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PubMedDate not supplied

[Cloning of the gene for thermostable Thermus aquaticus YT1 DNA polymerase and its expression in Escherichia coli].

Using the phasmid vector pSL5, the genomic DNA fragment of T. aquaticus YT1 which contained the thermostable DNA polymerase (Taq-polymerase) gene was cloned. The BglII fragment of this genome locus was subcloned in the BamHI site of the pUC19 plasmid. To optimize the Taq-polymerase gene expression in E. coli cells, the gene was cloned in the correct reading frame regarding the initiation ATG codon of the pPR-TGATG-1 expression vector. The gene expression in this vector was controlled by the phage lambda PR promoter and the temperature-sensitive phage lambda repressor. We used PCR to amplify the short 5'-end fragment of the Taq-polymerase gene coding for the part into which an artificial SacI site was introduced. This site has been used for cloning the PCR product into the pPR-TGATG-1 vector, and the missing gene part was cloned into the KpnI site of the PCR product from the natural cloned gene. The cells of the E. coli PVG-A1 strain, which was obtained in the end, expressed efficiently the Taq-polymerase gene at the nonpermissive temperature. The content of the recombinant Taq-polymerase in the cells was about 1-2% of total proteins. The purified nearly homogeneous Taq-polymerase amplified efficiently in the PCR DNA fragments up to 5.5 kb long and was useful in DNA sequencing the by Sanger method. The half-life of the purified Taq polymerase was about 60 min at 95 degrees C, it was active for at least 65 standard PCR circles. The specific activity of recombinant enzyme preparations was about 180-200,000 units per mg of protein. The E. coli PVG-A1 strain enables one to isolate up to 500,000 units of purified enzyme from 2 l of bacterial culture.

Bacteriophage lambda↗
PubMed1999

Cloning, expression and significance of MPT53 for identification of secreted proteins of Mycobacterium tuberculosis.

Based on our N -terminal amino acid sequence of MPT53 and a deduced DNA sequence, we searched for the corresponding gene in the Mycobacterium tuberculosis genomic sequence at the Sanger centre, localizing mpt53 close to mpt70 and mpt83. The gene was cloned and expressed, followed by purification of MPT53 to homogeneity from recombinant M. smegmatis culture fluid. In MPT53 there is 60 % identity with the active site of thioredoxin of M. tuberculosis (MPT46) with two cysteins in a CXXC motif, but MPT53 could not serve as an alternative substrate for thioredoxin reductase. Testing for IgM and IgG1 anti-MPT53 in cattle sera showed that MPT53 is immunogenic following natural and experimental infection with M. bovis. Cloning of mpt53 represents cloning of the last of the 10 proteins originally defined as "secreted proteins" of M. tuberculosis and M. bovis based on determination of their "Localization index" (LI) (J Gen Microbiol 1991;137 : 875-84). The need for a precise definition of the term "secreted protein" is discussed. So far we have observed full concordance between occurrence of an LI value indicating secretion of a protein and occurrence of a signal sequence in the corresponding gene. Signal sequence independent protein secretion in mycobacteria may occur for a limited number of proteins and remains to be established.

Amino Acid Sequence↗
PubMed2005

[Cloning of Human canstatin gene and expression of its recombinant protein].

