scholarly journals Evolutionary Trends of the Transposase-Encoding Open Reading Frames A and B (orfA and orfB) of the Mycobacterial IS6110 Insertion Sequence

PLoS ONE ◽  
2015 ◽  
Vol 10 (6) ◽  
pp. e0130161 ◽  
Author(s):  
Sara Thabet ◽  
Amine Namouchi ◽  
Helmi Mardassi
Keyword(s):  
Insertion Sequence ◽  
Open Reading Frames ◽  
Evolutionary Trends ◽  
Reading Frames

scholarly journals Bias between the Left and Right Inverted Repeats during IS911 Targeted Insertion

2008 ◽  
Vol 190 (18) ◽  
pp. 6111-6118 ◽  
Author(s):  
P. Rousseau ◽  
C. Loot ◽  
C. Turlan ◽  
S. Nolivos ◽  
M. Chandler
Keyword(s):  
Insertion Sequence ◽  
Regulatory Protein ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Functional Differences ◽  
Left And Right ◽  
Ordered Assembly ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

ABSTRACT IS911 is a bacterial insertion sequence composed of two consecutive overlapping open reading frames (ORFs [orfA and orfB]) encoding the transposase (OrfAB) as well as a regulatory protein (OrfA). These ORFs are bordered by terminal left and right inverted repeats (IRL and IRR, respectively) with several differences in nucleotide sequence. IS911 transposition is asymmetric: each end is cleaved on one strand to generate a free 3′-OH, which is then used as the nucleophile in attacking the opposite insertion sequence (IS) end to generate a free IS circle. This will be inserted into a new target site. We show here that the ends exhibit functional differences which, in vivo, may favor the use of one compared to the other during transposition. Electromobility shift assays showed that a truncated form of the transposase [OrfAB(1-149)] exhibits higher affinity for IRR than for IRL. While there was no detectable difference in IR activities during the early steps of transposition, IRR was more efficient during the final insertion steps. We show here that the differential activities between the two IRs correlate with the different affinities of OrfAB(1-149) for the IRs during assembly of the nucleoprotein complexes leading to transposition. We conclude that the two inverted repeats are not equivalent during IS911 transposition and that this asymmetry may intervene to determine the ordered assembly of the different protein-DNA complexes involved in the reaction.

scholarly journals Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (cehA) from Rhizobium sp. Strain AC100

2002 ◽  
Vol 68 (3) ◽  
pp. 1220-1227 ◽  
Author(s):  
Masayuki Hashimoto ◽  
Mitsuru Fukui ◽  
Kouichi Hayano ◽  
Masahito Hayatsu
Keyword(s):  
Nucleotide Sequence ◽  
Insertion Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Homology Search ◽  
Sequencing Analysis ◽  
Terminal Sequence ◽  
Homologous Sequences ◽  
Naphthyl Acetate ◽  
Reading Frames

ABSTRACT Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.

scholarly journals Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 484
Author(s):  
Michael Sadler ◽  
Melanie R. Mormile ◽  
Ronald L. Frank
Keyword(s):  
Insertion Sequence ◽  
Open Reading Frames ◽  
Insertion Sequences ◽  
Genome Plasticity ◽  
Mobile Dna ◽  
Dna Elements ◽  
Left And Right ◽  
Evolutionary Role ◽  
Reading Frames

Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying stages of decay, from nearly intact to an ends-only sequence. The loci were characterized with respect to two divergent open reading frames (ORF), tnpA and tnpB, and left and right ends of the elements. The tnpB ORF contains two nearly identical insert sequences that suggest recombination between tnpB ORF is occurring. From these results, insertion sequence activity can be inferred, including transposition capability and element interaction.

scholarly journals Genetic Characterization and Evolutionary Implications of a car Gene Cluster in the Carbazole Degrader Pseudomonas sp. Strain CA10

