scholarly journals Salmonellagenomic island 3 is an integrative and conjugative element and contributes to copper and arsenic resistance ofSalmonella enterica

2019 ◽  
Author(s):  
Nobuo Arai ◽  
Tsuyoshi Sekizuka ◽  
Yukino Tamamura ◽  
Masahiro Kusumoto ◽  
Atsushi Hinenoya ◽  
...  
Keyword(s):  
Mobile Genetic Element ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Sequencing Analysis ◽  
Arsenic Resistance ◽  
Filter Mating ◽  
Serovar Typhimurium ◽  
Resistance Island ◽  
Reading Frames ◽  
Integrative And Conjugative Element

ABSTRACTSalmonellagenomic island 3 (SGI3) was first described as a chromosomal island inSalmonella4,[5],12:i:-, a monophasic variant ofSalmonella entericasubsp.entericaserovar Typhimurium. The SGI3 DNA sequence detected fromSalmonella4,[5],12:i:-isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic resistance operon in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter mating experiments using theS. entericaserovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3′ end of the tRNA genespheVorpheR. The length of the target site was 52 or 55 bp, and a 55-bpattIsequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4compared with the recipient strains under anaerobic conditions. Resistance was defined by thecusgene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4compared with recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic resistance ofS. enterica.

scholarly journals SalmonellaGenomic Island 3 Is an Integrative and Conjugative Element and Contributes to Copper and Arsenic Tolerance ofSalmonella enterica

2019 ◽  
Vol 63 (9) ◽  
Author(s):  
Nobuo Arai ◽  
Tsuyoshi Sekizuka ◽  
Yukino Tamamura ◽  
Masahiro Kusumoto ◽  
Atsushi Hinenoya ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Trna Genes ◽  
Sequencing Analysis ◽  
Content Type ◽  
Arsenic Tolerance ◽  
Filter Mating ◽  
Serovar Typhimurium ◽  
Resistance Island ◽  
Reading Frames ◽  
Integrative And Conjugative Element

ABSTRACTSalmonellagenomic island 3 (SGI3) was first described as a chromosomal island inSalmonella4,[5],12:i:–, a monophasic variant ofSalmonella entericasubsp.entericaserovar Typhimurium. The SGI3 DNA sequence detected fromSalmonella4,[5],12:i:– isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic tolerance operon, in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter-mating experiments using theS. entericaserovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3′ end of the tRNA genespheVorpheR. The length of the target site was 52 or 55 bp, and a 55-bpattIsequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4compared to the recipient strains under anaerobic conditions. Tolerance was defined by thecusgene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4compared to recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic tolerance ofS. enterica.

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.

Genetic diversity of limonene synthase genes in Rongan kumquat (Fortunella crassifolia)

2020 ◽  
Vol 47 (5) ◽  
pp. 425
Author(s):  
Mengyu Liu ◽  
Xiaofeng Liu ◽  
Junhua Hu ◽  
Yang Xue ◽  
Xiaochun Zhao
Keyword(s):  
Large Family ◽  
Open Reading Frames ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Geranyl Diphosphate ◽  
Limonene Synthase ◽  
High Amino Acid ◽  
Main Component ◽  
Reading Frames

D-limonene is the main component of citrus essential oils. In the monoterpene biosynthetic pathway, geranyl diphosphate reacts with monoterpenes to form the prenyl-carbocation intermediate to produce d-limonene. In this study, d-limonene synthase (FcLS) genes were first isolated from Rongan kumquat (Fortunella crassifolia Swingle). Sequencing analysis revealed that the open reading frames of 18 FcLS genes contain 12 single nucleotide polymorphisms, which resulted in the variation of FcLS proteins, indicating that the limonene synthase genes are a large family in F. crassifolia. This phenomenon has not been reported in Citrus. The predicted FcLS proteins showed a high amino acid sequence identity with other Citrus limonene synthases and also had the typical structures of limonene synthase protein. FcLS1 was validated to be a functional d-limonene synthase by prokaryotic expression.

scholarly journals Genetic Identification of the Bacteriocins Produced by Enterococcus faecium IT62 and Evidence that Bacteriocin 32 Is Identical to Enterocin IT

2009 ◽  
Vol 53 (5) ◽  
pp. 1907-1911 ◽  
Author(s):  
Esther Izquierdo ◽  
Yimin Cai ◽  
Eric Marchioni ◽  
Saïd Ennahar
Keyword(s):  
Amino Acids ◽  
Genetic Analysis ◽  
Structural Gene ◽  
Enterococcus Faecium ◽  
Open Reading Frames ◽  
Genetic Identification ◽  
Leader Peptide ◽  
Sequencing Analysis ◽  
The One ◽  
Reading Frames

