一株南极嗜冷杆菌产丙酮酸脱氢酶的 性质研究及基因克隆

从南极普利兹湾深海沉积物中筛选到一株嗜冷杆菌7195。其16SrDNA序列分析表明谊菌株属于嗜冷杆菌属（Psychrobacter）,从该菌的全基因组DNA中克隆到编码丙酮酸脱氢酶系E1（PDHcEI）的完整ORF,全长为2817bp,使用DNAMAN5．1对其全长ORF的PDHcEI基因进行分析,PDHcE1基因编码一个由939AA残基组成、分子量预计为100663Da的PDHcEI蛋白质,与Psychrobacter sp．273—4的PDHcE1有78．53％的相似性。     

嗜热菌Thermus sp.YBJ-1的分离和淀粉酶基因的克隆

从西藏热泉水样分离得到一株嗜热菌(YBJ-1),其16S rDNA(1511bp)序列与栖热菌(Thermus scotoductus ITI-252T)的同源性为98％。通过PCR技术将Thermus sp．YBJ-1的淀粉酶基因(amyT)全长开放阅读框克隆到T载体。分析表明,amyT的ORF全长为1767bp,编码588个氨基酸。推导的氨基酸序列与嗜热脂肪芽孢杆菌的阿尔法环糊精酶(Bacillus stearothermophilus alpha-eyclodextrinase)和栖热菌Thermus sp．IM6501的麦芽糖淀粉酶(Thermus sp．IM6501 mahogenic amylase)分别有99％和96％的同源性,与嗜热脂肪芽孢杆菌的新普鲁兰酶(neopullulanase)的同源性为81％。     

南极耐冷 Pseudomonas sp. 7323低温脂肪酶的性质及基因克隆

 南极微生物是筛选低温酶的良好来源,但尚未得到充分的研究与开发.低温脂肪酶具有广阔的应用前景,其基因结构特征也具有重要的研究意义. 本文对南极微生物开展了低温脂肪酶产生菌的筛选、基因克隆及特征分析.采用功能筛选的方法,从南极普里兹湾深海沉积物中获得一株产低温脂肪酶的菌株7323,其最适温度和最高生长温度分别为20℃和30℃,属于耐冷菌.16S rDNA序列分析表明,该菌属于假单胞菌属（Pseudomonas）.通过设计引物扩增出的脂肪酶基因全长为1854　bp,该基因编码一个由617氨基酸、分子量预计为64466的蛋白质.氨基酸序列分析表明,该酶与Pseudomonas sp. UB48 的脂肪酶有89%的相似性,在催化区和C末端信号肽中存在高度保守的序列.纯化后的酶学性质研究表明,该脂肪酶的最适温度为35℃,最适pH值为9.0,为碱性低温酶.     

落地生根S-腺苷高半胱氨酸水解酶基因的克隆及生物信息学分析

为了解落地生根(Kalanchoe daigremontiana)的SAHH基因功能,采用RACE技术从其叶片克隆了SAHH的全长c DNA序列,命名为Kd SAHH。结果表明,Kd SAHH全长为1748 bp,含1458 bp完整的开放阅读框(ORF),推测编码485个氨基酸。预测落地生根SAHH蛋白分子量约为53 k Da,理论等电点为5.59~5.682。Scanprostie和DNAstar预测表明,落地生根SAHH蛋白在进化上非常保守,与苜蓿的亲缘关系较近。以黄羽扇豆为模板,利用SWISS-MODLE和Phyre程序模拟的落地生根SAHH蛋白亚基三维结构有一定差异。这些为落地生根Kd SAHH的表达和功能研究奠定了基础。     

