Multiple and reversible hydrogenases for hydrogen production by Escherichia coli: dependence on fermentation substrate,pH and the F0F1-ATPase

Molecular hydrogen (H₂) can be produced via hydrogenases during mixed-acid fermentation by bacteria. Escherichia coli possesses multiple (four) hydrogenases. Hydrogenase 3 (Hyd-3) and probably 4 (Hyd-4) with formate dehydrogenase H (Fdh-H) form two different H₂-evolving formate hydrogen lyase (FHL) pathways during glucose fermentation. For both FHL forms, the hycB gene coding small subunit of Hyd-3 is required. Formation and activity of FHL also depends on the external pH ([pH]_out) and the presence of formate. FHL is related with the F₀F₁-ATPase by supplying reducing equivalents and depending on proton-motive force. Two other hydrogenases, 1 (Hyd-1) and 2 (Hyd-2), are H₂-oxidizing enzymes during glucose fermentation at neutral and low [pH]_out. They operate in a reverse, H₂-producing mode during glycerol fermentation at neutral [pH]_out. Hyd-1 and Hyd-2 activity depends on F₀F₁. Moreover, Hyd-3 can also work in a reverse mode. Therefore, the operation direction and activity of all Hyd enzymes might determine H₂ production; some metabolic cross-talk between Hyd enzymes is proposed. Manipulating of different Hyd enzymes activity is an effective way to enhance H₂ production by bacteria in biotechnology. Moreover, a novel approach would be the use of glycerol as feedstock in fermentation processes leading to H₂ production, reduced fuels and other chemicals with higher yields than those obtained by common sugars.     

Multiple and reversible hydrogenases for hydrogen production by Escherichia coli: dependence on fermentation substrate, pH and the F(0)F(1)-ATPase

Molecular hydrogen (H(2)) can be produced via hydrogenases during mixed-acid fermentation by bacteria. Escherichia coli possesses multiple (four) hydrogenases. Hydrogenase 3 (Hyd-3) and probably 4 (Hyd-4) with formate dehydrogenase H (Fdh-H) form two different H(2)-evolving formate hydrogen lyase (FHL) pathways during glucose fermentation. For both FHL forms, the hycB gene coding small subunit of Hyd-3 is required. Formation and activity of FHL also depends on the external pH ([pH](out)) and the presence of formate. FHL is related with the F(0)F(1)-ATPase by supplying reducing equivalents and depending on proton-motive force. Two other hydrogenases, 1 (Hyd-1) and 2 (Hyd-2), are H(2)-oxidizing enzymes during glucose fermentation at neutral and low [pH](out). They operate in a reverse, H(2)-producing mode during glycerol fermentation at neutral [pH](out). Hyd-1 and Hyd-2 activity depends on F(0)F(1). Moreover, Hyd-3 can also work in a reverse mode. Therefore, the operation direction and activity of all Hyd enzymes might determine H(2) production; some metabolic cross-talk between Hyd enzymes is proposed. Manipulating of different Hyd enzymes activity is an effective way to enhance H(2) production by bacteria in biotechnology. Moreover, a novel approach would be the use of glycerol as feedstock in fermentation processes leading to H(2) production, reduced fuels and other chemicals with higher yields than those obtained by common sugars.     

Hydrogenase activity and proton-motive force generation by Escherichia coli during glycerol fermentation

Proton motive force (Δp) generation by Escherichia coli wild type cells during glycerol fermentation was first studied. Its two components, electrical—the membrane potential (?φ) and chemical—the pH transmembrane gradient (ΔpH), were established and the effects of external pH (pH_ex) were determined. Intracellular pH was 7.0 and 6.0 and lower than pH_ex at pH 7.5 and 6.5, respectively; and it was higher than pH_ex at pH 5.5. At high pH_ex, the increase of ?φ (?130 mV) was only partially compensated by a reversed ΔpH, resulting in a low Δp. At low pH_ex ?φ and consequently Δp were decreased. The generation of Δp during glycerol fermentation was compared with glucose fermentation, and the difference in Δp might be due to distinguished mechanisms for H⁺ transport through the membrane, especially to hydrogenase (Hyd) enzymes besides the F₀F₁-ATPase. H⁺ efflux was determined to depend on pH_ex; overall and N,N’-dicyclohexylcarbodiimide (DCCD)-inhibitory H⁺ efflux was maximal at pH 6.5. Moreover, ΔpH was changed at pH 6.5 and Δp was different at pH 6.5 and 5.5 with the hypF mutant lacking all Hyd enzymes. DCCD-inhibited ATPase activity of membrane vesicles was maximal at pH 7.5 and decreased with the hypF mutant. Thus, Δp generation by E. coli during glycerol fermentation is different than that during glucose fermentation. Δp is dependent on pH_ex, and a role of Hyd enzymes in its generation is suggested.     

