Enzymological aspects of the pathways for trimethylamine oxidation and C1 assimilation of obligate methylotrophs and restricted facultative methylotrophs

Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

BACKGROUND

Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes.

RESULTS

In this effort, we first update a second-generation genome-scale metabolic model (iCth446) for C. thermocellum by correcting cofactor dependencies, restoring elemental and charge balances, and updating GAM and NGAM values to improve phenotype predictions. The iCth446 model is next used as a scaffold to develop a core kinetic model (k-ctherm118) of the C. thermocellum central metabolism using the Ensemble Modeling (EM) paradigm. Model parameterization is carried out by simultaneously imposing fermentation yield data in lactate, malate, acetate, and hydrogen production pathways for 19 measured metabolites spanning a library of 19 distinct single and multiple gene knockout mutants along with 18 intracellular metabolite concentration data for a Δgldh mutant and ten experimentally measured Michaelis-Menten kinetic parameters.

CONCLUSIONS

The k-ctherm118 model captures significant metabolic changes caused by (1) nitrogen limitation leading to increased yields for lactate, pyruvate, and amino acids, and (2) ethanol stress causing an increase in intracellular sugar phosphate concentrations (~1.5-fold) due to upregulation of cofactor pools. Robustness analysis of k-ctherm118 alludes to the presence of a secondary activity of ketol-acid reductoisomerase and possible regulation by valine and/or leucine pool levels. In addition, cross-validation and robustness analysis allude to missing elements in k-ctherm118 and suggest additional experiments to improve kinetic model prediction fidelity. Overall, the study quantitatively assesses the advantages of EM-based kinetic modeling towards improved prediction of C. thermocellum metabolism and develops a predictive kinetic model which can be used to design biofuel-overproducing strains.

An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme

The universal Per-ARNT-Sim (PAS) domain functions as a signal transduction module involved in sensing diverse stimuli such as small molecules, light, redox state and gases. The highly evolvable PAS scaffold can bind a broad range of ligands, including haem, flavins and metal ions. However, although these ligands can support catalytic activity, to our knowledge no enzymatic PAS domain has been found. Here we report characterization of the first PAS enzyme: a haem-dependent oxidative N-demethylase. Unrelated to other amine oxidases, this enzyme contains haem, flavin mononucleotide, 2Fe-2S and tetrahydrofolic acid cofactors, and specifically catalyses the NADPH-dependent oxidation of dimethylamine. The structure of the α subunit reveals that it is a haem-binding PAS domain, similar in structure to PAS gas sensors. The dimethylamine substrate forms part of a highly polarized oxygen-binding site, and directly assists oxygen activation by acting as both an electron and proton donor. Our data reveal that the ubiquitous PAS domain can make the transition from sensor to enzyme, suggesting that the PAS scaffold can support the development of artificial enzymes.

Metabolic methanol: molecular pathways and physiological roles

Methanol has been historically considered an exogenous product that leads only to pathological changes in the human body when consumed. However, in normal, healthy individuals, methanol and its short-lived oxidized product, formaldehyde, are naturally occurring compounds whose functions and origins have received limited attention. There are several sources of human physiological methanol. Fruits, vegetables, and alcoholic beverages are likely the main sources of exogenous methanol in the healthy human body. Metabolic methanol may occur as a result of fermentation by gut bacteria and metabolic processes involving S-adenosyl methionine. Regardless of its source, low levels of methanol in the body are maintained by physiological and metabolic clearance mechanisms. Although human blood contains small amounts of methanol and formaldehyde, the content of these molecules increases sharply after receiving even methanol-free ethanol, indicating an endogenous source of the metabolic methanol present at low levels in the blood regulated by a cluster of genes. Recent studies of the pathogenesis of neurological disorders indicate metabolic formaldehyde as a putative causative agent. The detection of increased formaldehyde content in the blood of both neurological patients and the elderly indicates the important role of genetic and biochemical mechanisms of maintaining low levels of methanol and formaldehyde.