嗜热菌Thermus sp. YBJ-1的分离和淀粉酶基因的克隆

从西藏热泉水样分离得到一株嗜热菌（YBJ-1）,其16S Rdna（1511bp）序列与栖热菌（Thermus scotoductus ITI252T）的同源性为98%。 通过PCR技术将Thermus sp. YBJ-1的淀粉酶基因(amyT)全长开放阅读框克隆到T载体。分析表明, amyT的ORF全长为1767bp,编码588个氨基酸。推导的氨基酸序列与嗜热脂肪芽孢杆菌的阿尔法环糊精酶（Bacillus stearothermophilus alpha cyclodextrinase） 和栖热菌Thermus sp.IM6501的麦芽糖淀粉酶（Thermus sp.IM6501 maltogenic amylase）分别有99%和96%的同源性,与嗜热脂肪芽孢杆菌的新普鲁兰酶（neopullulanas）的同源性为81%。     

芽孢杆菌Bacillus sp. S-1壳聚糖酶基因的克隆与序列分析

从连云港海滩晒虾蟹壳的泥土里筛选出一株产壳聚糖酶能力较高的菌株S-1,根据其形态特征、生理生化以及16S rDNA鉴定,初步认定该菌为芽孢杆菌属（Bacillus）。利用NCBI数据库中已经报道的Bacillus壳聚糖酶序列设计兼并引物,以菌株Bacillus sp. S-1的基因组DNA为模板进行聚合酶链式反应（PCR）,克隆到壳聚糖酶基因的部分序列;利用Clontech公司Universal GenomeWalker试剂盒构建该菌株的基因组步移文库,根据已测定的序列信息设计特异性引物,结合两步法PCR技术分别克隆两端未知序列,拼接获得壳聚糖酶基因的全长序列（该基因全长1362 bp编码453个氨基酸,注册号：EU924147）,并对该序列进行了生物信息学方面的分析。     

粗毛栓菌诱变菌株SAH-12漆酶基因的克隆与序列分析

粗毛栓菌Trametes gallica诱变菌株SAH-12是通过紫外诱变选育得到的漆酶高产菌株。为了对其漆酶基因进行研究和利用,采用cDNA末端快速扩增(Rapid Amplification of cDNA Ends,RACE)技术,从T.gallica诱变菌株SAH-12分离得到漆酶基因全长cDNA Lacc1(GenBank accession No.DQ431716)及其对应的结构基因Lac1(DQ431715)。该基因属于真菌漆酶基因家族,与来自出发菌T.gallica漆酶基因lacA(AY875867)在成熟肽编码区的同源性最高(一致性为98%)。Lacc1全长1891bp,由40bp的5'-UTR、1554bp的完整ORF和297bp的3'-UTR构成,具有polyA加尾信号AATACA和59bp的polyA结构;其完整ORF可编码21个氨基酸残基组成的信号肽和496个氨基酸残基组成的成熟蛋白。在Lacc1基因的推导氨基酸序列中有4个潜在的N-糖基化位点和4个参与二硫键形成的Cys残基,且含有真菌漆酶Ⅰ、Ⅱ、Ⅲ型铜离子结合区的4个高度保守序列。结构基因Lac1全长2338bp,含10个内含子和11个外显子,各内含子长度在51bp～76bp之间,且其序列均符合5'-gt……ag-3'规则。     

二色补血草硫氧还蛋白(Trx)的克隆和表达分析

从二色补血草cDNA文库中分离出1个硫氧还蛋白基因全长cDNA序列。基因全长1138bp,其中,5’非翻译（UTR）区128bp,3＇非翻译区212bp,开放阅读框（ORF）全长798bp,编码265个氨基酸,编码蛋白的分子量为28．58kDa,理论等电点（pI）为9．68。BlastP分析表明二色补血草Trx与拟南芥Trx序列同源性为52％,与葡萄7h序列同源性为76％,从11个物种的氨基酸多序列比对可以看出Trx氨基酸序列保守性较高。实时定量RT-PCR方法检测低温、NaCl和PEG胁迫不同时间后的基因在二色补血草中表达模式的结果表明,NaCl能诱导Trx基因在二色补血草叶中表达,胁迫24h后达到高峰,而聚乙二醇和低温处理则抑制Trx在二色补血草根和叶的表达。     

