Molecular cloning and nucleotide sequencing of organophosphorus insecticide hydrolase gene from Arthrobacter sp. strain B-5

The organophosphorus insecticide hydrolase (OPH) gene of Arthrobacter sp. strain B-5, isolated from turf green soil was cloned into Escherichia coli JM109. Three clones, termed EpB511, EpB521 and EpB531, exhibiting OPH activity were obtained. However, these three clones showed lower OP-degrading ability than strain B-5. A 7.7-kb inserted fragment of the plasmid pB521 harbored by EpB521 was subcloned, resulting in construction of a plasmid, pB526, carrying the 2.6-kb inserted fragment with OP-degrading ability. In this sequence, an open reading frame (ORF) that encodes a 43,607 Da polypeptide composed of 415 amino acids was identified. The N-terminal amino acid sequence deduced from the nucleotide sequence was identical to that of purified OPHs. The deduced amino acid sequence was compared with the sequences in the data bank and a 58.1% amino acid identity was found with the aryldialkylphosphatase from Nocardia sp. strain B-1, an enzyme that possesses catalytic functions similar to OPH.     

Cloning and expression of the N-acetylmuramidase gene from Streptomyces rutgersensis H-46

The N-acetylmuramidase SR1 gene from Streptomyces rutgersensis H-46 was cloned in Escherichia coli JM109 and expressed in E. coli BL21(DE3)pLysS. An open reading frame included the leader peptide region encoding a polypeptide of 65 amino acid residues and the mature SR1 enzyme region encoding a polypeptide of 209 amino acid residues. The overall G + C content of the mature enzyme gene was 67.6%, with 98.1% of G or C in the third position of the codons. The calculated molecular weight of the mature enzyme was 23,057 Da. The amino acid sequence of the mature enzyme showed a significant level of identity with bacteriolytic enzymes from Streptomyces globisporus (50.9% identity), Chalaropsis species (40.2% identity) and Saccharopolyspora erythraea (31.0% identity). The mature enzyme gene cloned into plasmid pET26b carrying a signal peptide, peIB, was expressed in E. coli BL21(DE3)pLysS. The signal peptide region was cleaved during the production of the enzyme. Specific activity of the enzyme purified from the transformant was almost identical to that of the native enzyme. Furthermore, the SR1 enzyme gene cloned with the leader peptide gene into plasmid pET28a was also expressed in E. coli. In this case, a proform-like protein was partially processed; 35 amino acid residues were cleaved but 30 amino acid residues remained. This proform like protein has approximately one-nineteenth the activity of the native enzyme. These results indicated that the native SR1 enzyme was produced in the following manner in the cells of S. rutgersensis H-46. The SR1 enzyme gene was translated to a pre-proform protein followed by the deletion of a signal peptide. Finally, the proform-like protein was processed by deletion of the remaining leader peptide.     

Isolation, characterization, and molecular cloning of a thermostable xylitol oxidase from Streptomyces sp. IKD472

A thermophilic bacterium, Streptomyces sp. IKD472, that can oxidize xylitol was isolated from a hot spring and was found to produce xylitol oxidase. The purified enzyme was a monomeric protein with an apparent molecular weight of 43 k as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis and gel filtration. This novel enzyme is capable of catalyzing the oxidation of one mole of xylitol to form one mole each of xylose and hydrogen peroxide. Since the V(max)K(m) value for xylitol was two and four times higher than those for galactitol and n-sorbitol, respectively, the enzyme was designated as xylitol oxidase. The enzyme was stable in the pH range from 5.5 to 10.5 and at temperatures up to 65 degrees C. The optimal temperature and pH were 55 degrees C and pH 7.5, respectively. Xylitol oxidase bound one mole of FAD as a coenzyme per mole of protein. The amino acid sequence of the NH2 terminus and the fragments obtained by lysylendpeptidase digestion of xylitol oxidase were determined for preparation of synthetic oligonucleotides as hybridization probes. A 2.8-kb chromosomal fragment hybridizing to the probes was cloned into pUC18 in Escherichia coli. The gene consists of an open reading frame of 1245 by that encodes a protein containing 415 amino acids with a molecular weight of 44,730 but without the conserved nucleotide-binding sequence, Gly-X-Gly-X-X-Gly. The amino acid sequence has 70% identity to putative oxidoreductase from Streptomyces coelicolar, 51% to sorbitol oxidase from Streptomyces sp., and 26% to L-gulonolactone oxidase from rat in terms of the overall amino acid sequence. DNA manipulation of the cloned gene in E. coli, by alteration of a strong promoter and a synthesized ribosome-binding sequence at an appropriate position, resulted in overproduction of xylitol oxidase 100 times more than that produced in the original Streptomyces sp. IKD472. The enzyme properties of recombinant xylitol oxidase were the same as those of the authentic enzyme. Stable xylitol oxidases, which allow easier quantitative analysis of xylitol, are useful for clinical applications.     