Enhanced hydrogen and 1,3‐propanediol production from glycerol by fermentation using mixed cultures

The conversion of glycerol into high value products, such as hydrogen gas and 1,3‐propanediol (PD), was examined using anaerobic fermentation with heat‐treated mixed cultures. Glycerol fermentation produced 0.28 mol‐H₂/mol‐glycerol (72 mL‐H₂/g‐COD) and 0.69 mol‐PD/mol‐glycerol. Glucose fermentation using the same mixed cultures produced more hydrogen gas (1.06 mol‐H₂/mol‐glucose) but no PD. Changing the source of inoculum affected gas production likely due to prior acclimation of bacteria to this type of substrate. Fermentation of the glycerol produced from biodiesel fuel production (70% glycerol content) produced 0.31 mol‐H₂/mol‐glycerol (43 mL H₂/g‐COD) and 0.59 mol‐PD/mol‐glycerol. These are the highest yields yet reported for both hydrogen and 1,3‐propanediol production from pure glycerol and the glycerol byproduct from biodiesel fuel production by fermentation using mixed cultures. These results demonstrate that production of biodiesel can be combined with production of hydrogen and 1,3‐propanediol for maximum utilization of resources and minimization of waste. Biotechnol. Bioeng. 2009; 104: 1098–1106. © 2009 Wiley Periodicals, Inc.     

Characterization of <Emphasis Type="Italic">Escherichia coli</Emphasis> [NiFe]-Hydrogenase Distribution During Fermentative Growth at Different pHs

The contribution made by each of the three active [NiFe]-hydrogenases (Hyd) of Escherichia coli during fermentation of glucose or glycerol in peptone-based medium at different pHs was analysed. The activities of the hydrogen-oxidizing Hyd-1 and Hyd-2 enzymes showed a reciprocal dependence on the pH of the medium while Hyd-3, a key component of the hydrogen-evolving formate hydrogenlyase complex, was mainly active at pH 6.5. Our findings identify the conditions during fermentation of glucose or glycerol under which each [NiFe]-hydrogenase is optimally active and demonstrate a previously unrecognized dependence on Hyd-1 activity at low pH.     

Oxidative and Reductive Routes of Glycerol and Glucose Fermentation by Escherichia coli Batch Cultures and Their Regulation by Oxidizing and Reducing Reagents at Different pHs

Glycerol and glucose fermentation redox routes by Escherichia coli and their regulation by oxidizing and reducing reagents were investigated at different pHs. Cell growth was followed by decrease of pH and redox potential (E _h ). During glycerol utilization at pH 7.5 ?pH, the difference between initial and end pH, was lower compared with glucose fermentation. After 8 h growth, during glycerol utilization E _h dropped down to negative values (?150 mV) but during glucose fermentation it was positive (+50 mV). In case of glycerol H₂ was evolved at the middle log phase while during glucose fermentation H₂ was produced during early log phase. Furthermore, upon glycerol utilization, oxidizer potassium ferricyanide (1 mM) inhibited both cell growth and H₂ formation. Reducing reagents dl-dithiothreitol (3 mM) and dithionite (1 mM) inhibited growth but stimulated H₂ production. The findings point out the importance of reductive conditions for glycerol fermentation and H₂ production by E. coli.     

Carbon sources-dependent carotenoid production in metabolically engineered <Emphasis Type="Italic">Escherichia coli</Emphasis>

The effects of three phosphoenolpyruvate (PEP)-dependent PTS carbon sources (glucose, mannose and maltose) and three non-PTS carbon sources (glycerol, galactose, and lactose) on the formation of four carotenoids with diverse structures and on the cell growth of the recombinant Escherichia coli were investigated. The biosynthetic pathways of four carotenoids, C₃₀ diapolycopene, C₃₀ diapotorulene, C₄₀ lycopene, and C₄₀ beta-carotene, were engineered in E. coli. The resulting E. coli cells were grown in a mineral medium supplemented with each of the six carbon sources. Among the six carbon sources, non-PTS glycerol showed the highest performance in production of all four carotenoid structures, whereas PTS glucose showed the lowest performance. Based on the conversion yield, carotenoid-producing capability, and the cell density, we found that there was no close correlation between PTS and non-PTS transport mechanism and carotenoid formations in E. coli.     

