Catalytic triad of intracellular poly(3-hydroxybutyrate) depolymerase (PhaZ1) in Ralstonia eutropha H16

The amino acid sequence of an intracellular poly[D(-)-3-hydroxybutyrate] (PHB) depolymerase (PhaZ1) from Ralstonia eutropha H16 was compared with the sequences of various proteins using the BLAST search. It showed a number of matches including with intracellular PHB depolymerases, conserved hypothetical proteins, and PHB synthases. From an alignment of these proteins, we constructed nine mutants: C87A, S118A, H120Q, C183A, C183S, D355A, D356A, C370A, and H388Q. The C183A, D355A, and H388Q mutants lost their activities, but C183S and the other mutants did not. C183, D355, and H388 in PhaZ1 were positioned similarly to the amino acids of the catalytic triad of PHB synthase. These results indicated that C183, D355, and H388 make up the catalytic triad of PhaZ1.     

Cloning and sequence analysis of poly(tetramethylene succinate) depolymerase from Acidovorax delafieldii strain BS-3

A gene encoding poly(tetramethylene succinate), PBS, depolymerase, pbsA, has been cloned from Acidovorax delafieldii strain BS-3 chromosomal DNA. The clone expressed in Escherichia coli showed the ability to degrade both PBS and poly[(tetramethylene succinate)-co-adipate] that are kinds of biodegradable plastics. PBS depolymerase was considered to be a kind of lipase, since it also degrades olive oil. It had no apparent hydrophobic-amino-acid-rich region which exists in other known plastic-degrading enzymes. From the result of amino acid homology search, PbsA was found to have some similarities with lipases of Streptomyces sp. and Mollaxella sp. In the motif surrounding the active site Ser residue (Gly-X1-Ser-X2-Gly), PbsA was revealed to have a Trp residue in the X1 position instead of His which is most likely found in other bacterial lipases.     

Characterization of two 3-hydroxybutyrate dehydrogenases in poly(3-hydroxybutyrate)-degradable bacterium, Ralstonia pickettii T1

Two D-(-)-3-hydroxybutyrate (3HB) dehydrogenases, BDH1 and BDH2, were isolated and purified from a poly(3-hydroxybutyrate) (PHB)-degradable bacterium, Ralstonia pickettii T1. BDH1 activity increased in R. pickettii T1 cells grown on several organic acids as a carbon source but not on 3HB, whereas BDH2 activity markedly increased in the same cells grown on 3HB or PHB. To examine their biochemical properties, bdh1 and bdh2 were cloned and overexpressed in Escherichia coli, and their purified products were characterized. The kinetic parameters indicate that BDH1 is more suitable for converting acetoacetate to 3HB than BDH2, whereas BDH2 is more efficient for the reverse reaction than BDH1. Thus, R. pickettii T1 contains two BDHs with different biochemical properties and physiological roles: BDH1 for cell growth on organic acids other than 3HB and BDH2 for cell growth on 3HB or PHB.     

Cloning and sequence analysis of a gene (aly PG) encoding poly(alpha-L-guluronate)lyase from Corynebacterium sp. strain ALY-1

The aly PG gene, coding for a poly alpha-l-guluronate lyase (PG lyase) of Corynebacterium strain ALY-1, was cloned and sequenced. The gene consists of 768 bp encoding a signal peptide of 32 amino acids and a mature protein of 224 amino acids. Two disulfide bond cross-linkages were found to be formed between Cys-4 and Cys-51 and between Cys-200 and Cys-206 in the native PG lyase molecule. The deduced amino acid sequence of the Corynebacterium sp. aly PG gene exhibited 29% homology toward that of the Klebsiella pneumoniae, subsp. aerogenes aly A gene, with two conserved regions (the amino acid sequences from Y-102 to M-110 and from Y-221 to Q-229).     