OBJECTIVE: To clone human canstatin gene and express its recombinant protein. METHODS: The total RNA was extracted from human placenta. The canstatin gene fragment was synthesized and amplified from the total RNA by RT-PCR. The resulting product was cloned into pUCm-T vector and transformed into E.coli DH5alpha through electroporation. The gene was sequenced by the Sanger Dideoxy-mediated chain-termination method, and then the canstatin cDNA was cloned into the BamHI and HindIII sites of plasmid pET-22b (+) and transformed into E.coli BL21 where it was induced to express proteins by isopropyl-1-thio-b-Dgalactopyranoside (IPTG). RESULTS: The extracted total RNA was separated into three clear bands indicating 28S, 18S, and 5S after electrophoresis. The canstatin gene fragment was synthesized and amplified from the total RNA by RT-PCR. The resulting products were cloned into pUCm-T vectors, and then were transformed into E.coli DHSa. After an over night culture, both blue and white colonies were found on the agar plate. Six white colonies were selected and cut by BamHI and HindIII. The plasmids DNA in one white colony showed one band near the location of primary plasmid after digested by BamHI and two bands near the locations of primary plasmid and objective gene fragment after digested by HindIII. The cloned gene in this white colony was sequenced and demonstrated to have the same sequence as that of canstatin gene in GenBank. Then canstatin cDNA was cut down from pUCm-T with BamHI and HindIII and ligated into the vector pET-22b (+). The resultant plasmid pET-22b (+)/canstatin was then transformed into E.coli BL21. White colonies were found on LB agar plate. Seven of them were selected and their plasmids were digested with both BamHI and HindIII. After electrophoresis, all selected colonies showed two specific bands, one was found near the location of primary plasmids, and the other near that of objective gene fragment. After IPTG induction, there was a new protein band about Mr 24 000 on SDS-PAGE. As estimated by densitometry, the percentage of the expressed product over total bacterial proteins was 18.2%, 18.8%, 23.0% and 23.4%, respectively, 1, 2, 3, and 4 hours after induction. CONCLUSION: Human canstatin gene was successfully cloned and its recombinant proteins were expressed in this study.

Base Sequence↗
PubMed2006

Novel porcine repetitive elements.

BACKGROUND: Repetitive elements comprise approximately 45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals. RESULTS: We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI). These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute), covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats. CONCLUSION: The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.

Animals↗
PubMed2001

Characterization of a Plasmodium falciparum erythrocyte-binding protein paralogous to EBA-175.

A member of a Plasmodium receptor family for erythrocyte invasion was identified on chromosome 13 from the Plasmodium falciparum genome sequence of the Sanger Centre (Cambridge, U.K.). The protein (named BAEBL) has homology to EBA-175, a P. falciparum receptor that binds specifically to sialic acid and the peptide backbone of glycophorin A on erythrocytes. Both EBA-175 and BAEBL localize to the micronemes, organelles at the invasive ends of the parasites that contain other members of the family. Like EBA-175, the erythrocyte receptor for BAEBL is destroyed by neuraminidase and trypsin, indicating that the erythrocyte receptor is a sialoglycoprotein. Its specificity, however, differs from that of EBA-175 in that BAEBL can bind to erythrocytes that lack glycophorin A, the receptor for EBA-175. It has reduced binding to erythrocytes with the Gerbich mutation found in another erythrocyte, sialoglycoprotein (glycophorin C/D). The interest in BAEBL's reduced binding to Gerbich erythrocytes derives from the high frequency of the Gerbich phenotype in some regions of Papua New Guinea where P. falciparum is hyperendemic.

Animals↗
PubMed1990

Analysis of ENU-induced mutations at the Adh locus in Drosophila melanogaster.

N-Ethyl-N-nitrosourea (ENU) was used to induce mutations in the Drosophila melanogaster, alcohol dehydrogenase (Adh) gene. Flies were treated with ENU and mated to homozygous intragenic Adh null mutants; Adh null mutations were selected by exposure of the F1 generation to 1-penten-3-ol. Fourteen Adh null mutations were recovered which included 11 from spermatozoa, 2 from oocytes and 1 from a premeiotic spermatocyte. 2 mutations from spermatozoa and 1 of the mutations from oocytes were multilocus deficiencies which included the Adh locus as determined by complementation tests. The remaining 11 intragenic Adh null mutations were sequenced using the Sanger dideoxy method. One Adh null mutation induced in an oocyte was an AT to TA transversion and the mutation induced in a premeiotic spermatocyte was a GC to AT transition, both of which resulted in a single amino acid substitution. The 11 null mutations induced in spermatozoa were a data set in which both the dose of ENU and the treated germ-cell stage were held constant; therefore, only these 11 mutations were used to calculate the mutation frequency and compare the mutations at the Adh locus with those recovered in other studies. The dose of ENU induced a sex-linked recessive lethal frequency approximately 300 times that of the spontaneous frequency; therefore, these mutations were assumed to have been induced by ENU. 2 of the 11 mutations induced in spermatozoa were multilocus deficiencies and 9 were intragenic mutations. 7 of the 9 intragenic mutations were GC to AT transitions which resulted in 5 single amino acid substitutions, 1 premature translation termination codon, and 1 splice site mutation.(ABSTRACT TRUNCATED AT 400 WORDS)