ABSTRACT Enterococcus faecium IT62, a strain isolated from ryegrass in Japan, produces three bacteriocins (enterocins L50A, L50B, and IT) that have been previously purified and the primary structures of which have been determined by amino acid sequencing (E. Izquierdo, A. Bednarczyk, C. Schaeffer, Y. Cai, E. Marchioni, A. Van Dorsselaer, and S. Ennahar, Antimicrob. Agents Chemother., 52:1917-1923, 2008). Genetic analysis showed that the bacteriocins of E. faecium IT62 are plasmid encoded, but with the structural genes specifying enterocin L50A and enterocin L50B being carried by a plasmid (pTAB1) that is separate from the one (pTIT1) carrying the structural gene of enterocin IT. Sequencing analysis of a 1,475-bp region from pTAB1 identified two consecutive open reading frames corresponding, with the exception of 2 bp, to the genes entL50A and entL50B, encoding EntL50A and EntL50B, respectively. Both bacteriocins are synthesized without N-terminal leader sequences. Genetic analysis of a sequenced 1,380-bp pTIT1 fragment showed that the genes entIT and entIM, encoding enterocin IT and its immunity protein, respectively, were both found in E. faecium VRE200 for bacteriocin 32. Enterocin IT, a 6,390-Da peptide made up of 54 amino acids, has been previously shown to be identical to the C-terminal part of bacteriocin 32, a 7,998-Da bacteriocin produced by E. faecium VRE200 whose structure was deduced from its structural gene (T. Inoue, H. Tomita, and Y. Ike, Antimicrob. Agents Chemother., 50:1202-1212, 2006). By combining the biochemical and genetic data on enterocin IT, it was concluded that bacteriocin 32 is in fact identical to enterocin IT, both being encoded by the same plasmid-borne gene, and that the N-terminal leader peptide for this bacteriocin is 35 amino acids long and not 19 amino acids long as previously reported.

scholarly journals Identification of Proteins Associated with Murine Cytomegalovirus Virions

2004 ◽  
Vol 78 (20) ◽  
pp. 11187-11197 ◽  
Author(s):  
Lisa M. Kattenhorn ◽  
Ryan Mills ◽  
Markus Wagner ◽  
Alexandre Lomsadze ◽  
Vsevolod Makeev ◽  
...  
Keyword(s):  
Gene Prediction ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Open Reading Frames ◽  
Murine Cytomegalovirus ◽  
Prediction Algorithm ◽  
Sequencing Analysis ◽  
Protein Coding ◽  
Coding Potential ◽  
Reading Frames

ABSTRACT Proteins associated with the murine cytomegalovirus (MCMV) viral particle were identified by a combined approach of proteomic and genomic methods. Purified MCMV virions were dissociated by complete denaturation and subjected to either separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and in-gel digestion or treated directly by in-solution tryptic digestion. Peptides were separated by nanoflow liquid chromatography and analyzed by tandem mass spectrometry (LC-MS/MS). The MS/MS spectra obtained were searched against a database of MCMV open reading frames (ORFs) predicted to be protein coding by an MCMV-specific version of the gene prediction algorithm GeneMarkS. We identified 38 proteins from the capsid, tegument, glycoprotein, replication, and immunomodulatory protein families, as well as 20 genes of unknown function. Observed irregularities in coding potential suggested possible sequence errors in the 3′-proximal ends of m20 and M31. These errors were experimentally confirmed by sequencing analysis. The MS data further indicated the presence of peptides derived from the unannotated ORFs ORFc225441-226898 (m166.5) and ORF105932-106072. Immunoblot experiments confirmed expression of m166.5 during viral infection.

scholarly journals Complete DNA Sequence and Comparative Analysis of the 50-Kilobase Virulence Plasmid of Salmonella entericaSerovar Choleraesuis

2001 ◽  
Vol 69 (4) ◽  
pp. 2612-2620 ◽  
Author(s):  
Takeshi Haneda ◽  
Nobuhiko Okada ◽  
Noriko Nakazawa ◽  
Takatoshi Kawakami ◽  
Hirofumi Danbara
Keyword(s):  
Comparative Analysis ◽  
Systemic Infection ◽  
Open Reading Frames ◽  
Virulence Plasmid ◽  
Sequence Element ◽  
E Coli ◽  
Virulence Plasmids ◽  
Serovar Typhimurium ◽  
Insertion Sequence Element ◽  
Reading Frames

ABSTRACT The complete nucleotide sequence of pKDSC50, a large virulence plasmid from Salmonella enterica serovar Choleraesuis strain RF-1, has been determined. We identified 48 of the open reading frames (ORFs) encoded by the 49,503-bp molecule. pKDSC50 encodes a known virulence-associated operon, the spv operon, which is composed of genes essential for systemic infection by nontyphoidalSalmonella. Analysis of the genetic organization of pKDSC50 suggests that the plasmid is composed of several virulence-associated genes, which include the spvRABCD genes, plasmid replication and maintenance genes, and one insertion sequence element. A second virulence-associated region including the pef(plasmid-encoded fimbria) operon and rck (resistance to complement killing) gene, which has been identified on the virulence plasmid of S. enterica serovar Typhimurium, was absent. Two different replicon regions, similar to the RepFIIA and RepFIB replicons, were found. Both showed high similarity to those of the pO157 plasmid of enterohemorrhagic Escherichia coliO157:H7 and the enteropathogenic E. coli (EPEC) adherence factor plasmid harbored by EPEC strain B171 (O111:NM), as well as the virulence plasmids of Salmonella serovars Typhimurium and Enteritidis. Comparative analysis of the nucleotide sequences of the 50-kb virulence plasmid of serovar Choleraesuis and the 94-kb virulence plasmid of serovar Typhimurium revealed that 47 out of 48 ORFs of the virulence plasmid of serovar Choleraesuis are highly homologous to the corresponding ORFs of the virulence plasmid of serovar Typhimurium, suggesting a common ancestry.

