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PubMed2003

Identification of genetic loci required for capsular expression in Vibrio vulnificus.

Transposon mutagenesis of an encapsulated, virulent strain of Vibrio vulnificus 1003(O) led to the identification of four genetic regions that are essential to capsular polysaccharide (CPS) expression and virulence. Of the four regions, three are believed to be part of a capsule gene locus comprised of biosynthesis, polymerization, and transport genes clustered on a single chromosomal fragment. Genes indicating a Wzy-dependent system of polymerization and transmembrane export are present, suggesting that the CPS of V. vulnificus is lipid linked. The fourth region, while it contains a gene essential for CPS expression, is characteristic of an integron-gene cassette region, similar to the super integron of V. cholerae. It is not believed to be part of a CPS gene locus and is located in a region of the chromosome separate from the putative CPS loci. It is comprised of open reading frames (ORFs) carrying genes of unknown function surrounded by direct repeats. This region also contains IS492, an insertion sequence located numerous times throughout a region of the genome, demonstrating a restriction fragment length polymorphism among an encapsulated and nonencapsulated morphotype of V. vulnificus. Collectively, 22 ORFs were recognized: 13 capsule synthesis genes, 4 insertion sequences, 1 truncated biosynthesis gene, and 4 genes of unknown function. This study has led to the identification of previously unrecognized genetic loci that may help to increase the understanding of capsular genetics and antigenic diversity among V. vulnificus strains.

Animals↗
PubMed2001

Transmission dynamics and molecular characterization of Mycobacterium tuberculosis isolates with low copy numbers of IS6110.

Population-based analysis of Mycobacterium tuberculosis transmission in Houston, Tex., over 5 years identified 377 patients infected with an isolate containing one to four copies of IS6110. The isolates were analyzed by spoligotyping and assigned to one of three major genetic groups based on nucleotide polymorphisms in codons katG 463 and gyrA 95. Prospectively obtained patient interviews were reviewed to assess epidemiologic links between apparently clustered patients. A total of 13 groups of isolates with the same IS6110 profile were identified, representing 326 of the 377 patients (86.5%; range 2 to 113 patients). In contrast, 28 groups of isolates containing 334 patients (88.6%) had the same spoligotype (range, 2 to 143 patients). Combination of IS6110 profile and spoligotype data identified 31 clusters with 300 patients (79.6%; range, 2 to 82 patients). All 377 isolates belonged to major genetic group 1 (77 patients) or genetic group 2 (300 patients); no major genetic group 3 isolates were identified. Among the 228 patients interviewed, 33 patients (14.5%) were directly linked to another patient in the same cluster. Possible epidemiologic links were also found among 11 patients. Moreover, many clusters consisted of individuals with the same ethnicity. In conclusion, we confirmed that IS6110 profiling and spoligotyping together provide enhanced molecular discrimination of M. tuberculosis isolates with low copy numbers of IS6110. Identification of epidemiologic links among some of the patients verified that the combination of these two methods reliably indexes tuberculosis transmission.

Bacterial Typing Techniques↗
PubMed1988

Identification of a repeated sequence in the genome of the sea urchin which is transcribed by RNA polymerase III and contains the features of a retroposon.

A repeated sequence element which is located about 200 nucleotides upstream from the protein-coding portion of the muscle actin gene (probably within a large 5' intron) in the genome of the sea urchin, Strongylocentrotus purpuratus has been characterized, and shown to contain the sequence features which indicate that it has been transposed by means of an RNA intermediate. This retroposon-like sequence, SURF1-1, is a member of a family which is dispersed and repeated about 800 times in the genome, referred to as SURF1 (sea urchin retroposon family 1). In vitro transcription of this sequence by RNA polymerase III defines a 300 nucleotide transcription unit which is bounded by a short direct repeated sequence. The 3' end of this unit contains a simple 21 nucleotide A+T-rich sequence characteristic of retroponons, and a consensus B box portion of an internal RNA polymerase III promotor is located 60 to 80 nucleotides downstream from the two sites of transcription initiation. This sequence also contains a 40 nucleotide region that is related to several tRNA sequences (containing the B box), and a 79 nucleotide sequence which is homologous to a repeated sequence previously shown to be present within the 3' untranslated portions of the Spec1 and Spec2 mRNAs of this species (1). Analysis of transcripts of this sequence family in RNA from several embryonic stages indicates that its expression is highest at 11 hours postfertilization (about 128 cells) and drops as development proceeds. Furthermore, most or all, transcription of this sequence family in nuclei isolated from 11 hour embryos is by RNA polymerase III, and is from the same strand which is transcribed in vitro.