Alcohol Dehydrogenase↗
PubMed1993

Sequencing two DNA templates in five channels by digital compression.

By applying algebraic coding methods to the Sanger dideoxynucleotide procedure, DNA sequences of two templates can be determined simultaneously in only five reactions and data channels. A 5:2 data compression is accomplished by instantaneous source coding of nucleotide sequence pairs into one set of 5-bit block codes. A general algebraic expression, 2n-1 > or = 4f, describes conditions under which f DNA templates can be sequenced using n channels. Such compression sequencing is accurate and efficient, as demonstrated by manual 35S autoradiographic detection and automated on-line analysis using fluorescent-labeled primers. Symmetric 5:2 compression is especially useful when comparing two closely related sequences.

Automation↗
PubMedDate not supplied

Molecular characterization of a DNA probe, U6.2, located close to the fragile X locus.

A new DNA probe, U6.2, defining locus DXS304, was recently shown to be closely linked to the fragile X locus (FRAXA). It is polymorphic with a number of different enzymes, all of which are in complete linkage disequilibrium, which suggests an insertion/deletion type of polymorphism. Using the method of Sanger, we have sequenced 1,102 bp of the cloned U6.2 fragment. Analysis of the sequence showed there was a long direct repeat of 121 bp and two long inverted repeats. The first was 19 bp long, and the second was a palindromic invert of 20 bp. Such repeats could promote recombination in this region and could have been involved in the suggested insertion/deletion event that created the polymorphism detected at locus DXS304. Long fragments were observed using pulsed field gel electrophoresis (PFGE), but no length variations were seen. The sequence of U6.2 will be useful in developing a polymerase chain reaction (PCR) based assay for the restriction fragment length polymorphism (RFLP) detected at locus DXS304 which should assist with carrier detection and prenatal diagnosis of the fragile X syndrome.

Alleles↗
PubMed1991

A phagemid vector library for cloning DNA with four-nucleotide 5' or 3' overhangs.

A phagemid vector library for cloning DNA with four nucleotide 5' or 3' overhangs has been constructed. This library is based on the pT7T3 vector (Pharmacia) which is a modification of the phagemid pTZ18U vector. We have chosen pT7T3 as the parent vector because it can be used for Sanger's dideoxy sequencing and for the generation of RNA probes with either the T7 or T3 promoter. Each member of the cloning vector series pBM has recognition sites for both of the restriction enzymes BspM1 and BstX1 in addition to the basic multiple cloning sites. BspM1 recognizes the sequence 5'...ACCTGC NNNN/NNNN...3' whereas BstX1 recognizes the sequence 5'...CCAN NNNN/NTGG...3'. Thus these two sites can be overlapped, so that only 256 vectors (instead of 512 vectors) need be constructed to cover all the theoretical possible combinations of sites which give complementary cohesive ends for cloning DNA with four nucleotide 5' or 3' overhangs. This vector library can be used for amplification cloning of DNA in a tandem array by choosing appropriate vectors which have nonpalindromic sequences. We have obtained approximately 200 members of the 256 possible clones and have organized the vectors using a MacIntosh HyperCard program for easy retrieval.

Base Sequence↗
PubMed2000

Genomics of Bordetella pertussis toxins.