交替假单胞菌(Pseudoalteromonas sp.)DY3菌株产内切葡聚糖酶的性质研究及基因克隆

从深海样品ESO109中分离到一株具有高内切葡聚糖酶活力的细菌DY3,16SrDNA序列分析表明该菌与交替假单胞菌属(Pseudoalteromonas sp．)的Pseudoalteromonas citrea和Pseudoalteromonas elyakovii的同源性为99％。PCR扩增DY3的内切葡聚糖酶基因celX全长1479bp,编码一个492AA的蛋白质。酶的氨基酸序列分析表明CelX与Rseudoalteromonas haloplanktis的内切葡聚糖酶CelG有95％的相似性,包括一个糖基水解酶家族5的催化结构域,一个连接序列和位于C端的的CBM5结构域。对酶性质的初步研究发现,CelX的最适温度为40℃,酶的最适pH在6～7之间。     

产植酸酶菌株的筛选及其植酸酶基因的克隆

从土壤中筛选到产植酸酶活性较高的烟曲霉菌株WY-2,其植酸酶最适pH为5.5,最适温度为55℃。通过对烟曲霉WY-2植酸酶基因进行PCR扩增,获得了一个1.5kb大小的特异性产物,将其克隆到载体pMD18-T中。测序结果分析表明,该基因片段含有植酸酶基因完整的阅读框架(ORF),基因全长1459bp,其中包含一个61bp的内含子,编码465个氨基酸,有7个潜在的糖基化位点,5′端有一编码26个氨基酸的信号肽序列。该基因与已报道的烟曲霉ATCC34625植酸酶基因有91%同源性,编码的氨基酸序列同源性为91%。     

A novel R-stereoselective amidase from Pseudomonas sp. MCI3434 acting on piperazine-2-tert-butylcarboxamide.

A novel amidase acting on (R,S)-piperazine-2-tert-butylcarboxamide was purified from Pseudomonas sp. MCI3434 and characterized. The enzyme acted R-stereoselectively on (R,S)-piperazine-2-tert-butylcarboxamide to yield (R)-piperazine-2-carboxylic acid, and was tentatively named R-amidase. The N-terminal amino acid sequence of the enzyme showed high sequence identity with that deduced from a gene named PA3598 encoding a hypothetical hydrolase in Pseudomonas aeruginosa PAO1. The gene encoding R-amidase was cloned from the genomic DNA of Pseudomonas sp. MCI3434 and sequenced. Analysis of 1332 bp of the genomic DNA revealed the presence of one open reading frame (ramA) which encodes the R-amidase. This enzyme, RamA, is composed of 274 amino acid residues (molecular mass, 30 128 Da), and the deduced amino acid sequence exhibits homology to a carbon-nitrogen hydrolase protein (PP3846) from Pseudomonas putida strain KT2440 (72.6% identity) and PA3598 protein from P. aeruginosa strain PAO1 (65.6% identity) and may be classified into a new subfamily in the carbon-nitrogen hydrolase family consisting of aliphatic amidase, beta-ureidopropionase, carbamylase, nitrilase, and so on. The amount of R-amidase in the supernatant of the sonicated cell-free extract of an Escherichia coli transformant overexpressing the ramA gene was about 30 000 times higher than that of Pseudomonas sp. MCI3434. The intact cells of the E. coli transformant could be used for the R-stereoselective hydrolysis of racemic piperazine-2-tert-butylcarboxamide. The recombinant enzyme was purified to electrophoretic homogeneity from cell-free extract of the E. coli transformant overexpressing the ramA gene. On gel-filtration chromatography, the enzyme appeared to be a monomer. It had maximal activity at 45 degrees C and pH 8.0, and was completely inactivated in the presence of p-chloromercuribenzoate, N-ethylmaleimide, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Ag+, Cd2+, Hg2+, or Pb2+. RamA had hydrolyzing activity toward the carboxamide compounds, in which amino or imino group is connected to beta- or gamma-carbon, such as beta-alaninamide, (R)-piperazine-2-carboxamide (R)-piperidine-3-carboxamide, D-glutaminamide and (R)-piperazine-2-tert-butylcarboxamide. The enzyme, however, did not act on the other amide substrates for the aliphatic amidase despite its sequence similarity to RamA.     