Actins↗
PubMed1997

[Search for insertion mutations disrupting mitosis using a transposon from the reporter gene in Drosophila melanogaster].

Transpositions of the vector P[lArB] into the regions 78D, 61F, and 85F of chromosome 3, which result in various anomalies of mitoses in neural ganglions of homozygous larvae, were obtained by insertion mutagenesis. The tissue specificity of regulatory elements controlling the reporter gene was studied by staining for the activity of beta-galactosidase reporter gene of the vector P[lArB]. These regulatory elements are suggested to be the enhancers of the genes carrying insertions. In all studied mutants, staining for beta-galactosidase was found in tissues containing actively proliferating cells. The staining of germarium in adult female ovaries was the most pronounced. The germarium staining pattern was used for the identification of novel insertions leading to mitosis abnormalities. The P1003 (99F) insertion was found, which according to preliminary data leads to an increase in the mitotic index and anomalies of chromosome structure in neuroblasts of homozygous larvae. In addition, the 22w (42A) insertion leading to chromosome arrest in metaphase was found.

Animals↗
PubMed1985

Retroviral characteristics of the long terminal repeat of murine E.Tn sequences.

E.Tn sequences form a family of long moderately repeated sequences which are abundantly transcribed in the pluripotent cell lineage between day 3.5 and 7.5 of early mouse embryogenesis. The structure of the long terminal repeat (LTR) bordering the E.Tn sequences has been investigated by nucleotide sequencing, primer extension and S1 mapping experiments. This has allowed the identification of U3, R and U5 domains, and of several other structural features all of which are characteristics of retroviral LTRs.

Animals↗
PubMed1994

Identification of bacterial cell-surface virulence determinants with TnphoA.

Insertion mutagenesis using TnphoA has proved to be a potent device for the creation of easily screened knockout mutations in genes encoding virulence determinants in a variety of pathogenic bacteria. Initial identification of genes with TnphoA directly initiates more sophisticated genetic and biochemical studies on these factors essential to our understanding of bacterial pathogenesis.

Alkaline Phosphatase↗
PubMed1982

Structural organization of the corticotropin-beta-lipotropin precursor gene.

The human and the bovine corticotropin (ACTH)-beta-lipotropin (LPH) precursor gene have been isolated and characterized. Both genes consist of three exons which are divided by two large introns at exactly the same positions. One of the introns is inserted within the segment transcribed into the 5'-untranslated region of the mRNA, and the other interrupts the protein-coding sequence near the signal peptide region. The largest exon encodes most of the protein sequence which includes the three repeated melanotropin (MSH) peptides and other biologically active peptides such as ACTH and beta-endorphin. Thus, there is no apparent correspondence between the repetitive structure of the precursor protein and the structural organization of its gene. Comparison of the nucleotide sequences of the human and the bovine gene reveals that three regions are highly conserved, i.e., the region extending from the signal peptide to gamma-MSH, the ACTH region and the beta-MSH/beta-endorphin region. This suggests that the peptide(s) in the amino-terminal region, including gamma-MSH, may be of physiological importance, as is the case for ACTH and beta-endorphin. The different biologically active component peptides of the ACTH-beta-LPH precursor, encoded by a single gene, seem to be involved in the defense mechanism of the living organism by acting coordinately in the central nervous system as well as in peripheral tissues. The identification of the mRNA encoding the ACTH-beta-LPH precursor in a human ectopic ACTH-producing tumor is also reported.

Adrenocorticotropic Hormone↗
PubMed2005

Identification of StiR, the first regulator of secondary metabolite formation in the myxobacterium Cystobacter fuscus Cb f17.1.

