Biochemical and molecular characterization of the oxidative branch of glycerol utilization by Citrobacter freundii

Identification and biochemical characterization of an ATP-dependent dihydroxyacetone kinase from Trypanosoma cruzi

Dihydroxyacetone (DHA) can be used as an energy source by many cell types; however, it is toxic at high concentrations. The enzyme dihydroxyacetone kinase (DAK) has shown to be involved in DHA detoxification and osmoregulation. Among protozoa of the genus Trypanosoma, T. brucei, which causes sleeping sickness, is highly sensitive to DHA and does not have orthologous genes to DAK. Conversely, T. cruzi, the etiological agent of Chagas Disease, has two putative ATP-dependent DAK (TcDAKs) sequences in its genome. Here we show that T. cruzi epimastigote lysates present a DAK specific activity of 27.1 nmol/min/mg of protein and that this form of the parasite is able to grow in the presence of 2 mM DHA. TcDAK gene was cloned and the recombinant enzyme (recTcDAK) was expressed in Escherichia coli. An anti-recTcDAK serum reacted with a protein of the expected molecular mass of 61 kDa in epimastigotes. recTcDAK presented maximal activity using Mg⁺², showing a Km of 6.5 μM for DHA and a K_0.5 of 124.7 μM for ATP. As it was reported for other DAKs, recTcDAK activity was inhibited by FAD with an IC₅₀ value of 0.33 mM. In conclusion, TcDAK is the first DAK described in trypanosomatids confirming another divergent metabolism between T. brucei and T. cruzi.

In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli

Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H₂ , complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H₂ evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H₂ evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.

Growth of the acetogenic bacterium Acetobacterium woodii on glycerol and dihydroxyacetone

More than 2 million tons of glycerol are produced during industrial processes each year and, therefore, glycerol is an inexpensive feedstock to produce biocommodities by bacterial fermentation. Acetogenic bacteria are interesting production platforms and there have been few reports in the literature on glycerol utilization by this ecophysiologically important group of strictly anaerobic bacteria. Here, we show that the model acetogen Acetobacterium woodii DSM1030 is able to grow on glycerol, but contrary to expectations, only for 2-3 transfers. Transcriptome analysis revealed the expression of the pdu operon encoding a propanediol dehydratase along with genes encoding bacterial microcompartments. Deletion of pduAB led to a stable growth of A. woodii on glycerol, consistent with the hypothesis that the propanediol dehydratase also acts on glycerol leading to a toxic end-product. Glycerol is oxidized to acetate and the reducing equivalents are reoxidized by reducing CO₂ in the Wood-Ljungdahl pathway, leading to an additional acetate. The possible oxidation product of glycerol, dihydroxyacetone (DHA), also served as carbon and energy source for A. woodii and growth was stably maintained on that compound. DHA oxidation was also coupled to CO₂ reduction. Based on transcriptome data and enzymatic analysis we present the first metabolic and bioenergetic schemes for glycerol and DHA utilization in A. woodii.

Self-Synchronized Oscillatory Metabolism of Clostridium pasteurianum in Continuous Culture

By monitoring the real-time gas production (CO2 and H2) and redox potential at high sampling frequency in continuous culture of Clostridium pasteurianum on glycerol as sole carbohydrate, the self-synchronized oscillatory metabolism was revealed and studied. The oscillations in CO2 and H2 production were in sync with each other and with both redox potential and glycerol in the continuous stirred tank reactor (CSTR). There is strong evidence that the mechanism for this is in the regulation of the oxidative pathway of glycerol metabolism, including glycolysis, and points toward complex, concerted cycles of enzyme inhibition and activation by pathway intermediates and/or redox equivalents. The importance of understanding such an “oscillatory metabolism” is for developing a stable and highly productive industrial fermentation process for butanol production, as unstable oscillations are unproductive. It is shown that the oscillatory metabolism can be eradicated and reinstated and that the period of oscillations can be altered by modification of the operating parameters. Synchronized oscillatory metabolism impacted the product profile such that it lowered the selectivity for butanol and increased the selectivity for ethanol. This elucidates a possible cause for the variability in the product profile of C. pasteurianum that has been reported in many previous studies.

