Isolation and characterization of Bacillus sp. INT005 accumulating polyhydroxyalkanoate (PHA) from gas field soil

A gram-positive bacterium (designated strain INT005) that accumulated polyhydroxyalkanoate (PHA) was isolated from gas field soil. From its morphological and physiological properties and the partial nucleotide sequence (about 500 bp) of its 16S rDNA, it was suggested that strain INT005 was similar to several species of the genus Bacillus. We confirmed that strain INT005 is a Bacillus sp. The PHA productivities of strain INT005 were higher than those of Bacillus megaterium and Ralstonia eutropha at 37-45 degrees C reported to date, and it was suggested that the PHA synthase of INT005 may exhibit moderate thermostability. The bacterium had the ability to produce poly(3-hydroxybutyrate), poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3-hydroxybutyrate-co-3-hydroxyhexanoate), poly(3-hydroxybutyrate-co-4-hydroxybutyrate-co-3-hydroxyhexanoate), and poly(3-hydroxybutyrate-co-6-hydroxyhexanoate-co-3-hydroxyhexanoate) from the appropriate carbon sources. The PHA synthase from INT005 showed similar substrate specificity to those of class I and III PHA synthases and strain INT005 produced PHAs with various monomer compositions. From the analysis of monomer composition and PHA accumulation in the presence of acrylic acid, it was suggested that de novo fatty acid synthesis and beta-oxidation are involved in the PHA synthesis of Bacillus sp. INT005. Since Bacillus sp. INT005 could synthesize PHA even at 45 degrees C and PHAs with various monomer compositions, and only one report on the cloning of the synthesis-related genes from a Bacillus species (B. megaterium) has been published;Bacillus sp. INT005 is thought to be very valuable source of PHA synthesis-related genes.     

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.     

Precise control of repeating unit composition in biodegradable poly(3-hydroxyalkanoate) polymers synthesized by Escherichia coli

The composition of medium-chain-length (MCL) poly(3-hydroxyalkanoate) (PHA) biopolymers is normally an uncontrollable random mixture of repeating units with differing side chain lengths. Attempts to generate MCL PHA homopolymers and control repeating unit composition have been published in native PHA-producing organisms but have limited ranges for the different sizes of repeating units that can be synthesized. In this study, a new Escherichia coli-based system that exhibits control over repeating unit composition for both MCL PHAs and short-chain-length (SCL) PHAs has been developed, covering an unprecedented range of repeating units. The fadB and fadJ genes from the β-oxidation pathway were eliminated from the chromosome of E. coli LS5218. The subsequent blockage in β-oxidation caused a buildup of enoyl-CoA intermediates, which were converted to PHAs by an (R)-specific enoyl-CoA hydratase (PhaJ4) and PHA synthase [PhaC1(STQK)] expressed from a plasmid DNA construct. Fatty acid substrates were converted to PHAs with repeating units equal in the number of carbon atoms to the fatty acid substrate. The broad substrate specificities of the PhaJ4 and PhaC1(STQK) enzymes allowed for the production of homopolymers with strict control over the repeating unit composition from substrates of four to twelve carbons in length. Polymers were purified and analyzed by GC, GC-MS, and NMR for structural composition and by DSC, TGA, and GPC for thermal and physical characteristics. This study marks the development of the first single biological system to achieve consistent repeating unit control over such a broad range of repeating units in PHAs.     

Improved polyhydroxybutyrate (PHB) production in transgenic tobacco by enhancing translation efficiency of bacterial PHB biosynthetic genes

Polyhydroxybutyrate [P(3HB)] was produced in the transgenic tobacco harboring the genes encoding acetoacetyl-CoA reductase (PhaB) and polyhydroxyalkanoate synthase (PhaC) from Ralstonia eutropha (Cupriavidus necator) with optimized codon usage for expression in tobacco. P(3HB) contents in the transformants (0.2mg/g dry cell weight in average) harboring the codon-optimized phaB gene was twofold higher than the control transformants harboring the wild-type phaB gene. The immunodetection revealed an increased production of PhaB in leaves, indicating that the enhanced expression of PhaB was effective to increase P(3HB) production in tobacco. In contrast, codon-optimization of the phaC gene exhibited no apparent effect on P(3HB) production. This result suggests that the efficiency of PhaB-catalyzed reaction contributed to the flux toward P(3HB) biosynthesis in tobacco leaves.     