Myxobacteria are well established as proficient producers of natural products with numerous biological activities. Although some knowledge has been gained regarding the biosynthesis of secondary metabolites in this class of bacteria, almost nothing is known about the underlying regulatory mechanisms. In order to identify regulatory elements, we submitted the argyrin and stigmatellin producer Cystobacter fuscus to a random transposon mutagenesis strategy and screened 1,000 mutants for the occurrence of strains showing remarkably increased or decreased production of these compounds. In addition to the identification of the stigmatellin biosynthetic gene cluster, a novel positive regulator (stiR) of stigmatellin production was identified after transposon recovery. In order to exclude secondary mutagenesis effects, a double cross-over mutagenesis strategy was applied to the strain resulting in the repeated generation of the transposon genotype. This strain was shown to be equally effected in natural product biosynthesis.

DNA Transposable Elements↗
PubMed1999

Identification of genes in an extraintestinal isolate of Escherichia coli with increased expression after exposure to human urine.

The identification of genes with increased expression in vivo may lead to the identification of novel or unrecognized virulence traits and/or recognition of environmental signals involved in modulating gene expression. Our laboratory is studying an extraintestinal isolate of Escherichia coli as a model pathogen. We had previously used human urine ex vivo to identify the unrecognized urovirulence genes guaA and argC and to establish that arginine and guanine (or derivatives) were limiting in this body fluid (T. A. Russo et al., Mol. Microbiol. 22:217-229, 1996). In this study, we have continued with this approach and identified three additional genes that have increased expression in human urine relative to Luria-Bertani (LB) medium. Expression of ure1 (urine-responsive element) is increased a mean of 47.6-fold in urine but completely suppressed by exogenous glucose. This finding suggests that ure1 is regulated by catabolite repression and that limiting glucose in urine is a regulatory signal. ure1 is present in the E. coli K-12 genome, but its function is unknown. Although disruption of ure1 results in diminished growth in human urine, limiting concentrations of amino acids, nucleosides, or iron (Fe), or changes in osmolarity or pH do not affect the expression of ure1. Therefore, Ure1 appears to have a role independent of the synthesis or uptake of these nutrients and does not appear to be involved in osmoprotection. iroN(E. coli) is a novel E. coli gene with 77% DNA homology to a catecholate siderophore receptor gene recently identified in Salmonella. Its expression is increased a mean of 27.2-fold in urine and is repressed by exogenous Fe and a urinary pH of 5.0. This finding supports the contention that Fe is a limiting element in urine and that alteration of pH can affect gene expression. It is linked to the P-pilus (prs) and F1C fimbrial (foc) gene clusters on a pathogenicity island and appears to have been acquired by IS1230-mediated horizontal transmission. The homologous iroN(E. coli) sequence is significantly more prevalent in urinary tract and blood isolates of E. coli compared to fecal isolates. Last, the expression of ArtJ, an arginine periplasmic binding protein, is increased a mean of 16.6-fold in urine. This finding implicates arginine concentrations as limited in urine and, in combination with previous data demonstrating that argC is important for urovirulence, suggests that the ability of E. coli to synthesize or acquire arginine is important for urovirulence. ure1, iroN(E. coli), and artJ all have increased expression in human blood and ascites relative to LB medium as well. The identification of these genes increases our understanding of regulatory signals present in human urine, blood, and ascites. Ure1, IroN(E. coli), and ArtJ also warrant further evaluation as virulence traits both within and outside the urinary tract.

Ascites↗
PubMedDate not supplied

[Thermosensitive vector derived from RP1 plasmid for detection of transposable elements].