Impact of acetolactate synthase inactivation on 1,3-propanediol fermentation by Klebsiella pneumoniae

1,3-Propanediol (1,3-PDO) is an important compound that is mainly used in industry for polymer production. Fermentation of 1,3-PDO from glycerol by Klebsiella pneumoniae is accompanied by formation of 2,3-butanediol (2,3-BDO) as one of the main byproduct. The first step in the formation of 2,3-BDO from pyruvate is catalyzed by acetolactate synthase (ALS), an enzyme that competes with 1,3-PDO oxidoreductase for the cofactor NADH. This study aimed to analyze the impact of engineering the 2,3-BDO formation pathway via inactivation of ALS on 1,3-PDO fermentation by K. pneumoniae HSL4. An ALS mutant was generated using Red recombinase assisted gene replacement. The ALS specific activities of K. pneumoniae ΔALS were notably lower than that of the wild-type strain. Fed-batch fermentation of the mutant strain resulted in a 1,3-PDO concentration, productivity and conversion of 72.04 g L^–1, 2.25 g L^–1 h^–1, and 0.41 g g^–1, increase by 4.71%, 4.65% and 1.99% compared with the parent strain. Moreover, inactivation of ALS decreased meso-2,3-BDO formation to trace amounts, significantly increased 2S,3S-BDO and lactate production, and a pronounced redistribution of intracellular metabolic flux was apparent.

Rei1-like protein regulates nutritional metabolism and transport required for the asexual cycle in vitro and in vivo of a fungal insect pathogen

Rei1 is a cytoplasm-specific pre-60S subunit export factor that functions exclusively in cold-sensitive yeast growth but remains unexplored in filamentous fungi. Here, we report that Rei1-like BbRei1 is localized in both cytoplasm and nucleus and acts as a vital regulator in Beauveria bassiana. Deletion of BbRei1 resulted in delayed conidial germination, abnormally polarized germlings, severe growth defects on various carbon/nitrogen sources and reduced conidiation capacity as well as low temperature-sensitive growth. In ΔBbrei1, greatly attenuated virulence correlated with reduced activities of enzymes secreted for cuticular penetration and blocked formation of hyphal bodies in vivo essential for facilitation of host mummification. Revealed by transcriptomic analysis, 560 and 840 genes were significantly up- and down-regulated in ΔBbrei1 versus wild-type respectively, representing 13.5% of the fungal genome. Many repressed genes were involved in metabolism and transport of carbohydrates and amino acids. However, electrophoretic mobility shift assays presented no interactions of purified BbRei1 with 14 promoter DNA fragments. Conclusively, BbRei1 plays a pivotal role in gene expression and metabolism of nutrients and energy essential for the asexual cycle in vitro and in vivo of B. bassiana and functions much beyond the role for the yeast Rei1 in cold-sensitive cell growth.

Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry

Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.

Globally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.

IMPORTANCE Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.

Metabolome and molecular basis for carbohydrate increase and nitrate reduction in burley tobacco seedlings by glycerol through upregulating carbon and nitrogen metabolism

Burley tobacco (Nicotiana Tabacum) is a chlorophyll-deficiency mutant. Nitrate is one precursor of tobacco-specific nitrosamines (TSNAs) and is largely accumulated in burley tobacco. To decrease nitrate accumulation in burley tobacco, glycerol, a polyhydric alcohol compound and physiological regulating material, was sprayed and its effects were investigated based on metabolomic technology and molecular biology. The results showed that glucose, glutamine and glutamic acid increased by 2.6, 5.1 and 196, folds, respectively, in tobacco leaves after glycerol application. Nitrate content was significantly decreased by 12-16% and expression of eight genes responsible for carbon and nitrogen metabolism were up-regulated with glycerol applications under both normal and 20% reduced nitrogen levels (P < 0.01). Leaf biomass of plants sprayed with glycerol and 20% nitrogen reduction was equivalent to that of no glycerol control with normal nitrogen application. Carbohydrates biosynthesis, nitrate transport and nitrate assimilation were enhanced in glycerol sprayed burley tobacco seedlings which might contribute to reduced nitrate and increased carbohydrates contents. In conclusion, glyerol spray coupled with 20% nitrogen reduction would be an effective method to reduce nitrate accumulation in burley tobacco.