Genomics of Methylotrophy in Gram-Positive Methylamine-Utilizing Bacteria

Gram-positive methylotrophic bacteria have been known for a long period of time, some serving as model organisms for characterizing the specific details of methylotrophy pathways/enzymes within this group. However, genome-based knowledge of methylotrophy within this group has been so far limited to a single species, Bacillus methanolicus (Firmicutes). The paucity of whole-genome data for Gram-positive methylotrophs limits our global understanding of methylotrophy within this group, including their roles in specific biogeochemical cycles, as well as their biotechnological potential. Here, we describe the isolation of seven novel strains of Gram-positive methylotrophs that include two strains of Bacillus and five representatives of Actinobacteria classified within two genera, Arthrobacter and Mycobacterium. We report whole-genome sequences for these isolates and present comparative analysis of the methylotrophy functional modules within these genomes. The genomic sequences of these seven novel organisms, all capable of growth on methylated amines, present an important reference dataset for understanding the genomic basis of methylotrophy in Gram-positive methylotrophic bacteria. This study is a major contribution to the field of methylotrophy, aimed at closing the gap in the genomic knowledge of methylotrophy within this diverse group of bacteria.

Methylotrophic autotrophy in Beijerinckia mobilis

Representatives of the genus Beijerinckia are known as heterotrophic, dinitrogen-fixing bacteria which utilize a wide range of multicarbon compounds. Here we show that at least one of the currently known species of this genus, i.e., Beijerinckia mobilis, is also capable of methylotrophic metabolism coupled with the ribulose bisphosphate (RuBP) pathway of C1 assimilation. A complete suite of dehydrogenases commonly involved in the sequential oxidation of methanol via formaldehyde and formate to CO2 was detected in cell extracts of B. mobilis grown on CH3OH. Carbon dioxide produced by oxidation of methanol was further assimilated via the RuBP pathway as evidenced by reasonably high activities of phosphoribulokinase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Detection and partial sequence analysis of genes encoding the large subunits of methanol dehydrogenase (mxaF) and form I RubisCO (cbbL) provided genotypic evidence for methylotrophic autotrophy in B. mobilis.

Formation of 3-hexuloses in aldol reactions, analysis of the products as their O-isopropylidene derivatives by GC–MS

A method for analysis of mixtures of 3-hexuloses by gas chromatography mass spectrometry of their di-O-isopropylidene derivatives has been elaborated. The origin of characteristic fragment ions in the mass spectra is suggested on the basis of the spectra of d(12) analogues, obtained by acetonation with acetone-d(6) and on MS/MS investigations. The method has been applied to product mixtures from aldol reactions between glycero-tetrulose and glycolaldehyde and between 2-pentuloses and formaldehyde. An interesting result is the formation of ribo-3-hexulose with a high degree of stereoselectivity in alkali catalysed reaction between erythro-2-pentulose and formaldehyde.

Synthesis of 3-hexuloses from 1,2:5,6-di-O-isopropylidenehexitols

A simple, but low-yielding method for the synthesis of 3-hexuloses has been elaborated. Oxidation of 1,2:5,6-di-O-isopropylidenehexitols with bromine in the presence of barium carbonate, followed by mild-acid hydrolysis of the oxidation products gave the free hexuloses. Oxidation occurred at only one of the carbon atoms bearing free hydroxyl groups. From the D-mannitol derivative, D-arabino-3-hexulose was obtained via the di-O-isopropylidene derivative, whereas the D-glucitol derivative gave a mixture of the 1,2:5,6-di-O-isoprpylidene derivatives of L-xylo- and D-ribo-3-hexulose, separable by column chromatography. Mild-acid hydrolysis of the oxidation products afforded the free hexuloses.

The primary structure of Hyphomicrobium X dimethylamine dehydrogenase. Relationship to trimethylamine dehydrogenase and implications for substrate recognition

The gene encoding dimethylamine dehydrogenase from Hyphomicrobium X has been cloned and over-expressed in Escherichia coli. Using the chemically determined protein sequence, primers were designed to amplify DNA fragments encoding the proximal and distal parts of the gene. These fragments were used to synthesise two probes and the dmd gene was cloned as part of two BamHI fragments isolated from digested genomic DNA. The sequence of the complete open reading frame was determined on both strands and contained 2211 bp coding for a protein of 736 amino acids, including the N-terminal methionine residue that is removed when expressed in the native host. The molecular mass of the processed apoprotein predicted from the DNA sequence is 82,523 Da. Dimethylamine dehydrogenase is closely related to the trimethylamine dehydrogenase of Methylophilus methylotrophus W3A1 (63.5% identical) and other class I FMN-binding beta 8 alpha 8 barrel flavoproteins. Residues in the active site of trimethylamine dehydrogenase that are known, or implicated, to be important in catalysis are conserved in dimethylamine dehydrogenase. Sequence alignment of dimethylamine and trimethylamine dehydrogenases suggests that the specificity for secondary and tertiary amines resides in a single amino acid substitution in a substrate-binding aromatic bowl located in the active site of the enzymes.