Purification, characterization and gene cloning of thermostable O-acetyl-L-homoserine sulfhydrylase forming gamma-cyano-alpha-aminobutyric acid

A thermophilic and cyanide ion-tolerant bacterium, Bacillus stearothermophilus CN3 isolated from a hot spring in Japan, was found to produce thermostable gamma-cyano-alpha-aminobutyric acid synthase. The enzyme was purified and characterized. The purified enzyme has a molecular mass of approximately 180 kDa and consists of four identical subunits. It was stable in the pH range of 6.0 to 10.5 and up to 60 degrees C. The enzyme catalyzed the gamma-replacement reaction of O-acetyl-L-homo-serine with cyanide ions. The gene encoding the gamma-cyano-alpha-aminobutyric acid synthase was isolated from B. stearothermophilus CN3. Sequence homology analysis revealed that the gamma-cyano-alpha-aminobutyric acid synthase from the bacterium is O-acetyl-L-homoserine sulfhydrylase. A recombinant plasmid, constructed by ligation of the cloned gene and an expression vector, was introduced into Escherichia coli JM109. The transformed E. coli cells overexpressed gamma-cyano-alpha-aminobutyric acid synthase. The heat stable gamma-cyano-alpha-aminobutyric acid synthase can be applied to the synthesis of [5-11C]L-glutamic acid used as a tracer for positron emission tomography.     

Enzyme-catalyzed poly(3-hydroxybutyrate) synthesis from acetate with CoA recycling and NADPH regeneration in Vitro

We established a novel enzyme-catalyzed poly(3-hydroxybutyrate) [P(3HB)] synthesis system capable of recycling CoA on the basis of the P(3HB) biosynthetic pathway in Ralstonia eutropha. The system includes purified beta-ketothiolase (PhaA), NADPH-dependent acetoacetyl-CoA reductase (PhaB), PHA synthase (PhaC), acetyl-CoA synthetase (Acs) and glucose dehydrogenase (GDH). In this system, acetyl-CoA was synthesized from acetate and CoA by Acs and ATP, and then two molecules of acetyl-CoA were condensed by PhaA to synthesize acetoacetyl-CoA, which was converted to (R)-3-hydroxybutyryl-CoA (3HBCoA) by PhaB and NADPH. The 3HBCoA was polymerized by PhaC and converted to P(3HB). In this system, the CoA molecules that were released during the condensation and polymerization reactions catalyzed by PhaA and PhaC, respectively, were reused successfully for the synthesis of acetyl-CoA. In addition, NADPH, which was consumed in the reduction of acetoacetyl-CoA, was regenerated by the action of GDH. In this system, the yield of P(3HB) synthesized from acetate as the substrate was 5.6 mg in a 5-ml reaction mixture, and the weight-average molecular weight and polydispersity were 6.64 x 10(6) and 1.36, respectively. Furthermore, CoA was reused at least 26 times, and NADPH was also regenerated at least 26 times during 24 h of reaction.     

Purification, characterization and gene cloning of thermostable O-acetyl-L-serine sulfhydrylase forming beta-cyano-L-alanine

A thermophilic and cyanide ion-tolerant bacterium, Bacillus stearothermophilus CN3 isolated from a hot spring in Japan, was found to produce thermostable beta-cyano-L-alanine synthase. The enzyme catalyzes the synthesis of beta-cyano-L-alanine from O-acetyl-L-serine and cyanide ions. The purified enzyme has a molecular mass of approximately 70 kDa and consists of two identical subunits. It was stable in the pH range of 6.0 to 10.0 and up to 70 degrees C. The enzyme also catalyzes the synthesis of various beta-substituted-L-alanine derivatives from O-acetyl-L-serine and nucleophilic reagents. The gene encoding the beta-cyano-L-alanine synthase was isolated from B. stearothermophilus CN3. Sequence homology analysis revealed that the beta-cyano-L-alanine synthase of the bacterium is O-acetyl-L-serine sulfhydrylase. A recombinant plasmid, constructed by ligation of the cloned gene and an expression vector, pKK223-3, was introduced into E. coli JM109. The transformed E. coli cells overexpressed beta-cyano-L-alanine synthase. Heat stable beta-cyano-L-alanine synthase can be applied to the synthesis of [4-11C]l-2,4-diaminobutyric acid as a tracer for positron emission tomography.     

