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PubMed1997

Proline-rich-protein promoters direct LacZ expression to the granular convoluted tubular cells of the submandibular gland in adult transgenic mice.

The ability of two mouse PRP gene promoters to direct the expression of the bacterial lacZ reporter gene was tested in transgenic mice. Transgenes A1-lacZ and C1-lacZ consisted of 8.2 kb A1 and 7.8 kb C1 PRP promoters respectively fused to the lacZ coding sequence. A1 and C1 are two A-type PRP genes isolated from the inbred SWR mice, which show the same gene structure and similar sequence to the closely related MP2 and M14 PRP genes previously cloned from outbred CD-1 mice. We here show that both A1-lacZ and C1-lacZ transgenes have very similar expression patterns: (1) they expressed the lacZ gene in all 14 established transgenic lines under normal (non-stimulated) conditions; (2) the expression was restricted to the granular convoluted tubular cells of the submandibular glands; (3) the expression was developmentally regulated beginning at sexual maturation and lasting to at least 1.5 years of age; and (4) expression in some lines was probably influenced by sex hormones, since higher expression was found in males than in females. A1-lacZ and C1-lacZ are the first transgenes derived from the PRP/GRP (glutamine/glutamic acid-rich protein) gene superfamily to be expressed in the granular convoluted tubular cells (with known endocrine functions), rather than in the acinar cells (with mainly exocrine functions) of the submandibular glands.

Animals↗

PubMed1997

Molecular cloning, chromosomal localization, and expression of murine dipeptidyl peptidase I.

Dipeptidyl peptidase I (DPPI) is a lysosomal cysteine protease that catalyzes the sequential removal of dipeptides from the amino termini of various protein substrates. We have isolated a cDNA coding for murine DPPI from mouse thymus and spleen cDNA libraries. The deduced amino acid sequence codes for a protein of 462 amino acid residues; comparison of this deduced sequence with that of rat and human DPPI revealed 90.1% and 77.8% identity, respectively. Using DPPI cDNA, we obtained two BAC (Bacterial Artificial Chromosome) clones that contained the murine DPPI locus. The DPPI gene consists of seven exons and 6 introns, and spans approximately 20 kilobases. Using fluorescence in situ chromosome hybridization, we localized murine DPPI to chromosome 7D3-E1.1. We determined that DPPI protein is widely distributed in mouse tissues, although its relative abundance varies from tissue to tissue. In contrast to previous reports, we show here that DPPI mRNA and protein levels and enzymatic activity are unchanged during in vitro T cell activation, implying that this enzyme is not rate-limiting for granzyme processing.

Amino Acid Sequence↗

PubMed1989

Monoclonal antibodies for affinity purification of IL-6/IFN- beta 2 and for neutralization of HGF activity.

Two types of recombinant human IL-6 (rIL-6) were used for the development of specific monoclonal antibodies. The first was produced in E. coli and used for immunization, the second was produced in Chinese Hamster Ovary Cells (CHO) and used for screening. The complete translated sequence of the cDNA coding for human IL-6 was fused, in phase, to protein-A and the hybrid gene was fused to the strong lambda PR promoter. This protein was purified from bacterial extracts by chromatography on rabbit IgG-Sepharose columns. After six injections of the purified protein into mice, sera were tested for their binding titer in a solid phase radioimmunassay (sRIA) and for the specificity of binding by Western blots. In the sRIA, crude supernatants of CHO cells (harboring a plasmid containing the human IL-6 gene and expressing high levels of IL-6 but no protein-A or any bacterial antigen) were bound to a solid support, reacted with supernatants of the hybridomas and finally detected with [125I]-goat anti-mouse antibodies. Spleen cells derived from a mouse showing the highest binding titer were fused to mouse myeloma cells. The hybridomas were screened by the sRIA and several positive clones were isolated and characterized. One of the clones was found to neutralize the hybridoma growth factor activity of the rIL-6 from both sources. The same clone was also used for Western blots and for affinity purification of both natural and recombinant IL-6 (E. coli and CHO).

Animals↗

PubMed2004

DNAskew: statistical analysis of base compositional asymmetry and prediction of replication boundaries in the genome sequences.

Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

Algorithms↗

PubMed1990

Identification of three genes coding for aminoglycoside-modifying enzymes by means of the polymerase chain reaction.

A polymerase chain reaction (PCR) was devised for the simultaneous identification of three widespread aminoglycoside-acetylating enzymes (AACs), namely, AAC(3)-I, AAC(3)-II and AAC(3)-IV. Three sets of 20-mer DNA primers were constructed, based on the nucleotide sequences of the genes coding these enzymes. Each of the three gene regions contained a unique restriction site. This property was used to confirm the specificity of the reactions. Evolutionarily-well-conserved sequences of the 16S rRNA bacterial genes were used to construct two 20-mer primers, which served as positive controls for the amplification reactions. Tests of twenty reference strains, containing ten different aminoglycoside-modifying enzymes, confirmed the specificity and the sensitivity of the method. The PCR method confirmed the presence of the aacC2 gene in 63 clinical strains, in which susceptibility data and colony hybridization had previously suggested the presence of the gene.

Acetylation↗

PubMed1990

Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1(M.SssI).

We describe here the cloning, characterization and expression in E. coli of the gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). This enzyme methylates completely and exclusively CpG sequences. The Spiroplasma gene was transcribed in E. coli using its own promoter. Translation of the entire message required the use of an opal suppressor, suggesting that UGA triplets code for tryptophan in Spiroplasma. Sequence analysis of the gene revealed several UGA triplets, in a 1158 bp long open reading frame. The deduced amino acid sequence revealed in M.SssI all common domains characteristic of bacterial cytosine DNA methylases. The putative sequence recognition domain of M.SssI showed no obvious similarities with that of the mouse DNA methylase, in spite of their common sequence specificity. The cloned enzyme methylated exclusively CpG sequences both in vivo and in vitro. In contrast to the mammalian enzyme which is primarily a maintenance methylase, M.SssI displayed de novo methylase activity, characteristic of prokaryotic cytosine DNA methylases.

Amino Acid Sequence↗

PubMed1996

Molecular data suggest an early acquisition of the mitochondrion endosymbiont.

The three deepest branching eucaryotic lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microspora, Metamonada and Parabasala. They are followed by either the Euglenozoa (e.g. Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eucaryotes. To investigate the hypothesis of an even earlier timing of the mitochondrion endosymbiosis we have amplified a partial cpn-60 coding region from the parabasalid Trichomonas vaginalis and the first such sequence from a percolozoan, Naegleria fowleri. Analysis of predicted protein sequences reveals a high degree of sequence similarity (> or = 40%) with a selection of published bacterial and mitochondrial cpn-60s for both taxa. Both sequences were recovered within a strongly supported monophyletic group, otherwise defined by mitochondrial sequences, which systematically clustered with alpha-proteobacteria. These results provide compelling evidence that the ancestor of T. vaginalis once contained the endosymbiont which gave rise to mitochondria, and suggest that this symbiosis probably occurred before the Trichomonas lineage diverged from the main eukaryote trunk. It also makes feasible the published hypothesis that the Trichomonas hydrogenosome might represent a biochemically modified mitochondrion. Analysis of the N. fowleri cpn-60 did not support the hypothesis that the mitochondrion-containing Percolozoa represent an earlier branch in the cpn-60 tree than Trichomonas or Trypanosoma.

Animals↗

PubMed1990

Expression and assembly of mature apotransacylase (E2b) of bovine branched-chain alpha-keto acid dehydrogenase complex in Escherichia coli. Demonstration of transacylase activity and modification by lipoylation.

