scholarly journals Nucleotide Sequence of Plasmid pCNB1 from Comamonas Strain CNB-1 Reveals Novel Genetic Organization and Evolution for 4-Chloronitrobenzene Degradation

2007 ◽  
Vol 73 (14) ◽  
pp. 4477-4483 ◽  
Author(s):  
Ying-Fei Ma ◽  
Jian-Feng Wu ◽  
Sheng-Yue Wang ◽  
Cheng-Ying Jiang ◽  
Yun Zhang ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Resistance Genes ◽  
Gene Deletion ◽  
Degradation Pathway ◽  
Open Reading Frames ◽  
Mercury Resistance ◽  
Dna Molecules ◽  
Chromate Resistance ◽  
Reverse Transcription Pcr ◽  
Reading Frames

ABSTRACT The nucleotide sequence of a new plasmid pCNB1 from Comamonas sp. strain CNB-1 that degrades 4-chloronitrobenzene (4CNB) was determined. pCNB1 belongs to the IncP-1β group and is 91,181 bp in length. A total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pCNB1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4CNB. The 4CNB degradative genes and arsenate resistance genes were located on an extraordinarily large transposon (44.5 kb), proposed as TnCNB1. TnCNB1 was flanked by two IS1071 elements and represents a new member of the composite I transposon family. The 4CNB degradative genes within TnCNB1 were separated by various truncated genes and genetic homologs from other DNA molecules. Genes for chromate resistance were located on another transposon that was similar to the Tn21 transposon of the class II replicative family that is frequently responsible for the mobilization of mercury resistance genes. Resistance to arsenate and chromate were experimentally confirmed, and transcriptions of arsenate and chromate resistance genes were demonstrated by reverse transcription-PCR. These results described a new member of the IncP-1β plasmid family, and the findings suggest that gene deletion and acquisition as well as genetic rearrangement of DNA molecules happened during the evolution of the 4CNB degradation pathway on pCNB1.

scholarly journals The Nucleotide Sequence of Shiga Toxin (Stx) 2e-Encoding Phage φP27 Is Not Related to Other Stx Phage Genomes, but the Modular Genetic Structure Is Conserved

2002 ◽  
Vol 70 (4) ◽  
pp. 1896-1908 ◽  
Author(s):  
Jürgen Recktenwald ◽  
Herbert Schmidt
Keyword(s):  
Nucleotide Sequence ◽  
Shiga Toxin ◽  
Phage Genome ◽  
Genetic Recombination ◽  
Genome Structure ◽  
Open Reading Frames ◽  
Functional Modules ◽  
Phage Propagation ◽  
Reading Frames ◽  
Lambdoid Phages

ABSTRACT In this study we determined the complete nucleotide sequence of Shiga toxin 2e-encoding bacteriophage φP27, isolated from the Shiga toxin-producing Escherichia coli patient isolate 2771/97. φP27 is integrated as a prophage in the chromosomal yecE gene. This integration generates identity segments of attL and attR sites with lengths of 11 nucleotides. The integrated prophage genome has a size of 42,575 bp. We identified 58 open reading frames (ORFs), each with a length of >150 nucleotides. The deduced proteins of 44 ORFs showed significant homologies to other proteins present in sequence databases, whereas 14 putative proteins did not. For 29 proteins, we could deduce a putative function. Most of these are related to the basic phage propagation cycle. The φP27 genome represents a mosaic composed of genetic elements which are obviously derived from related and unrelated phages. We identified five short linker sequences of 22 to 151 bp in the φP27 sequence which have also been detected in a couple of other lambdoid phages. These linkers are located between functional modules in the phage genome and are thought to play a role in genetic recombination. Although the overall DNA sequence of φP27 is not highly related to other known phages, the data obtained demonstrate a typical lambdoid genome structure.

scholarly journals Ferrous Iron- and Sulfur-Induced Genes in Sulfolobus metallicus

2007 ◽  
Vol 73 (8) ◽  
pp. 2491-2497 ◽  
Author(s):  
Stephan Bathe ◽  
Paul R. Norris
Keyword(s):  
Reverse Transcription ◽  
Ferrous Iron ◽  
Subtractive Hybridization ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Reverse Transcription Pcr ◽  
Genes Encoding ◽  
Induced Genes ◽  
Reading Frames ◽  
Sulfur Oxygenase Reductase

ABSTRACT Genes of Sulfolobus metallicus that appeared to be upregulated in relation to growth on either ferrous iron or sulfur were identified using subtractive hybridization of cDNAs. The genes upregulated during growth on ferrous iron were found in a cluster, and most were predicted to encode membrane proteins. Quantitative reverse transcription-PCR of cDNA showed upregulation of most of these genes during growth on ferrous iron and pyrite compared to results during growth on sulfur. The highest expression levels observed included those for genes encoding proteins with similarities to cytochrome c oxidase subunits and a CbsA-like cytochrome. The genes identified here that may be involved in oxidation of ferrous iron by S. metallicus are termed fox genes. Of three available genomes of Sulfolobus species (S. tokodaii, S. acidocaldarius, and S. solfataricus), only that of S. tokodaii has a cluster of highly similar open reading frames, and only S. tokodaii of these three species was also able to oxidize ferrous iron. A gene encoding sulfur oxygenase-reductase was identified as the source of the dominant transcript in sulfur-grown cells of S. metallicus, with the predicted protein showing high identities to the previously described examples from S. tokodaii and species of Acidianus.

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 Mapping the regions carrying the three contiguous antibiotic resistance genes aadE, sat4, and aphA-3 in the genomes of staphylococci.

