Identification and Characterization of IS1411, a New Insertion Sequence Which Causes Transcriptional Activation of the Phenol Degradation Genes inPseudomonas putida

ABSTRACT A new insertion sequence (IS element), IS1411, was identified downstream of the phenol degradation genes pheBAthat originated from plasmid DNA of Pseudomonas sp. strain EST1001. According to sequence analysis, IS1411 belongs to a new family of IS elements that has recently been named the ISL3 family (J. Mahillon and M. Chandler, Microbiol. Mol. Biol. Rev. 62:725–774, 1998). IS1411 generates 8-bp duplication of the target DNA and carries 24-bp inverted repeats (IRs), highly homologous to the IRs of other IS elements belonging to this family. IS1411 was discovered as a result of insertional activation of promoterless pheBA genes in Pseudomonas putida due to the presence of outward-directed promoters at the left end of IS1411. Both promoters located on the IS element have sequences that are similar to the consensus sequence ofEscherichia coli ς70. IS1411 can produce IS circles, and the circle formation is enhanced when two copies of the element are present in the same plasmid.

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An essential Saccharomyces cerevisiae gene homologous to SNF2 encodes a helicase-related protein in a new family

Molecular and Cellular Biology ◽

10.1128/mcb.12.4.1893-1902.1992 ◽

1992 ◽

Vol 12 (4) ◽

pp. 1893-1902

Author(s):

B C Laurent ◽

X Yang ◽

M Carlson

Keyword(s):

Saccharomyces Cerevisiae ◽

Amino Acids ◽

Binding Site ◽

Transcriptional Activation ◽

Nucleoside Triphosphate ◽

Related Protein ◽

New Family ◽

Eukaryotic Proteins ◽

Beta Galactosidase

The Saccharomyces cerevisiae SNF2 gene affects the expression of many diversely regulated genes and has been implicated in transcriptional activation. We report here the cloning and characterization of STH1, a gene that is homologous to SNF2. STH1 is essential for mitotic growth and is functionally distinct from SNF2. A bifunctional STH1-beta-galactosidase protein is located in the nucleus. The predicted 155,914-Da STH1 protein is 72% identical to SNF2 over 661 amino acids and 46% identical over another stretch of 66 amino acids. Both STH1 and SNF2 contain a putative nucleoside triphosphate-binding site and sequences resembling the consensus helicase motifs. The large region of homology shared by STH1 and SNF2 is conserved among other eukaryotic proteins, and STH1 and SNF2 appear to define a novel family of proteins related to helicases.

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A homolog of human transcription factor NF-X1 encoded by the Drosophila shuttle craft gene is required in the embryonic central nervous system.

Molecular and Cellular Biology ◽

10.1128/mcb.16.1.192 ◽

1996 ◽

Vol 16 (1) ◽

pp. 192-201 ◽

Cited By ~ 27

Author(s):

N D Stroumbakis ◽

Z Li ◽

P P Tolias

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Transcription Factor ◽

Consensus Sequence ◽

Preliminary Evidence ◽

Phenotypic Characterization ◽

Binding Motif ◽

New Family

NF-X1 is a novel cytokine-inducible transcription factor that has been implicated in the control of immune responses in humans, presumably by regulating expression of class II major histocompatibility genes. Here we report the cloning and genetic characterization of the first reported NF-X1 homolog, which is encoded by the Drosophila melanogaster shuttle craft (stc) gene. The deduced sequence of the fly and human proteins defines a new family of molecules distinguished by a novel cysteine-rich DNA-binding motif (consisting of seven copies of the consensus sequence Cx3Cx3LxCGx0-5HxCx3CHxGxCx2Cx7-9CxC). We have identified and begun a phenotypic characterization of mutations in the stc gene. stc mutants die at the end of embryogenesis, when they appear to be incapable of coordinating the typical peristaltic contraction waves normally required for embryos to hatch into feeding first instar larvae. Preliminary evidence indicates that the resulting lethality of this behavioral defect is accompanied by subtle morphological abnormalities in the central nervous system, where in wild-type embryos, STC protein is normally localized in the nuclei of repeated cell clusters within each neuromere and brain lobe. Thus, the NF-X1 homolog encoded by the Drosophila stc gene defines a new family of putative transcription factors and plays an essential role in the completion of embryonic development. This study presents the first in vivo genetic analysis of a member of this new protein family.

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TheSinorhizobium melilotiinsertion sequence (IS) elements ISRm102F34-1/ISRm7and ISRm220-13-5belong to a new family of insertion sequence elements

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.1999.tb13441.x ◽

1999 ◽

Vol 172 (1) ◽

pp. 1-7 ◽

Cited By ~ 8

Author(s):

Werner Selbitschka ◽

Sanae Zekri ◽

Gerald SchrÃ¶der ◽

Alfred PÃ¼hler ◽

NicolÃ¡s Toro

Keyword(s):

Insertion Sequence ◽

Is Elements ◽

New Family ◽

Sequence Elements ◽

Insertion Sequence Elements

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An essential Saccharomyces cerevisiae gene homologous to SNF2 encodes a helicase-related protein in a new family.

