Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production.

Klebsiella oxytoca is an important microorganism for nitrogen fixation and chemical production. Here, we report an annotated draft genome of K. oxytoca strain M5al that contains 5,256 protein-coding genes and 95 structural RNAs, which provides a genetic basis for a better understanding of the physiology of this species.

Recombinant glutamine synthetase (GS) from C. glutamicum existed as both hexamers & dedocamers and C-terminal His-tag enhanced inclusion bodies formation in E. coli.

In order to investigate the effect of his-tag on glutamine synthetase (GS, EC 6.3.1.2) from Corynebacterium glutamicum, recombinant Escherichia coli strains overexpressing GSIM, HGSIM (GS fused with N-terminal his-tag), GSIMH (GS fused with C-terminal his-tag), and HGSIMH (GS fused with N-terminal & C-terminal his-tags) were constructed, respectively. Under similar expression conditions, GSIM and HGSIM were partially solubly expressed; no soluble GSIMH and HGSIMH were observed, based on the result of SDS-PAGE. Gel filtration of purified soluble HGSIM showed that hexamers and dedocamers coexisted in the quaternary structure of GS from C. glutamicum. Combined this result with the analysis of two GS crystal structure models, we hypothesized that C-terminal residues participated in GS folding after translation on ribosome. After the folding process, C-terminal residues were released again and exposed to solvent. Fused C-terminal his-tag interrupted the GS to fold into its correct conformation so that inclusion bodies formed.

Characterization of glycerol dehydratase expressed by fusing its alpha- and beta-subunits.

The gdh and gdhr genes, encoding B(12)-dependent glycerol dehydratase (GDH) and glycerol dehydratase reactivase (GDHR), respectively, in Klebsiella pneumoniae, were cloned and expressed in E. coli. Part of the beta-subunit was lost during GDH purification when co-expressing alpha, beta and gamma subunit. This was overcome by fusing the beta-subunit to alpha- or gamma-subunit with/without the insertion of a linker peptide between the fusion moieties. The kinetic properties of the fusion enzymes were characterized and compared with wild type enzyme. The results demonstrated that the fusion protein GDHALB/C, constructed by linking the N-terminal of beta-subunit to the C-terminal of alpha subunit through a (Gly(4)Ser)(4) linker peptide, had the greatest catalytic activity. Similar to the wild-type enzyme, GDHALB/C underwent mechanism-based inactivation by glycerol during catalysis and could be reactivated by GDHR.

Introduction of an NADH regeneration system into Klebsiella oxytoca leads to an enhanced oxidative and reductive metabolism of glycerol.

Redox cofactors play crucial roles in the metabolic and regulatory network of living organisms. We reported here the effect of introducing a heterogeneous NADH regeneration system into Klebsiella oxytoca on cell growth and glycerol metabolism. Expression of fdh gene from Candida boidinii in K. oxytoca resulted in higher intracellular concentrations of both NADH and NAD(+) during the fermentation metaphase, with the ratio of NADH to NAD(+) unaltered and cell growth unaffected, interestingly different from that in engineered Escherichia coli, Lactococcus lactis, and others. Metabolic flux analysis revealed that fluxes to 1,3-propanediol, ethanol, and lactate were all increased, suggesting both the oxidative and reductive metabolisms of glycerol were enhanced. It demonstrates that in certain microbial system NADH availability can be increased with NADH to NAD(+) ratio unaltered, providing a new strategy to improve the metabolic flux in those microorganisms where glycolysis is not the only central metabolic pathways.

Novel redox potential-based screening strategy for rapid isolation of Klebsiella pneumoniae mutants with enhanced 1,3-propanediol-producing capability.

This report describes a novel redox potential (oxidoreduction potential [ORP])-based screening strategy for the isolation of mutants of Klebsiella pneumoniae which have an increased ability to produce 1,3-propanediol (1,3-PD). This method can be described as follows: first, to determine an ORP range which is preferred for the wild-type strain to grow and to produce 1,3-PD; second, to subject a chemically mutagenized culture to a reduced ORP level which is deleterious for the wild-type strain. Colonies that showed high specific growth rates at deleterious ORP levels were selected, and their abilities to produce 1,3-PD were investigated. In an ORP-based screening experiment where the ORP was controlled at -280 mV, 4 out of 11 isolated strains were recognized as positive mutant strains. A mutant which is capable of producing higher concentrations of 1,3-PD was subjected to fed-batch fermentations for further characterization. Its preferred ORP level (-280 mV) was significantly lower than that of its parent (-190 mV). The highest 1,3-PD concentration of the mutant was 915 mmol liter(-1), which was 63.1% higher than that of the parent. Metabolic-flux analysis suggested that the intracellular reductive branch of the mutant was strengthened, which improved 1,3-PD biosynthesis. The procedure and results presented here provide a novel method of screening for strains with improved product formation.