Cloning and sequencing of a chitinase gene from Vibrio alginolyticus H-8

A gene from Vibrio alginolyticus H-8, encoding chitinase, designated as chitinase B, was cloned by the shot-gun method using pUC118 and sequenced. The open reading frame consisted of 846 amino acids including a signal peptide. The molecular mass of the enzyme estimated based on the amino acid sequence data was 90 kDa. The N-terminal amino acid sequence of the enzyme was different from that of chitinase C1 which we had previously reported. This cloned chitinase B was considered one out of four chitinases (A, B, D, and E) which had been newly isolated from the culture broth and cell extract of V. alginolyticus H-8. The gene contained a chitin-binding domain and typical conserved regions of chitinases reported previously. The deduced amino acid sequence of the cloned chitinase B showed high sequence homology with the chitinase from V. parahaemolyticus (84% identity) and the chitinase from V. anguillarum (76.6%), but low sequence homology with the chitinase from V. harveyi (24.4%), and the chitodextrinase from V. furnissii (23.9%). Chitinase E found in cell extract is considered an intracellular chitinase which is different from chitodextrinases.     

大豆rbcL基因克隆、序列分析及原核表达

利用叶绿体基因组保守性的特征,根据菜豆、豌豆、烟草的rbcL基因序列设计引物,从大豆叶绿体DNA中克隆rbcL基因,全长序列为1488bp,包括1449bp的开放阅读框,编码482个氨基酸。相似性比较显示,此序列与其它10个物种rbcL基因核苷酸的同源性为85．37％～95．31％,氨基酸的同源性为90．87％-96．47％。将该基因与表达载体pET-30a（＋）连接,转化大肠杆菌Rosseta感受态细胞,PCR和酶切鉴定筛选阳性克隆,阳性菌液IPTG诱导后经10％SDS—PAGE分析,结果显示,诱导表达出分子量约为60kD的特异融合蛋白。     

草莓轻型黄边病毒外壳蛋白抗原表位预测、克隆、表达及其免疫原性分析

应用IEDB、DNAStar、DNAMAN和Snap Gene等生物信息学工具对草莓轻型黄边病毒外壳蛋白的氨基酸残基序列进行分析。选择一段抗原性较强的肽段(位于外壳蛋白27~38氨基酸残基处),依据大肠杆菌(Escherichia coli)的密码子偏好性化学合成了该肽段的DNA编码序列(AE)。AE片段克隆至E.coli表达载体pET32a(+)的Eco RⅠ和XhoⅠ位点,获得重组质粒pET32a(+)-AE。含AE片段的开放阅读框长561 bp,编码了一个187氨基酸残基的重组融合蛋白,理论分子质量为20.29kD。重组质粒pET32a(+)-AE分别在E.coli BL21(DE3)和E.coli Rosetta中进行了诱导表达和条件优化。重组融合蛋白在E.coli Rosetta中的最佳表达条件为1.5 mmol/L异丙基-β-D-硫代半乳糖苷(isopropyl β-D-1-thiogalactopyranoside,IPTG)、35℃诱导表达2 h,产率为13.22 mg/L;在E.coli BL21(DE3)中的最佳表达条件是为0.5 mmol/L IPTG、30℃诱导表达2 h,产率为9.55 mg/L。重组融合蛋白经十二烷基硫酸钠-聚丙烯酰胺凝胶电泳分离、质谱鉴定表明,其含有所预测的草莓轻型黄边病毒外壳蛋白抗原表位肽段AE。AE重组融合蛋白经Ni~(2+)亲和色谱纯化、EK酶切、分子筛除去融合蛋白标签后,免疫产蛋鸡。从免疫鸡所产鸡蛋中提取鸡卵黄免疫球蛋白(immunoglobulin of yolk,Ig Y),Dot-Blot检测抗体结合活性。结果表明,所提取的IgY可特异性识别AE肽段和SMYEV外壳蛋白。这一结果表明所预测的AE肽段具有较好的免疫原性。     