A biochemical study of the intermediary carbon metabolism of Shewanella putrefaciens

Cell extracts were used to determine the enzymes involved in the intermediary carbon metabolism of several strains of Shewanella putrefaciens. Enzymes of the Entner-Doudoroff pathway (6-phosphogluconate dehydratase and 2-keto-3-deoxy-6-phosphogluconate aldolase) were detected, but those of the Embden-Meyerhof-Parnas pathway were not. While several tricarboxylic acid cycle enzymes were present under both aerobic and anaerobic conditions, two key enzymes (2-oxoglutarate dehydrogenase and pyruvate dehydrogenase) were greatly diminished under anaerobic conditions. Extracts of cell grown anaerobically on formate as the sole source of carbon and energy were positive for hydroxypyruvate reductase, the key enzyme of the serine pathway in other methylotrophs, while no hexulose synthase activity was seen.

The Entner-Doudoroff pathway: history, physiology and molecular biology

The Entner-Doudoroff pathway is now known to be very widely distributed in nature. Biochemical and physiological studies show that the Entner-Doudoroff pathway can operate in a linear and catabolic mode, in a 'cyclic' mode, in a modified mode involving non-phosphorylated intermediates, or in alternative modes involving C1 metabolism and anabolism. Molecular and genetic analyses of the Entner-Doudoroff pathway in Zymomonas mobilis, Escherichia coli and Pseudomonas aeruginosa have led to an improved understanding of some fundamental aspects of metabolic controls. It can be argued that the Entner-Doudoroff pathway is more primitive than Embden-Meyerhof-Parnas glycolysis.

Oxidative and assimilative enzyme activities in continuous cultures of the obligate methylotroph Methylobacillus flagellatum

In methanol-limited continuous cultures of the obligate methylotrophic bacterium Methylobacillus flagellatum grown at rates from 0.05 to 0.63 h-1, and also in an oxyturbidostat culture of M. flagellatum growing at the rate of 0.73 h-1, levels of methanol dehydrogenase, enzymes of formaldehyde oxidation (both linear and cyclic) and assimilation (RuMP cycle), a number of intermediary metabolism and TCA cycle enzymes and also 'dye-linked' formaldehyde dehydrogenase were determined. It was shown that the activities of dissimilatory enzymes, with the exception of 'dye-linked' formaldehyde dehydrogenase, decreased with increasing growth rate. Activities of assimilative enzymes and activities of the TCA cycle enzymes detected as well as the 'dye-linked' formaldehyde dehydrogenase activity, increased with increasing growth rate. A periplasmic location was shown for the latter enzyme and a role in formaldehyde detoxification was proposed.

Inhibition by trimethylamine of methylamine oxidation by Paracoccus denitrificans and bacterium W3A1

Trimethylamine, a common substrate for methylotrophic growth, specifically inhibited methylamine-dependent respiration by Paracoccus denitrificans and bacterium W3A1. These effects were caused by the specific inhibition by trimethylamine of the periplasmic quinoprotein methylamine dehydrogenase. Steady-state kinetic analysis of the effect of trimethylamine on methylamine oxidation by methylamine dehydrogenase indicated that the inhibition was a mixed type. Apparent Ki values for trimethylamine of 1.1 mM and 4.7 mM, respectively, were obtained for the P. denitrificans and bacterium W3A1 enzymes. Methylamine-dependent oxygen consumption by each bacterium was inhibited either by preincubation of cells with trimethylamine prior to the addition of substrate or by addition of trimethylamine to actively respiring cells. Formate-dependent respiration was not inhibited by trimethylamine. A scheme is proposed which describes a regulatory role for trimethylamine in the metabolism and dissimilation of methylamine by methylotrophic bacteria.

Physiology and genetics of methylotrophic bacteria

Methylotrophic bacteria comprise a broad range of obligate aerobic microorganisms, which are able to proliferate on (a number of) compounds lacking carbon-carbon bonds. This contribution will essentially be limited to those organisms that are able to utilize methanol and will cover the physiological, biochemical and genetic aspects of this still diverse group of organisms. In recent years much progress has been made in the biochemical and genetic characterization of pathways and the knowledge of specific reactions involved in methanol catabolism. Only a few of the genetic loci hitherto found have been matched by biochemical experiments through the isolation or demonstration of specific gene products. Conversely, several factors have been identified by biochemical means and were shown to be involved in the methanol dehydrogenase reaction or subsequent electron transfer. For the majority of these components, their genetic loci are unknown. A comprehensive treatise on the regulation and molecular mechanism of methanol oxidation is therefore presented, followed by the data that have become available through the use of genetic analysis. The assemblage of methanol dehydrogenase enzyme, the role of pyrrolo-quinoline quinone, the involvement of accessory factors, the evident translocation of all these components to the periplasm and the dedicated link to the electron transport chain are now accepted and well studied phenomena in a few selected facultative methylotrophs. Metabolic regulation of gene expression, efficiency of energy conservation and the question whether universal rules apply to methylotrophs in general, have so far been given less attention. In order to expand these studies to less well known methylotrophic species initial results concerning such area as genetic mapping, the molecular characterization of specific genes and extrachromosomal genetics will also pass in review.