Microbial production of D-mannitol and D-fructose from glycerol

In view of the recent development that some petrochemical products are efficiently available as substrates for the fermentation industry, glycerol manufactured from propylene by chemical synthesis would also be hoped for the purpose. This paper describes some of the factors influencing mannitol production from glycerol by Torulopsis yeasts and a microbial conversion of glycerol to D -fructose via mannitol, in which two sequential steps of yeast and Acetobacter fermentation are involved. Torulopsis mannitofaciens CBS 5981 and Torulopsis vcrsatilis CBS 1752, exceptionally good mannitol producers, were selected for the study. High concentrations of nitrogen sources and KH₂PO₄ in the medium markedly decreased mannitol yield in spite of good utilization of the substrate. T. mannitofaciens produced mannitol in yield of 31% of the glycerol consumed at optimal condition. The fermentation by washed yeast cells gave much higher mannitol yield of more than 50%. A sequential fermentation process was carried out without isolation and purification of the intermediate and yielded.51.7%. D -fructose from the glycerol.     

Optimization of carotenoid production by Umbelopsis ramanniana

Umbelopsis ramanniana was investigated to increase carotenoid production. Nine different carbon sources and six different nitrogen sources were evaluated for the maximum carotenoid production. The most effective nitrogen and carbon sources were KNO₃ and lactose, respectively. Then, the optimization of medium components for enhancement of carotenoid production by Umbelopsis ramanniana was achieved using Plackett–Burman design. Box–Behnken response surface methodology was applied to further optimize carotenoid and biomass production. Carbon to nitrogen ratio, lactose concentration, and shaking speed were studied as variables in Box–Behnken design. The optimum conditions for carotenoid and biomass production were determined as 32.42 g/L of lactose concentration, 20:1 of carbon to nitrogen ratio, and shaking speed of 130 rpm. The maximum carotenoid and biomass production under optimized conditions were 1141 μg/L (β-carotene-Eq) and 13.14 g/L, respectively. When compared to the control fermentation, carotenoid, and biomass production were increased by about 2 and 1.3 folds, respectively.     

Formate and glucose stimulation of methane and hydrogen production in rumen liquor

Membrane-inlet mass spectrometry was used to investigate the effects of increasing the concentration of the rumen metabolites, formate and glucose, upon CH₄ and H₂ production during fermentation by unfractionated rumen liquor. Additions of formate up to 3.6 mM stimulated CH₄ and then excess H₂ production. Each addition caused a large accumulation of H₂ (>40 µM), which returned to in situ concentrations after periods of more than 1 h. Glucose additions up to 2.0 mM gave linear increases in CH₄ and H₂ production. The conversion of substrate carbon into CH₄ was found to decrease from 34% to 9% for formate, as concentrations were increased (1.6–3.6 mM); approximately 13.5% of the glucose carbon was converted to CH₄.     

Enhanced methane and hydrogen production from municipal solid waste and agro-industrial by-products co-digested with crude glycerol

The effects of crude glycerol on the performance of single-stage anaerobic reactors treating different types of organic waste were examined. A reactor treating the organic fraction of municipal solid waste produced 1400 mL CH₄/d before the addition of glycerol and 2094 mL CH₄/d after the addition of glycerol. An enhanced methane production rate was also observed when a 1:4 mixture of olive mill wastewater and slaughterhouse wastewater was supplemented with crude glycerol. Specifically, by adding 1% v/v crude glycerol to the feed, the methane production rate increased from 479 mL/d to 1210 mL/d. The extra glycerol-COD added to the feed did not have a negative effect on the reactor performance in either case. Supplementation of the feed with crude glycerol also had a significant positive effect on anaerobic fermentation reactors. Hydrogen yield was 26 mmole H₂/g VS added and 15 mmole H₂/g VS added in a reactor treating the organic fraction of municipal solid waste and a 1:4 mixture of olive mill and slaughterhouse wastewater. The addition of crude glycerol to the feed enhanced hydrogen yield at 2.9 mmole H₂/g glycerol added and 0.7 mmole H₂/g glycerol added.     