Biochemical and genetic characterization of a D(-)-3-hydroxybutyrate dehydrogenase from Acidovorax sp. strain SA1

D(-)-3-hydroxybutyrate dehydrogenase (BDH; EC 1.1.1.30) from a poly(D(-)-3-hydroxybutyrate) (PHB) degrading bacterium, Acidovorax sp. SA1, was purified using Toyopearl DEAE-650M, red-Sepharose CL-4B, and Q Sepharose FF. The molecular mass of the enzyme was estimated as 27 kDa by SDS-PAGE and 110 kDa by gel filtration. The gene encoding BDH was cloned and sequenced, and expressed in Escherichia coli. The gene product was purified in two steps with a high yield. The N-terminal amino acid sequence of the enzyme purified from E. coli agreed with that of the purified enzyme from strain SA1. The BDH of strain SA1 had high amino acid sequence homology to that of Ralstonia eutropha H16. The Km values for D(-)-3-hydroxybutyrate and NAD+ in the oxidation reaction were 4.5 x 10(-4) M and 8.9 x 10(-5) M, respectively. The Km values for acetoacetate and NADH in the reduction reaction were 2.4 x 10(-4) M and 2.9 x 10(-5) M, respectively.     

Cloning and sequencing of the ornithine carbamoyltransferase gene from Pachysolen tannophilus

A fragment of DNA from a yeast Pachysolen tannophilus, bearing the ornithine carbamoyltransferase gene (OCTase, EC 2.1.3.3) has been cloned from a genomic library by functional complementation of the Escherichia coli OCT-negative mutant. The gene was located within the cloned segment of DNA and its coding sequence identified by DNA sequencing. This has indicated that P. tannophilus OCT gene encodes a 347 amino acid polypeptide, which shows 60% identity to the homologous Saccharomyces cerevisiae protein. The amino acid composition of its N-terminus indicates that this protein is translocated across the mitochondrial membrane. The gene can be expressed in E. coli as well as in S. cerevisiae. Comparison with other OCTases confirms a high degree of conservation among these proteins.     

Cloning and sequence analysis of the estA gene encoding enzyme for producing (R)-beta-acetylmercaptoisobutyric acid from Pseudomonas aeruginosa 1001

The estA gene encoding the enzyme that catalyzes the production of (R)-beta-acetylmercaptoisobutyric acid from (R,S)-ester from Pseudomonas aeruginosa 1001, was cloned in Escherichia coli and its nucleotide sequence was determined, revealing the presumed open reading frame encoding a polypeptide of 316 amino acid residues (948 nucleotides). The overall A + T and C + G compositions were 32.59% and 67.41%, respectively. The amino acid sequence of the estA gene product showed a significant similarity with that of the triacylglycerol lipase from Psychrobacter immobilis (38% identity), triacylglycerol lipase from Moraxella sp. (36% identity), and two forms of carboxyl esterases from Acinetobacter calcoaceticus (17% and 17% identities). The deduced amino acid sequences have a pentapeptide consensus sequence, G-X-S-X-G, having an active serine residue, and another active site, dipeptides H-G, located at 70-100 amino acids upstream of the G-X-S-X-G consensus sequence.     