Nitrogen metabolism in the facultative methylotroph Arthrobacter P1 grown with various amines or ammonia as nitrogen sources

The metabolism of trimethylamine (TMA) and dimethylamine (DMA) in Arthrobacter P1 involved the enzymes TMA monooxygenase and trimethylamine-N-oxide (TMA-NO) demethylase, and DMA monooxygenase, respectively. The methylamine and formaldehyde produced were further metabolized via a primary amine oxidase and the ribulose monophosphate (RuMP) cycle. The amine oxidase showed activity with various aliphatic primary amines and benzylamine. The organism was able to use methylamine, ethylamine and propylamine as carbon- and nitrogen sources for growth. Butylamine and benzylamine only functioned as nitrogen sources. Growth on glucose with ethylamine, propylamine, butylamine and benzylamine resulted in accumulation of the respective aldehydes. In case of ethylamine and propylamine this was due to repression by glucose of the synthesis of the aldehyde dehydrogenase(s) required for their further metabolism. Growth on glucose/methylamine did not result in repression of the RuMP cycle enzyme hexulose-6-phosphate synthase (HPS). High levels of this enzyme were present in the cells and as a result formaldehyde did not accumulate. Ammonia assimilation in Arthrobacter P1 involved NADP-dependent glutamate dehydrogenase (GDH), NAD-dependent alanine dehydrogenase (ADH) and glutamine synthetase (GS) as key enzymes. In batch cultures both GDH and GS displayed highest levels during growth on acetate with methylamine as the nitrogen source. A further increase in the levels of GS, but not GDH, was observed under ammonia-limited growth conditions in continuous cultures with acetate or glucose as carbon sources.

[Regulation of PEP-carboxylase of the facultative methylotrop Acetobacter sp. MB 58]

Acetobacter sp. MB 58 assimilates methanol via the fructose-1,6-bisphosphate variant of the hexulose phosphate pathway. Glyceraldehyde-3-phosphate originates as net product of an assimilation loop involving the regeneration of the C1-acceptor ribulose-5-phosphate and must be available for the de novo synthesis of the C1-acceptor as well as for the oxidative glycolysis. It is made probable in a regulatory model that this is accomplished via alternating anabolic and catabolic phases which are controlled by concerted action of PEP-carboxylase and pyruvate kinase. Whereas Ac-CoA is a crucial effector and alpha-ketoglutarate and aspartate are inhibitors for the PEP-carboxylase, the pyruvate kinase is assumed to be regulated by energy charge.

Derivation of Aromatic Amino Acid Mutants from a Methanol-Utilizing Yeast, Hansenula polymorpha

Three classes of mutants, deregulated to enhance the flow of aromatic intermediates through the tryptophan biosynthetic branch, were obtained. 5-Fluorotryptophan, an antimetabolite of tryptophan, was employed to obtain one class of deregulated mutants. By sequential resistance development, three resistant mutants were isolated. Hansenula polymorpha strains showed greater sensitivity to 5-fluorotryptophan when growing on methanol than when growing on glucose. Yeast extract stimulated the production of total indole metabolites (indoles) by wild-type and mutant strains, with each 5-fluorotryptophan mutant producing higher amounts of these metabolites than its predecessor. Two other mutant classes were isolated: (i) a mutant resistant to anthranilate (an inhibitory intermediate in the tryptophan biosynthetic branch) and (ii) a phenylalanine-plus-tyrosine bradytroph. Each of these produced a higher extracellular titer of total indoles than its immediate parent. With respect to the overproduction of indoles, resistance to 5-fluorotryptophan was a more useful selection method than were anthranilate resistance and phenylalanine-plus-tyrosine bradytrophy.