Phenol/cresol degradation by the thermophilic Bacillus thermoglucosidasius A7: cloning and sequence analysis of five genes involved in the pathway

Bacillus thermoglucosidasius A7 degraded phenol at 65 degrees C via the meta cleavage pathway. Five enzymes used in the metabolism of phenol were cloned from B. thermoglucosidasius A7 into pUC18. Nine open reading frames were present on the 8.1kb insert, six of which could be assigned a function in phenol degradation using database homologies and enzyme activities. The phenol hydroxylase is a two-component enzyme encoded by pheA1 and pheA2. The larger component (50kDa) has 49% amino acid identity with the 4-hydroxyphenylacetate hydroxylase of Escherichia coli, while the smaller component (19kDa) is most related (30% amino acid identity) to the styrene monoxygenase component B from Pseudomonas fluorescens. Both components were neccessary for activity. The catechol 2, 3-dioxygenase encoded by pheB has 45% amino acid identity with dmpB of Pseudomonas sp. CF600 and could be assigned to superfamily I, family 2 and a new subfamily of the Eltis and Bolin grouping. The 2-hydroxymuconic acid semialdehyde hydrolase (2HMSH), encoded by pheC, revealed the highest amino acid identity (36%) to the equivalent enzyme from Pseudomonas sp. strain CF600, encoded by dmpD. Based on sequence identity, pheD and pheE were deduced to encode the 2-hydroxypenta-2,4-dienoate hydratase (2HDH), demonstrating 45% amino acid identity to the gene product of cumE from Pseudomonas fluorescens and the acetaldehyde dehydrogenase (acylating) demonstrating 57% amino acid identity to the gene product of bphJ from Pseudomonas LB400.     

Cloning and Characterization of the Gene Encoding Endo-β-1,3-glucanase from Arthrobacter sp. NHB-10

The gluA gene, encoding an endo-β-1,3-glucanase from Arthrobacter sp. (strain NHB-10), was cloned and analyzed. The deduced endo-β-1,3-glucanase amino acid sequence was 750 amino acids long and contained a 42 amino acid signal peptide with a mature protein of 708 amino acids. There was no similarity to known endo-β-1,3-glucanases, but GluA was partially similar to two fungal exo-β-1,3-glucanases in glycoside hydrolase (GH) family 55. Of five possible residues for catalysis and two motifs in two β-helix heads of GH family 55, three residues and one motif were conserved in GluA, suggesting that GluA is the first bacterial endo-β-1,3-glucanase in GH family 55. Significant similarity was also found to two proteins of unknown function from Streptomyces coelicolor A3(2) and S. avermitilis.     

Nucleotide sequence and expression of clcD, a plasmid-borne dienelactone hydrolase gene from Pseudomonas sp. strain B13.