Bordetella pertussis, the etiologic agent of whooping cough, produces numerous toxins including pertussis toxin (PTX), adenylate cyclase toxin (AC), dermonecrotic toxin (DNT) and tracheal cytotoxin (TCT). PTX is composed of five different subunits organised in a typical A-B type structure of which the A part possesses an enzymatic ADP-ribosyltransferase activity and the B moiety expresses receptor-binding activity. The secretion of this toxin requires nine other genes (ptl) organised in an operon together with the five structural genes of PTX. To further characterise the genetic locus of this major virulence factor, we analysed the ptx/ptl upstream and downstream sequences. Comparison of these regions between three species of Bordetella (B. pertussis, Bordetella parapertussis and Bordetella bronchiseptica) revealed differences in the upstream region. Analysis of two strains of B. bronchiseptica naturally lacking the ptx genes showed that only the ptx/ptl genes were deleted in these strains, and that the upstream and downstream regions were conserved. Upstream of the PTX structural genes and the promoter, an open reading frame (bugT) was identified, the product of which is homologous with putative proteins from several other Gram-negative organisms. Detailed analysis of the genome of B. pertussis which is currently sequenced at the Sanger Centre revealed the presence of 90 genes coding for proteins homologous to BugT, which qualifies the bug gene family as the most populated one of Bordetella. These bug genes are located in various genetic environments, including the proximities of genes coding for other toxins, such as DNT and AC. The Bug proteins are highly conserved in terms of size and periodicity of predicted secondary structure elements, but have also a high variability in their amino acid composition reflected in their wide range of isoelectric points. The function of these genes which is currently unknown is under investigation. To characterise the expression and regulation of these genes, as well as of novel putative B. pertussis virulence factors, we designed a transcriptional fusion vector to be inserted in precise locations of the B. pertussis chromosome by homologous recombination. The reporter gene present in this vector allowed us to show that at least some of the bug genes are expressed.

Adenylate Cyclase Toxin↗
PubMed2003

Purification and properties of the Dictyostelium calpain-like protein, Cpl.

Calpains are intracellular, cysteine proteases found in plants, animals, and fungi. There is emerging evidence that they are important mediators of cell adhesion and motility in animal cells. Because the cellular slime mold, Dictyostelium discoideum, is a genetically tractable model for cell adhesion and motility, we have investigated whether a calpain-like protein is expressed in this organism. Contig 13130 (Sanger Institute Dictyostelium sequencing project) was identified as a three-exon gene that encodes a calpain-like protein. Using a custom peptide antibody to assay for the presence of this putative protein, we identified Dictyostelium calpain-like protein (Cpl) and purified it to near homogeneity. Cpl is a 72278 Da cytosolic protein. Weak caseinolytic activity inhibitable by cysteine protease inhibitors was copurified with Cpl immunoreactivity, and purified Cpl appeared to undergo autoproteolysis upon transfer to inhibitor-free buffer. The major cleavage, generating a 51291 Da form, occurred after Pro 189. The Cpl domain structure resembles mammalian calpain 10, comprising an N-terminal catalytic domain followed by tandem calpain D-III domains. The putative catalytic domain appears to possess His and Gln active site residues, instead of the canonical His and Asn residues in calpains. The active site Cys has not yet been identified, and definitive proof of a proteolytic function awaits further study. Its phylogenetic distribution in D. discoideum and several protists suggests that the calpain D-III domain evolved early in eukaryotic cells.

Amino Acid Sequence↗
PubMed1992

The recognition of DNA cleavage sites by porcine spleen topoisomerase II.

The cutting sites specificity of topoisomerase II from porcine spleen were determined by a modified Sanger's DNA sequencing method. The topoisomerase II prefers to cut DNA at the 3' side of A and leave 5' protruding end with two staggering bases. Through the free energy analysis for DNA duplex, we also found that the topoisomerase II seemed cut DNA preferably at energetically unstable regions. So it is concluded that the specific DNA cutting by porcine spleen topoisomerase II has two structural recognition factors: one is to localize around the energetically unstable region and another is to act at the 3' side of A base.