吸水链霉菌valG基因的克隆与表达

为提高井冈霉素A的产量,本实验尝试构建吸水链霉菌的多拷贝基因菌株.根据吸水链霉菌（Streptomyces hygroscopicus subsp.jinggangensis）的糖基转移酶基因（valG）序列设计了1对引物.PCR扩增编码糖基转移酶（ValG）的1269 bp基因后,利用TA克隆构建克隆质粒pMD-19-valG.测序正确后经双酶切构建穿梭质粒pIJ8630-valG.再次测序验证后,经质粒DNA转化吸水链霉菌感受态细胞将pIJ8630-valG导入吸水链霉菌中.PCR检测证实重组菌构建成功.HPLC检测发酵产物,发现井冈霉素A的产量达到了1.17 mg/mL,比出发菌株提高了11.2％,valG基因得到表达,为进一步利用valG构建新的高产菌株奠定了基础.     

Cloning and heterologous expression of the Candida albicans gene PMI 1 encoding phosphomannose isomerase

Using a DNA fragment derived from the Saccharomyces cerevisiae phosphomannose isomerase (PMI) structural gene as a probe against a random ordered array library of genomic DNA from the pathogenic fungus Candida albicans, we have cloned the C. albicans PMI 1 gene. This gene, which is unique in the C. albicans genome, can functionally complement PMI-deficient mutants of both S. cerevisiae and Escherichia coli. The DNA sequence of the PMI 1 gene predicts a protein with 64·1% identity to PMI from S. cerevisiae. Sequential gene disruption of PMI 1 produces a strain with an auxotrophic requirement for D-mannose. The heterologous expression of the PMI 1 gene at levels up to 45% of total cell protein in E. coli leads to partitioning of the enzyme between the soluble and particulate fractions. The protein produced in the soluble fraction is indistinguishable in kinetic properties from the material isolated from C. albicans cells. The nucleotide sequence data reported here will appear in the EMBL database under Accession Number X82024.     

Regulating the molar fraction of 4-hydroxybutyrate in poly(3-hydroxybutyrate-4-hydroxybutyrate) biosynthesis by Ralstonia eutropha using propionate as a stimulator

The regulation of the molar fraction of 4-hydroxybutyrate (4-HB) in the poly(3-hydroxybutyrate-4-hydroxybutyrate) [P(3HB-4HB)] biosynthesis by Ralstonia eutropha (formerly Alcaligenes eutrophus) was attempted by the supplemental addition of propionate. The molar fraction of 4-HB in P(3HB-4HB) was increased significantly from 12.3 to 51.8 mol% by the addition of a small amount of propionate along with gamma-butyrolactone commonly used as a precursor for the biosynthesis of P(3HB-4HB). The mechanism of regulation by propionate was investigated by measuring the variation of enzyme activities related to the biosynthesis of P(3HB-4HB) and the level of intermediate metabolite acetyl-CoA. PHB synthase activity was induced significantly by propionate, and the acetyl-CoA concentration also increased significantly due to the additional supply of propionate. The overflowing acetyl-CoA seems to cause an inhibitory effect on the ketolysis reaction catalysing the lysis of 4-hydroxybutyryl-CoA to two molecules of acetyl-CoA; consequently, the 4-HB fraction available for polymerization increased. Accordingly, the molar fraction of 4-HB in P(3HB-4HB) biosynthesis seems to be regulated by both an increased 4-HB fraction and an activated PHB synthase due to the supplemental addition of propionate as a stimulator.     

Improvement of poly(3-hydroxybutyrate) [P(3HB)] production in Corynebacterium glutamicum by codon optimization, point mutation and gene dosage of P(3HB) biosynthetic genes

In our previous study, a system for producing poly(3-hydroxybutyrate) [P(3HB)] was established by introducing a polyhydroxyalkanoate (PHA) biosynthetic gene operon (phaCAB Re) derived from Ralstonia eutropha into Corynebacterium glutamicum. In this study, two experimental strategies have been applied to improve P(3HB) production in recombinant C. glutamicum. One is a codon optimization of the N-terminal-coding region of the PHA synthase (PhaC Re) gene focusing on the codon usage preference for the translation system of C. glutamicum. The other is the replacement of wild-type phaC Re with a modified gene encoding a mutation of Gly4Asp (G4D), which enhanced the production of PhaC Re and P(3HB) in Escherichia coli. The introduction of these engineered PHA synthase genes into C. glutamicum enhanced the production of PhaC(Re) and P(3HB). Interestingly, we found that these gene modifications also caused increases in the concentration of the translation products of the genes encoding monomer-supplying enzymes, beta-ketothiolase (PhaA Re) and acetoacetyl-CoA reductase (PhaB Re). This finding prompted us to carry out a gene dosage of phaAB Re for a double plasmid system, and the highest production (52.5 wt%) of P(3HB) was finally achieved by combining the gene dosage of phaAB Re with codon optimization. The molecular weight of P(3HB) was also increased by approximately 2-fold, as was P(3HB) content. Microscopic observation revealed that the volume of the cells accumulating P(3HB) was increased by more than 4-fold compared with the non-P(3HB)-accumulating cells without filamentous morphologenesis observed in E. coli.     