2001 ◽  
Vol 183 (12) ◽  
pp. 3663-3679 ◽  
Author(s):  
Hideaki Nojiri ◽  
Hiroyo Sekiguchi ◽  
Kana Maeda ◽  
Masaaki Urata ◽  
Sei-Ichiro Nakai ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Insertion Sequence ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
The Novel ◽  
Gene Duplications ◽  
Homology Searching ◽  
Reading Frames ◽  
Strain Ca10 ◽  
Recombination Gene

ABSTRACT The nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of thecarAaAaBaBbCAc(ORF7)Ad genes of carbazole-degrading Pseudomonas sp. strain CA10 were determined. Thirty-two open reading frames (ORFs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (carAaAaBaBbCAcAdDFE) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. The high identities (68 to 83%) with the enzymes involved in 3-(3-hydroxyphenyl)propionic acid degradation were observed only for CarFE. This observation, together with the fact that two ORFs are inserted between carDand carFE, makes it quite likely that thecarFE genes were recruited from another locus. In the 21-kb region upstream from carAa, aromatic-ring-hydroxylating dioxygenase genes (ORF26, ORF27, and ORF28) were found. Inductive expression in carbazole-grown cells and the results of homology searching indicate that these genes encode the anthranilate 1,2-dioxygenase involved in carbazole degradation. Therefore, these ORFs were designated antABC. Four homologous insertion sequences, IS5car1 to IS5car4, were identified in the neighboring regions ofcar and ant genes. IS5car2and IS5car3 constituted the putative composite transposon containing antABC. One-ended transposition of IS5car2 together with the 5′ portion ofantA into the region immediately upstream ofcarAa had resulted in the formation of IS5car1 and ORF9. In addition to the insertion sequence-dependent recombination, gene duplications and presumed gene fusion were observed. In conclusion, through the above gene rearrangement, the novel genetic structure of the cargene cluster has been constructed. In addition, it was also revealed that the car and ant gene clusters are located on the megaplasmid pCAR1.

scholarly journals Identification of Genetic Loci Required for Capsular Expression in Vibrio vulnificus

2003 ◽  
Vol 71 (3) ◽  
pp. 1091-1097 ◽  
Author(s):  
Amy B. Smith ◽  
Ronald J. Siebeling
Keyword(s):  
Unknown Function ◽  
Gene Locus ◽  
Insertion Sequence ◽  
Capsular Polysaccharide ◽  
Vibrio Vulnificus ◽  
Virulent Strain ◽  
Gene Cassette ◽  
Open Reading Frames ◽  
Genetic Loci ◽  
Reading Frames

ABSTRACT 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.

scholarly journals Genetic Basis for Lipopolysaccharide O-Antigen Biosynthesis in Bordetellae

1999 ◽  
Vol 67 (8) ◽  
pp. 3763-3767 ◽  
Author(s):  
Andrew Preston ◽  
Andrew G. Allen ◽  
Joanna Cadisch ◽  
Richard Thomas ◽  
Kim Stevens ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Genetic Basis ◽  
Genetic Locus ◽  
Bordetella Bronchiseptica ◽  
Open Reading Frames ◽  
Bordetella Parapertussis ◽  
O Antigen ◽  
Surface Polysaccharide ◽  
Reading Frames

ABSTRACT Bordetella bronchiseptica and Bordetella parapertussis express a surface polysaccharide, attached to a lipopolysaccharide, which has been called O antigen. This structure is absent from Bordetella pertussis. We report the identification of a large genetic locus in B. bronchiseptica and B. parapertussis that is required for O-antigen biosynthesis. The locus is replaced by an insertion sequence in B. pertussis, explaining the lack of O-antigen biosynthesis in this species. The DNA sequence of the B. bronchiseptica locus has been determined and the presence of 21 open reading frames has been revealed. We have ascribed putative functions to many of these open reading frames based on database searches. Mutations in the locus in B. bronchiseptica andB. parapertussis prevent O-antigen biosynthesis and provide tools for the study of the role of O antigen in infections caused by these bacteria.