Cloning and expression of chitin deacetylase gene from a Deuteromycete, Colletotrichum lindemuthianum

The chitin deacetylase gene was cloned from cDNA of Colletotrichum lindemuthianum ATCC 56676, and the open reading frame consisted of a possible prepro-sequence of 27 amino acids at the N-terminus and a mature chitin deacetylase. The deduced amino acid sequence of the mature enzyme revealed 26% identity and 46% similarity with a chitin deacetylase from Mucor rouxii. The molecular mass of the protein estimated from the amino acid sequence data was 24.3 kDa, which was in good agreement with the MALDI-TOF MS analysis data of the purified protein (24.17-24.36 kDa). The gene product was overexpressed in Escherichia coli cells as a fusion protein with six histidine residues at its C-terminus. The fusion protein formed inclusion bodies, but chitin deacetylase activity was restored from the inclusion bodies by a simple renaturation step with 8 M urea treatment. The recombinant enzyme was purified by affinity chromatography and gel filtration steps, and had a final specific activity of 4.22 units mg(-1) of protein. Trypsin digestion of the recombinant enzyme resulted in 2.1-fold increase in activity, suggesting that the removal of the prepro-domain from the recombinant enzyme resulted in an increase in its activity.     

Processing of XynE (110-kDa) of Aeromonas caviae ME-1 to 72-kDa xylanase in Escherichia coli transformant

An extracellular 72-kDa xylanase from an Escherichia coli transformant that harbored pXED30 carrying xynE of Aeromonas caviae ME-1 was purified by extraction following SDS-PAGE to electrophoretic homogeneity. The analysis of N-terminal 10 amino acid residues (Gly-Ala-Arg-Ala-Gln-Ala-Ala-Ala-Asp-Val) revealed a 72-kDa product derived by the cleavage of Gly26-Gly27 at the N-terminal region of 110 kDa XynE. The 72-kDa xylanase from A. caviae ME-1 was found to have the same sequence as that of the N-terminal 10 amino acid residues. When OmpT-deficient E. coli mutants were used as hosts, the 72-kDa xylanase was detected in cell-free extracts, but not in the culture supernatant, suggesting that OmpT is not involved in the cleavage at the C-terminal region, but is involved in the secretion of 72-kDa xylanase to the culture medium.     

Molecular cloning and characterization of thermostable beta-lactam acylase with broad substrate specificity from Bacillus badius

The gene (pac) encoding beta-lactam acylase from Bacillus badius was cloned and expressed in Escherichia coli. The pac gene was identified by polymerase chain reaction (PCR) using degenerated primers, on the basis of conserved amino acid residues. By using single specific primer PCR (SSP-PCR) and direct genome sequencing, a complete pac gene with its promoter region was obtained. The ORF consisted of 2415 bp and the deduced amino acid sequence indicated that the enzyme is synthesized as a preproenzyme with a signal sequence, an alpha-subunit, a spacer peptide and a beta-subunit. The pac gene was expressed with its own promoter in different E. coli host strains and a maximum recombinant PAC (1820 U l(-1)) was obtained in E. coli DH5alpha. The recombinant PAC was purified by Ni-NTA chromatography and the purified PAC had two subunits with apparent molecular masses of 25 and 62 kDa. This enzyme exhibited a high thermostability with a maximum activity at 50 degrees C. This enzyme showed stability over a wide pH range (pH 6.0-8.5) with a maximum activity at pH 7.0 and activity on a wide beta-lactam substrate range. The K(m) values obtained for the hydrolysis of penicillin G and a chromogenic substrate, 6-nitro-3-phenylacetylamidobenzoic acid, from B. badius PAC were 39 and 41 microM, respectively. The PAC activity was competitively inhibited by PAA (K(i), 108 microM) and noncompetitively by 6-APA (K(i), 17 mM). The constitutive production of B. badius PAC in E. coli and its easier purification together with the advantageous properties, such as thermostability, pH stability and broad substrate specificity, make this as a novel enzyme suitable for beta-lactam industry.     