Toxicity of dihydroxyacetone is exerted through the formation of methylglyoxal in Saccharomyces cerevisiae: effects on actin polarity and nuclear division

Dihydroxyacetone (DHA) is the smallest ketotriose, and it is utilized by many organisms as an energy source. However, at higher concentrations, DHA becomes toxic towards several organisms including the budding yeast Saccharomyces cerevisiae. In the present study, we show that DHA toxicity is due to its spontaneous conversion to methylglyoxal (MG) within yeast cells. A mutant defective in MG-metabolizing enzymes (glo1Δgre2Δgre3Δ) exhibited higher susceptibility to DHA. Intracellular MG levels increased following the treatment of glo1Δgre2Δgre3Δ cells with DHA. We previously reported that MG depolarized the actin cytoskeleton and changed vacuolar morphology. We herein demonstrated the depolarization of actin and morphological changes in vacuoles following a treatment with DHA. Furthermore, we found that both MG and DHA caused the morphological change in nucleus, and inhibited the nuclear division. Our results suggest that the conversion of DHA to MG is a dominant contributor to its cytotoxicity.

Improvement of glycerol catabolism in Bacillus licheniformis for production of poly-γ-glutamic acid

Bacillus licheniformis WX-02 is a well-studied strain to produce poly-γ-glutamic acid (γ-PGA) with numerous applications. This study is to improve WX-02 strain's capability of assimilating glycerol, a major byproduct of biofuels industries, through metabolic manipulation. Through gene knockout, the GlpK pathway was identified as the sole functional glycerol catabolism pathway, while the DhaK pathway was inactive for this strain under either aerobic or anaerobic conditions. The enhancement of glycerol utilization was attempted by substituting the native glpFK promoter with the constitutive promoter (P43), ytzE promoter (PytzE), and bacABC operon promoter (PbacA), respectively. The glycerol consumptions of the corresponding mutant strains WX02-P43glpFK, WX02-PytzEglpFK, and WX02-PbacAglpFK were 30.9, 26.42, and 18.8% higher than that of the WX-02 strain, respectively. The γ-PGA concentrations produced by the three mutant strains were 33.71, 23.39, and 30.05% higher than that of WX-02 strain, respectively. When biodiesel-derived crude glycerol was used as the carbon source, the mutant WX02-P43glpFK produced 16.63 g L^-1 of γ-PGA, with a productivity of 0.35 g L^-1 h^-1. Collectively, this study demonstrated that glycerol can be used as an effective substrate for producing γ-PGA by metabolic engineering B. licheniformis strains.

Implications of glycerol metabolism for lipid production

Triacylglycerol (TAG) is an important product in oil-producing organisms. Biosynthesis of TAG can be completed through either esterification of fatty acids to glycerol backbone, or through esterification of 2-monoacylglycerol. This review will focus on the former pathway in which two precursors, fatty acid and glycerol-3-phosphate (G3P), are required for TAG formation. Tremendous progress has been made about the enzymes or genes that regulate the biosynthetic pathway of TAG. However, much attention has been paid to the fatty acid provision and the esterification process, while the possible role of G3P is largely neglected. Glycerol is extensively studied on its usage as carbon source for value-added products, but the modification of glycerol metabolism, which is directly associated with G3P synthesis, is seldom recognized in lipid investigations. The relevance among glycerol metabolism, G3P synthesis and lipid production is described, and the role of G3P in glycerol metabolism and lipid production are discussed in detail with an emphasis on how G3P affects lipid production through the modulation of glycerol metabolism. Observations of lipid metabolic changes due to glycerol related disruption in mammals, plants, and microorganisms are introduced. Altering glycerol metabolism results in the changes of final lipid content. Possible regulatory mechanisms concerning the relationship between glycerol metabolism and lipid production are summarized.