Animals↗
PubMed1997

Lactose carrier mutants of Escherichia coli with changes in sugar recognition (lactose versus melibiose).

The purpose of this research was to identify amino acid residues that mediate substrate recognition in the lactose carrier of Escherichia coli. The lactose carrier transports the alpha-galactoside sugar melibiose as well as the beta-galactoside sugar lactose. Mutants from cells containing the lac genes on an F factor were selected by the ability to grow on succinate in the presence of the toxic galactoside beta-thio-o-nitrophenylgalactoside. Mutants that grew on melibiose minimal plates but failed to grow on lactose minimal plates were picked. In sugar transport assays, mutant cells showed the striking result of having low levels of lactose downhill transport but high levels of melibiose downhill transport. Accumulation (uphill) of melibiose was completely defective in all of the mutants. Kinetic analysis of melibiose transport in the mutants showed either no change or a greater than normal apparent affinity for melibiose. PCR was used to amplify the lacY DNA of each mutant, which was then sequenced by the Sanger method. The following six mutations were found in the lacY structural genes of individual mutants: Tyr-26-->Asp, Phe-27-->Tyr, Phe-29-->Leu, Asp-240-->Val, Leu-321-->Gln, and His-322-->Tyr. We conclude from these experiments that Tyr-26, Phe-27, Phe-29 (helix 1), Asp-240 (helix 7), Leu-321, and His-322 (helix 10) either directly or indirectly mediate sugar recognition in the lactose carrier of E. coli.

Amino Acids↗
PubMed2004

Genetic analysis of chs1+ and chs2+ encoding chitin synthases from Schizosaccharomyces pombe.

To explore the function of chitin in Schizosaccharomyces pombe, we have cloned chs1+ and chs2+, encoding putative chitin synthases, based on sequences in the Sanger Centre database. The synthetic lethal phenotype of the S. cerevisiae chs1 chs2 chs3 mutant was complemented by expression of S. pombe chs1+ or chs1+, indicating that both chs1+ and chs2+ in fact encode chitin synthase. The homothallic Deltachs1 strain formed abnormal asci that contained 1, 2, or 3 spores, while the Deltachs2 strain had no noticeable phenotype. The chs1 chs2 double disruptant looked similar phenotypically to the Deltachs1 strain. The Chs2-GFP fusion protein predominantly localized at the septum after the septum was formed during vegetative growth. The level of chs2+ mRNA increased just before the septum was formed. Levels of Chs2-13Myc synthesis also changed during the cell cycle. Thus, chs1+ is required for proper spore formation, and chs2+ is perhaps involved in septum formation.

Benzenesulfonates↗
PubMed2001

[Construction of eukaryotic expression plasmid pcDNA3-gtfB expressing glucosyltransferase B of Streptococcus mutans].

