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PubMed2005

Cloning of a CACTA transposon-like insertion in intron I of tomato invertase Lin5 gene and identification of transposase-like sequences of Solanaceae species.

Very few CACTA transposon-like sequences have been described in Solanaceae species. Sequence information has been restricted to partial transposase (TPase)-like fragments, and no target gene of CACTA-like transposon insertion has been described in tomato to date. In this manuscript, we report on a CACTA transposon-like insertion in intron I of tomato (Lycopersicon esculentum) invertase gene Lin5 and TPase-like sequences of several Solanaceae species. Consensus primers deduced from the TPase region of the tomato CACTA transposon-like element allowed the amplification of similar sequences from various Solanaceae species of different subfamilies including Solaneae (Solanum tuberosum), Cestreae (Nicotiana tabacum) and Datureae (Datura stramonium). This demonstrates the ubiquitous presence of CACTA-like elements in Solanaceae genomes. The obtained partial sequences are highly conserved, and allow further detection and detailed analysis of CACTA-like transposons throughout Solanaceae species. CACTA-like transposon sequences make possible the evaluation of their use for genome analysis, functional studies of genes and the evolutionary relationships between plant species.

Amino Acid Sequence↗
PubMed2003

Identification of Listeria monocytogenes genes involved in salt and alkaline-pH tolerance.

The capacity of Listeria monocytogenes to tolerate salt and alkaline stresses is of particular importance, as this pathogen is often exposed to such environments during food processing and food preservation. We screened a library of Tn917-lacZ insertional mutants in order to identify genes involved in salt and/or alkaline tolerance. We isolated six mutants sensitive to salt stress and 12 mutants sensitive to salt and alkaline stresses. The position of the insertion of the transposon was located in 15 of these mutants. In six mutants the transposon was inserted in intergenic regions, and in nine mutants it was inserted in genes. Most of the genes have unknown functions, but sequence comparisons indicated that they encode putative transporters.

Bacterial Proteins↗
PubMed1992

Identification of the gene (aroK) encoding shikimic acid kinase I of Escherichia coli.

DNA sequence analysis has revealed that an unidentified open reading frame (ufr1) is present immediately preceding the aroB gene of Escherichia coli. The predicted protein product of urf1 contains a consensus ATP-binding-site sequence and shows 34% amino acid homology to shikimate kinase II in a 97-amino-acid region. Inactivation of urf1 by insertion of an antibiotic resistance gene had a polar effect on aroB, indicating that these two genes constitute a transcriptional unit. The auxotrophic requirements of a strain mutant for both urf1 and aroL (encoding shikimate kinase II) are consistent with shikimate kinase deficiency. We propose that urf1 encodes shikimate kinase I and that it be designated aroK.

Amino Acid Sequence↗
PubMed1989

Direct selection for curing and deletion of Rhizobium plasmids using transposons carrying the Bacillus subtilis sacB gene.

We have constructed derivatives of the transposon Tn5 carrying the mob site (oriT) of plasmid RP4, and an nptI-sacB-sacR cassette [Ried and Collmer, Gene 57 (1987) 239-246]. The mob site, in conjunction with the antibiotic-resistance markers carried on the transposons, allows identification of transposon inserts in cryptic plasmids by mobilisation to other strains. The sacB-sacR genes allow direct selection for the loss or curing of plasmids, because only strains which no longer contain an active sacB gene are able to grow on media containing sucrose. We have tested these transposons in four strains of Rhizobium leguminosarum and two strains of Rhizobium meliloti, and have been able to demonstrate curing of several large cryptic plasmids, and generation of large deletions in many other plasmids. This method has enabled us to show that the R. leguminosarum plasmids pRL12JI and pR1eVF39f carry auxotrophic markers, and that the plasmid pR1eVF39c carries genes which affect colony morphology.

Bacillus subtilis↗
PubMed1990

Characterization of a Listeria monocytogenes-specific protein capable of inducing delayed hypersensitivity in Listeria-immune mice.

Recovery of the host after infection by the intracellular pathogen Listeria monocytogenes is dependent on cell-mediated immunity. Little is known of the nature of listerial antigens that induce cell-mediated responses in the infected host. In this study we report on the identification and cloning of an Escherichia coli recombinant encoding a listerial antigen, designated ImaA, capable of eliciting a specific delayed-type hypersensitivity response in Listeria-immune mice. Nucleotide sequencing of the Listeria DNA insert in plasmid pLM10 showed that the ImaA gene product consisted of 170 amino acids with a molecular weight of 17,994. The predicted amino acid sequence suggests that the protein is localized to the bacterial plasma membrane or cell wall. The ImaA gene was unique to the pathogenic species L. monocytogenes and Listeria ivanovii; it was not present in any other species of the genus Listeria.

