Effect of oxygen on the metabolism of Zymomonas mobilis

Respiration is essential for aerobic growth of Zymomonas mobilis ZM4

IMPORTANCE

A key to producing next-generation biofuels is to engineer microbes that efficiently convert non-food materials into drop-in fuels, and to engineer microbes effectively, we must understand their metabolism thoroughly. Zymomonas mobilis is a bacterium that is a promising candidate biofuel producer, but its metabolism remains poorly understood, especially its metabolism when exposed to oxygen. Although Z. mobilis respires with oxygen, its aerobic growth is poor, and disruption of genes related to respiration counterintuitively improves aerobic growth. This unusual result has sparked decades of research and debate regarding the function of respiration in Z. mobilis. Here, we used a new set of mutants to determine that respiration is essential for aerobic growth and likely protects the cells from damage caused by oxygen. We conclude that the respiratory pathway of Z. mobilis should not be deleted from chassis strains for industrial production because this would yield a strain that is intolerant of oxygen, which is more difficult to manage in industrial settings.

Zymomonas mobilis ZM4 Utilizes an NADP+-Dependent Acetaldehyde Dehydrogenase To Produce Acetate

Zymomonas mobilis is a promising bacterial host for biofuel production, but further improvement has been hindered because some aspects of its metabolism remain poorly understood. For example, one of the main by-products generated by Z. mobilis is acetate, but the pathway for acetate production is unknown. Acetaldehyde oxidation has been proposed as the major source of acetate, and an acetaldehyde dehydrogenase was previously isolated from Z. mobilis via activity guided fractionation, but the corresponding gene has never been identified. We determined that the locus ZMO1754 (also known as ZMO_RS07890) encodes an NADP⁺-dependent acetaldehyde dehydrogenase that is responsible for acetate production by Z. mobilis. Deletion of this gene from the chromosome resulted in a growth defect in oxic conditions, suggesting that acetaldehyde detoxification is an important role of acetaldehyde dehydrogenase. The deletion strain also exhibited a near complete abolition of acetate production, both in typical laboratory conditions and during lignocellulosic hydrolysate fermentation. Our results show that ZMO1754 encodes the major acetate-forming acetaldehyde dehydrogenase in Z. mobilis, and we therefore rename the gene aldB based on functional similarity to the Escherichia coli acetaldehyde dehydrogenase. IMPORTANCE Biofuel production from nonfood crops is an important strategy for reducing carbon emissions from the transportation industry, but it has not yet become commercially viable. An important avenue to improve biofuel production is to enhance the characteristics of fermentation organisms by decreasing by-product formation via genetic engineering. Here, we identified and deleted a metabolic pathway and associated gene that lead to acetate formation in Zymomonas mobilis. Acetate is one of the major by-products generated during ethanol production by Z. mobilis, so this information may be used in the future to develop better strains for commercial biofuel production.

Ethanologenesis and respiration in a pyruvate decarboxylase-deficient Zymomonas mobilis

Objective

Zymomonas mobilis is an alpha-proteobacterium with a rapid ethanologenic pathway, involving Entner–Doudoroff (E–D) glycolysis, pyruvate decarboxylase (Pdc) and two alcohol dehydrogenase (ADH) isoenzymes. Pyruvate is the end-product of the E–D pathway and the substrate for Pdc. Construction and study of Pdc-deficient strains is of key importance for Z. mobilis metabolic engineering, because the pyruvate node represents the central branching point, most novel pathways divert from ethanol synthesis. In the present work, we examined the aerobic metabolism of a strain with partly inactivated Pdc.

Results

Relative to its parent strain the mutant produced more pyruvate. Yet, it also yielded more acetaldehyde, the product of the Pdc reaction and the substrate for ADH, although the bulk ADH activity was similar in both strains, while the Pdc activity in the mutant was reduced by half. Simulations with the kinetic model of Z. mobilis E-D pathway indicated that, for the observed acetaldehyde to ethanol production ratio in the mutant, the ratio between its respiratory NADH oxidase and ADH activities should be significantly higher, than the measured values. Implications of this finding for the directionality of the ADH isoenzyme operation in vivo and interactions between ADH and Pdc are discussed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05625-5.

Acetaldehyde Stimulation of the Growth of Zymomonas mobilis Subjected to Ethanol and Other Environmental Stresses: Effect of Other Metabolic Electron Acceptors and Evidence for a Mechanism

Ethanol-stressed cultures of Z. mobilis showed greatly reduced lag times in growth when supplemented with small amounts of acetaldehyde. This effect could be mimicked by other metabolic electron acceptors, including propionaldehyde and oxygen, indicating a redox-based mechanism. Added propionaldehyde was rapidly and stoichiometrically converted to 1-propanol, suggesting that added acetaldehyde is also reduced during early growth. Acetaldehyde addition measurably accelerated glycolysis in nongrowing cells and also slightly stimulated cultures subjected to temperature change, osmotic shock and salt and acetate stress. Acetaldehyde’s stimulatory effect appears to be due to its ability to accelerate glycolysis via its effect on the cellular redox balance. Acetaldehyde reduction opposes the drain on NAD+ concentrations caused by oxidation of the added ethanol, accounting for the particularly strong effect on ethanol-stressed cells. This study provides evidence for our earlier proposed redox-based mechanism for acetaldehyde’s ability to reduce the lag phase of environmentally stressed cultures and suggests that the effect may have applications in industrial fermentations, especially those inhibited by ethanol and toxic compounds present in, for instance, lignocellulosic hydrolysates.