XJT-9503高温中性蛋白酶基因Gp1的克隆、表达及序列分析

试验根据地衣芽孢杆菌XJT9503的高温中性蛋白酶酶蛋白所测定的N-端及部分肽段氨基酸序列及质谱分析结果设计了PCR引物,用PCR方法从地衣芽孢杆菌XJT9503中扩增了高温中性蛋白酶基因Gp1,对所获得的基因进行序列分析测定,并与蛋白酶的氨基酸序列分析对比。GP1基因全序列共1129bp,包括整个阅读框,共编码376个氨基酸。将扩增的DNA片段插入到大肠杆菌载体pET-28a中,构建成重组分泌型表达载体pGp1。并在大肠杆菌宿主BL21中得到表达。SDS-PAGE分析显示产物的分子量为27.0×103,同核酸序列测定所推导的值相符。同时,对地衣芽孢杆菌XJT9503中性蛋白酶基因序列进行了测定和比较分析,发现与地衣芽孢杆菌6816丝氨酸蛋白酶和地衣芽孢杆菌1411T角蛋白水解酶基因的同源性为97%。     

A novel flavin adenine dinucleotide (FAD) containing d-lactate dehydrogenase from the thermoacidophilic crenarchaeota Sulfolobus tokodaii strain 7: purification, characterization and expression in Escherichia coli

Dye-linked D-lactate dehydrogenase activity was found in the crude extract of a continental thermoacidophilic crenarchaeota, Sulfolobus tokodaii strain 7, and was purified 375-fold through four sequential chromatography steps. With a molecular mass of about 93 kDa, this enzyme was a homodimer comprised of identical subunits with molecular masses of about 48 kDa. The enzyme retained its full activity after incubation at 80 degrees C for 10 min and after incubation at pHs ranging from 6.5 to 10.0 for 30 min at 50 degrees C. The preferred substrate for this enzyme was D-lactate, with 2,6-dichloroindophenol serving as the electron acceptor. Using high-performance liquid chromatography (HPLC), the enzyme's prosthetic group was determined to be flavin adenine dinucleotide (FAD). Its N-terminal amino acid sequence was MLEGIEYSQGEEREDFVGFKIKPKI. Using that sequence and previously reported genome information, the gene encoding the enzyme (ST0649) was identified. It was subsequently cloned and expressed in Escherichia coli and found to encode a polypeptide of 440 amino acids with a calculated molecular weight of 49,715. The amino acid sequence of this dye-linked D-lactate dehydrogenase showed higher homology (39% identity) with that of a glycolate oxidase subunit homologue from Archaeoglobus fulgidus, but less similarity (32% identity) to D-lactate dehydrogenase from A. fulgidus. Taken together, our findings indicate that the dye-linked D-lactate dehydrogenase from S. tokodaii is a novel type of FAD containing D-lactate dehydrogenase.     

Effect of pepsin-treated bovine and goat caseinomacropeptide on Escherichia coli and Lactobacillus rhamnosus in acidic conditions

Caseinomacropeptide (CMP) is a 7-kDa phosphoglycopolypeptide released from κ-casein during milk digestion and in the cheesemaking process. The objective of the study was to analyze the effect of pepsin-treated CMP from cow and goat milk on the resistance of Escherichia coli and Lactobacillus rhamnosus during acid stress. Bacterial cells in the exponential growth phase were suspended in acidified phosphate buffered saline with or without pepsin-treated CMP. Viability was determined during a 90-min incubation period. Pepsin-treated CMP exhibited bactericidal activity at pH 3.5 when added in a dose-dependent manner to E. coli, decreasing survival by more than 90% within 15 min at 0.25 mg/mL. At pH >4.5, the bactericidal activity disappeared, indicating that pepsin-treated CMP was efficient at low pH only. The effectiveness of pepsin-treated CMP at pH 3.5 was not affected by the presence of glycoconjugates linked to CMP or by the bovine or caprine origin of milk. In contrast, L. rhamnosus, a probiotic, was more resistant to acid stress when pepsin-treated bovine or caprine CMP was added to the media. Viability reached 50% after 60 min of incubation at pH 3 compared with 5% survival in the media without added pepsin-treated CMP. Neither glycosylation extent nor sequence variations between CMP from bovine milk and caprine milk affected the protective activity of hydrolyzed CMP toward L. rhamnosus. This suggests that encrypted bioactive peptides released by the pepsin treatment of CMP had an antibacterial effect on E. coli in acidic media, but improved the resistance of L. rhamnosus to acid stress. The peptide fragment accountable for bactericidal activity is the N-terminal region κ-casein f(106-124).     