[Expression and characterization of formate dehydrogenase gene in Klebisella pneumoniae].

Glycerol can be converted to 1,3-propanediol by the anaerobic fermentation of Klebsiella pneumoniae, during which reducing equivalent NADH was consumed. Therefore, the availability of NADH would be critical for the yield of 1, 3-propanediol. In this paper, formate/formate dehydrogenase system was used for the regeneration of in vivo NADH and the improvement of 1, 3-propanediol production. Formate Dehydrogenase gene (fdh) was amplified from Candida boidinii genome by PCR and the purified PCR product was inserted into the vector pMD18-T Simple to construct plasmid pMD18-T Simple-fdh, which was transformed into Escherichia coli DH5alpha and recombinants were selected by blue-white selection. From the transformant the fdh gene was separated and inserted into pMALTM-p2X to construct expression vector pMAL-p2X-fdh, which was transformed into Klebsiella pneumoniae YMU2 and a recombinant strain Klebsiella pneumoniae F-l was obtained. The plasmid stability of strain F-l and the conditions of fdh expression induced by IPTG were studied. It was demonstrated that the plasmid had good stability, and 0.5mmol/L IPTG would induce the expression of protein encoded by fdh gene with the molecular weight of 40.2kDa. The enzyme activity reached 5.47U/mg crude protein when K. pneumoniae F-I was induced for 4h by 0.5mmol/L IPTG. Compared with that of the parent strain K. pneumoniae YMU2, the yield of 1,3-propanediol of recombinant strain F-1 increased by 12.5% in the anaeribic bioreactor.

Inactivation of aldehyde dehydrogenase: a key factor for engineering 1,3-propanediol production by Klebsiella pneumoniae.

Production of 1,3-propanediol (1,3-PD) from glycerol by Klebsiella pneumoniae is restrained by ethanol formation. The first step in the formation of ethanol from acetyl-CoA is catalyzed by aldehyde dehydrogenase (ALDH), an enzyme that competes with 1,3-PD oxidoreductase for the cofactor NADH. This study aimed to improve the production of 1,3-PD by engineering the ethanol formation pathway. An inactivation mutation of the aldA gene encoding ALDH in K. pneumoniae YMU2 was generated by insertion of a tetracycline resistance marker. Inactivation of ALDH resulted in a nearly abolished ethanol formation but a significantly improved 1,3-PD production. Metabolic flux analysis revealed that a pronounced redistribution of intracellular metabolic flux occurred. The final titer, the productivity of 1,3-PD and the yield of 1,3-PD relative to glycerol of the mutant strain reached 927.6 mmol L(-1), 14.05 mmol L(-1)h(-1) and 0.699 mol mol(-1), respectively, which were much higher than those of the parent strain. In addition, the specific 1,3-PD-producing capability (1,3-PD produced per gram of cells) of the mutant strain was 2-fold that of the parent strain due to a lower growth yield of the mutant. By increasing NADH availability, this study demonstrates an important metabolic engineering approach to improve the efficiency of oxidoreduction-coupled bioprocesses.

[Effects of carnitine acetyltransferase gene knockout on long chain dicarboxylic acid production and metabolism of Candida tropicalis].

Candida tropicalis can assimilate n-alkane as a sole carbon source and produce dicarboxylic acids (DCAs). The synthesis of DCAs is thought to be reduced by beta-oxidation. Carnitine acetyltransferase (CAT) is the major enzyme to transfer DCAs into beta-oxidative pathway, then DCAs would be catalyzed to generate ATP to supply cells with energy. A homologous recombination plasmid was constructed, in which CAT gene was disrupted by inserting hygromycin B resistance gene. This plasmid was used to transform Candida tropicalis wild type strain F10-1, and one single CAT gene knockout strain was obtained. Comparing with the wild type, the recombinant increased DCA13 yield and molar conversion of alkane by 13.0% and 11.8%, respectively, and decreased unnecessary consumption of DCAs in beta-oxidation.

[Measurement of intracellular pH in long-chain dicarboxylic acid-producing yeast Candida tropicalis and its growth activity].