Cloning and secretive expression of the gene encoding the proteinaceous alpha-amylase inhibitor paim from Streptomyces corchorusii

A gene encoding the proteinaceous alpha-amylase inhibitor Paim was cloned and sequenced. Southern analysis and the amino acid sequence deduced from the cloned gene indicated that Paim isoforms were encoded in the same gene. When the gene was expressed in Escherichia coli and Streptomyces lividans, recombinant Paim inhibitors were produced in the periplasmic space and in the culture supernatant, respectively. The purified inhibitors had different N-terminal sequences from those of the authentic inhibitors.     

Production and characterization of biodegradable terpolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) by Alcaligenes sp. A-04

The production of the terpolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate), P(3HB-co-3HV-co-4HB), by Alcaligenes sp. A-04 was investigated to determine the superior biodegradable polymer properties over those of poly(3-hydroxybutyrate), P(3HB), and its copolymers. The highest terpolymer content of 68% (w/w) was produced by Alcaligenes sp. A-04 at 60 h by shake-flask cultivation. The terpolymer with 93 mol% 4HB mole fraction units was produced when the cultivation time was extended to 96 h. Moreover, it was found that Alcaligenes sp. A-04 could utilize 1,4-butanediol for the synthesis of 3HB and 4HB monomers as well as the sodium salt of 4-hydroxybutyrate. The terpolymer content was 30% (w/w) and the composition was P(33%3HB-co-16%3HV-co-51%4HB). Next, terpolymers with 4HB mole fraction units ranging from 50 to 90 mol% were produced by varying the medium composition and cultivation time. The thermal and mechanical properties of the resulting terpolymers were different from those of the copolymers with a similar mole fraction of monomer units. The terpolymer P(4%3HB-co-3%3HV-co-93%4HB) showed an elongation of 430%, a toughness of 33 MPa, and Young's modulus of 127 MPa similar to those of low-density polyethylene. The terpolymer P(11%3HB-co-34%3HV-co-55%4HB) showed Young's Modulus of 618 MPa similar to that of polypropylene.     

Enzymatic synthesis of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) with CoA recycling using polyhydroxyalkanoate synthase and acyl-CoA synthetase

We succeeded in developing a novel method for in vitro poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3 HB-co-4 HB)] synthesis with CoA recycling using polyhydroxyalkanoate synthase and an acyl-CoA synthetase. Using this method, the monomer compositions in P(3 HB-co-4 HB)s could be controlled strictly by the ratios of the monomers in the reaction mixtures.     

Cloning, sequence analysis, and expression in Escherichia coli of gene encoding N-Benzyl-3-pyrrolidinol dehydrogenase from Geotrichum capitatum

The gene encoding N-benzyl-3-pyrrolidinol dehydrogenase (DDBJ/EMBL/GenBank accession no. AB294179), a useful biocatalyst for producing (S)-N-benzyl-3-pyrrolidinol, was cloned from the genomic DNA of Geotrichum capitatum JCM 3908. The gene contained an open reading frame consisting of 1023 nucleotides corresponding to 340 amino acid residues. The subunit molecular weight was calculated to be 39,000. The predicted amino acid sequence did not have significant similarity to those of N-benzyl-3-pyrrolidinone reductases reported previously. From 30 mM N-benzyl-3-pyrrolidinone, (S)-N-benzyl-3-pyrrolidinol was obtained with a yield >99.9% and an enantiomeric excess >99.9% in 1-h and 2-h reactions without NADH addition by the resting cells of Escherichia coli HB 101 strains harboring the expression plasmids pSG-POBS and pSF-POBS that possess the glucose dehydrogenase gene and formate dehydrogenase gene as an NADH-reproducing system, respectively, besides the N-benzyl-3-pyrrolidinol dehydrogenase gene. N-Benzyl-3-pyrrolidinol dehydrogenase activity (0.56 U/mg) was observed in E. coli (pSG-POBS), which was 17-fold the specific activity observed in G. capitatum JCM 3908.     