Molecular and Cellular Biology ◽

10.1128/mcb.12.4.1893 ◽

1992 ◽

Vol 12 (4) ◽

pp. 1893-1902 ◽

Cited By ~ 109

Author(s):

B C Laurent ◽

X Yang ◽

M Carlson

Keyword(s):

Saccharomyces Cerevisiae ◽

Amino Acids ◽

Binding Site ◽

Transcriptional Activation ◽

Nucleoside Triphosphate ◽

Related Protein ◽

New Family ◽

Eukaryotic Proteins ◽

Beta Galactosidase

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Molecular characterization of imipenem-resistant, cfiA-positive Bacteroides fragilis isolates from the USA, Hungary and Kuwait

Journal of Medical Microbiology ◽

10.1099/jmm.0.05452-0 ◽

2004 ◽

Vol 53 (5) ◽

pp. 413-419 ◽

Cited By ~ 50

Author(s):

József Sóki ◽

Eleonóra Fodor ◽

David W. Hecht ◽

Richard Edwards ◽

Vincent O. Rotimi ◽

...

Keyword(s):

Insertion Sequence ◽

Inhibitory Concentration ◽

Bacteroides Fragilis ◽

Carbapenem Resistance ◽

Activation Mechanism ◽

Nucleotide Sequencing ◽

Is Elements ◽

Activation Mechanisms ◽

The Usa

Fifteen Bacteroides fragilis isolates from the USA, Hungary and Kuwait were examined for carbapenem resistance, for carbapenemase activity and, with the use of various PCR-based methods and nucleotide sequencing, for cfiA genes and activating insertion sequence (IS) elements. All the B. fragilis isolates were cfiA-positive, 10 of the cfiA genes being upregulated by IS elements that are already known. Of these 10, one was of a novel type (designated IS943) and two further ones (IS614B and IS614C) were suspected hybrids of IS612, IS614 and IS942. There were five cfiA-positive imipenem-resistant B. fragilis isolates with elevated imipenem MICs (minimal inhibitory concentration) that harboured no IS insertion upstream of the cfiA gene, but produced carbapenemase; these isolates might possess a novel activation mechanism. On the basis of the available phenotypic and genotypic evidence, the present data suggest that there are at least two cfiA activation mechanisms among B. fragilis isolates.

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Characterization of IS1547, a New Member of the IS900 Family in the Mycobacterium tuberculosis Complex, and Its Association with IS6110

Journal of Bacteriology ◽

10.1128/jb.181.3.1021-1024.1999 ◽

1999 ◽

Vol 181 (3) ◽

pp. 1021-1024 ◽

Cited By ~ 16

Author(s):

Z. Fang ◽

C. Doig ◽

N. Morrison ◽

B. Watt ◽

K. J. Forbes

Keyword(s):

Mycobacterium Tuberculosis ◽

Insertion Sequence ◽

Insertion Site ◽

Is Elements ◽

Insertion Sites ◽

Inverted Terminal Repeats ◽

Terminal Repeats ◽

Polymorphic Restriction ◽

Different Strains

ABSTRACT Unlike classically defined insertion sequence (IS) elements, which are delimited by their inverted terminal repeats, some IS elements do not have inverted terminal repeats. Among this group of atypical IS elements, IS116, IS900, IS901, and IS1110 have been proposed as members of the IS900 family of elements, not only because they do not have inverted terminal repeats but also because they share other features such as homologous transposases and particular insertion sites. In this study, we report a newly identified IS sequence, IS1547, which was first identified in a clinical isolate of Mycobacterium tuberculosis. Its structure, insertion site, and putative transposase all conform with the conventions of the IS900family, suggesting that it is a new member of this family. IS1547 was detected only in isolates of the M. tuberculosis complex, where it had highly polymorphic restriction fragment length polymorphism patterns, suggesting that it may be a useful genetic marker for identifying isolates of the M. tuberculosis complex and for distinguishing different strains ofM. tuberculosis. ipl is a preferential locus for IS6110 insertion where there are eight known different insertion sites for IS6110. Surprisingly, the DNA sequence of ipl is now known to be a part of IS1547, meaning that IS1547 is a preferential site for IS6110 insertion.

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Serotype 1a O-Antigen Modification: Molecular Characterization of the Genes Involved and Their Novel Organization in the Shigella flexneriChromosome

Journal of Bacteriology ◽

10.1128/jb.181.15.4711-4718.1999 ◽

1999 ◽

Vol 181 (15) ◽

pp. 4711-4718 ◽

Cited By ~ 35

Author(s):

Pradip Adhikari ◽

Gwen Allison ◽

Belinda Whittle ◽

Naresh K. Verma

Keyword(s):

Sequence Analysis ◽

Molecular Characterization ◽

Insertion Sequence ◽

Shigella Flexneri ◽

Pathogenicity Islands ◽

Is Elements ◽

O Antigen ◽

Phage Dna

ABSTRACT The factors responsible for serotype 1a O-antigen modification inShigella flexneri were localized to a 5.8-kb chromosomalHindIII fragment of serotype 1a strain Y53. The entire 5.8-kb fragment and regions up- and downstream of it (10.6-kb total) were sequenced. A putative three-gene operon, which showed homology with other serotype conversion genes, was identified and shown to confer serotype 1a O-antigen modification. The serotype conversion genes were flanked on either side by phage DNA. Multiple insertion sequence (IS) elements were located within and upstream of the phage DNA in a composite transposon-like structure. Host DNA homologous to the dsdC and the thrW proA genes was located upstream of the IS elements and downstream of the phage DNA, respectively. The sequence analysis indicates that the organization of the 10.6-kb region of the Y53 chromosome is unique and suggests that the serotype conversion genes were originally brought into the host by a bacteriophage. Several features of this region are also characteristic of pathogenicity islands.

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