Amino Acid Sequence↗
PubMed1990

Molecular biology of Crohn's disease mycobacteria.

A Glasgow surgeon, T.K. Dalziel, published a detailed description of chronic enteritis in humans in 1913. He proposed that the disease was caused by the same organisms as those responsible for chronic enteritis, Johne's disease, in animals described a few years earlier (1895). Dalziel's dilemma was that he could see acid-fast bacilli in the diseased animal tissues but not in the diseased human tissues. Little real progress in the medical understanding of the causes of chronic enteritis in humans occurred over the next half a century or more. From 1978, a decade of research in many laboratories using improved methods for the culture of environmental mycobacteria showed that these could be grown in bacillary form from about one in five cases of Crohn's disease, from the same proportion of cases of ulcerative colitis, and from about one in ten control tissues. Spheroplasts were grown from two in five cases of Crohn's disease, one in five cases of ulcerative colitis, and rarely from control tissues. The nature of these agents was often uncertain. We describe work which began in 1985 and led rapidly to the identification of IS900, a DNA repetitive element in an uncharacterized Crohn's disease mycobacterial isolate. With other isolates, these were then shown by DNA fingerprinting to be indistinguishable from Mycobacterium paratuberculosis, Johne's bacillus. Similar techniques also demonstrated the wood-pigeon strain of M. avium in some Crohn's disease cultures. This bacillus can also cause chronic enteritis in calves. IS900 is the first of a family of unusual DNA insertion sequences which extend widely throughout environmental mycobacteria. Use of assays based on PCR amplification of highly specific DNA sequences from these insertional elements, and recombinant and synthetic peptides from their predicted proteins, will revolutionize the detection and characterization of these agents. These methods, applied to animal, human and environmental samples, will indicate new ways for the prevention and treatment of chronic enteritis, as well as other disorders associated with infections by environmental mycobacteria.

Actinomycetales↗
PubMed1985

Identification of the Escherichia coli deoR and cytR gene products.

The protein products encoded by the Escherichia coli deoR and cytR structural genes have been identified based on results obtained from E. coli maxicells harboring (i) recombinant plasmids carrying wild-type deoR and cytR genes, (ii) deletion derivatives of the deoR+ and cytR+ plasmids, (iii) plasmids containing site-specific mutations in the deoR and cytR structural genes, and (iv) plasmids which have transposon Tn1000 inserted into the deoR and cytR structural genes. Analysis of the protein profiles obtained from all the maxicell experiments demonstrated that the deoR gene encodes a protein with a subunit molecular weight of 30,500 and that the product of the cytR gene is a protein with a subunit molecular weight of 37,000.

Base Sequence↗
PubMed1985

Analysis of the ruv locus of Escherichia coli K-12 and identification of the gene product.

The ruv gene of Escherichia coli, which is associated with inducible mechanisms of DNA repair and recombination, has been cloned into the low-copy plasmid vector pHSG415. The recombinant plasmid pPVA101 fully complements the DNA repair-deficient phenotype of ruv mutants. Restriction endonuclease analysis of this plasmid revealed a 10.6-kilobase (kb) HindIII DNA insert which contained a 7.7-kb PstI fragment identified as being from the chromosomal ruv region. Deletion analysis and Tn1000 insertional inactivation of ruv function located the ruv coding region to a 2.2-kb section of the cloned DNA fragment. A comparison of the proteins encoded by ruv wild-type and mutant plasmids identified the gene product as a protein of molecular weight 41,000.

Bacterial Proteins↗
PubMed1987

Identification of the DNA sequence required for transposition immunity of the gamma delta sequence.

A plasmid containing the transposon gamma delta sequence was immune to further insertion of gamma delta (transposition immunity). Plasmids carrying a fragment containing either 0.2 kilobase pairs of the gamma end or 0.4 kilobase pairs of the delta end of the gamma delta sequence were immune, and other parts of the gamma delta sequence did not confer immunity. The terminal 38-base-pair (bp) sequence of the delta end of the gamma delta was sufficient to confer immunity, the 38-bp sequence of the gamma end conferred only moderate immunity, and the terminal 35-bp sequence, which was completely identical at both the gamma and delta ends, was insufficient to confer immunity.

Base Sequence↗
PubMed1994

A family of vectors that facilitate transposon and insertional mutagenesis of cloned genes in yeast.