检测产志贺毒素大肠杆菌的菌落PCR方法

针对产志贺毒素大肠杆菌的毒力基因stx 设计特异性引物,并建立一种菌落PCR 方法。菌落PCR 模拟实验证实,该方法特异性强,能良好的扩增出O157 的stx1 和stx2 基因,而普通大肠杆菌、蜡样芽孢杆菌、金黄色葡萄球菌则无PCR 扩增产物。应用分子检测初筛、选择性培养、菌落PCR 相结合的方法,检测实际食品样品,分离检测到一株携带 stx1 的产志贺毒素大肠杆菌。本实验建立的菌落PCR 方法可应用于食品检验。     

Poly[(R)-3-hydroxybutyrate] formation in Escherichia coli from glucose through an enoyl-CoA hydratase-mediated pathway

In this study, a new metabolic pathway for the synthesis of poly[(R)-3-hydroxybutyrate] [P(3HB)] was constructed in a recombinant Escherichia coli strain that utilized forward and reverse reactions catalyzed by two substrate-specific enoyl-CoA hydratases, R-hydratase (PhaJ) and S-hydratase (FadB), to epimerize (S)-3HB-CoA to (R)-3HB-CoA via a crotonyl-CoA intermediate. The R-hydratase gene (phaJ(Ac)) from Aeromonas caviae was coexpressed with the PHA synthase gene (phaC(Re)) and 3-ketothiolase gene (phaA(Re)) from Ralstonia eutropha in fadR mutant E. coli strains (CAG18497 and LS5218), which had constitutive levels of the beta-oxidation multienzyme FadB(Ec). When grown on glucose as the sole carbon source, the cells accumulated P(3HB) up to an amount 6.5 wt% of the dry cell weight, whereas the control cells without phaJ(Ac) or fadR mutation accumulated significantly smaller amounts of P(3HB). These results suggest that PhaJ(Ac) and FadB(Ec) played an important role in supplying monomers for P(3HB) synthesis in the pathway. Furthermore, by using this pathway, a P(3HB)-concentration-dependent fluorescent staining screening technique was developed to rapidly identify cells that possess active R-hydratase.     

中度嗜盐菌Bacillus sp.XJ1-05 α-淀粉酶基因的克隆和原核表达

本实验室从新疆盐湖分离得到一株产α-淀粉酶中度嗜盐菌Bacillus sp.XJ1-05,根据已报道的α-淀粉酶基因(α-AMY)序列的保守区域设计引物,从中度嗜盐菌Bacillus sp.XJ1-05基因组中扩增出α-淀粉酶基因片段,将α-淀粉酶基因纯化后克隆到pGM-T载体上测序,结果表明α-淀粉酶基因片段长约1500bp,与地衣芽孢杆菌Bacillus licheniformis的α-淀粉酶基因序列的同源性为95%,两种序列具有一定的同源性。按正确的阅读框架将α-淀粉酶基因片段定向克隆到表达载体pET-32a上,将重组质粒转化到大肠杆菌BL21(DE3)菌株,经IPTG诱导表达,SDS-PAGE电泳表明,α-淀粉酶基因能在大肠杆菌BL21中成功表达,确定表达蛋白的相对分子量为61kD左右,与理论推导的分子量相一致;构建的大肠杆菌工程菌,所产生的α-淀粉酶是包涵体,通过超声波粉碎仪粉碎后,测α-淀粉酶酶活为原菌的1.8倍。     

坛装黄酒贮存过程中污染微生物的分离鉴定

该研究对坛装贮存黄酒关键污染微生物进行分离纯化和鉴定。利用梯度稀释法和划线纯化法得到编号为B001、B002、B003的3株细菌和编号为F004、F005、F006的3株真菌。通过形态学特征观察、生理生化鉴定和分子生物学鉴定方法对分离菌株进行鉴定。结果表明,细菌B001、B002、B003分别为解淀粉芽孢杆菌（Bacillus amyloliquefaciens）、铜绿假单胞菌（Pseudomonas aeruginosa）和假肠膜明串珠菌（Leuconostoc pseudomesenteroides）,真菌F004、F005、F006分别为头状螺旋地霉（Saprochaete capitate）、爪哇正青霉（Eupenicillium javanicum）及红曲菌（Monascus sp.）。     

Cloning of alanine racemase genes from Pseudomonas fluorescens strains and oligomerization states of gene products expressed in Escherichia coli