Two bacterial glycosphingolipid synthases responsible for the synthesis of glucuronosylceramide and α-galactosylceramide

Bacterial glycosphingolipids such as glucuronosylceramide and galactosylceramide have been identified as ligands for invariant natural killer T cells and play important roles in host defense. However, the glycosphingolipid synthases required for production of these ceramides have not been well-characterized. Here, we report the identification and characterization of glucuronosylceramide synthase (ceramide UDP-glucuronosyltransferase [Cer-GlcAT]) in Zymomonas mobilis, a Gram-negative bacterium whose cellular membranes contain glucuronosylceramide. On comparing the gene sequences that encode the diacylglycerol GlcAT in bacteria and plants, we found a homologous gene that is widely distributed in the order Sphingomonadales in the Z. mobilis genome. We first cloned the gene and expressed it in Escherichia coli, followed by protein purification using nickel-Sepharose affinity and gel filtration chromatography. Using the highly enriched enzyme, we observed that it has high glycosyltransferase activity with UDP-glucuronic acid and ceramide as sugar donor and acceptor substrate, respectively. Cer-GlcAT deletion resulted in a loss of glucuronosylceramide and increased the levels of ceramide phosphoglycerol, which was expressed in WT cells only at very low levels. Furthermore, we found sequences homologous to Cer-GlcAT in Sphingobium yanoikuyae and Bacteroides fragilis, which have been reported to produce glucuronosylceramide and α-galactosylceramide, respectively. We expressed the two homologs of the cer-glcat gene in E. coli and found that each gene encodes Cer-GlcAT and Cer-galactosyltransferase, respectively. These results contribute to the understanding of the roles of bacterial glycosphingolipids in host-bacteria interactions and the function of bacterial glycosphingolipids in bacterial physiology.

High Productivity Ethanol from Solid-State Fermentation of Steam-Exploded Corn Stover Using Zymomonas mobilis by N2 Periodic Pulsation Process Intensification

Solid-state fermentation, featured by water-saving, eco-friendly and high concentration product, is a promising technology in lignocellulosic ethanol industry. However, in solid-state fermentation system, large gas content inside the substrate directly leads to high oxygen partial pressure and inhibits ethanol fermentation. Z. mobilis can produce ethanol from glucose near the theoretical maximum value, but this ethanol yield would be greatly decreased by high oxygen partial pressure during solid-state fermentation. In this study, we applied N₂ periodic pulsation process intensification (NPPPI) to ethanol solid-state fermentation, which displaced air with N₂ and provided a proper anaerobic environment for Z. mobilis. Based on the water state distribution, the promotion effects of NPPPI on low solid loading and solid-state fermentation were analyzed to confirm the different degrees of oxygen inhibition in ethanol solid-state fermentation. During the simultaneous saccharification solid-state fermentation, the NPPPI group achieved 45.29% ethanol yield improvement and 30.38% concentration improvement compared with the control group. NPPPI also effectively decreased 58.47% of glycerol and 84.24% of acetic acid production and increased the biomass of Z. mobilis. By coupling the peristaltic enzymatic hydrolysis and fed-batch culture, NPPPI made the ethanol yield and concentration reach 80.11% and 55.06 g/L, respectively, in solid-state fermentation.

Potential of Zymomonas mobilis as an electricity producer in ethanol production

BACKGROUND

Microbial fuel cell (MFC) convokes microorganism to convert biomass into electricity. However, most well-known electrogenic strains cannot directly use glucose to produce valuable products. Zymomonas mobilis, a promising bacterium for ethanol production, owns special Entner-Doudoroff pathway with less ATP and biomass produced and the low-energy coupling respiration, making Z. mobilis a potential exoelectrogen.

RESULTS

A glucose-consuming MFC is constructed by inoculating Z. mobilis. The electricity with power density 2.0 mW/m² is derived from the difference of oxidation-reduction potential (ORP) between anode and cathode chambers. Besides, two-type electricity generation is observed as glucose-independent process and glucose-dependent process. For the sake of enhancing MFC efficiency, extracellular and intracellular strategies are implemented. Biofilm removal and addition of c-type cytochrome benefit electricity performance and Tween 80 accelerates the electricity generation. Perturbation of cellular redox balance compromises the electricity output, indicating that redox homeostasis is the principal requirement to reach ideal voltage.

CONCLUSION

This study identifies potential feature of electricity activity for Z. mobilis and provides multiple strategies to enhance the electricity output. Therefore, additional electricity generation will benefit the techno-economic viability of the commercial bulk production for biochemicals or biofuels in an efficient and environmentally sustainable manner.

Applying a New REFINE Approach in Zymomonas mobilis Identifies Novel sRNAs That Confer Improved Stress Tolerance Phenotypes

As global controllers of gene expression, small RNAs represent powerful tools for engineering complex phenotypes. However, a general challenge prevents the more widespread use of sRNA engineering strategies: mechanistic analysis of these regulators in bacteria lags far behind their high-throughput search and discovery. This makes it difficult to understand how to efficiently identify useful sRNAs to engineer a phenotype of interest. To help address this, we developed a forward systems approach to identify naturally occurring sRNAs relevant to a desired phenotype: RNA-seq Examiner for Phenotype-Informed Network Engineering (REFINE). This pipeline uses existing RNA-seq datasets under different growth conditions. It filters the total transcriptome to locate and rank regulatory-RNA-containing regions that can influence a metabolic phenotype of interest, without the need for previous mechanistic characterization. Application of this approach led to the uncovering of six novel sRNAs related to ethanol tolerance in non-model ethanol-producing bacterium Zymomonas mobilis. Furthermore, upon overexpressing multiple sRNA candidates predicted by REFINE, we demonstrate improved ethanol tolerance reflected by up to an approximately twofold increase in relative growth rate compared to controls not expressing these sRNAs in 7% ethanol (v/v) RMG-supplemented media. In this way, the REFINE approach informs strain-engineering strategies that we expect are applicable for general strain engineering.