Effect of substrate loading on hydrogen production during anaerobic fermentation by Clostridium thermocellum 27405

We have investigated hydrogen (H₂) production by the cellulose-degrading anaerobic bacterium, Clostridium thermocellum. In the following experiments, batch-fermentations were carried out with cellobiose at three different substrate concentrations to observe the effects of carbon-limited or carbon-excess conditions on the carbon flow, H₂-production, and synthesis of other fermentation end products, such as ethanol and organic acids. Rates of cell growth were unaffected by different substrate concentrations. H₂, carbon dioxide (CO₂), acetate, and ethanol were the main products of fermentation. Other significant end products detected were formate and lactate. In cultures where cell growth was severely limited due to low initial substrate concentrations, hydrogen yields of 1 mol H₂/mol of glucose were obtained. In the cultures where growth ceased due to carbon depletion, lactate and formate represented a small fraction of the total end products produced, which consisted mainly of H₂, CO₂, acetate, and ethanol throughout growth. In cultures with high initial substrate concentrations, cellobiose consumption was incomplete and cell growth was limited by factors other than carbon availability. H₂-production continued even in stationary phase and H₂/CO₂ ratios were consistently greater than 1 with a maximum of 1.2 at the stationary phase. A maximum specific H₂ production rate of 14.6 mmol g dry cell⁻¹ h⁻¹ was observed. As cells entered stationary phase, extracellular pyruvate production was observed in high substrate concentration cultures and lactate became a major end product.     

Rhodobacter sphaeroides RV cultivation and hydrogen production in a one- and two-stage chemostat

Rhodobacter sphaeroides RV cultivation and hydrogen production were studied in a one- and two-stage chemostat using lactic acid as substrate. Light saturation was observed when light intensities equal to or above 10 klx were applied. Under light saturation, the two-stage chemostat appeared to be very effective for hydrogen production, allowing complete nitrogen removal by bacterial growth in the first reactor. The hydrogen evolution rate in the second reactor was up to 75 ml H₂ (g dry weight)^–1 h^–1. Accumulation of storage material was observed in the second reactor of the two-stage chemostat under a large carbon excess and limiting light irradiance. The optimal hydraulic residence time was 15 h for both stages, leading to a total hydrogen production about 40% higher than in the one-stage chemostat. Under increasing influent ammonium and yeast extract concentrations, opposite trends of decreasing bacterial activity and increasing concentration resulted in a linear increase of the overall hydrogen production to 1.4–1.6lH₂ (l reactor)^–1 day^–1. Hydrogen production quickly fell when nitrogen was not completely metabolised. The hydrogen evolution rate was also found to depend on lactic acid concentration, and maximum bacterial activity was observed at 100 mM influent lactic acid.     

Transcriptional control of hydrogen production during mixed carbon fermentation by hydrogenases 4 (hyf) and 3 (hyc) in Escherichia coli

Escherichia coli molecular hydrogen (H(2)) production was studied during mixed carbon (glucose and glycerol) fermentation at pH 6.5. Wild type cells in the assays supplemented with glucose produced H(2) at ~2 fold lower level than cells grown on glucose only. When compared to the wild type, H(2) production in the assays added with glucose was decreased by ~2 fold in fhlA, hyfG and double fhlA hyfG mutants and by ~1.5 fold in hyaB, hybC, and double hyaB hybC mutants. However, in the assays with glycerol, no measurable H(2) production was detected. Taken together, these results suggest that during mixed carbon fermentation, H(2) could be produced with low efficiency via Hyd-3 and Hyd-4. This is a novel finding for Hyd-4 activity at pH 6.5. The insignificant decrease of H(2) production in the strains with defects in Hyd-1 and Hyd-2 was probably due to an interaction between the Hyd enzymes and their organization in the bacterial membrane. In the glucose assays, H(2) production in the wild type cells was inhibited ~2 fold by 0.3mM N,N'-dicyclohexylcarbodiimide (DCCD), an inhibitor of the F(0)F(1)-ATPase. This inhibition was the same for fhlA and hyfG fhlA mutants but not hyaB, hybC, hyfG or hyaB hybC mutants. The results indicate that the FhlA protein coded by the fhlA gene might interact with the F(0)F(1)-ATPase. We propose that this interaction is mediated by mixed carbon fermentation.     

Hydrogenases for biological hydrogen production

Biological H₂ production offers distinctive advantages for environmental protection over existing physico-chemical methods. This study focuses specifically on hydrogenases, a class of enzymes that serves to effectively catalyze H₂ formation from protons or oxidation to protons. It reviews the classification schemes (i.e. [NiFe]-, [FeFe]-, and [Fe]-hydrogenases) and properties of these enzymes, which are essential to understand the mechanisms for H₂ production, the control of cell metabolism, and subsequent increases in H₂ production. There are five kinds of biological hydrogen production methods, categorized based upon the light energy requirement, and feedstock sources. The genetic engineering work on hydrogenase to enhance H₂ production is reviewed here. Further discussions in this study include nitrogenase, an enzyme that normally catalyzes the reduction of N₂ to ammonia but is also able to produce H₂ under photo-heterotrophic conditions, as well as other applicable fields of hydrogenase other than H₂ production.     