The involvement of the transposable DNA element of E. coli K12 chromosome in integrative recombination of RP1 plasmid was studied. Using temperature sensitive for replication plasmid RP1ts12--the derivative of RP1 which contains mutated transposon Tnl, it was shown that integration of RP1 into host chromosome and Hfr formation may occur according to a mechanism mediated by chromosome IS-elements. Plasmids that are desintegrated from the chromosome of these Hfrs contain discrete DNA segments (IS-elements) and possess elevated frequency of integration into chromosome of rec+ cells. The latter was used for selection of RP1ts12 recombinants carrying chromosome IS. For identification of IS involved in RP1 integration the number of independent RP1ts 12 recombinants was subjected to restriction and heteroduplex analysis. By analysing recombinants integrated into bacterial chromosome with frequency 5 X 10(-3), a new IS-element of E. coli K12 designated IS111 was discovered. IS111-element is about 1500bp of length, contains Smal, Pst1 and BamH1 restriction endonuclease sites and was found in the same position on the plasmid RP1 in two different orientations. IS-elements that have been revealed in a number of other RP1ts12 recombinants were preliminary identified as IS1-like elements. One recombinants plasmid was found to have an IS5-like elements. The activity of IS-elements inserted into RP1ts12 in recA-dependent integrative recombination was estimated. From the data of absolute and relative RP1ts12 integration frequencies mediated by IS111, IS1- and IS5-like elements a conclusion was made about the absence of E. coli K12 chromosome IS-elements in RP1 plasmid. The Hfr-formation and chromosomal gene transfer by recombinant plasmids RP1ts12: IS111 were studied. The possibility to use insertion RP1ts12 derivatives for the estimation of copies number, mapping and definition of orientation of IS-elements in bacterial chromosome and the possibilities for detection of transposable DNA elements using RP1ts12 in a wide range of gram-negative bacteria are discussed.

Bacterial Proteins↗
PubMed1984

The molecular basis of I-R hybrid dysgenesis in Drosophila melanogaster: identification, cloning, and properties of the I factor.

We have analyzed two mutations of the white-eye gene, which arose in flies subject to I-R hybrid dysgenesis. These mutations are associated with insertions of apparently identical 5.4 kb sequences, which we have cloned. We believe that these insertions are copies of the I factor controlling I-R hybrid dysgenesis. The I factor is not a member of the copia-like or fold-back classes of transposable elements and has no sequence homology with the P factor that controls P-M dysgenesis. All strains of D. melanogaster contain I-factor sequences. Those present in reactive strains must represent inactive I elements. I elements have a remarkably similar sequence organization in all reactive strains and are located in peri-centromeric regions. Inducer strains appear to contain both I elements, located in peri-centromeric regions, and 10-15 copies of the complete I factor at sites on the chromosome arms.

Animals↗
PubMed2002

Efficient gene identification and targeted gene disruption in the wheat blotch fungus Mycosphaerella graminicola using TAGKO.

TAGKO ( transposon- arrayed gene knock out) is a highly efficient method for gene discovery and gene function assignment in the rice blast fungus Magnaporthe grisea. Here, we report the application of genome-wide TAGKO to the wheat blotch fungus Mycosphaerella graminicola, including the successful development of electroporation-based transformation for this fungus. A M. graminicola genomic cosmid library was constructed and a pool of 250 cosmid clones was mutagenized by in vitro transposition. Sequence analysis identified 5,110 unique insertion events in the M. graminicola genome. Eleven transposon-tagged cosmid clones (TAGKO clones) were chosen and transformed into the wild-type strain by electroporation. Ten TAGKO clones out of 11 produced gene-specific mutants at a targeting frequency of 15-28%, significantly higher than that of conventional gene-disruption constructs. The remaining clone failed to produce viable mutants, thereby providing indirect evidence for the identification of an essential gene.

Ascomycota↗
PubMed2006

Rapid identification of non-essential genes for in vitro replication of Marek's disease virus by random transposon mutagenesis.

Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that induces rapid-onset T-cell lymphomas in poultry. The MDV genome encodes more than 100 genes. However, the role of many of these genes in virus replication is not known. The construction of an infectious bacterial artificial chromosome (BAC) clone of the highly oncogenic RB-1B strain of MDV has been described previously. Virus reconstituted from the BAC clone induced rapid-onset lymphomas in chickens very similar to the wildtype viruses. In this paper, the construction of a high-density random transposon-insertion mutant library of the RB-1B BAC clone using a high throughput in vitro transposon mutagenesis technique is described. Furthermore a PCR screening method, using primers specific for the transposon sequence and the MDV gene(s) of interest, was developed for the rapid identification of specific insertion mutants. The application of the screening method to identify some of the non-essential genes for MDV replication in vitro is described.