Zymomonas mobilis metabolism: Novel tools and targets for its rational engineering

Zymomonas mobilis is an α-proteobacterium that interests the biofuel industry due to its perfect ethanol fermentation yields. From its first description as a bacterial isolate in fermented alcoholic beverages to date, Z. mobilis has been rigorously studied in directions basic and applied. The Z. mobilis powerful Entner-Doudoroff glycolytic pathway has been the center of rigorous biochemical studies and, aside from ethanol, it has attracted interest in terms of high-added-value chemical manufacturing. Energetic balances and the effects of respiration have been explored in fundamental directions as also in applications pursuing strain enhancement and the utilization of alternative carbon sources. Metabolic modeling has addressed the optimization of the biochemical circuitry at various conditions of growth and/or substrate utilization; it has been also critical in predicting desirable end-product yields via flux redirection. Lastly, stress tolerance has received particular attention, since it directly determines biocatalytical performance at challenging bioreactor conditions. At a genetic level, advances in the genetic engineering of the organism have brought forth beneficial manipulations in the Z. mobilis gene pool, e.g., knock-outs, knock-ins and gene stacking, aiming to broaden the metabolic repertoire and increase robustness. Recent omic and expressional studies shed light on the genomic content of the most applied strains and reveal landscapes of activity manifested at ambient or reactor-based conditions. Studies such as those reviewed in this work, contribute to the understanding of the biology of Z. mobilis, enable insightful strain development, and pave the way for the transformation of Z. mobilis into a consummate organism for biomass conversion.

Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4

Zymomonas mobilis is a bacterium that produces ethanol from glucose at up to 97% of theoretical efficiency on a carbon basis. One factor contributing to the high efficiency of ethanol production is that Z. mobilis has a low biomass yield. The low biomass yield may be caused partly by the low ATP yield of the Entner-Doudoroff (ED) glycolytic pathway used by Z. mobilis, which produces only one ATP per glucose consumed. To test the hypothesis that ATP yield limits biomass yield in Z. mobilis, we attempted to introduce the Embden-Meyerhof-Parnas (EMP) glycolytic pathway (with double the ATP yield) by expressing phosphofructokinase (Pfk I) from Escherichia coli. Expression of Pfk I caused growth inhibition and resulted in accumulation of mutations in the pfkA gene. Co-expression of additional EMP enzymes, fructose bisphosphate aldolase (Fba) and triose phosphate isomerase (Tpi), with Pfk I did not enable EMP flux, and resulted in production of glycerol as a side product. Further analysis indicated that heterologous reactions may have operated in the reverse direction because of native metabolite concentrations. This study reveals how the metabolomic context of a chassis organism influences the range of pathways that can be added by heterologous expression.

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production

Zymomonas mobilis is an aerotolerant anaerobe and prolific ethanologen with attractive characteristics for industrial bioproduct generation. However, there is currently insufficient knowledge of the impact that environmental factors have on flux through industrially relevant biosynthetic pathways. Here, we examined the effect of oxygen exposure on metabolism and gene expression in Z. mobilis by combining targeted metabolomics, mRNA sequencing, and shotgun proteomics. We found that exposure to oxygen profoundly influenced metabolism, inducing both transient metabolic bottlenecks and long-term metabolic remodeling. In particular, oxygen induced a severe but temporary metabolic bottleneck in the methyl erythritol 4-phosphate pathway for isoprenoid biosynthesis caused by oxidative damage to the iron-sulfur cofactors of the final two enzymes in the pathway. This bottleneck was resolved with minimal changes in expression of isoprenoid biosynthetic enzymes. Instead, it was associated with pronounced upregulation of enzymes related to iron-sulfur cluster maintenance and biogenesis (i.e., flavodoxin reductase and the suf operon). We also detected major changes in glucose utilization in the presence of oxygen. Specifically, we observed increased gluconate production following exposure to oxygen, accounting for 18% of glucose uptake. Our results suggest that under aerobic conditions, electrons derived from the oxidation of glucose to gluconate are diverted to the electron transport chain, where they can minimize oxidative damage by reducing reactive oxygen species such as H2O2. This model is supported by the simultaneous upregulation of three membrane-bound dehydrogenases, cytochrome c peroxidase, and a cytochrome bd oxidase following exposure to oxygen. IMPORTANCE Microbially generated biofuels and bioproducts have the potential to provide a more environmentally sustainable alternative to fossil-fuel-derived products. In particular, isoprenoids, a diverse class of natural products, are chemically suitable for use as high-grade transport fuels and other commodity molecules. However, metabolic engineering for increased production of isoprenoids and other bioproducts is limited by an incomplete understanding of factors that control flux through biosynthetic pathways. Here, we examined the native regulation of the isoprenoid biosynthetic pathway in the biofuel producer Zymomonas mobilis. We leveraged oxygen exposure as a means to perturb carbon flux, allowing us to observe the formation and resolution of a metabolic bottleneck in the pathway. Our multi-omics analysis of this perturbation enabled us to identify key auxiliary enzymes whose expression correlates with increased production of isoprenoid precursors, which we propose as potential targets for future metabolic engineering.