Bacterial alanine racemase (EC 5.1.1.1) is a pyridoxal 5'-phosphate-dependent enzyme. Almost all eubacteria known to date possess a biosynthetic alr gene and some bacteria have an additional catabolic dadX gene. On the basis of the subunit structure, alanine racemases are classified into two types, monomeric and homodimeric. Alanine racemase genes were cloned from two distinct Pseudomonas fluorescens strains, the psychrotrophic TM5-2 strain and the soil-borne LRB3W1 strain, by means of complementing an Escherichia coli alanine racemase-deficient mutant. From the cloning results, both strains are likely to possess only one alanine racemase gene, dadX, in the same manner as the other P. fluorescens strains. Gene organization surrounding the dadX gene is highly conserved among Pseudomonas strains. The gene for D-amino acid dehydrogenase is located adjacent to the dadX gene in both strains. The DadX alanine racemases were expressed in E. coli as C-terminal His-tagged fusion proteins and purified to homogeneity. The catalytic activity of LRB3W1 DadX was higher than that of TM5-2 DadX. The association states of P. fluorescens DadX subunits in the E. coli alanine racemase-deficient mutant were analyzed by gel filtration chromatography. Alanine racemase subunits were demonstrated to exist as both monomers and dimers. The enzyme was in a monomer-dimer equilibrium, and the catalytic activity of the enzyme was proportional to the equilibrium association constant for dimerization.     

芽孢杆菌发酵液的抑菌活性及葡聚糖酶的基因克隆、表达分析

通过液培法和菌丝生长速率法,探究茯苓粉培养基（ABP培养基）诱导芽孢杆菌CmRh1产葡聚糖酶的发酵上清液对苹果炭疽病菌的抑制作用;采用PCR技术克隆葡聚糖内切酶基因,异源表达并初步验证其功能;采用在线生物信息学对芽孢杆菌葡聚糖酶的理化性质、信号肽、跨膜区、保守结构域、二级和三级结构、亚细胞定位等进行预测。结果表明：茯苓粉培养基（ABP培养基）诱导的芽孢杆菌CmRh1发酵上清液对苹果炭疽病菌具有一定的抑菌效果,抑菌率分别为16.07%和14.03%;从芽孢杆菌CmRh1菌株克隆到1个葡聚糖内切酶基因（Glu4）,开放阅读框（Open Reading Frame,ORF）为1500 bp,编码499 aa。生物信息学预测,Glu4是1个含有信号肽和1个跨膜结构域稳定的亲水性蛋白质,其分子量约为55 kDa,理论等电点为7.14;保守结构域预测,Glu4属于GH5型纤维素酶家族;二级结构元件主要包括α螺旋、延伸链、β转角和无规则卷曲,三级结构为典型的β-三明治结构,符合葡聚糖内切酶的结构特征;Glu4亚细胞定位于细胞外,是一个典型的分泌蛋白。SDSPAGE结合Western blot结果显示...     

Antibacterial activity of Bacillus amyloliquefaciens phage endolysin without holin conjugation

To characterize the enzymatic activity and antibacterial activity of endolysin encoded by a Bacillus amyloliquefaciens phage, the open reading frame encoding endolysin was amplified by PCR and cloned into the expression plasmid pET21d(+). The resultant plasmid was used to transform Escherichia coli JM109(DE3). Production of endolysin in the cytosol facilitated cell lysis without coproduction of holin, which is considered to degrade or alter the cytoplasmic membrane. The phage endolysin was overexpressed and purified. Although the specific activity of the purified phage endolysin towards lyophilized Micrococcus luteus cells was 1/11 of the activity of chicken egg white lysozymes, the endolysin showed stronger antibacterial activity towards E. coli W3110, E. coli JM109(DE3) and Pseudomonas aeruginosa PAO1 than chicken egg white lysozymes. The antibacterial activity of the endolysin towards these three bacterial strains was marked when EDTA was added to the endolysin solution.     

Production and purification of a bacteriocin peptide produced by Lactococcus sp. strain GM005, isolated from Miso-paste

Lactococcus sp. GM005 was isolated from Miso-paste and was found to produce a bacteriocin with strong antibacterial activity. A culture of Lactococcus sp. GM005, maintained at 30 degrees C and a constant pH of 6.0, exhibited bacteriocin activity eightfold higher than that of a culture grown under pH-uncontrolled conditions. GM005 bacteriocin was purified to homogeneity on SDS-PAGE by hydrophobic column chromatography and gel filtration. The estimated molecular weight of GM005 bacteriocin was approximately 9.6 kDa based on gel-filtration analysis, and was approximately 2.4 kDa based on tricine-SDS-PAGE analysis, indicating a tetrametric structure. N-terminal amino acid analysis revealed that the N-terminal end was blocked. Amino acid composition analysis revealed a high proportion of hydrophobic amino acid residues and lanthionine. This differs from the composition of some antibiotics. GM005 bacteriocin exhibits a bactericidal activity against Lactobacillus sakei JCM1157T.     