Model-aided atpE gene knockout strategy in Escherichia coli for enhanced succinic acid production from glycerol

Succinic acid is an important platform chemical with a variety of applications. Model-guided metabolic engineering strategies in Escherichia coli for strain improvement to increase succinic acid production using glucose and glycerol remain largely unexplored. Herein, we report what are, to our knowledge, the first metabolic knockout of the atpE gene to have increased succinic acid production using both glucose and alternative glycerol carbon sources in E. coli. Guided by a genome-scale metabolic model, we engineered the E. coli host to enhance anaerobic production of succinic acid by deleting the atpE gene, thereby generating additional reducing equivalents by blocking H⁺ conduction across the mutant cell membrane. This strategy produced 1.58 and .49 g l^?1 of succinic acid from glycerol and glucose substrate, respectively. This work further elucidates a model-guided and/or system-based metabolic engineering, involving only a single-gene deletion strategy for enhanced succinic acid production in E. coli.     

Combinatorial assembly of ferredoxin-linked modules in Escherichia coli yields a testing platform for Rnf-complexes

The Rnf complex is a membrane-bound ferredoxin(Fd):NAD(P)⁺ oxidoreductase (Fno) that couples Fd oxidation to vectorial H⁺/Na⁺ transport across the cytoplasmic membrane. Here, we produced two putative Rnf-complexes from Clostridioides difficile (Cd-Rnf) and Clostridium ljungdahlii (Cl-Rnf) for the first time in Escherichia coli. A redox-responsive low-expression system enabled Rnf assembly in the membranes of E. coli as confirmed by in vitro activity measurements. To study the physiological effects of Rnf on the metabolism of E. coli, we assembled additional Fd-dependent enzymes by plasmid-based multigene expression: (a) an Fd-linked butyrate pathway (But) from C. difficile, (b) an [FeFe]-hydrogenase (Hyd) to modulate the redox state of Fd, and (c) heterologous ferredoxins as electron carriers. The hydrogenase efficiently modulated butyrate formation by H₂-mediated Fd reoxidation under nitrogen. In its functionally assembled state, Rnf severely impaired cell growth. Including Hyd in the But/Rnf background, in turn, restored normal growth. Our findings suggest that Rnf mediates reverse electron flow from NADH to Fd, which requires E. coli’s F-type ATPase to function in its reverse, ATP hydrolyzing direction. The reduced Fd is then reoxidized by endogenous Fd:NAD(P)H oxidoreductase (Fpr), which regenerates NADH and, thereby, initiates a futile cycle fueled by ATP hydrolysis. The introduction of hydrogenase interrupts this futile cycle under N₂ by providing an efficient NAD(P)⁺-independent Fd reoxidation route, whereas under H₂, Hyd outcompetes Rnf for Fd reduction. This is the first report of an Rnf complex being functionally produced and physiologically investigated in E. coli.     

Escherichia coli genome-scale metabolic gene knockout of lactate dehydrogenase (ldhA), increases succinate production from glycerol

Genome-scale metabolic model (GEM) of Escherichia coli has been published with applications in predicting metabolic engineering capabilities on different carbon sources and directing biological discovery. The use of glycerol as an alternative carbon source is economically viable in biorefinery. The use of GEM for predicting metabolic gene deletion of lactate dehydrogenase (ldhA) for increasing succinate production in Escherichia coli from glycerol carbon source remained largely unexplored. Here, I hypothesized that metabolic gene knockout of ldhA in E. coli from glycerol could increase succinate production. A proof-of-principle strain was constructed and designated as E. coli BMS5 (ΔldhA), by predicting increased succinate production in E. coli GEM and confirmed the predicted outcomes using wet cell experiments. The mutant GEM (ΔldhA) predicted 11% increase in succinate production from glycerol compared to its wild-type model (iAF1260), and the E. coli BMS5 (ΔldhA) showed 1.05 g/l and its corresponding wild-type produced .05 g/l (23-fold increase). The proof-of-principle strain constructed in this study confirmed the aforementioned hypothesis and further elucidated the fact that E. coli GEM can prospectively and effectively predict metabolic engineering interventions using glycerol as substrate and could serve as platform for new strain design strategies and biological discovery.