A cDNA clone encoding the entire transacylase (E2b) precursor of the bovine branched-chain alpha-keto acid dehydrogenase complex (Griffin, T. A., Lau, K. S., and Chuang, D. T. (1988) J. Biol. Chem. 263, 14008-14014) was used to construct a prokaryotic expression vector for recombinant mature E2b. The overexpression in Escherichia coli correlates with the presence near the 5'-terminus of the mature E2b coding region (nucleotides 20 to 28) of the sequence 5'-TCAAACT-CT-3'. It has been proposed that this sequence is involved in secondary mRNA recognition through interaction with the 5'-terminus of the bacterial 16 S rRNA. The mature E2b protein has transacylase activity when assayed with exogenous dihydrolipoamide and [1-14C] isovaleryl-CoA as substrates. However, the recombinant protein has no attached lipoic acid. This was established by the absence of radiolabel incorporation when transformed E. coli cells were grown in a medium containing DL-[2-3H]lipoic acid. The recombinant mature E2b protein was purified to greater than 95% purity in one step using Sepharose 4B column chromatography. The purified recombinant protein was shown to have a cubic 24-mer structure by electron microscopy and to possess a specific activity similar to that of the purified natural bovine E2b. The purified recombinant mature E2b was lipoylated in vitro in the presence of 2 mM ATP using a mitochondrial extract prepared from bovine liver. The above results provide the first evidence that the proper folding and assembly of mature bovine E2b is independent of the attachment of lipoyl moieties and that mammalian lipoylation activity is present in mitochondria.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗

PubMed2003

Pathogenicity mechanisms of prokaryotic cells: an evolutionary view.

The success of pathogenic microbes depends on their ability to colonize host tissues and to counter host defense mechanisms. Microorganisms can produce overwhelming infection because of their relatively short generation times, and because they have evolved powerful mechanisms for generating phenotypic diversity as an efficient strategy for adapting to rapidly responding immune system defenses and the broad range of polymorphisms characteristic of different host tissues. Bacterial evolution may not be a continuous process, but more of a succession of temporally spaced major events. These events cause a non-gradual sequence of adaptations to a given environment. The pathogenicity islands are genetically unstable elements, and many of the genes coding for the adhesins, toxins and other virulence factors are present in pathogenicity islands, which almost certainly had former lives as accessory elements or as parts thereof, or were borne on functional accessory elements. Novel genes are also acquired by transduction (mediated by bacteriophages, plasmids or transposons), by conjugation (DNA transfer between cells) or by transformation (natural DNA uptake). Horizontal gene transfer from other species is a major source of variation and is fundamental to the genetic theory of adaptive evolution in prokaryotes.

Bacteria↗

PubMed1983

Cloning of the gene for C protein, a low molecular weight spore-specific protein from Bacillus megaterium.

The structural gene for C protein, a low molecular weight spore-specific protein from Bacillus megaterium, has been cloned in Escherichia coli. Expression of the C-protein gene in E. coli requires an external transcription promoter and prevention of termination of transcription prior to transcription of all or part of the sequence coding for the C protein. The gene for the C protein is within a 5-kilobase DNA fragment, but this fragment does not code for either of the other two major low molecular weight spore proteins, suggesting that the structural genes for these proteins are not tightly linked.

Bacillus megaterium↗

PubMed1980

The expression in E. coli of synthetic repeating polymeric genes coding for poly(L-aspartyl-L-phenylalanine).

Two dodecadeoxynucleotides of defined sequence have been synthesised by phosphotriester methodology. They can be polymerised to give a double stranded DNA which codes, when read in the correct phase, for the repeating dipeptide poly(aspartyl-phenylalanine). This polymeric DNA has been cloned in E. coli K12 using as vector a plasmid having a controllable bacterial promoter upstream of the insertion site. Clones containing genes coding for up to 150 repeats of (aspartyl-phenylalanine) have been isolated and characterised. The polymeric inserts appear to be stable over many generations and are expressed in E. coli under the control of the bacterial promoter, to give a polymer of phenylalanine and aspartic acid which may be broken down enzymically to yield aspartyl-phenylalanine.

Amino Acid Sequence↗

PubMed2002

Antigenic heterogeneity of the hepatitis C virus NS5A protein.