Pathway Construction in Corynebacterium glutamicum and Strain Engineering To Produce Rare Sugars from Glycerol

Rare sugars are valuable natural products widely used in pharmaceutical and food industries. In this study, we expected to synthesize rare ketoses from abundant glycerol using dihydroxyacetone phosphate (DHAP)-dependent aldolases. First, a new glycerol assimilation pathway was constructed to synthesize DHAP. The enzymes which convert glycerol to 3-hydroxypropionaldehyde and l-glyceraldehyde were selected, and their corresponding aldehyde synthesis pathways were constructed in vivo. Four aldol pathways based on different aldolases and phosphorylase were gathered. Next, three pathways were assembled and the resulting strains synthesized 5-deoxypsicose, 5-deoxysorbose, and 5-deoxyfructose from glucose and glycerol and produce l-fructose, l-tagatose, l-sorbose, and l-psicose with glycerol as the only carbon source. To achieve higher product titer and yield, the recombinant strains were further engineered and fermentation conditions were optimized. Fed-batch culture of engineered strains obtained 38.1 g/L 5-deoxypsicose with a yield of 0.91 ± 0.04 mol product per mol of glycerol and synthesized 20.8 g/L l-fructose, 10.3 g/L l-tagatose, 1.2 g/L l-sorbose, and 0.95 g/L l-psicose.

The role of 1,3-propanediol production in fermentation of glycerol by Clostridium pasteurianum

Waste crude glycerol from biodiesel production can be used to produce biobutanol using Clostridium pasteurianum with the main products being n-butanol, 1,3-propanediol (PDO) and ethanol. There has been much discrepancy and mystery around the cause and effect of process parameters on the product distribution, thus a better understanding of the pathway regulation is required. This study shows that as process pH decreased, the rate of cell growth and CO2 production also decreased, resulting in slower fermentations, increased duration of butanol production and higher butanol concentrations and yields. The production rate of PDO was multi-modal and the role of PDO appears to function in redox homeostasis. The results also showed that C. pasteurianum displayed little biphasic behavior when compared to Clostridia spp. typically used in ABE fermentation due to the alternative glycolysis-independent reductive pathway of PDO production, rendering it suitable for a continuous fermentation process.

Carbon-rich wastes as feedstocks for biodegradable polymer (polyhydroxyalkanoate) production using bacteria

Research into the production of biodegradable polymers has been driven by vision for the most part from changes in policy, in Europe and America. These policies have their origins in the Brundtland Report of 1987, which provides a platform for a more sustainable society. Biodegradable polymers are part of the emerging portfolio of renewable raw materials seeking to deliver environmental, social, and economic benefits. Polyhydroxyalkanoates (PHAs) are naturally-occurring biodegradable-polyesters accumulated by bacteria usually in response to inorganic nutrient limitation in the presence of excess carbon. Most of the early research into PHA accumulation and technology development for industrial-scale production was undertaken using virgin starting materials. For example, polyhydroxybutyrate and copolymers such as polyhydroxybutyrate-co-valerate are produced today at industrial scale from corn-derived glucose. However, in recent years, research has been undertaken to convert domestic and industrial wastes to PHA. These wastes in today's context are residuals seen by a growing body of stakeholders as platform resources for a biobased society. In the present review, we consider residuals from food, plastic, forest and lignocellulosic, and biodiesel manufacturing (glycerol). Thus, this review seeks to gain perspective of opportunities from literature reporting the production of PHA from carbon-rich residuals as feedstocks. A discussion on approaches and context for PHA production with reference to pure- and mixed-culture technologies is provided. Literature reports advocate results of the promise of waste conversion to PHA. However, the vast majority of studies on waste to PHA is at laboratory scale. The questions of surmounting the technical and political hurdles to industrialization are generally left unanswered. There are a limited number of studies that have progressed into fermentors and a dearth of pilot-scale demonstration. A number of fermentation studies show that biomass and PHA productivity can be increased, and sometimes dramatically, in a fermentor. The relevant application-specific properties of the polymers from the wastes studied and the effect of altered-waste composition on polymer properties are generally not well reported and would greatly benefit the progress of the research as high productivity is of limited value without the context of requisite case-specific polymer properties. The proposed use of a waste residual is advantageous from a life cycle viewpoint as it removes the direct or indirect effect of PHA production on land usage and food production. However, the question, of how economic drivers will promote or hinder advancements to demonstration scale, when wastes generally become understood as resources for a biobased society, hangs today in the balance due to a lack of shared vision and the legacy of mistakes made with first generation bioproducts.