This report describes two sets of plasmid vectors that facilitate the identification of regions of complementation in cloned genomic inserts via transposon or insertional mutagenesis. The first set contains ARS-H4 CEN6, a yeast selectable nutritional marker (HIS3, TRP1 or URA3), and neo for selection in Escherichia coli. These plasmids lack the Tn3 transposition immunity region present in pBR322 derived vectors, and are permissive recipients for Tn3 transposon mutagenesis. The second family of plasmids described facilitate gene disruption procedures performed in vitro. These vectors carry disruption cassettes that contain different yeast selectable markers (HIS3, LEU2, TRP1 or URA3) adjacent to the Tn5 neo gene. These genes can be excised as a cassette on a common restriction fragment and introduced into any desired restriction site with selection for kanamycin resistance.

Cloning, Molecular↗
PubMed1995

Structure of the int-5, a novel MMTV integration genomic locus containing mouse early transposon LTR homology region.

Previous studies have reported the cloning and identification of the int-5, a novel mouse mammary tumor virus (MMTV) integration locus involved in mammary tumorigenesis. Here we report the characterization of the 5.5 kb region from this novel MMTV integration site. Our results show that the region after the MMTV integration site, a 258 bp sequence is homologous (100%) to the mouse early transposon (mETn) long-terminal repeat and other sequences of the this transposon are not present in the 5.5 kb region. Our results also show for the first time the tumor specific expression of mETn and expression of the region downstream of the MMTV integration site that is homologous to mETn-LTR in D2 mammary tumors.

Animals↗
PubMed1996

Spectrum of somatic mutation at the hypoxanthine phosphoribosyltransferase (hprt) gene of healthy people.

Understanding the significance of somatic mutations requires knowledge of the mutations that occur in vivo in healthy people. The molecular characterization of mutations in the hypoxanthine phosphoribosyltransferase (hprt) gene in 217 independent T-lymphocyte mutants from 172 donors, including smoking and non-smoking males and females, reveals a broad spectrum of in vivo somatic mutation occurring in a population of healthy people. Identification of the DNA alteration in individual mutant clones was accomplished using either one or a combination of multiplex polymerase chain reaction analysis of genomic DNA, sequencing of cDNA, and genomic DNA sequencing. The total spectrum consists of 59% (128/217) base substitutions: 126 simple and two tandem CC>TT base substitutions; 39% (85/217) deletion/insertion type mutations: 30 frameshifts, 26 small (3-200 basepairs) and 27 large deletions, and two duplications; and the remaining 2% (4/217) complex mutations involving the deletion of one to 11 basepairs which are replaced by 1 to 10 basepairs. No significant difference was detected between the base substitution spectra for the smokers and the non-smokers. Analysis of the number of mutations occurring at any one base position led to the identification of three hotspots for mutations at basepairs 197, 508 and 617, in the hprt gene coding region. Spontaneous deamination of CpG may be implicated in the creation of basepair 508 as a hotspot since all mutations detected are C>T transitions resulting in the nonsense mutation, TAG. At basepairs 197 and 617 both G>T transversions and G>A transitions were found indicating that at least two mechanisms were involved in creating mutations at these positions. Comparison of the mutation spectra from two populations can provide insight into the origin of the mutations. This study provides an excellent base for comparison of mutation spectra in other human populations.

Adult↗
PubMed2001

VpsR, a Member of the Response Regulators of the Two-Component Regulatory Systems, Is Required for Expression of vps Biosynthesis Genes and EPS(ETr)-Associated Phenotypes in Vibrio cholerae O1 El Tor.

The rugose colonial variant of Vibrio cholerae O1 El Tor produces an exopolysaccharide (EPS(ETr)) that enables the organism to form a biofilm and to resist oxidative stress and the bactericidal action of chlorine. Transposon mutagenesis of the rugose variant led to the identification of vpsR, which codes for a homologue of the NtrC subclass of response regulators. Targeted disruption of vpsR in the rugose colony genetic background yielded a nonreverting smooth-colony morphotype that produced no detectable EPS(ETr) and did not form an architecturally mature biofilm. Analysis of two genes, vpsA and vpsL, within the vps cluster of EPS(ETr) biosynthesis genes revealed that their expression is induced above basal levels in the rugose variant, compared to the smooth colonial variant, and requires vpsR. These results show that VpsR functions as a positive regulator of vpsA and vpsL and thus acts to positively regulate EPS(ETr) production and biofilm formation.

Amino Acid Sequence↗
PubMed1982

[Formation of stable Hfr strains in R factor RP1 integration with the chromosome of E. coli K12 recA and their use for R-plasmid selection].