The effect of sequence variability between different types of hepatitis C virus (HCV) on the antigenic properties of the NS5 protein was studied by using recombinant proteins. A strong antigenic region was identified within the HCV NS5A protein at amino acids 2212 to 2313. Forty-five unique sequences encompassing this region were selected from GenBank and were compared to each other. The results of this analysis showed that the primary structure of this strong antigenic region is highly variable. Percent homology between different genotype sequences varied from 40.4 to 72.5%. Thirteen representative sequences from all six HCV genotypes were selected to design synthetic genes coding for this antigenic region. These genes were assembled by PCR from synthetic oligonucleotides and expressed in Escherichia coli as hybrid proteins with glutathione S-transferase. All 13 fusion proteins were purified from bacterial lysates and used to test a panel of anti-HCV positive sera (n = 91) obtained from patients infected with HCV genotypes 1 through 6. All but two proteins immunoreacted with 62 to 93% of HCV anti-NS5-positive serum samples. Although a variable degree of genotype-specific antigenic reactivity was detected, only one protein demonstrated a noticeable preference to immunoreact with antibodies against the homologous HCV genotype. On the other hand, closely related proteins derived from the same subtype or genotype immunoreacted with significantly different efficiency with HCV antibodies. Thus, sequence variability has a profound effect on the antigenic properties of the NS5A immunodominant regions. This observation should be taken into consideration in the development of diagnostic tests for the efficient detection of anti-HCV activity in serum specimens.

Amino Acid Sequence↗

PubMed1991

Relationship between tryptophan biosynthesis and indole-3-acetic acid production in Azospirillum: identification and sequencing of a trpGDC cluster.

Screening the tryptophan (Trp)-dependent indole-3-acetic acid (IAA) production of different Azospirillum species revealed that A. irakense KA3 released 10 times less IAA into the medium than A. brasilense Sp7. A cosmid library of strain Sp7 was transferred into A. irakense KA3 with the aim of characterizing genes involved in IAA biosynthesis. Trp-dependent IAA production was increased in two transconjugants which both contained an identical 18.5 kb HindIII fragment from Sp7. After Tn5 mutagenesis, cosmids carrying Tn5 insertions at 36 different positions of the 18.5 kb fragment were isolated and transferred into strain KA3. IAA production by the recipient strains was screened by HPLC. The Tn5 insertions of 4 clones with decreased IAA production were mapped on a 2 kb SalI-SphI fragment. Recombination of Tn5 insertions at this locus into the genome of strain Sp7 led to Trp auxotrophic mutants. A 5.2 kb EcoRI-SalI fragment including the 2 kb SalI-SphI fragment was sequenced and six open reading frames were identified. Three of them were clustered and their deduced amino acid sequences showed significant similarity to TrpG, TrpD and TrpC, which are enzymes involved in tryptophan biosynthesis. One of the remaining open reading frames probably encodes an acetyltransferase. The region responsible for the enhanced Trp-dependent IAA production in strain KA3 corresponded to trpD, coding for the phosphoribosyl anthranilate transferase.

Acetyltransferases↗

PubMed1988

Effects of 3' end deletions from the Vibrio harveyi luxB gene on luciferase subunit folding and enzyme assembly: generation of temperature-sensitive polypeptide folding mutants.

Ten recombinant plasmids have been constructed by deletion of specific regions from the plasmid pTB7 that carries the luxA and luxB genes, encoding the alpha and beta subunits of luciferase from Vibrio harveyi, such that luciferases with normal alpha subunits and variant beta subunits were produced in Escherichia coli cells carrying the recombinant plasmids. The original plasmid, which conferred bioluminescence (upon addition of exogenous aldehyde substrate) on E. coli carrying it, was constructed by insertion of a 4.0-kb HindIII fragment of V. harveyi DNA into the HindIII site of plasmid pBR322 [Baldwin, T.O., Berends, T., Bunch, T. A., Holzman, T. F., Rausch, S. K., Shamansky, L., Treat, M. L., & Ziegler, M. M. (1984) Biochemistry 23, 3663-3667]. Deletion mutants in the 3' region of luxB were divided into three groups: (A) those with deletions in the 3' untranslated region that left the coding sequences intact, (B) those that left the 3' untranslated sequences intact but deleted short stretches of the 3' coding region of the beta subunit, and (C) those for which the 3' deletions extended from the untranslated region into the coding sequences. Analysis of the expression of luciferase from these variant plasmids has demonstrated two points concerning the synthesis of luciferase subunits and the assembly of those subunits into active luciferase in E. coli. First, deletion of DNA sequences 3' to the translational open reading frame of the beta subunit that contain a potential stem and loop structure resulted in dramatic reduction in the level of accumulation of active luciferase in cells carrying the variant plasmids, even though the luxAB coding regions remained intact.

Amino Acid Sequence↗

PubMed1997

Insertional mutagenesis of a peptide synthetase gene that is responsible for hepatotoxin production in the cyanobacterium Microcystis aeruginosa PCC 7806.

