suited for the coassimilation of various organic substrates such as glycolate, acetate, propionate, 3-hydroxypropionate, lactate, butyrate, or succinate. To test this possibility, we added these compounds at a 5 mM concentration to autotrophically pregrown cells. Although the provided amounts of H(2) and CO(2) allowed continuing photoautotrophic growth, cells immediately consumed most substrates at rates equaling the rate of autotrophic carbon fixation. Using [(14)C]acetate, half of the labeled organic carbon was incorporated into cell mass. Our data suggest that C. aurantiacus uses the 3-hydroxypropionate bi-cycle, together with the glyoxylate cycle, to channel organic substrates into the central carbon metabolism. Enzyme activities of the 3-hydroxypropionate bi-cycle were marginally affected when cells were grown heterotrophically with such organic substrates. The 3-hydroxypropionate bi-cycle in Chloroflexi is unique and was likely fostered in an environment in which traces of organic compounds can be coassimilated. Other bacteria living under oligotrophic conditions acquired genes of a rudimentary 3-hydroxypropionate bi-cycle, possibly for the same purpose. Examples are Chloroherpeton thalassium, Erythrobacter sp. strain NAP-1, Nitrococcus mobilis, and marine gammaproteobacteria of the OM60/NOR5 clade such as Congregibacter litoralis.