Metabolic engineering of Gluconobacter oxydans 621H for increased biomass yield

The obligatory aerobic acetic acid bacterium Gluconobacter oxydans incompletely oxidizes carbon sources regio- and stereoselectively in the periplasm and therefore is used industrially for oxidative biotransformations, e. g., in vitamin C production. However, it has a very low biomass yield as the oxidized products largely remain in the medium and cannot be used for anabolism. Cytoplasmic carbon metabolism occurs via the pentose phosphate pathway and the Entner-Doudoroff pathway, whereas glycolysis and the tricarboxylic acid cycle are incomplete. Acetate is formed as an end product via pyruvate decarboxylase and acetaldehyde dehydrogenase. In order to increase the biomass yield from glucose, we sequentially replaced (i) gdhS encoding the cytoplasmic NADP-dependent glucose dehydrogenase by the Acetobacter pasteurianus sdhCDABE genes for succinate dehydrogenase and the flavinylation factor SdhE (strain IK001), (ii) pdc encoding pyruvate decarboxylase by a second ndh gene encoding a type II NADH dehydrogenase (strain IK002.1), and (iii) gdhM encoding the membrane-bound PQQ-dependent glucose dehydrogenase by sucCD from Gluconacetobacter diazotrophicus encoding succinyl-CoA synthetase (strain IK003.1). Analysis of the strains under controlled cultivation conditions in bioreactors revealed for IK003.1 that neither gluconate nor 2-ketogluconate was formed, but some 5-ketogluconate. Acetate formation was eliminated, and comparable amounts of pyruvate were formed instead. CO₂ formation by IK003.1 was more than doubled compared to the reference strain. Growth of IK003.1 was retarded, but the biomass yield of this strain was raised by 60%. IK003.1 serves as suitable host for oxidative biotransformations and for further metabolic engineering.

The Low Energy-Coupling Respiration in Zymomonas mobilis Accelerates Flux in the Entner-Doudoroff Pathway

Performing oxidative phosphorylation is the primary role of respiratory chain both in bacteria and eukaryotes. Yet, the branched respiratory chains of prokaryotes contain alternative, low energy-coupling electron pathways, which serve for functions other than oxidative ATP generation (like those of respiratory protection, adaptation to low-oxygen media, redox balancing, etc.), some of which are still poorly understood. We here demonstrate that withdrawal of reducing equivalents by the energetically uncoupled respiratory chain of the bacterium Zymomonas mobilis accelerates its fermentative catabolism, increasing the glucose consumption rate. This is in contrast to what has been observed in other respiring bacteria and yeast. This effect takes place after air is introduced to glucose-consuming anaerobic cell suspension, and can be simulated using a kinetic model of the Entner-Doudoroff pathway in combination with a simple net reaction of NADH oxidation that does not involve oxidative phosphorylation. Although aeration hampers batch growth of respiring Z. mobilis culture due to accumulation of toxic byproducts, nevertheless under non-growing conditions respiration is shown to confer an adaptive advantage for the wild type over the non-respiring Ndh knock-out mutant. If cells get occasional access to limited amount of glucose for short periods of time, the elevated glucose uptake rate selectively improves survival of the respiring Z. mobilis phenotype.

Reconstruction of a charge balanced genome-scale metabolic model to study the energy-uncoupled growth of Zymomonas mobilis ZM1

Zymomonas mobilisis an ethanologenic bacterium and is known to be an example microorganism with energy-uncoupled growth. The reconstructed metabolic model indicate that resistance to intracellular pH reduction could be the main reason for uncoupled growth.

Structure of the Zymomonas mobilis respiratory chain: oxygen affinity of electron transport and the role of cytochrome c peroxidase

The genome of the ethanol-producing bacterium Zymomonas mobilis encodes a bd-type terminal oxidase, cytochrome bc1 complex and several c-type cytochromes, yet lacks sequences homologous to any of the known bacterial cytochrome c oxidase genes. Recently, it was suggested that a putative respiratory cytochrome c peroxidase, receiving electrons from the cytochrome bc1 complex via cytochrome c552, might function as a peroxidase and/or an alternative oxidase. The present study was designed to test this hypothesis, by construction of a cytochrome c peroxidase mutant (Zm6-perC), and comparison of its properties with those of a mutant defective in the cytochrome b subunit of the bc1 complex (Zm6-cytB). Disruption of the cytochrome c peroxidase gene (ZZ60192) caused a decrease of the membrane NADH peroxidase activity, impaired the resistance of growing culture to exogenous hydrogen peroxide and hampered aerobic growth. However, this mutation did not affect the activity or oxygen affinity of the respiratory chain, or the kinetics of cytochrome d reduction. Furthermore, the peroxide resistance and membrane NADH peroxidase activity of strain Zm6-cytB had not decreased, but both the oxygen affinity of electron transport and the kinetics of cytochrome d reduction were affected. It is therefore concluded that the cytochrome c peroxidase does not terminate the cytochrome bc1 branch of Z. mobilis, and that it is functioning as a quinol peroxidase.

Discovery of ethanol-responsive small RNAs in Zymomonas mobilis

Zymomonas mobilis is a bacterium that can produce ethanol by fermentation. Due to its unique metabolism and efficient ethanol production, Z. mobilis has attracted special interest for biofuel energy applications; an important area of study is the regulation of those specific metabolic pathways. Small RNAs (sRNAs) have been studied as molecules that function as transcriptional regulators in response to cellular stresses. While sRNAs have been discovered in various organisms by computational prediction and experimental approaches, their discovery in Z. mobilis has not yet been reported. In this study, we have applied transcriptome analysis and computational predictions to facilitate identification and validation of 15 novel sRNAs in Z. mobilis. We furthermore characterized their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4, and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed, respectively. Importantly, when we tested the effect of ethanol stress on the expression of sRNAs in Z. mobilis, Zms2, Zms6, and Zms18 showed differential expression under 5% ethanol stress conditions. These data suggest that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.