Intracellular pH (pHi) has an important influence on the metabolic activity of cells or cellular processes. The intracellular pH (pHi) of long-chain alpha,omega-dicarboxylic acid-producing Candida tropicalis was determined by fluorescence technique using a pH-sensitive fluorescent probe 5(6)-carboxyfluorescein diacetate. Optimal loading conditions of the fluorescent probe into the cells were experimentally determined. Effects of extracellular pH and carbon sources for growth on pHi in the cell grown in a flask were studied; the results indicated that extracellular pH has a slight influence on pHi, whereas carbon sources such as sucrose, glucose, acetic acid, and n-tridecane showed moderate influences. Further work on the relationship between the cell growth activity and pHi was carried out in a 5 L bioreactor. The time course of specific rates of the cell growth, glucose consumption, CO2 production, and pH gradients across cell plasma membrane were plotted, where the cell growth was improved by the higher pHi at 8 - 12 h. The measured pHi values were varied from 5.72 to 6.15 at medium pH 6.0 in which glucose and sodium acetate were used together as carbon source. The investigation of pHi can be helpful for understanding its effects on the kinetics of the metabolic steps involved in the synthesis rate of alpha,omega-dicarboxylic acid and alpha,omega-dicarboxylic acid transport across plasma membranes.

Intracellular pH and metabolic activity of long-chain dicarylic acid-producing yeast Candida tropicalis.

The intracellular pH (pH(i) of alpha-omega-dicarylic acid producing Candida tropicalis was determined by a fluorescence technique using the pH-sensitive fluorescent probe 5(6)-carboxyfluorescein diacetate. Fermentations with n-tridecane substrate to produce alpha,omega-tridecanedioic acid were carried out in a 5-l bioreactor in which growth and production were separated. During the growth phase, the measured pH(i) values were varied from 5.65 to 6.15 in all the experiments performed under different constant pH-operating conditions. The specific rates of growth, sucrose consumption, CO2 production, and O2 consumption were correlated with pH(i). Cytochrome P450 monooxygenase (P450), which catalyzes n-alkane hydroxylation, was only slightly expressed during the growth phase. During the first 6 h of the production phase, P450 activity was induced rapidly accompanying higher pH(i). A much higher level of P450 activity was observed at pH(i) of 6.55+/-0.15 for all the fermentations, with maximum productivity (1.919 g/l/h) occurring when using an optimal pH-control strategy. However, P450 activity, tridecanedioic acid productivity, and pH(i) decreased progressively during the latter part of the production phase, as a consequence of the metabolic activity changes of the cells. Even though culture pH has only a slight influence on pH(i), the metabolic activity of C. tropicalis is sensitive to the variations in pH(i). The measured pH(i) varied from 6.1 to 6.7 during the production phase for all the fermentations. Thus, both tridecanedioic acid productivity and P450 activity are correlated with pH(i) or pH gradients across the cell membrane.

[Effects of H2O2 addition on cell growth and product formation in long-chain dicarboxylic acid fermentation].

When Candida tropicalis was cultivated in shakig-flask with the H2O2 addition, DCA (Dicarboxylic Acid, DCA) concentration was increased, especially at 2 mmol/L H2O2 concentration. The cytochrome P450 activity assays indicated that H2O2 addition significantly increased the activities of cytochrome P450 and DCA production positively correlated with the activities of cytochrome P450. The study on the cell growth demonstrated that the H2O2 addition inhibited the cell growth rate. However, the retarding effect was not irreversible since the cell growth rate could recover slowly to the original level after the H2O2 addition was halted. The mechanism of inducement on cytochrome P450 by H2O2 addition was also discussed in this article.

Isolation and enzyme determination of Candida tropicalis mutants for DCA production.

Techniques, named two-step enrichment and double-time replica-plating method (TEDR), are described that allow a mutated population of Candida tropicalis to be enriched efficiently for mutants deficient in the alkane degradation pathway (Alk(-)) and to be selected easily for mutants increasing in the DCA (dicarboxylic acids) excretion pathway. After C. tropicalis was mutated with ethyl methane sulphonate and ultraviolet, the Alk(-) mutants were enriched (the first step enrichment, up to eightfold in one round of enrichment) by treatment with nystatin in medium SEL1-1. The mutagen-treated cells were then cultured in medium YPD containing chlorpromazine for further enriching (the second-step enrichment, up to threefold in one round) the mutants with an increasing capacity of alpha- and omega-oxidation. On the other hand, the Alk(-) mutants were readily isolated by the SEL1 replica-plating method by using alkane or glucose as the sole carbon source. A total of 43 Alk(-) mutants were isolated from 2x10(8) mutagen-treated cells. In the following steps, by using SEL2 replica plating, the screening studies showed that of the 43 Alk(-) mutants, 11 strains could accumulate DCA greatly from alkane, and strains 1-12 and 1-3, especially, could produce nearly three times as much DCA as the wild-type organism could. The results showed that the strains had more cytochrome P450 activity and a higher converting capacity of alkane.