Fermentative production of (R)-(-)-3-hydroxybutyrate using 3-hydroxybutyrate dehydrogenase null mutant of Ralstonia eutropha and recombinant Escherichia coli

Two systems, one using an (R)-(-)-3-hydroxybutyrate dehydrogenase (BDH) null mutant of Ralstonia eutropha and the other using a recombinant Escherichia coli strain containing a synthetic poly[(R)-(-)-3-hydroxybutyrate] (PHB) operon and an extracellular PHB depolymerase gene, were used for the fermentative production of (R)-(-)-3-hydroxybutyrate (3HB). The concentration of 3HB in the culture supernatant of the mutant R. eutropha system reached about 30 mM after 5 d under anaerobic conditions, although it was about 4-10 mM under aerobic conditions. On the other hand, the 3HB concentration in the culture supernatant of the recombinant E. coli system reached about 70 mM after 4 d, indicating that about 70% of the glucose added was converted to 3HB.     

牛凝乳酶基因的克隆与表达

为了获得大量高纯度高活性的凝乳酶制剂,采用基因工程方法,从犊牛皱胃黏膜细胞中克隆得到凝乳酶基因,然后将此基因插入原核表达载体pTWIN1中,使之与几丁质结合域(CBD)-内含肽(intein)融合,从而获得原核表达质粒:pTWIN1/EchybF2.经转化大肠杆菌BL21(DE3)后,在IPTG诱导下进行凝乳酶的表达.SDS-PAGE电泳分析和酶活性实验结果显示,CBD-intein-EchybF2融合蛋白在BL21(DE3)中获得高效表达,在低温诱导时主要以可溶性蛋白的形式存在,并具有凝乳活性.     

Cloning and expression of the gene encoding the thermophilic NAD(P)H-FMN oxidoreductase coupling with the desulfurization enzymes from Paenibacillus sp. A11-2

The gene encoding the NAD(P)H-flavin oxidoreductase (flavin reductase) which couples with the thermophilic dibenzothiophene (DBT)-desulfurizing monooxygenases of Paenibacillus sp. A11-2 was cloned in Escherichia coli and designated tdsD. Nucleotide sequence analysis suggested that the gene product consisted of 200 amino acids and showed about 30%, 27% and 26% amino acid sequence similarity to the major flavin reductase of Vibrio fischeri, the NADH dehydrogenase of Thermus thermophilus and several oxygen-insensitive NAD(P)H nitroreductases in the Enterobacteriaceae family, respectively. Both the growing and resting recombinant E. coli, in which tdsD was coexpressed with a set of desulfurizing genes, showed a rate of DBT removal about 5 times higher than the recombinants lacking tdsD. Maximal desulfurization was observed close to 45 degrees C and 55 degrees C in the resting cells and in the cell-free extraction reaction with the tdsD-coexpressing recombinants, respectively. In an organic/aqueous biphasic system, the coexpression of tdsD also markedly enhanced the rate of DBT removal.     

Taxonomic characterization and metabolic analysis of the Halomonas sp. KM-1, a highly bioplastic poly(3-hydroxybutyrate)-producing bacterium