The inefficient aerobic energetics of Zymomonas mobilis: identifying the bottleneck

To investigate the mechanisms of Zymomonas mobilis uncoupled aerobic metabolism, growth properties of the wild-type strain Zm6 were compared to those of its respiratory mutants cytB and cydB, and the effects of the ATPase inhibitor DCCD on growth and intracellular ATP concentration were studied. The effects of the ATPase inhibitor DCCD on growth and intracellular ATP concentration strongly indicated that the apparent lack of oxidative phosphorylation in aerobically growing Z. mobilis culture might be caused by the ATP hydrolyzing activity of the H(+) -dependent ATPase in all analyzed strains. Aerobic growth yields of the mutants, and their capacity of oxidative ATP synthesis with ethanol were closely similar, not supporting presence of one major, yet energetically inefficient electron transport branch causing the observed poor aerobic growth and lack of oxidative phosphorylation in Z. mobilis. We suggest that rapidly operating Entner-Doudoroff pathway generates too high phosphorylation potential for the weakly coupled respiratory system to shift the H(+) -dependent ATPase toward ATP synthesis.

Biotechnological potential of respiring Zymomonas mobilis: a stoichiometric analysis of its central metabolism

The active, yet energetically inefficient electron transport chain of the ethanologenic bacterium Zymomonas mobilis could be used in metabolic engineering for redox-balancing purposes during synthesis of certain products. Although several reconstructions of Z. mobilis metabolism have been published, important aspects of redox balance and aerobic catabolism have not previously been considered. Here, annotated genome sequences and metabolic reconstructions have been combined with existing biochemical evidence to yield a medium-scale model of Z. mobilis central metabolism in the form of COBRA Toolbox model files for flux balance analysis (FBA). The stoichiometric analysis presented here suggests the feasibility of several metabolic engineering strategies for obtaining high-value products, such as glycerate, succinate, and glutamate that would use the electron transport chain to oxidize the excess NAD(P)H, generated during synthesis of these metabolites. Oxidation of the excess NAD(P)H would also be needed for synthesis of ethanol from glycerol. Maximum product yields and the byproduct spectra have been estimated for each product, with glucose, xylose, or glycerol as the carbon substrates. These novel pathways represent targets for future metabolic engineering, as they would exploit both the rapid Entner-Doudoroff glycolysis, and the energetically uncoupled electron transport of Z. mobilis.

Electron transport and oxidative stress in Zymomonas mobilis respiratory mutants

The ethanol-producing bacterium Zymomonas mobilis is of great interest from a bioenergetic perspective because, although it has a very high respiratory capacity, the respiratory system does not appear to be primarily required for energy conservation. To investigate the regulation of respiratory genes and function of electron transport branches in Z. mobilis, several mutants of the common wild-type strain Zm6 (ATCC 29191) were constructed and analyzed. Mutant strains with a chloramphenicol-resistance determinant inserted in the genes encoding the cytochrome b subunit of the bc (1) complex (Zm6-cytB), subunit II of the cytochrome bd terminal oxidase (Zm6-cydB), and in the catalase gene (Zm6-kat) were constructed. The cytB and cydB mutants had low respiration capacity when cultivated anaerobically. Zm6-cydB lacked the cytochrome d absorbance at 630 nm, while Zm6-cytB had very low spectral signals of all cytochromes and low catalase activity. However, under aerobic growth conditions, the respiration capacity of the mutant cells was comparable to that of the parent strain. The catalase mutation did not affect aerobic growth, but rendered cells sensitive to hydrogen peroxide. Cytochrome c peroxidase activity could not be detected. An upregulation of several thiol-dependent oxidative stress-protective systems was observed in an aerobically growing ndh mutant deficient in type II NADH dehydrogenase (Zm6-ndh). It is concluded that the electron transport chain in Z. mobilis contains at least two electron pathways to oxygen and that one of its functions might be to prevent endogenous oxidative stress.

Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations

BACKGROUND

Zymomonas mobilis ZM4 (ZM4) produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. Z. mobilis performs best under anaerobic conditions, but is an aerotolerant organism. However, the genetic and physiological basis of ZM4's response to various stresses is understood poorly.

RESULTS

In this study, transcriptomic and metabolomic profiles for ZM4 aerobic and anaerobic fermentations were elucidated by microarray analysis and by high-performance liquid chromatography (HPLC), gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) analyses. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Greater amounts of other end-products such as acetate, lactate, and acetoin were detected under aerobic conditions and at 26 h there was only 1.7% of the amount of ethanol present aerobically as there was anaerobically. In the early exponential growth phase, significant differences in gene expression were not observed between aerobic and anaerobic conditions via microarray analysis. HPLC and GC analyses revealed minor differences in extracellular metabolite profiles at the corresponding early exponential phase time point. Differences in extracellular metabolite profiles between conditions became greater as the fermentations progressed. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 contained lower levels of amino acids such as alanine, valine and lysine, and other metabolites like lactate, ribitol, and 4-hydroxybutanoate under anaerobic conditions relative to aerobic conditions. Stationary phase microarray analysis revealed that 166 genes were significantly differentially expressed by more than two-fold. Transcripts for Entner-Doudoroff (ED) pathway genes (glk, zwf, pgl, pgk, and eno) and gene pdc, encoding a key enzyme leading to ethanol production, were at least 30-fold more abundant under anaerobic conditions in the stationary phase based on quantitative-PCR results. We also identified differentially expressed ZM4 genes predicted by The Institute for Genomic Research (TIGR) that were not predicted in the primary annotation.