The clcD structural gene encodes dienelactone hydrolase (EC 3.1.1.45), an enzyme that catalyzes the conversion of dienelactones to maleylacetate. The gene is part of the clc gene cluster involved in the utilization of chlorocatechol and is carried on a 4.3-kilobase-pair BglII fragment subcloned from the Pseudomonas degradative plasmid pAC27. A 1.9-kilobase-pair PstI-EcoRI segment subcloned from the BglII fragment was shown to carry the clcD gene, which was expressed inducibly under the tac promoter at levels similar to those found in 3-chlorobenzoate-grown Pseudomonas cells carrying the plasmid pAC27. In this study, we present the complete nucleotide sequence of the clcD gene and the amino acid sequence of dienelactone hydrolase deduced from the DNA sequence. The NH2-terminal amino acid sequence encoded by the clcD gene from plasmid pAC27 corresponds to a 33-residue sequence established for dienelactone hydrolase encoded by the Pseudomonas sp. strain B13 plasmid pWR1. A possible relationship between the clcD gene and pcaD, a Pseudomonas putida chromosomal gene encoding enol-lactone hydrolase (EC 3.1.1.24) is suggested by the fact that the gene products contain an apparently conserved pentapeptide neighboring a cysteinyl side chain that presumably lies at or near the active sites; the cysteinyl residue occupies position 60 in the predicted amino acid sequence of dienelactone hydrolase.     

Comparative studies of genes encoding thermostable L-2-halo acid dehalogenase from Pseudomonas sp. strain YL, other dehalogenases, and two related hypothetical proteins from Escherichia coli.

We have determined the nucleotide sequence of the gene encoding thermostable L-2-halo acid dehalogenase (L-DEX) from the 2-chloroacrylate-utilizable bacterium Pseudomonas sp. strain YL. The open reading frame consists of 696 nucleotides corresponding to 232 amino acid residues. The protein molecular weight was estimated to be 26,179, which was in good agreement with the subunit molecular weight of the enzyme. The gene was efficiently expressed in the recombinant Escherichia coli cells: the amount of L-DEX corresponds to about 49% of the total soluble proteins. The predicted amino acid sequence showed a high level of similarity to those of L-DEXs from other bacterial strains and haloacetate dehalogenase H-2 from Moraxella sp. strain B (38 to 57% identity) but a very low level of similarity to those of haloacetate dehalogenase H-1 from Moraxella sp. strain B (10%) and haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 (12%). By searching the protein amino acid sequence database, we found two E. coli hypothetical proteins similar to the Pseudomonas sp. strain YL L-DEX (21 to 22%).     

Cloning and expression of a conjugated bile acid hydrolase gene from Lactobacillus plantarum by using a direct plate assay.

The conjugated bile acid hydrolase gene from the silage isolate Lactobacillus plantarum 80 was cloned and expressed in Escherichia coli MC1061. For the screening of this hydrolase gene within the gene bank, a direct plate assay developed by Dashkevicz and Feighner (M. P. Dashkevicz and S. D. Feighner, Appl. Environ. Microbiol. 53:331-336, 1989) was adapted to the growth requirements of E. coli. Because of hydrolysis and medium acidification, hydrolase-active colonies were surrounded with big halos of precipitated, free bile acids. This phenomenon was also obtained when the gene was cloned into a multicopy shuttle vector and subsequently reintroduced into the parental Lactobacillus strain. The cbh gene and surrounding regions were characterized by nucleotide sequence analysis. The deduced amino acid sequence was shown to have 52% similarity with a penicillin V amidase from Bacillus sphaericus. Preliminary characterization of the gene product showed that it is a cholylglycine hydrolase (EC 3.5.1.24) with only slight activity against taurine conjugates. The optimum pH was between 4.7 and 5.5. Optimum temperature ranged from 30 to 45 degrees C. Southern blot analysis indicated that the cloned gene has similarity with genomic DNA of bile acid hydrolase-active Lactobacillus spp. of intestinal origin.     

Cloning and expression of a conjugated bile acid hydrolase gene from Lactobacillus plantarum by using a direct plate assay.