OBJECTIVE: Glucosyltransferase (GTF) of Streptococcus mutans is considered as a cariogenic virulence factor due to its ability to synthesize glucan, which facilitate sucrose-depended adherence and cell-to-cell accumulation of bacteria. In this study, gtfB, the target gene fragment which encodes multiple catalytic sites and antigen epitopes of GTF, was recombined into eukaryotic expression vector pcDNA3. The feasibility of the recombination plasmid pcDNA3-gtfB used as gene vaccine will be investigated in further study. METHODS: The target gene fragment gtfB (904-4578 bp) was obtained by standard PCR amplification while genome DNA of streptococcus mutans GS-5 was used as template. Then the PCR products were extracted and purified from low-melting temperature agarose. The gtfB and plasmid pcDNA3 were cut by Kpn I, Xho I, and the digested products were extracted and purified again for recombination. The purified gtfB and plasmid pcDNA3 were recombined by T4 DNA ligase, ligation products were transformed into competent cell, Escherichia coli JM109. Transformed colonies were screened by Ampr LB plate, then recombined plasmids were isolated and identified by restricted endonuclease cutting and Sanger dideoxy DNA sequencing. RESULTS: Identified by agarose gel electrophoresis, the target gene-gtfB obtained PCR amplification had the same molecular size (36 kb) as predicted. It was indicated that recombined plasmids contained inserted gtfB gene fragment by restricted endonuclease cut analysis, the sequencing data also indicated that inserted gtfB gene had correct DNA sequence and orientation according to DNA sequence of Streptococcus mutans GS-5 (gene bank M17361). CONCLUSION: Inserted gene-gtfB of recombined plasmid pcDNA3-gtfB encoded multiple catalytic sites and epitopes. It was proved that these epitopes had high immune antigenicity and that antiserum could significantly inhibit the synthesis of water-insoluble glucans and water-soluble glucan. In vitro adherence experiment also indicated that it could inhibit streptococcus mutans adherence to saliva-coated hydroxyapatite. Vector pcDNA3 was high expressing eukaryotic vector, and could stimulate antigen-representing cell. It was suggested that recombined plasmid pcDNA3-gtfB had high immune antigenicity and immune responsiveness, and this supported its use as gene vaccine candidates in the development of anti-caries vaccines.

Dental Caries↗
PubMed2003

[Construction of plant expression plasmid of chimera SBR-CT delta A1].

OBJECTIVE: The purpose of this study is to construct plant expression plasmid containing the gene encoding chimera SBR-CT delta A1. METHODS: The target gene fragment P2, including the gene-encoded chimera SBR-CT delta A1 (3,498-5,378 bp), was obtained by standard PCR amplification. The PCR products were ligated with pGEM-easy vector through TA clone to form plasmid pTSC. The plasmid pTSC and plasmid pPOKII were digested by restricted endonuclease BamHI and KpnI, and the digested products were extracted and purified for recombination. Then the purified P2 and plasmid pPOKII were recombined by T4 DNA ligase to form recombinant plasmid pROSC; inserting bar gene into the plasmid and form pROSB plasmid. The recombined plasmids were isolated and identified by restricted endonuclease cutting and Sanger dideoxy DNA sequencing. RESULTS: P2 gene was linked to pPOKII plasmid and formed recombinant plasmid pROSC. The DNA sequence and orientation were corrected. And bar gene was inserted into pPOSC and form recombinant plasmid pROSB. CONCLUSION: Plant expression vector pROSC and pROSB containing the gene encoding chimera SBR-CT delta A1, which may provide useful experiment foundation for further study on edible vaccine against caries have been successfully constructed.

Adhesins, Bacterial↗
PubMed2004

[Construction of eukaryotic expression plasmid pSecTag2B-msBlyS expressing mouse soluble B lymphocyte stimulator].

OBJECTIVE: The purpose of this study was to clone the soluble form of the mouse BlyS (msBlyS) and insert it into a eukaryotic expression vector pSecTag2B in order to further elucidat the antitumor activity induced by msBlyS expressed by the recombined plasmid pSecTag2B-msBlyS. METHODS: Full length cDNA of mouse soluble BlyS (msBlyS) was amplified by reverse transcription-PCR from total RNA of mouse spleen. The PCR product was ligated directly with linearized vector pCR2.1 supplied in the TA cloning kit. The recombined plasmid pCR2.1-msBlyS which was selected and identified using blue-white screening method and restriction map analysis and the purified original plasmid pSecTag2B were both cut by HindIII and EcoR I. The digested fragments were extracted and purified from low-melting temperature agarose and ligated by T4DNA ligase. The recombined plasmid pSecTag2B-msBlyS were isolated and identified by restricted endonuclease cutting and Sanger dideoxy DNA sequencing. RESULTS: The sequencing data indicated that inserted msBlyS gene had correct DNA sequence and orientation. CONCLUSION: Eukaryotic expression vector pSecTag2B. Expressing mouse BlyS have successfully been cloned. This will provide us an opportunity to do further research work on BlyS.

Animals↗