CONCLUSION

High oxygen concentrations present during Z. mobilis fermentations negatively influence fermentation performance. The maximum specific growth rates were not dramatically different between aerobic and anaerobic conditions, yet oxygen did affect the physiology of the cells leading to the buildup of metabolic byproducts that ultimately led to greater differences in transcriptomic profiles in stationary phase.

NADH dehydrogenase deficiency results in low respiration rate and improved aerobic growth of Zymomonas mobilis

The respiratory chain of the ethanol-producing bacterium Zymomonas mobilis is able to oxidize both species of nicotinamide cofactors, NADH and NADPH. A mutant strain with a chloramphenicol-resistance determinant inserted in ndh (encoding an NADH : CoQ oxidoreductase of type II) lacked the membrane NADH and NADPH oxidase activities, while its respiratory D-lactate oxidase activity was increased. Cells of the mutant strain showed a very low respiration rate with glucose and no respiration with ethanol. The aerobic growth rate of the mutant was elevated; exponential growth persisted longer, resulting in higher biomass densities. For the parent strain a similar effect of aerobic growth stimulation was achieved previously in the presence of submillimolar cyanide concentrations. It is concluded (i) that the respiratory chain of Z. mobilis contains only one functional NAD(P)H dehydrogenase, product of the ndh gene, and (ii) that inhibition of respiration, whether resulting from a mutation or from inhibitor action, stimulates Z. mobilis aerobic growth due to redirection of the NADH flux from respiration to ethanol synthesis, thus minimizing accumulation of toxic intermediates by contributing to the reduction of acetaldehyde to ethanol.

Physiology of Zymomonas mobilis: some unanswered questions

The ethanol-producing bacterium Zymomonas mobilis can serve as a model organism for the study of rapid catabolism and inefficient energy conversion in bacteria. Some basic aspects of its physiology still remain poorly understood. Here, the energy-spilling pathways during uncoupled growth, the structure and function of electron transport chain, and the possible reasons for the inefficient oxidative phosphorylation are analysed. Also, the interaction between ethanol synthesis and respiration is considered. The search for mechanisms of futile transmembrane proton cycling, as well as identification of respiratory electron transport complexes, like the energy-coupling NAD(P)H:quinone oxidoreductase and the cyanide-sensitive terminal oxidase(s), are outlined as the key problems for further research of Z. mobilis energy metabolism.

High efficiency ethanol fermentation by entrapment of Zymomonas mobilis into LentiKatsR

AIMS

To examine the potential of Zymomonas mobilis entrapped into polyvinylalcohol (PVA) lens-shaped immobilizates in batch and continuous ethanol production.

METHODS AND RESULTS

Cells, free or immobilized in PVA hydrogel-based lens-shaped immobilizates - LentiKats, were cultivated on glucose medium in a 1 l bioreactor. In comparison with free cell cultivation, volumetric productivity of immobilized batch culture was nine times higher (43.6 g l(-1) h(-1)). The continuously operated system did not improve the efficiency (volumetric productivity of the immobilized cells 30.7 g l(-1) h(-1)).

CONCLUSIONS

We demonstrated Z. mobilis capability, entrapped into LentiKats, in the cost-efficient batch system of ethanol production.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results reported here emphasize the potential of bacteria in combination with suitable fermentation technology in industrial scale. The innovation compared with traditional systems is characterized by excellent long-term stability, high volumetric productivity and other technological advantages.

The paradoxical cyanide-stimulated respiration of Zymomonas mobilis: cyanide sensitivity of alcohol dehydrogenase (ADH II)

The respiratory inhibitor cyanide stimulates growth of the ethanologenic bacterium Zymomonas mobilis, perhaps by diverting reducing equivalents from respiration to ethanol synthesis, thereby minimizing accumulation of toxic acetaldehyde. This study sought to identify cyanide-sensitive components of respiration. In aerobically grown, permeabilized Z. mobilis cells, addition of 200 microM cyanide caused gradual inhibition of ADH II, the iron-containing alcohol dehydrogenase isoenzyme, which, in aerobic cultures, might be oxidizing ethanol and supplying NADH to the respiratory chain. In membrane preparations, NADH oxidase was inhibited more rapidly, but to a lesser extent, than ADH II. The time-course of inhibition of whole-cell respiration resembled that of NADH oxidase, yet the inhibition was almost complete, and was accompanied by an increase of intracellular NADH concentration. Cyanide did not significantly affect the activity of ADH I, the zinc-containing alcohol dehydrogenase isoenzyme. When an aerobic batch culture was grown in the presence of 200 microM cyanide, cyanide-resistant ADH II activity was observed, its appearance correlating with the onset of respiration. It is concluded that the membrane-associated respiratory chain, but not ADH II, is responsible for the whole-cell cyanide sensitivity, while the cyanide-resistant ADH II is needed for respiration in the presence of cyanide, and represents an adaptive response of Z. mobilis to cyanide, analogous to the induction of alternative terminal oxidases in other bacteria.

Ethanol cycle in an ethanologenic bacterium

A novel redox cycle is suggested, performing interconversion between acetaldehyde and ethanol in aerobically growing ethanologenic bacterium Zymomonas mobilis. It is formed by the two alcohol dehydrogenase (ADH) isoenzymes simultaneously catalyzing opposite reactions. ADH I is catalyzing acetaldehyde reduction. The local reactant ratio at its active site probably is shifted towards ethanol synthesis due to direct channeling of NADH from glycolysis. ADH II is oxidizing ethanol. The net result of the cycle operation is NADH shuttling from glycolysis to the membrane respiratory chain, and ensuring flexible distribution of reducing equivalents between the ADH reaction and respiration.