Purification and properties of glucose-6-phosphate dehydrogenase (NADP+/NAD+) and 6-phosphogluconate dehydrogenase (NADP+/NAD+) from methanol-grown Pseudomonas C

Glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate:NADPH+ 1-oxidoreductase, EC 1.1.1.49) and 6-phosphogluconate dehydrogenase (6-phospho-D-gluconate:NADP+ 2-oxidoreductase, EC 1.1.1943) have been purified from methanol-grown Pseudomonas C. Glucose-6-phosphate dehydrogenase exhibits activity with either NADP+ or NAD+ as coenzymes, V NADP+ = 0.96 V NAD+.Km values of 22, 290, and 250 microns are obtained for NADP+, NAD+ and glucose 6-phosphate (NADP+ as the coenzyme), respectively. ATP inhibits Glc-6P dehydrogenase activity with NAD+ as coenzyme and to a less extent the activity with DANP+. In the presence of MgCl2, ATP inhibition of Blc-6P dehydrogeanse activity is abolished. 6-Phosphogluconate dehydrogenase has a dual specificity for both NADP+ or NAD+ as coenzymes, V NADP+ = 1.66 V NAD+.Km values of 20, 500 and 100 microns are obtained for NADP+, NAD+ and 6-phosphogluconate (NADP+ as the coenzyme), respectively. With NAD+ as the coenzyme ATP inhibits 6-phosphogluconate dehydrogeanse activity, while with NADP+ as the coenzyme, activity was less affected. The possible role of these enzymes in the metabolism of one-carbon (C1)-compounds in Pseudomonas C is discussed and compared with other methylotrophic microorganisms.

Properties of the methane mono-oxygenase from extracts of Methylosinus trichosporium OB3b and evidence for its similarity to the enzyme from Methylococcus capsulatus (Bath)

1. The methane mono-oxygenase from Methylosinus trichosporium OB3b was soluble. The only suitable electron donor was NAD(P)H, neither sodium L-ascorbate nor electrons derived from the oxidation of methanol could substitute for NAD(P)H. Evidence is presented for the existence of an NAD+-linked formaldehyde dehydrogenase. 2. Mono-oxygenase activity was not inhibited by a range of potential inhibitors including potassium cyanide, amytal, carbon monoxide or various metal-chelating agents, although 8-hydroxyquinoline and ethyne were effective in this respect. 3. Although the enzyme preparations were unstable on storage, the crude extract could be resolved into two components by ion-exchange chromatography. Activity could be restored to one of the components on addition of purified components from Methylococcus capsulatus (Bath). 4. Cross-reactivity of mono-oxygenase components and other similarities between the enzymes from M. trichosporium and M. capsulatus are discussed. The properties of the M. trichosporium methane mono-oxygenase reported here are contrasted with the properties of the same enzyme reported by others.

Purification and properties of glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase from a methanol-utilizing yeast, Candida boidinii

Glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate: NADP oxidoreductase, EC 1.1.1.49) and 6-phosphogluconate dehydrogenase (6-phospho-D-gluconate: NADP oxidoreductase, EC 1.1.1.44) were purified approx. 1700 fold and 330 fold, respectively, from Candida boidinii grown on methanol. The final enzyme preparations were homogeneous as judged by polyacrylamide gel electrophoresis. The molecular weights of the enzymes were estimated to be 118 000 and 110 000, respectively. Both enzymes are composed of two probably identical subunits and the molecular weights of the polypeptide chains were calculated to be 61 000 and 58 000, respectively. From a consideration of enzyme activities and types of inhibition by different metabolites the role of these two enzymes in glucose- and methanol-metabolism is discussed.

3-Hexulosephosphate synthase from Methylomonas aminofaciens 77a. Purification, properties and kinetics

3-Hexulosephosphate synthase (D-arabino-3-hexulose 6-phosphate formaldehyde lyase) was purified from an obligate methylotroph, Methylomonas aminofaciens, to homogeneity as judged by polyacrylamide gel electrophoresis and analytical ultracentrifugation. The molecular weight was determined to be 45 000-47 000 by sedimentation velocity and gel filtration. The enzyme appears to be composed of two identical subunits (Mr = 23 000). A bivalent cation is required for the activation and stabilization of the enzyme. The enzyme is specific for formaldehyde and D-ribulose 5-phosphate. The optimum pH is 8.0 (isoelectric point, pH 5.1) and the optimum temperature is 45 degrees C. Initial velocity studies are consistent with a sequential mechanism. The Michaelis constants are 0.29 mM for formaldehyde and 0.059 mM for D-ribulose 5-phosphate.