大肠杆菌苹果酸脱氢酶基因mdh的克隆、高效表达及酶学性质

以大肠杆菌基因组DNA为模板,扩增得到苹果酸脱氢酶(mdh)编码基因mdh,构建了重组菌pET-28a-mdh/BL21并成功表达了mdh,大小约36 000。选用Ni柱亲和层析法纯化具有活性的苹果酸脱氢酶(mdh),纯化后比酶活达到112.5 U/mg,纯化倍数达2.62倍,回收率为59%。并对该酶的酶学性质进行了初步研究,其中反应最适pH值为6.0,在pH值2.0~6.0范围内稳定;反应最适温度为37℃,在42℃以下酶的稳定性较好。K+对酶有明显的激活作用,Cu2+对酶有抑制作用,Hg2+和Zn2+对酶有很强的抑制作用。醇类对酶的活力影响不大,丙三醇可显著提高酶的热稳定性。酶动力学参数以草酰乙酸为底物的Km为0.235 mmol/L,Vmax为0.47μmol/(L.min)。     

Development and validation of an HPLC-based screening method to acquire polyhydroxyalkanoate synthase mutants with altered substrate specificity

A rapid and convenient method for the compositional analysis of polyhydroxyalkanoate (PHA) was developed using high-performance liquid chromatography (HPLC) and alkaline sample pretreatment in a 96-well plate format. The reliability of this system was confirmed by the fact that a mutant with a D171G mutation of Aeromonas caviae PHA synthase (PhaC(Ac)), which gained higher reactivity toward 3-hydroxyhexanoate (3HHx), was selected from the D171X mutant library. Together with D171G mutant, several single mutants showing high reactivity toward 3HHx were isolated by the HPLC assay. These new mutants and double mutants combined with an N149S mutation were used to synthesize P(3-hydroxybutyrate-co-3HHx) in Ralstonia eutropha PHB(-)4 from soybean oil as carbon source, achieving higher levels of 3HHx fraction than the wild-type enzyme. Based on these results, the high-throughput screening system will serve as a powerful tool for exploring new and beneficial mutations responsible for regulating copolymer composition of PHA.     

农用抗生素高产菌株的筛选分离及诱变育种

该实验分离得到4株产农用抗生素菌株,编号1#～4#。 以厚垣镰孢霉（Fusarium chlamydosporum）、枯草芽孢杆菌（Bacillus subtilis）、大肠杆菌（Escherichia coli）、金黄色葡萄球菌（Staphylococcus aureus）作为指示菌,测定其发酵液的抑菌活性,并对抑菌 活性菌株进行诱变育种。 结果表明,菌株1#对枯草芽孢杆菌（B. subtilis）和金黄色葡萄球菌（S. aureus）抑菌圈直径＞10 mm,抑菌 活性较好。 采用紫外诱变、重金属激活沉默基因复活诱变两种方法诱变菌株1#后,对厚垣镰孢霉、枯草芽孢杆菌、大肠杆菌、金黄 色葡萄球菌抑菌作用分别增加了25.68%、32.11%、34.85%、28.28%。 形态学观察及生理生化实验结果初步鉴定菌株1#为链霉菌属（Streptomyces sp.）。     

大肠杆菌中表达Cry1C基因及其重组表达产物的纯化及复性

通过PCR方法将苏云金芽孢杆菌Cry1C基因从原始质粒中克隆出来。由于Cry1C基因携带了大量大肠杆菌稀有密码子,因此用PCR方法对其前86个密码子进行修改,以提高其在大肠杆菌BL21(DE3)中的表达量。Cry1C蛋白在大肠杆菌BL21(DE3)中以包涵体形式大量表达,将包涵体用8mol/L尿素溶解并用His TrapTM FF凝胶柱纯化。所得纯化蛋白在复性缓冲液中复性折叠,最终得到可溶并有生物活性(由三化螟活性实验验证)的蛋白。Cry1C蛋白纯度可达99.2%。     

密苏里游动放线菌葡萄糖异构酶基因xylA的克隆及其表达条件的优化

为克隆、表达密苏里游动放线菌葡萄糖异构酶(GI)基因xylA,并对其诱导表达条件进行初步优化。采用Slowdown PCR方法克隆得到密苏里游动放线菌(Actinoplanes missouriensis)CICIM B0118(A)的葡萄糖异构酶基因xylA,构建pET-28a(+)-xylA 表达载体,并转化至E. coli BL21 (DE3),经异丙基-β -D- 硫代半乳糖苷(IPTG)诱导表达,并对其表达产物进行SDS-PAGE 电泳。结果表明,融合蛋白分子质量约为45kD。在诱导时间9h、0.6mmol/L IPTG、30℃和OD600nm 值为0.8 的最适培养条件下,酶比活力最高达到62.42U/mL。