Cyanide inhibits respiration yet stimulates aerobic growth of Zymomonas mobilis

Potassium cyanide at submillimolar concentrations (20-500 microM) inhibited the high respiration rates of aerobic cultures of Zymomonas mobilis but, remarkably, stimulated culture growth. In batch culture, after an extended lag phase, exponential growth persisted longer, resulting in higher biomass densities. In aerobic chemostat cultures, elevated biomass concentration was observed in the presence of cyanide. This growth stimulation effect is attributed to decreased production of the inhibitory metabolite acetaldehyde at lowered respiration rates, when more reducing equivalents are channelled to alcohol dehydrogenase. Growth in the presence of cyanide did not alter the membrane cytochrome content. In non-growing cyanide-preincubated cells, with ethanol as the respiratory substrate, cyanide increased ATP levels; in such cells, a large part of the cyanide-sensitive respiration was inhibited within a few seconds after ethanol addition, while inhibition of the rest of respiration took several minutes. The more cyanide-sensitive respiration was apparently energy-nongenerating, and was absent in membrane preparations. Pelleting of membranes from cell-free extracts produced 'soluble' fractions in which a b-type haem was detectable by reduced minus oxidized difference spectroscopy. The function of the Z. mobilis respiratory chain in cell growth and respiratory protection, and the possible physiological role of aerobic generation of inhibitory metabolites, are discussed.

Exceptional characteristics of heterotetrameric (alpha 2 beta 2) E1p of the pyruvate dehydrogenase complex from Zymomonas mobilis: expression from an own promoter and a lipoyl domain in E1 beta

In the pyruvate dehydrogenase complex (PDHC) of Zymomonas mobilis the beta subunit of the pyruvate dehydrogenase (E1p) as well as the acetyltransferase (E2p) contain an N-terminal lipoyl domain. Both lipoyl domains were acetylated in vitro using 2-14C-pyruvate as a substrate, demonstrating that both lipoyl domains can accept acetyl groups from the E1 component. As previously shown the structural genes (pdhA alpha beta, pdhB, lpd) encoding the pyruvate dehydrogenase complex of Z. mobilis are located in two distinct gene clusters, pdhA alpha beta and pdhB-orf2-lpd (U. Neveling et al. (1998) J. Bacteriol. 180, 1540-1548). Analysis of pdh gene expression using lacZ fusions revealed that the DNA fragments upstream of pdhA alpha, pdhB and lpd each have promoter activities. These pdh promoter activities were 7-30-fold higher in Z. mobilis than in Escherichia coli.

Membrane D-lactate oxidase in Zymomonas mobilis: evidence for a branched respiratory chain

Respiratory chain composition of the ethanol-producing bacterium Zymomonas mobilis was studied. Its membrane D-lactate oxidase was characterised. With NADH, but not D-lactate as substrate, a cytochrome o-like component was seen in CO difference spectra. Chlorpromazine specifically inhibited reduction of cytochrome d, while myxothiazol eliminated the cytochrome o-like features in CO difference spectra. It is suggested that electrons from NADH are distributed between branches terminated by the cytochrome o-like component, cytochrome a, and cytochrome d. With D-lactate, electrons are transported to cytochrome a, or an unidentified CN(-)-sensitive oxidase, and cytochrome d.

Purification of the pyruvate dehydrogenase multienzyme complex of Zymomonas mobilis and identification and sequence analysis of the corresponding genes

The pyruvate dehydrogenase (PDH) complex of the gram-negative bacterium Zymomonas mobilis was purified to homogeneity. From 250 g of cells, we isolated 1 mg of PDH complex with a specific activity of 12.6 U/mg of protein. Analysis of subunit composition revealed a PDH (E1) consisting of the two subunits E1alpha (38 kDa) and E1beta (56 kDa), a dihydrolipoamide acetyltransferase (E2) of 48 kDa, and a lipoamide dehydrogenase (E3) of 50 kDa. The E2 core of the complex is arranged to form a pentagonal dodecahedron, as shown by electron microscopic images, resembling the quaternary structures of PDH complexes from gram-positive bacteria and eukaryotes. The PDH complex-encoding genes were identified by hybridization experiments and sequence analysis in two separate gene regions in the genome of Z. mobilis. The genes pdhAalpha (1,065 bp) and pdhAbeta (1,389 bp), encoding the E1alpha and E1beta subunits of the E1 component, were located downstream of the gene encoding enolase. The pdhB (1,323 bp) and lpd (1,401 bp) genes, encoding the E2 and E3 components, were identified in an unrelated gene region together with a 450-bp open reading frame (ORF) of unknown function in the order pdhB-ORF2-lpd. Highest similarities of the gene products of the pdhAalpha, pdhAbeta, and pdhB genes were found with the corresponding enzymes of Saccharomyces cerevisiae and other eukaryotes. Like the dihydrolipoamide acetyltransferases of S. cerevisiae and numerous other organisms, the product of the pdhB gene contains a single lipoyl domain. The E1beta subunit PDH was found to contain an amino-terminal lipoyl domain, a property which is unique among PDHs.