Chromosomes, Artificial, Bacterial↗
PubMed2004

Newly developed primers for the detection of Mycobacterium avium subspecies paratuberculosis.

Recent publications reported the existence of IS900 like sequences in mycobacteria different from Mycobacterium avium subspecies paratuberculosis (Map). The primers used for IS900 detection of Map have amplified these sequences causing false positive results. In this study, we have developed two new PCR assays for the detection of Map. The first assay is based on the IS900 sequence using primers different from the ones previously reported, the second assay on the f57 sequence. The specificity of the tests was checked by analysis of 190 mycobacterial isolates (74 Map and 116 non-Map isolates). All Map strains were positive and all non-Map strains were negative. Serial dilutions of Map bacteria were used to assess the sensitivity of the assays. We achieved a sensitivity of 1CFU per PCR for both assays. In addition, a PCR-simulating computer programme was used to evaluate the specificity of the new IS900 primers. The combination of the two PCR assays has proven to be useful for the identification of Map but validation on a large range of clinical samples still needs to be done.

Animals↗
PubMed2002

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.

Animals↗
PubMed1989

Detection of mutations in human type I collagen mRNA in osteogenesis imperfecta by indirect RNase protection.

A method for detecting a wide variety of mutations within type I collagen has been developed and evaluated on a series of patients with osteogenesis imperfecta. RNA, extracted from the nuclear and cytoplasmic compartment of cultured fibroblasts from affected individuals, is hybridized with antisense single-stranded cDNA to the alpha 1(I) mRNA. The hybrid is digested with RNase A and T1 under varying degrees of stringency. The resistant RNA bands are separated by electrophoresis in agarose, transferred to nitrocellulose, and hybridized with antisense cRNA colinear with the protecting probe. This approach is capable of detecting previously defined mutations such as 252-base pair deletion and a 1-base pair mismatch within the alpha 1(I) mRNA. The method appears to be particularly useful in detecting abnormalities of RNA processing that behave as an insert or deletion within the mature mRNA. The procedure should be generally applicable for the identification and localization of any mutation within an entire gene if the gene is expressed as an RNA and a complete cDNA for the mRNA is available.

Chromosome Deletion↗
PubMed1988

Identification of genes involved in growth autonomy of hematopoietic cells by analysis of factor-independent mutants.

The factor-dependent myeloid precursor cell line D35 mutates spontaneously at a frequency greater than 2.4 x 10(-7) to growth factor autonomy. This frequency could be increased at least 20-fold by retrovirus insertional mutagenesis. The isolation and characterization of factor-independent mutants allowed the identification of genes involved in growth autonomy. Mutants could be subdivided into two sets: those that secreted a stimulating factor (10/11) and those that did not (1/11). In one case, the factor released was distinct from previously characterized growth factors. In most mutants (6/9), the activation of a growth factor gene was associated with rearrangement that could be attributed to the insertion of a transposable-like element either 5' or 3' of the factor coding region in all cases examined, excluding oncogene involvement. All factor-independent mutants were tumorigenic, consistent with the hypothesis that growth-factor independence initiated by aberrant growth factor gene activation is an important and early step in tumorigenesis.

Alleles↗
PubMed1982

Evolution of the D-ribose operon on Escherichia coli B/r.

The D-ribose operon (rbs) of Escherichia coli K-12 maps at 83 min and is inducible. The rbs operon of E. coli B/r maps at 2 min and is constitutive. Evidence is presented showing that a second inducible copy of the rbs operons is present in E. coli B/r mapping at 83 min. The data indicated that the duplication of the rbs operon represented a transposition of the 83-min region to 2 min. The identification of a second copy of the rbs operon in B/r and the determination of its inducibility were based on the reactivation, through mutagenesis, of inducible rbs expression, mapping by P1 transduction of the mutation site to 83 min, and merodiploid complementation analysis of the D-ribokinase expression in E. coli B/r. We also show that the rbs transposition to 2-min continued to generate transposable elements coding for the 1- to 2-min region of the chromosome and transposing onto extrachromosomal DNA target molecules such as pBR322.

Chromosome Mapping↗