Key enzymes catalyzing glycerol to 1,3-propanediol

Biodiesel can replace petroleum diesel as it is produced from animal fats and vegetable oils, and it produces about 10 % (w/w) glycerol, which is a promising new industrial microbial carbon, as a major by-product. One of the most potential applications of glycerol is its biotransformation to high value chemicals such as 1,3-propanediol (1,3-PD), dihydroxyacetone (DHA), succinic acid, etc., through microbial fermentation. Glycerol dehydratase, 1,3-propanediol dehydrogenase (1,3-propanediol-oxydoreductase), and glycerol dehydrogenase, which were encoded, respectively, by dhaB, dhaT, and dhaD and with DHA kinase are encompassed by the dha regulon, are the three key enzymes in glycerol bioconversion into 1,3-PD and DHA, and these are discussed in this review article. The summary of the main research direction of these three key enzyme and methods of glycerol bioconversion into 1,3-PD and DHA indicates their potential application in future enzymatic research and industrial production, especially in biodiesel industry.

Bioinformatics and Molecular Biological Characterization of a Hypothetical Protein SAV1226 as a Potential Drug Target for Methicillin/Vancomycin-Staphylococcus aureus Infections

Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Bifunctional homodimeric triokinase/FMN cyclase: contribution of protein domains to the activities of the human enzyme and molecular dynamics simulation of domain movements

Mammalian triokinase, which phosphorylates exogenous dihydroxyacetone and fructose-derived glyceraldehyde, is neither molecularly identified nor firmly associated to an encoding gene. Human FMN cyclase, which splits FAD and other ribonucleoside diphosphate-X compounds to ribonucleoside monophosphate and cyclic X-phosphodiester, is identical to a DAK-encoded dihydroxyacetone kinase. This bifunctional protein was identified as triokinase. It was modeled as a homodimer of two-domain (K and L) subunits. Active centers lie between K1 and L2 or K2 and L1: dihydroxyacetone binds K and ATP binds L in different subunits too distant (≈ 14 Å) for phosphoryl transfer. FAD docked to the ATP site with ribityl 4'-OH in a possible near-attack conformation for cyclase activity. Reciprocal inhibition between kinase and cyclase reactants confirmed substrate site locations. The differential roles of protein domains were supported by their individual expression: K was inactive, and L displayed cyclase but not kinase activity. The importance of domain mobility for the kinase activity of dimeric triokinase was highlighted by molecular dynamics simulations: ATP approached dihydroxyacetone at distances below 5 Å in near-attack conformation. Based upon structure, docking, and molecular dynamics simulations, relevant residues were mutated to alanine, and kcat and Km were assayed whenever kinase and/or cyclase activity was conserved. The results supported the roles of Thr(112) (hydrogen bonding of ATP adenine to K in the closed active center), His(221) (covalent anchoring of dihydroxyacetone to K), Asp(401) and Asp(403) (metal coordination to L), and Asp(556) (hydrogen bonding of ATP or FAD ribose to L domain). Interestingly, the His(221) point mutant acted specifically as a cyclase without kinase activity.

Dihydroxyacetone metabolism in Haloferax volcanii

Dihydroxyacetone (DHA) is a ketose sugar that can be produced by oxidizing glycerol. DHA in the environment is taken up and phosphorylated to DHA-phosphate by glycerol kinase or DHA kinase. In hypersaline environments, it is hypothesized that DHA is produced as an overflow product from glycerol utilization by organisms such as Salinibacter ruber. Previous research has demonstrated that the halobacterial species Haloquadratum walsbyi can use DHA as a carbon source, and putative DHA kinase genes were hypothesized to be involved in this process. However, DHA metabolism has not been demonstrated in other halobacterial species, and the role of the DHA kinase genes was not confirmed. In this study, we examined the metabolism of DHA in Haloferax volcanii because putative DHA kinase genes were annotated in its genome, and it has an established genetic system to assay growth of mutant knockouts. Experiments in which Hfx. volcanii was grown on DHA as the sole carbon source demonstrated growth, and that it is concentration dependent. Three annotated DHA kinase genes (HVO_1544, HVO_1545, and HVO_1546), which are homologous to the putative DHA kinase genes present in Hqm. walsbyi, as well as the glycerol kinase gene (HVO_1541), were deleted to examine the effect of these genes on the growth of Hfx. volcanii on DHA. Experiments demonstrated that the DHA kinase deletion mutant exhibited diminished, but not absence of growth on DHA compared to the parent strain. Deletion of the glycerol kinase gene also reduced growth on DHA, and did so more than deletion of the DHA kinase. The results indicate that Hfx. volcanii can metabolize DHA and that DHA kinase plays a role in this metabolism. However, the glycerol kinase appears to be the primary enzyme involved in this process. BLASTp analyses demonstrate that the DHA kinase genes are patchily distributed among the Halobacteria, whereas the glycerol kinase gene is widely distributed, suggesting a widespread capability for DHA metabolism.