scholarly journals Chromosomal Arm Replacement in Streptomyces griseus

2003 ◽  
Vol 185 (3) ◽  
pp. 1120-1124 ◽  
Author(s):  
Tetsuya Uchida ◽  
Mariko Miyawaki ◽  
Haruyasu Kinashi
Keyword(s):  
Dna Repair ◽  
Deletion Mutant ◽  
Streptomyces Griseus ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequencing Analysis ◽  
Chromosomal Deletion ◽  
Terminal Inverted Repeats ◽  
Left And Right ◽  
Reading Frames

ABSTRACT UV irradiation of Streptomyces griseus 2247 yielded a new chromosomal deletion mutant, MM9. Restriction and sequencing analysis revealed that homologous recombination between two similar lipoprotein-like open reading frames, which are located 450 and 250 kb from the left and right ends, respectively, caused chromosomal arm replacement. As a result, new 450-kb terminal inverted repeats (TIRs) were formed in place of the original 24-kb TIRs. Frequent homologous recombinations in Streptomyces strains suggest that telomere deletions can usually be repaired by recombinational DNA repair functioning between the intact and deleted TIR sequences on the same chromosome.

scholarly journals Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes.

1992 ◽  
Vol 12 (1) ◽  
pp. 229-239 ◽  
Author(s):  
R Marschalek ◽  
J Hofmann ◽  
G Schumann ◽  
R Gösseringer ◽  
T Dingermann
Keyword(s):  
Dictyostelium Discoideum ◽  
Trna Gene ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Long Terminal Repeats ◽  
Retrotransposable Element ◽  
Position Specificity ◽  
Terminal Repeats ◽  
Orientation Specificity ◽  
Reading Frames

Different Dictyostelium discoideum strains contain between 2 and 200 copies of a retrotransposable element termed DRE (Dictyostelium repetitive element). From the analysis of more than 50 elements, it can be concluded that DRE elements always occur 50 +/- 3 nucleotides upstream of tRNA genes. All analyzed clones contain DRE in a constant orientation relative to the tRNA gene, implying orientation specificity as well as position specificity. DRE contains two open reading frames which are flanked by nonidentical terminal repeats. Long terminal repeats (LTRs) are composed of three distinct modules, called A, B, and C. The tRNA gene-proximal LTR is characterized by one or multiple A modules followed by a single B module (AnB). With respect to the distal LTR, two different subforms of DRE have been isolated. The majority of isolated clones contains a distal LTR composed of a B module followed by a C module (BC), whereas the distal LTR of the other subform contains a consecutive array of a B module, a C module, a slightly altered A module, another B module, and another C module (BC.ABC). Full-length as well as smaller transcripts from DRE elements have been detected, but in comparison with the high copy number in D. discoideum strains derived from the wild-type strain NC4, transcription is rather poor.

scholarly journals Identification of GtgE, a Novel Virulence Factor Encoded on the Gifsy-2 Bacteriophage of Salmonella enterica Serovar Typhimurium

2002 ◽  
Vol 184 (19) ◽  
pp. 5234-5239 ◽  
Author(s):  
Theresa D. Ho ◽  
Nara Figueroa-Bossi ◽  
Minhua Wang ◽  
Sergio Uzzau ◽  
Lionello Bossi ◽  
...  
Keyword(s):  
Virulence Factor ◽  
Salmonella Enterica ◽  
Virulence Genes ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Systemic Infection ◽  
Open Reading Frames ◽  
Effector Protein ◽  
Protein Sequence Analysis ◽  
Serovar Typhimurium ◽  
Reading Frames

ABSTRACT The Gifsy-2 temperate bacteriophage of Salmonella enterica serovar Typhimurium contributes significantly to the pathogenicity of strains that carry it as a prophage. Previous studies have shown that Gifsy-2 encodes SodCI, a periplasmic Cu/Zn superoxide dismutase, and at least one additional virulence factor. Gifsy-2 encodes a Salmonella pathogenicity island 2 type III secreted effector protein. Sequence analysis of the Gifsy-2 genome also identifies several open reading frames with homology to those of known virulence genes. However, we found that null mutations in these genes did not individually have a significant effect on the ability of S. enterica serovar Typhimurium to establish a systemic infection in mice. Using deletion analysis, we have identified a gene, gtgE, which is necessary for the full virulence of S. enterica serovar Typhimurium Gifsy-2 lysogens. Together, GtgE and SodCI account for the contribution of Gifsy-2 to S. enterica serovar Typhimurium virulence in the murine model.

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