In a brief previous report, the gram-negative moderately halophilic bacterium, Halomonas sp. KM-1, that was isolated in our laboratory was shown to produce the bioplastic, poly(3-hydroxybutyrate) (PHB), using biodiesel waste glycerol (Kawata and Aiba, Biosci. Biotechnol. Biochem., 74, 175-177, 2010). Here, we further characterized this KM-1 strain and compared it to other Halomonas strains. Strain KM-1 was subjected to a polyphasic taxonomic study. Strain KM-1 was rod-shaped and formed colonies on a plate that were cream-beige in color, smooth, opaque, and circular with entire edges. KM-1 grew under environmental conditions of 0.1%-10% (w/v) NaCl, pH 6.5-10.5 and at temperatures between 10°C and 45°C. The G+C content of strain KM-1 was 63.9 mol%. Of the 16 Halomonas strains examined in this study, the strain KM-1 exhibited the highest production of PHB (63.6%, w/v) in SOT medium supplemented with 10% glycerol, 10.0 g/L sodium nitrate and 2.0 g/L dipotassium hydrogen phosphate. The intracellular structures within which PHB accumulated had the appearance of intracellular granules with a diameter of approximately 0.5 μm, as assessed by electron microscopy. The intra- and extra-cellular metabolites of strain KM-1 were analyzed by capillary electrophoresis mass spectrometry. In spite of the high amount of PHB stored intra-cellularly, as possible precursors for PHB only a small quantity of 3-hydroxybutyric acid and acetyl CoA, and no quantity of 3-hydroxybutyl CoA, acetoacetyl CoA and acetoacetate were detected either intra- or extra-cellularly, suggesting highly efficient conversion of these precursors to PHB.     

Cloning and characterization of the lactate-specific inducible gene KlCYB2, encoding the cytochrome b(2) of Kluyveromyces lactis

In yeast the utilization of lactate requires two enzymes, the D and L-lactate ferricytochrome c oxidoreductase (D and L-LCR), which stereospecifically oxidize D- and L-lactate to pyruvate. These enzymes are nuclearly encoded and localized in mitochondria. In the yeast Kluyveromyces lactis, a mutant devoid of D- and L-LCR activities and unable to grow on racemic lactate was isolated. Transformation of the mutant with a K. lactis genomic library allowed the isolation of the KlCYB2 gene, restoring the growth on lactate and the L-LCR activity. The KlCYB2 gene and its flanking regions were sequenced (Accession No. AJ243324; EMBL/GenBank databases). The deduced amino acid sequence is highly homologous to the corresponding Saccharomyces cerevisiae and Hansenula anomala protein sequences previously characterized. The homology is missed in the N-terminal region, corresponding to the presequence cleaved during import into mitochondria. Analysis of KlCYB2 gene expression indicated that, in contrast to S. cerevisiae, the major regulatory feature is induction by lactate.     

微生物酯酶催化合成(R)-3-羟基丁酸乙酯

光学纯3-羟基丁酸乙酯(EHB)是重要有机中间体,可用以制备多种手性药物.以实验室保藏的巨大芽孢杆菌WZ009催化不对称水解反应合成光学纯(R)-3-EHB.考察了温度,pH,底物浓度、茵体添加量和拆分时间等因素对酶促反应的影响.确定最佳工艺条件为:温度T=30℃,pH=7.0,底物浓度为1％(质量体积比),茵体添加量为0.25 g/10 mL.在该条件下,反应2h后,转化率为55.5％,(R)-3-EHB e.e.s值达到99％以上,E值能达到66.巨大芽孢杆菌WZ009细胞具有较好的操作稳定性,可重复批次使用.该酶法制备(R)-3-EHB工艺具有良好的工业应用前景.     

Cloning, targeted disruption and heterologous expression of the Kluyveromyces marxianus endopolygalacturonase gene (EPG1)

The yeast Kluyveromyces marxianus strain BKM Y-719 produces an efficient pectin-degrading endopolygalacturonase (EPG) that cleaves the internal alpha-1,4-D-glycosidic linkages to yield oligomers of varying sizes. The EPG1 gene encoding this industrially important EPG was cloned by using the polymerase chain reaction (PCR) technique and degenerate primers to generate a 135 bp DNA fragment with which a genomic library was screened. The cloned fragment contained an open reading frame (ORF) of 1083 bp, encoding a 361 amino acid polypeptide. The predicted amino acid (aa) sequence of EPG showed similarity with polygalacturonases (PGs) of fungi. Analysis of the aa sequence indicated that the first 25 aa constitute a signal sequence and a motif (C218XGGHGXSIGSVG230) that is usually associated with a PG active site. Pulsed-field gel electrophoresis resolved chromosomal bands for K. marxianus BKM Y-719 and using chromoblotting it seems that EPG1 is present as only a single copy in the genome.