Several bloom-forming cyanobacterial genera produce potent inhibitors of eukaryotic protein phosphatases called microcystins. Microcystins are hepatotoxic cyclic heptapeptides and are presumed to be synthesized non-ribosomally by peptide synthetases. We identified putative peptide synthetase genes in the microcystin-producing strain Microcystis aeruginosa PCC 7806. Non-hepatotoxic strains of M. aeruginosa lack these genes. Strain PCC 7806 was transformed to chloramphenicol resistance. The antibiotic resistance cassette insertionally inactivated a peptide synthetase gene of strain PCC 7806 as revealed by Southern hybridization and DNA amplification. This is the first report of genetic transformation and mutation, by homologous recombination, of a bloom-forming cyanobacterium. Chemical and enzymatic analyses, including high-performance liquid chromatography (HPLC), mass spectrometry, amino acid activation, and protein phosphatase inhibition, revealed the inability of derived mutant cells to produce any variant of microcystin while maintaining their ability to synthesize other small peptides. The disrupted gene therefore encodes a peptide synthetase (microcystin synthetase) that is specifically involved in the biosynthesis of microcystins. Our results confirm that microcystins are synthesized non-ribosomally and that a basic difference between toxic and non-toxic strains of M. aeruginosa is the presence of one or more genes coding for microcystin synthetases.

Bacterial Proteins↗

PubMed1981

Codon catalog usage is a genome strategy modulated for gene expressivity.

The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added. One sequence, that of B. mori fibroin, is dropped due to uncertainty on the starting point for translation. Frequencies of all codons are given for each gene added and for each genome type in the total bank. A new series of correspondence analyses on codon use is presented, substantiating the genome hypothesis. Internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.

Amino Acid Sequence↗

PubMed2006

Enhancement of antibacterial activity of beta-lactam antibiotics by [P2W18O62]6-, [SiMo12O40]4-, and [PTi2W10O40]7- against methicillin-resistant and vancomycin-resistant Staphylococcus aureus.

The enhancement of antibacterial activity of beta-lactam antibiotics by polyoxometalates against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) was investigated by using K6[P2W18O62] . 14H2O (P2W18), K4[SiMo12O40] . 3H2O (SiMo12), and K7[PTi2W10O40] . 6H2O (PTi2W10). Susceptibility test by a beta-lactam-disk method showed the synergistic effect of the polyoxometalates in combination with oxacillin against both MRSA and VRSA. Energy dispersive X-ray analysis of the strain treated with P2W18 revealed localization of the polyoxometalate-tungsten atoms at the periphery of the cell, and the biological reduction of P2W18 and SiMo12 proceeded within both cells of MRSA and VRSA as far as they keep alive. These results indicate that the polyoxometalates can penetrate through the cell wall consisting of peptidoglycan layers and reach cytoplasmic membrane. The inhibitory effect of the polyoxometalates on both mecA- and pbp-induced mRNA expression of both MRSA and VRSA cells, verified by the RT-PCR-electrophoresis analysis, is observed, and the mechanism of the synergistic effect by the polyoxometalates is discussed in terms of the depression of penicillin-binding protein 2' (PBP2') coded by mecA gene.

Anti-Bacterial Agents↗

PubMed2006

Sequence analysis of the plasmid pColG from the Escherichia coli strain CA46.

The complete 4715 nucleotide sequence of the plasmid pColG from the Escherichia coli strain CA46, which was originally assumed to code for colicin G activity, has been determined. Based on the nucleotide sequence homology of the 1828bp replication region, with an average G+C content of 48%, pColG was classified as a ColE1-like plasmid. Computer assisted analysis of the remaining 2887bp nucleotide sequence with an average G+C content of 34% revealed three putative OFRs. To find out whether one or all of the three ORFs code for a possible bacteriocin, a DNA fragment encompassing these ORFs has been cloned and the recombinant colonies tested for bacteriocin production. None of the colonies had an inhibitory activity against E. coli strains DH5, HB101 and MC4100. The assumption that the plasmid pColG from the E. coli strain CA46 codes for a bacteriocin thus could not be confirmed.

Bacteriocins↗