Identification of the gene encoding a NAD(P)H-flavin oxidoreductase coupling with dibenzothiophene (DBT)-desulfurizing enzymes from the DBT-nondesulfurizing bacterium Paenibacillus polymyxa A-1

The gene encoding NAD(P)H-flavin oxidoreductase (flavin reductase), which couples efficiently with dibenzothiophene (DBT)-desulfurizing monooxygenases of Rhodococci, was cloned from a DBT-non-desulfurizing bacterium Paenibacillus polymyxa A-1 in Escherichia coli, and designated as flv. Cell-free extracts from the recombinant exhibited a flavin reductase activity about forty times higher than that of the E. coli carrying the vector DNA only. Nucleotide sequence analysis reveals that the gene product consists of 208 amino acids and showed about 27%, 32% and 21% identity in amino acid sequence with FRase I, the major flavin reductase of Vibrio fischeri, the NADH dehydrogenase of Thermus thermophilus and several members of the nitroreductase family, respectively. The coexpression of flv with two kinds of desulfurizing genes, dszABC and tdsABC, in E. coli enhanced the rate of DBT degradation by about 10 and 5 times as high as in the case without flv, respectively.     

Molecular cloning and expression of uricase gene from Arthrobacter globiformis in Escherichia coli and characterization of the gene product

Arthrobacter globiformis FERM BP-360 produces uricase (urate oxidase; EC 1.7.3.3) intracellularly. A genomic library of the bacterium, prepared in the plasmid vector pUC118, was screened with probes based on the amino acid sequence of the purified uricase. We found that a chimeric plasmid in the library, designated pUOD1, carries a 2.0-kb DNA insert from the Arthrobacter DNA that hybridizes with the probe. The DNA insert contains an ORF consisting of 302 amino acids with a calculated molecular mass of 33,858. The protein translated from the ORF displays the highest identity (67%) to uricase from a bacterium, Cellulomonas flavigena. X-ray fluorescence analysis showed that the Arthrobacter uricase contains copper ion. However, we found that the catalytic activity of uricase is inhibited by the excessive addition of copper ion. Although the production of A. globiformis uricase is induced by the addition of uric acid to the culture medium, Escherichia coli harboring pUOD1 produced 20-fold higher uricase than the original Arthrobacter strain, even without an inducer.     

Molecular cloning and characterization of a thermostable carboxylesterase from an archaeon, Sulfolobus shibatae DSM5389: non-linear kinetic behavior of a hormone-sensitive lipase family enzyme

A gene coding for an esterase (SshEstI, 915 bp in length) of the thermoacidophilic archaeon Sulfolobus shibatae DSM5389 was cloned, sequenced, and overexpressed in Escherichia coli JM109 cells as a soluble, catalytically active protein. The deduced amino acid sequence of SshEstI was consistent with a protein containing 305 amino acid residues with a molecular mass of 33 kDa. Sequence comparison studies indicated that SshEstI could be a member of the hormone-sensitive lipase family, in that it had the highest sequence similarity to esterases from Sulfolobus solfataricus (90% identity) and Archaeoglobus fulgidus (42%) and a lipase from Pseudomonas sp. B11-1 (38%). The recombinant enzyme was highly thermostable and retained more than 70% of its initial activity after incubation at 90 degrees C and pH 7.0 for 30 min. The recombinant enzyme catalyzed the hydrolysis of p-nitrophenyl (p-NP) esters with C2-C16 acyl chains but not the hydrolysis of triacylglycerides such as tributyrin and triolein. The enzymatic hydrolysis of p-NP acetate proceeded in a linear manner with time, whereas that of p-NP esters with acyl chains of C5 or longer showed a biphasic profile, where a rapid release of p-nitrophenol ( approximately 3 min) was followed by a slow, sustained release. These non-linear kinetics may be explained in terms of a very slow, presteady-state burst phenomenon of p-nitrophenol release or a hysteretic behavior of SshEstI with these substrates.