scholarly journals Complete DNA Sequence of Yersinia enterocolitica Serotype 0:8 Low-Calcium-Response Plasmid Reveals a New Virulence Plasmid-Associated Replicon

2001 ◽  
Vol 69 (7) ◽  
pp. 4627-4638 ◽  
Author(s):  
Norma J. Snellings ◽  
Michael Popek ◽  
Luther E. Lindler
Keyword(s):  
Yersinia Enterocolitica ◽  
Insertion Sequence ◽  
Open Reading Frames ◽  
Virulence Plasmid ◽  
Calcium Response ◽  
Is Elements ◽  
New Genes ◽  
Low Calcium ◽  
Reading Frames ◽  
Plasmid Replicons

ABSTRACT The complete nucleotide sequence and organization of theYersinia enterocolitica serotype 0:8 low-calcium-response (LCR) plasmid, pYVe8081, were determined. The 67,720-bp plasmid encoded all the genes known to be part of the LCR stimulon except for ylpA. Eight of 13 intact open reading frames of unknown function identified in pYVe8081 had homologues in Yersinia pestis plasmid pCD1 or inY. enterocolitica serotype 0:9 plasmid pYVe227. A region of approximately 17 kbp showed no DNA identity to pCD1 or pYVe227 and contained six potential new genes, a possible new replicon, and two intact insertion sequence (IS) elements. One intact IS element, ISYen1, was a new IS belonging to the IS256 family. Several vestigial IS elements appeared different from the IS distribution seen in the other LCR plasmids. The RepA proteins encoded by Y. enterocoliticaserotype 0:8 pYVeWA and pYVe8081 were identical. The putative pYVe8081 replicon showed significant homology to the IncL/M replicon of pMU407.1 but was only distantly related to the replicons of pCD1 and pYVe227. In contrast, the putative partitioning genes of pYVe8081 showed 97% DNA identity to the spy/sopABC loci of pCD1 and pYVe227. Sequence analysis suggests thatYersinia LCR plasmids are from a common ancestor but that Y. enterocolitica serotype 0:8 plasmid replicons may have evolved independently via cointegrate formation following a transposition event. The change in replicon structure is predicted to change the incompatibility properties of Y. enterocolitica serotype 0:8 plasmids from those of Y. enterocolitica serotype 0:9 and Y. pestis LCR plasmids.

scholarly journals A Plasmid-Borne blaOXA-58 Gene Confers Imipenem Resistance to Acinetobacter baumannii Isolates from a Lebanese Hospital

2008 ◽  
Vol 52 (11) ◽  
pp. 4115-4120 ◽  
Author(s):  
Raffaele Zarrilli ◽  
Domenico Vitale ◽  
Anna Di Popolo ◽  
Maria Bagattini ◽  
Ziad Daoud ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Insertion Sequence ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Open Reading Frames ◽  
Mosaic Structure ◽  
University Hospital ◽  
Origins Of Replication ◽  
Imipenem Resistance ◽  
Reading Frames

ABSTRACT We investigated the basis of the carbapenem resistance of 17 multidrug-resistant Acinetobacter baumannii clinical isolates collected from 2004 to 2005 at the Saint George University Hospital in Beirut, Lebanon. A. baumannii isolates were clonally related and were susceptible to colistin and trimethoprim-sulfamethoxazole, susceptible or intermediate to ampicillin-sulbactam and meropenem, and resistant to all other antimicrobials. Conjugation experiments demonstrated that resistance to imipenem could be transferred along with a plasmid containing the carbapenem-hydrolyzing oxacillinase bla OXA-58 gene. The plasmid that we called pABIR was 29,823 bp in size and showed a novel mosaic structure composed of two origins of replication, four insertion sequence (IS) elements, and 28 open reading frames. The bla OXA-58 gene was flanked by IS18 and ISAba3 elements at the 5′ and 3′ ends, respectively. The production of the carbapenem-hydrolyzing oxacillinase OXA-58 was apparently the only mechanism for carbapenem resistance in A. baumannii isolates causing the outbreak at the Lebanese Hospital.