Impurities of crude glycerol and their effect on metabolite production

Glycerol is a valuable raw material for the production of industrially useful metabolites. Among many promising applications for the use of glycerol is its bioconversion to high value-added compounds, such as 1,3-propanediol (1,3-PD), succinate, ethanol, propionate, and hydrogen, through microbial fermentation. Another method of waste material utilization is the application of crude glycerol in blends with other wastes (e.g., tomato waste hydrolysate). However, crude glycerol, a by-product of biodiesel production, has many impurities which can limit the yield of metabolites. In this mini-review we summarize the effects of crude glycerol impurities on various microbial fermentations and give an overview of the metabolites that can be synthesized by a number of prokaryotic and eukaryotic microorganisms when cultivated on glycerol.

Unraveling the dha cluster in Citrobacter werkmanii: comparative genomic analysis of bacterial 1,3-propanediol biosynthesis clusters

In natural 1,3-propanediol (PDO) producing microorganisms such as Klebsiella pneumoniae, Citrobacter freundii and Clostridium sp., the genes coding for PDO producing enzymes are grouped in a dha cluster. This article describes the dha cluster of a novel candidate for PDO production, Citrobacter werkmanii DSM17579 and compares the cluster to the currently known PDO clusters of Enterobacteriaceae and Clostridiaceae. Moreover, we attribute a putative function to two previously unannotated ORFs, OrfW and OrfY, both in C. freundii and in C. werkmanii: both proteins might form a complex and support the glycerol dehydratase by converting cob(I)alamin to the glycerol dehydratase cofactor coenzyme B12. Unraveling this biosynthesis cluster revealed high homology between the deduced amino acid sequence of the open reading frames of C. werkmanii DSM17579 and those of C. freundii DSM30040 and K. pneumoniae MGH78578, i.e., 96 and 87.5 % identity, respectively. On the other hand, major differences between the clusters have also been discovered. For example, only one dihydroxyacetone kinase (DHAK) is present in the dha cluster of C. werkmanii DSM17579, while two DHAK enzymes are present in the cluster of K. pneumoniae MGH78578 and Clostridium butyricum VPI1718.

From waste to plastic: synthesis of poly(3-hydroxypropionate) in Shimwellia blattae

In recent years, glycerol has become an attractive carbon source for microbial processes, as it accumulates massively as a by-product of biodiesel production, also resulting in a decline of its price. A potential use of glycerol in biotechnology is the synthesis of poly(3-hydroxypropionate) [poly(3HP)], a biopolymer with promising properties which is not synthesized by any known wild-type organism. In this study, the genes for 1,3-propanediol dehydrogenase (dhaT) and aldehyde dehydrogenase (aldD) of Pseudomonas putida KT2442, propionate-coenzyme A (propionate-CoA) transferase (pct) of Clostridium propionicum X2, and polyhydroxyalkanoate (PHA) synthase (phaC1) of Ralstonia eutropha H16 were cloned and expressed in the 1,3-propanediol producer Shimwellia blattae. In a two-step cultivation process, recombinant S. blattae cells accumulated up to 9.8% ± 0.4% (wt/wt [cell dry weight]) poly(3HP) with glycerol as the sole carbon source. Furthermore, the engineered strain tolerated the application of crude glycerol derived from biodiesel production, yielding a cell density of 4.05 g cell dry weight/liter in a 2-liter fed-batch fermentation process.