The conjugated bile acid hydrolase gene from the silage isolate Lactobacillus plantarum 80 was cloned and expressed in Escherichia coli MC1061. For the screening of this hydrolase gene within the gene bank, a direct plate assay developed by Dashkevicz and Feighner (M. P. Dashkevicz and S. D. Feighner, Appl. Environ. Microbiol. 53:331-336, 1989) was adapted to the growth requirements of E. coli. Because of hydrolysis and medium acidification, hydrolase-active colonies were surrounded with big halos of precipitated, free bile acids. This phenomenon was also obtained when the gene was cloned into a multicopy shuttle vector and subsequently reintroduced into the parental Lactobacillus strain. The cbh gene and surrounding regions were characterized by nucleotide sequence analysis. The deduced amino acid sequence was shown to have 52% similarity with a penicillin V amidase from Bacillus sphaericus. Preliminary characterization of the gene product showed that it is a cholylglycine hydrolase (EC 3.5.1.24) with only slight activity against taurine conjugates. The optimum pH was between 4.7 and 5.5. Optimum temperature ranged from 30 to 45 degrees C. Southern blot analysis indicated that the cloned gene has similarity with genomic DNA of bile acid hydrolase-active Lactobacillus spp. of intestinal origin.     

The lipA gene of Serratia marcescens which encodes an extracellular lipase having no N-terminal signal peptide.

The lipA gene encoding an extracellular lipase was cloned from the wild-type strain of Serratia marcescens Sr41. Nucleotide sequencing showed a major open reading frame encoding a 64.9-kDa protein of 613 amino acid residues; the deduced amino acid sequence contains a lipase consensus sequence, GXSXG. The lipase had 66 and 56% homologies with the lipases of Pseudomonas fluorescens B52 and P. fluorescens SIK W1, respectively, but did not show any overall homology with lipases from other origins. The Escherichia coli cells carrying the S. marcescens lipA gene did not secrete the lipase into the medium. The S. marcescens lipase had no conventional N-terminal signal sequence but was also not subjected to any processing at both the N-terminal and C-terminal regions. A specific short region similar to the regions of secretory proteins having no N-terminal signal peptide was observed in the amino acid sequence. Expression of the lipA gene in S. marcescens was affected by the carbon source and the addition of Tween 80.     

Cloning and sequencing of the fcbB gene encoding 4-chlorobenzoate-coenzyme A dehalogenase from Pseudomonas sp. DJ-12.

Pseudomonas sp. DJ-12 degrades 4-chlorobenzoate through hydrolytic dechlorination to produce 4-hydroxybenzoate and a chloride ion. The fcbB gene encoding the 4-chlorobenzoate-coenzyme A (4CBA-CoA) dehalogenase which catalyzes the nucleophilic substitution reaction to convert 4CBA-CoA to 4-hydroxybenzoate-coenzyme A (4HBA-CoA) in the consecutive steps of dechlorination was cloned from the chromosome of the organism. A nucleotide sequence analysis of the gene showed an open reading frame consisting of 810 nucleotides, which can encode for a polypeptide of molecular mass 30 kDa, containing 269 amino acid residues. A promoter-like sequence (-35 and -10 region) and a putative ribosome-binding sequence were identified. A deduced amino acid sequence of the 4CBA-CoA dehalogenase showed 86%, 50%, and 50% identity with those of corresponding enzymes in the Pseudomonas sp. CBS3, Arthrobacter sp. SU, and Arthrobacter sp. TM1, respectively.     

Cloning and characterization of the gene encoding endo-beta-1,3-glucanase from Arthrobacter sp. NHB-10

The gluA gene, encoding an endo-beta-1,3-glucanase from Arthrobacter sp. (strain NHB-10), was cloned and analyzed. The deduced endo-beta-1,3-glucanase amino acid sequence was 750 amino acids long and contained a 42 amino acid signal peptide with a mature protein of 708 amino acids. There was no similarity to known endo-beta-1,3-glucanases, but GluA was partially similar to two fungal exo-beta-1,3-glucanases in glycoside hydrolase (GH) family 55. Of five possible residues for catalysis and two motifs in two beta-helix heads of GH family 55, three residues and one motif were conserved in GluA, suggesting that GluA is the first bacterial endo-beta-1,3-glucanase in GH family 55. Significant similarity was also found to two proteins of unknown function from Streptomyces coelicolor A3(2) and S. avermitilis.