scholarly journals The tet39 Determinant and the msrE-mphE Genes in Acinetobacter Plasmids Are Each Part of Discrete Modules Flanked by Inversely Oriented pdif (XerC-XerD) Sites

2017 ◽  
Vol 61 (8) ◽  
Author(s):  
Grace A. Blackwell ◽  
Ruth M. Hall
Keyword(s):  
Insertion Sequence ◽  
Insertion Site ◽  
Tetracycline Resistance ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Content Type ◽  
System A ◽  
Genes Encoding ◽  
Putative Toxin ◽  
Reading Frames

ABSTRACT The tet39 tetracycline resistance determinant and the macrolide resistance genes msrE and mphE were found in an 18.2-kb plasmid, pS30-1, recovered from a global clone 2 (GC2) Acinetobacter baumannii isolate from Singapore, that conferred resistance to tetracycline and erythromycin. pS30-1 also contains mobA and mobC genes encoding MOBQ family proteins, but attempts to mobilize pS30-1 utilizing a coresident conjugative repAci6 plasmid were unsuccessful. Eight pdif sites, consisting of inversely oriented binding sites for the XerC and XerD recombinases separated by 6 bp, were detected in pS30-1. The tet39 determinant and the msrE-mphE gene pair are each surrounded by two pdif sites in inverse orientation. Identical regions in different contexts and many previously unnoticed pdif sites were found in a number of different plasmids in GenBank, showing that the tet39 and msrE-mphE dif modules are mobile. A putative toxin/antitoxin system, a gene encoding a serine recombinase, and open reading frames of unknown function were also part of dif modules in pS30-1. In general, modules with internal XerC or XerD sites alternate. Two copies of ISAjo2-1 (94% identical to ISAjo2) in pS30-1 were inserted 5 bp from a XerC site, and this appears to be the preferred insertion site for this insertion sequence (IS) group. Apparently, Acinetobacter plasmids exploit the Acinetobacter XerC-XerD recombinases to mobilize DNA units containing resistance and other genes, via an uncharacterized mechanism. The tet39 and msrE-mphE dif modules add to the oxa24 module and the oxa58 module redefined here, bringing the total of resistance gene-containing dif modules in Acinetobacter plasmids to four.

scholarly journals Molecular Characterization of IS1541Insertions in the Genome of Yersinia pestis

1998 ◽  
Vol 180 (1) ◽  
pp. 178-181 ◽  
Author(s):  
Monique Odaert ◽  
Annie Devalckenaere ◽  
Patrick Trieu-Cuot ◽  
Michel Simonet
Keyword(s):  
Yersinia Pestis ◽  
Hot Spots ◽  
Insertion Sequence ◽  
Single Copy ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Insertion Sites ◽  
Flanking Regions ◽  
Reading Frames

ABSTRACT The genome of Yersinia pestis, the causative agent of plague, contains at least 30 copies of an element, designated IS1541, which is structurally related to IS200(85% identity). One such element is inserted within the chromosomalinv gene (M. Simonet, B. Riot, N. Fortineau, and P. Berche, Infect. Immun. 64:375–379, 1996). We characterized other IS1541 insertions by cloning 14 different Y. pestis 6/69M loci carrying a single copy of this insertion sequence (IS) into Escherichia coli and, for each element, sequencing 250 bp of both flanking regions. In no case was this IS element inserted into large open reading frames; however, in eight cases, it was detected downstream (17 to 139 bp) of genes thought to be transcribed monocistronically or which constituted the last gene of an operon, and in only one case was it detected upstream (37 bp) of the first gene of an operon. Sequence analysis revealed stem-loop structures (ΔG, <−10 kcal) resembling rho-independent transcription terminators in 8 of the 14 insertion sites. These motifs might constitute hot spots for insertion of this IS1541element within the Y. pestis genome.

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