Incorporation of Listeria monocytogenes strains in raw milk biofilms

Biofilms develop successively on devices of milk production without sufficient cleaning and originate from the microbial community of raw milk. The established biofilm matrices enable incorporation of pathogens like Listeria monocytogenes, which can cause a continuous contamination of food processing plants. L. monocytogenes is frequently found in raw milk and non-pasteurized raw milk products and as part of a biofilm community in milk meters and bulk milk tanks. The aim of this study was to analyze whether different L. monocytogenes strains are interacting with the microbial community of raw milk in terms of biofilm formation in the same manner, and to identify at which stage of biofilm formation a selected L. monocytogenes strain settles best. Bacterial community structure and composition of biofilms were analyzed by a cloning and sequencing approach and terminal restriction fragment length polymorphism analysis (T-RFLP) based on the bacterial 16S rRNA gene. The chemical composition of biofilms was analyzed by Fourier transform infrared spectroscopy (FTIR), while settled L. monocytogenes cells were quantified by fluorescence in situ hybridization (FISH). Addition of individual L. monocytogenes strains to raw milk caused significant shifts in the biofilm biomass, in the chemical as well as in the bacterial community composition. Biofilm formation and attachment of L. monocytogenes cells were not serotype but strain specific. However, the added L. monocytogenes strains were not abundant since mainly members of the genera Citrobacter and Lactococcus dominated the bacterial biofilm community. Overall, added L. monocytogenes strains led to a highly competitive interaction with the raw milk community and triggered alterations in biofilm formation.

Molecular characterization of the glycerol-oxidative pathway of Clostridium butyricum VPI 1718

The glycerol oxidative pathway of Clostridium butyricum VPI 1718 plays an important role in glycerol dissimilation. We isolated, sequenced, and characterized the region coding for the glycerol oxidation pathway. Five open reading frames (ORFs) were identified: dhaR, encoding a putative transcriptional regulator; dhaD (1,142 bp), encoding a glycerol dehydrogenase; and dhaK (995 bp), dhaL (629 bp), and dhaM (386 bp), encoding a phosphoenolpyruvate (PEP)-dependent dihydroxyacetone (DHA) kinase enzyme complex. Northern blot analysis demonstrated that the last four genes are transcribed as a 3.2-kb polycistronic operon only in glycerol-metabolizing cultures, indicating that the expression of this operon is regulated at the transcriptional level. The transcriptional start site of the operon was determined by primer extension, and the promoter region was deduced. The glycerol dehydrogenase activity of DhaD and the PEP-dependent DHA kinase activity of DhaKLM were demonstrated by heterologous expression in different Escherichia coli mutants. Based on our complementation experiments, we proposed that the HPr phosphoryl carrier protein and His9 residue of the DhaM subunit are involved in the phosphoryl transfer to dihydroxyacetone-phosphate. DhaR, a potential regulator of this operon, was found to contain conserved transmitter and receiver domains that are characteristic of two-component systems present in the AraC family. To the best of our knowledge, this is the first molecular characterization of a glycerol oxidation pathway in a Gram-positive bacterium.

Relaxing the coenzyme specificity of 1,3-propanediol oxidoreductase from Klebsiella pneumoniae by rational design

1,3-Propanediol has wide applications for large volume markets, particularly in the polymer business. Microbial production of 1,3-propanediol has been considered as a competitor to the traditional petrochemical routes. However, the formation of 1,3-propanediol is limited by the amount of NADH supplied by the oxidative pathway of glycerol dismutation. Previous metabolic flux analysis revealed that relaxation of the coenzyme specificity of 1,3-propanediol oxidoreductase for both NADH and NADPH would increase the production of 1,3-propanediol as well as maintaining the NADH-NAD(+) circle. This work tried to accomplish such a relaxation by rational protein design. Overall binding free energy indicated that the electrostatic energy was the major force discriminating NADH from NADPH. Computational alanine-scanning mutagenesis of the active site residues illustrated that Asp41 was the key residue responsible for the coenzyme specificity. Compared with Asp41Ala, Asp41Gly could further weaken the repulsion between Asp41 and the phosphate group esterified to the 2'-hydroxyl group of the ribose at the adenine end of NADPH. Site-directed mutagenesis was conducted and the relaxation was successfully realized.

Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts

Violacein is a bacteria-originated indolocarbazole pigment with potential applications due to its various bioactivities such as anti-tumor, antiviral, and antifungal activities. However, stable mass production of this pigment is difficult due to its low productivities and the instability of wild-type violacein-producing strains. In order to establish a stable and efficient production system for violacein, the violacein synthesis pathway from a new species of Duganella sp. B2 was reconstructed in different bacterial strains including Escherichia coli, Citrobacter freundii, and Enterobacter aerogenes by using different vectors. The gene cluster that encodes five enzymes involved in the violacein biosynthetic pathway was first isolated from Duganella sp. B2, and three recombinant expression vectors were constructed using the T7 promoter or the alkane-responsive promoter PalkB. Our results showed that violacein could be stably synthesized in E. coli, C. freundii, and E. aerogenes. Interestingly, we found that there were great differences between the different recombinant strains, not only in the protein expression profiles pertaining to violacein biosynthesis but also in the productivity and composition of crude violacein. Among the host strains tested, the crude violacein production by the recombinant C. freundii strain reached 1.68 g L(-1) in shake flask cultures, which was 4-fold higher than the highest production previously reported in flask culture by other groups. To the best of our knowledge, this is the first report on the efficient production of violacein by genetically engineered strains.

Microbial conversion of glycerol to 1,3-propanediol by an engineered strain of Escherichia coli

In an effort to improve industrial production of 1,3-propanediol (1,3-PD), we engineered a novel polycistronic operon under the control of the temperature-sensitive lambda phage P(L)P(R) promoter regulated by the cIts857 repressor and expressed it in Escherichia coli K-12 ER2925. The genes for the production of 1,3-PD in Clostridium butyricum, dhaB1 and dhaB2, which encode the vitamin B(12)-independent glycerol dehydratase DhaB1 and its activating factor, DhaB2, respectively, were tandemly arrayed with the E. coli yqhD gene, which encodes the 1,3-propanediol oxidoreductase isoenzyme YqhD, an NADP-dependent dehydrogenase that can directly convert glycerol to 1,3-PD. The microbial conversion of 1,3-PD from glycerol by this recombinant E. coli strain was studied in a two-stage fermentation process. During the first stage, a novel high-cell-density fermentation step, there was significant cell growth and the majority of the metabolites produced were organic acids, mainly acetate. During the second stage, glycerol from the fresh medium was rapidly converted to 1,3-PD following a temperature shift from 30 degrees C to 42 degrees C. The by-products were mainly pyruvate and acetate. During this two-stage process, the overall 1,3-PD yield and productivity reached 104.4 g/liter and 2.61 g/liter/h, respectively, and the conversion rate of glycerol to 1,3-PD reached 90.2% (g/g). To our knowledge, this is the highest reported yield and productivity efficiency of 1,3-PD with glycerol as the sole source of carbon. Furthermore, the overall fermentation time was only 40 h, shorter than that of any other reports.

X-ray structures of the three Lactococcus lactis dihydroxyacetone kinase subunits and of a transient intersubunit complex

Bacterial dihydroxyacetone (Dha) kinases do not exchange the ADP for ATP but utilize a subunit of the phosphoenolpyruvate carbohydrate phosphotransferase system for in situ rephosphorylation of a permanently bound ADP-cofactor. Here we report the 2.1-angstroms crystal structure of the transient complex between the phosphotransferase subunit DhaM of the phosphotransferase system and the nucleotide binding subunit DhaL of the Dha kinase of Lactococcus lactis, the 1.1-angstroms structure of the free DhaM dimer, and the 2.5-angstroms structure of the Dha-binding DhaK subunit. Conserved salt bridges and an edge-to-plane stacking contact between two tyrosines serve to orient DhaL relative to the DhaM dimer. The distance between the imidazole Nepsilon2 of the DhaM His-10 and the beta-phosphate oxygen of ADP, between which the gamma-phosphate is transferred, is 4.9 angstroms. An invariant arginine, which is essential for activity, is appropriately positioned to stabilize the gamma-phosphate in the transition state. The (betaalpha)4alpha fold of DhaM occurs a second time as a subfold in the DhaK subunit. By docking DhaL-ADP to this subfold, the nucleotide bound to DhaL and the C1-hydroxyl of Dha bound to DhaK are positioned for in-line transfer of phosphate.