Analysis of thermoindependent derivatives of E. coli K12 JC1553 recA (p VD1) carrying a replication thermostable mutant pVD1 of R factor RP1 IncP Ap Km Tc showed that formation of about 5 per cent of them was associated with stable integration of the plasmid with the bacterial chromosome. The respective bacteria had the following features: (1) preserved all the markers of plasmid pVD1, (2) according to the data of the electrophoretic analysis had no extrachromosomal DNA on prolonged cultivation under nonselective conditions, (3) were effective donors of the chromosomal genes, (4) had a low rate of the plasmid marker transfer on crossing with R- recipient. The latter feature was suggested to be used as a test for identification of stable Hfr strains. Investigation of the properties of the transconjugants obtained on crossing of stable Hfr strains with R-recipients rec+ showed that same of them had plasmid DNA with a higher molecular mass as compared to that of plasmid pVD1 DNA. The presence of this DNA was connected with formation of R' plasmid as a result of an irregular exclusion of plasmid pVD1 from the chromosome of stable Hfr bacteria. On the basis of the results a simple method was proposed for selection of R' plasmids having a number of advantages over the classical ones. The perspectives of using thermostable derivatives of RP1 for cloning the chromosome genes are discussed.

Chromosomes, Bacterial↗
PubMed1987

The yeast ROAM mutation--identification of the sequences mediating host gene activation and cell-type control in the yeast retrotransposon, Ty.

When the yeast retrotransposon, Ty, integrates into the 5' flanking region of a gene it can activate the expression of that gene. At the same time the activated gene is brought under cell-type specific control such that expression is high in haploid a or alpha cells but low in a/alpha diploids. These Ty mediated mutations are known as ROAM mutations. In this study we have used a ROAM mutation created in vitro to identify the sequences within Ty that mediate this phenomenon. We show that a single activator located within the coding region of the Ty element is responsible for ROAM activation. This sequence, which is regulated by the mating type of the cell, differs from classical enhancer elements in that its activity is strictly orientation dependent. An independent activator located downstream of the ROAM sequence activated transcription only in the non-ROAM orientation. This sequence may be part of an internal promoter that controls expression of the sub-genomic 5.0kb Ty transcript.

DNA Transposable Elements↗
PubMed1987

Use of TnphoA to detect genes for exported proteins in Escherichia coli: identification of the plasmid-encoded gene for a periplasmic acid phosphatase.

The structural gene (appA) for the periplasmic acid phosphatase (optimum pH 2.5) of Escherichia coli was cloned into a plasmid by using a combination of in vivo and in vitro techniques. The position and orientation of the appA gene within the cloned DNA fragment were identified by using fusions to the alkaline phosphatase gene (phoA) generated by Tn5 IS50L::phoA (TnphoA) insertions. For TnphoA-generated hybrid proteins to have high enzymatic activity, it appears that the phoA gene must be fused to a target gene coding for a signal which promotes protein export. The approach used to identify the appA gene thus appears to provide a simple general means of selectively identifying genes encoding membrane and secreted proteins.

Acid Phosphatase↗
PubMed1992

Identification of an internal cis-element essential for the human L1 transcription and a nuclear factor(s) binding to the element.

L1 (LINE-1) is a long interspersed repetitive sequence derived from a retrotransposon. Transfection studies using the CAT gene as a reporter demonstrated that the first 155bp in the human L1 sequence contains an element(s) responsible for the promoter activity in HeLa cells. The transcription was shown to initiate at the first nucleotide of the L1 sequence in the transgene. Three prominent nuclear protein binding sites were found in the 5' region of the L1 sequence by DNaseI footprint analysis. One of the binding sites, designated as site A located at +3 to +26, was shown to be essential for the L1 transcription because the mutation at the site A caused almost complete loss of the promoter activity. A sequence AAGATGGCC at +11 to +19 in the site A was defined as a target core element for the protein binding. The site A-binding protein (designated TFL1-A) was found in various types of cells including an embryonic teratocarcinoma cell line. These results indicate that an internal short element located at the very 5' terminal of L1 sequence and the nuclear factor binding to the element play a crucial role in the transcription of human L1.

Amino Acid Sequence↗
PubMed1987

Identification of the structural gene encoding the SH-activated hemolysin of Listeria monocytogenes: listeriolysin O is homologous to streptolysin O and pneumolysin.

By immunoblotting with an antiserum raised against purified listeriolysin O, we have detected the presence of a truncated protein of 52 kilodaltons in culture supernatants of a Tn1545-induced nonhemolytic mutant of Listeria monocytogenes (J.L. Gaillard, P. Berche, and P. Sansonetti, Infect. Immun. 52:50-55, 1986). The region of insertion of the transposon has been cloned and sequenced. The transposon had inserted in an open reading frame the listeriolysin O gene. The deduced amino acid sequence of this open reading frame revealed that listeriolysin O is homologous to streptolysin O and pneumolysin, although homologies were not detectable at the DNA level.

Bacterial Proteins↗