A novel aerobic respiratory chain-linked NADH oxidase system in Zymomonas mobilis

Membrane vesicles prepared from Zymomonas mobilis oxidized NADH exclusively, whereas deamino-NADH was little oxidized. In addition, the respiratory chain-linked NADH oxidase system exhibited only a single apparent Km value of approximately 66 microM for NADH. The NADH oxidase was highly sensitive to the respiratory chain inhibitor 2-heptyl-4-hydroxyquinoline-N-oxide. However, the NADH:quinone oxidoreductase was not sensitive to 2-heptyl-4-hydroxyquinoline-N-oxide and was highly resistant to another respiratory chain inhibitor, rotenone. Electron transfer from NADH to oxygen generated a proton electrochemical gradient (inside positive) in inside-out membrane vesicles. In contrast, electron transfer from NADH to ubiquinone-1 generated no electrochemical gradient. These findings indicate that Z. mobilis possesses only NADH:quinone oxidoreductase lacking the energy coupling site.

Isoprenoid biosynthesis in bacteria: two different pathways?

The biosynthesis of isopentenylpyrophosphate, a central intermediate of isoprenoid formation, was investigated in six different bacterial organisms. Cell-free extracts of Myxococcus fulvus, Staphylococcus carnosus, Lactobacillus plantarum and Halobacterium cutirubrum converted [14C]acetyl-CoA or [14C]hydroxymethylglutaryl-CoA to [14C]mevalonic acid. Furthermore, [14C]mevalonic acid, [14C]mevalonate-5-phosphate and [14C]mevalonate-5-pyrophosphate were metabolized to [14C]isopentenylpyrophosphate. These data demonstrated the in vitro operation of acetoacetate pathway for the formation of isopentenylpyrophosphate in bacteria. In contrast, no intermediates of this reaction sequence could be detected using cell-free extracts of Zymomonas mobilis and Escherichia coli. These results indicate that at least two different pathways for the biosynthesis of isopentenylpyrophosphate are present in bacteria.

Zymomonas mobilis--science and industrial application

Zymomonas mobilis is undoubtedly one of the most unique bacterium within the microbial world. Known since 1912 under the names Termobacterium mobilis, Pseudomonas linderi, and Zymomonas mobilis, reviews on its uniqueness have been published in 1977 and 1988. The bacterium Zymomonas mobilis not only exhibits an extraordinarily uniqueness in its biochemistry, but also in its growth behavior, energy production, and response to culture conditions, as well as cultivation techniques used. This uniqueness caused great interest in the scientific, biotechnological, and industrial worlds. Its ability to couple and uncouple energy production in favor of product formation, to respond to physical and chemical environment manipulation, as well as its restricted product formation, makes it an ideal microorganism for microbial process development. This review explores the advances made since 1987, together with new developments in the pure scientific and applied commercial areas.

Mechanism of glutamate uptake in Zymomonas mobilis

The energetics of the anaerobic gram-negative bacterium Zymomonas mobilis, a well-known ethanol-producing organism, is based solely on synthesis of 1 mol of ATP per mol of glucose by the Entner-Doudoroff pathway. When grown in the presence of glucose as a carbon and energy source, Z. mobilis had a cytosolic ATP content of 3.5 to 4 mM. Because of effective pH homeostasis, the components of the proton motive force strongly depended on the external pH. At pH 5.5, i.e., around the optimal pH for growth, the proton motive force was about -135 mV and was composed of a pH gradient of 0.6 pH units (internal pH 6.1) and a membrane potential of about -100 mV. Measurement of these parameters was complicated since ionophores and lipophilic probes were ineffective in this organism. So far, only glucose transport by facilitated diffusion is well characterized for Z. mobilis. We investigated a constitutive secondary glutamate uptake system. Glutamate can be used as a nitrogen source for Z. mobilis. Transport of glutamate at pH 5.5 shows a relatively high Vmax of 40 mumol.min-1.g (dry mass) of cells-1 and a low affinity (Km = 1.05 mM). Glutamate is taken up by a symport with two H+ ions, leading to substantial accumulation in the cytosol at low pH values.

Expression of an L-alanine dehydrogenase gene in Zymomonas mobilis and excretion of L-alanine

An approach to broaden the product range of the ethanologenic, gram-negative bacterium Zymomonas mobilis by means of genetic engineering is presented. Gene alaD for L-alanine dehydrogenase (EC 1.4.1.1.) from Bacillus sphaericus was cloned and introduced into Z. mobilis. Under the control of the strong promoter of the pyruvate decarboxylase (pdc) gene, the enzyme was expressed up to a specific activity of nearly 1 mu mol . min -1 . mg of protein -1 in recombinant cells. As a results of this high L-alanine dehydrogenase activity, growing cells excreted up to 10 mmol of alanine per 280 mmol of glucose utilized into a mineral salts medium. By the addition of 85 mM NH4+ to the medium, growth of the recombinant cells stopped, and up to 41 mmol alanine was secreted. As alanine dehydrogenase competed with pyruvate decarboxylase (PDC) (EC 4.1.1.1.) for the same substrate (pyruvate), PDC activity was reduced by starvation for the essential PDC cofactor thiamine PPi. A thiamine auxotrophy mutant of Z. mobilis which carried the alaD gene was starved for 40 h in glucose-supplemented mineral salts medium and then shifted to mineral salts medium with 85 mM NH4+ and 280 mmol of glucose. The recombinants excreted up to 84 mmol of alanine (7.5 g/liter) over 25 h. Alanine excretion proceeded at an initial velocity of 238 nmol . min-1 . mg [dry weight]-1. Despite this high activity, the excretion rate seemed to be a limiting factor, as the intracellular concentration of alanine was as high as 260 mM at the beginning of the excretion phase and decreased to 80 to 90 mM over 24 h.