1997 ◽  
Vol 41 (5) ◽  
pp. 1024-1032 ◽  
Author(s):  
A Derbise ◽  
S Aubert ◽  
N El Solh
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Unknown Function ◽  
Antibiotic Resistance Genes ◽  
Open Reading Frames ◽  
Restriction Fragments ◽  
Internal Part ◽  
Reading Frames ◽  
Related Element

Tn5405 (12 kb) is a staphylococcal composite transposon delimited by two inverted copies of IS1182, one of which contains IS1181. The internal part of this transposon carries three antibiotic resistance genes, aphA-3, aadE, and sat4, and three open reading frames (ORFs), orfx, orfy, and orfz, of unknown function. The dispersion of Tn5405 and the genes and ORFs included in this transposon were investigated in 50 epidemiologically unrelated staphylococci carrying aphA-3. Twenty-three maps, distinguishable by the presence or absence of the investigated genes or ORFs and/or by the sizes of the restriction fragments carrying them, were identified. Four isolates carried Tn5405, and 15 other isolates contained a Tn5405-related element. IS1182 was not detected in the aphA-3 regions mapped in 31 isolates which carried the following combinations: orfx, orfy, aadE, sat4, and aphA-3 +/- orfz; orfy, aadE, sat4, and aphA-3 +/- orfz; and aadE, sat4, aphA-3, and orfz. In all isolates, the genes and ORFs investigated were in relative positions similar to those in Tn5405. Thus, the internal part of Tn5405 appeared to be partially conserved with the maintenance, in all of the isolates, of at least the three antibiotic resistance genes.

scholarly journals Complete Nucleotide Sequence and Genome Organization of Hibiscus Chlorotic Ringspot Virus, a New Member of the Genus Carmovirus: Evidence for the Presence and Expression of Two Novel Open Reading Frames

2000 ◽  
Vol 74 (7) ◽  
pp. 3149-3155 ◽  
Author(s):  
Mei Huang ◽  
Dora Chin-Yen Koh ◽  
Li-Juan Weng ◽  
Min-Li Chang ◽  
Yun-Kiam Yap ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Organization ◽  
Complete Nucleotide Sequence ◽  
Full Length ◽  
Open Reading Frames ◽  
Ringspot Virus ◽  
In Vitro Translation ◽  
Cdna Clones ◽  
High Amino Acid ◽  
Reading Frames

ABSTRACT The complete nucleotide sequence of hibiscus chlorotic ringspot virus (HCRSV) was determined. The genomic RNA (gRNA) is 3,911 nucleotides long and has the potential to encode seven viral proteins in the order of 28 (p28), 23 (p23), 81 (p81), 8 (p8), 9 (p9), 38 (p38), and 25 (p25) kDa. Excluding two unique open reading frames (ORFs) encoding p23 and p25, the ORFs encode proteins with high amino acid similarity to those of carmoviruses. In addition to gRNA, two 3′-coterminated subgenomic RNA (sgRNA) species were identified. Full-length cDNA clones derived from gRNA and sgRNA were constructed under the control of a T7 promoter. Both capped and uncapped transcripts derived from the full-length genomic cDNA clone were infectious. In vitro translation and mutagenesis assays confirmed that all the predicted ORFs except the ORF encoding p8 are translatable, and the two novel ORFs (those encoding p23 and p25) may be functionally indispensable for the viral infection cycle. Based on virion morphology and genome organization, we propose that HCRSV be classified as a new member of the genus Carmovirus in familyTombusviridae.

The Nucleotide Sequence of a 39 kb Segment of Yeast Chromosome IV: 12 New Open Reading Frames, Nine Known Genes and One Gene for Gly-tRNA

Yeast ◽  
1997 ◽  
Vol 13 (2) ◽  
pp. 163-169 ◽  
Author(s):  
ANDRÉ BAHR ◽  
SABINE MÖLLER-RIEKER ◽  
THOMAS HANKELN ◽  
CHRISTIANE KRAEMER ◽  
URSULA PROTIN ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Open Reading Frames ◽  
Yeast Chromosome ◽  
Reading Frames

scholarly journals Two C—P Lyase Operons in Pseudomonas stutzeri and Their Roles in the Oxidation of Phosphonates, Phosphite, and Hypophosphite

2004 ◽  
Vol 186 (14) ◽  
pp. 4730-4739 ◽  
Author(s):  
Andrea K. White ◽  
William W. Metcalf
Keyword(s):  
Insertion Site ◽  
Pseudomonas Stutzeri ◽  
Gene Organization ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
E Coli ◽  
Reverse Transcription Pcr ◽  
Transposon Insertion ◽  
Intergenic Sequences ◽  
Reading Frames

ABSTRACT DNA sequencing and analysis of two distinct C—P lyase operons in Pseudomonas stutzeri WM88 were completed. The htxABCDEFGHIJKLMN operon encodes a hypophosphite-2-oxoglutarate dioxygenase (HtxA), whereas the predicted amino acid sequences of HtxB to HtxN are each homologous to the components of the Escherichia coli phn operon, which encodes C—P lyase, although homologs of E. coli phnF and phnO are absent. The genes in the htx operon are cotranscribed based on gene organization, and the presence of the intergenic sequences is verified by reverse transcription-PCR with total RNA. Deletion of the htx locus does not affect the ability of P. stutzeri to grow on phosphonates, indicating the presence of an additional C—P lyase pathway in this organism. To identify the genes comprising this pathway, a Δhtx strain was mutagenized and one mutant lacking the ability to grow on methylphosphonate as the sole P source was isolated. A ca.-10.6-kbp region surrounding the transposon insertion site of this mutant was sequenced, revealing 13 open reading frames, designated phnCDEFGHIJKLMNP, which were homologous to the E. coli phn genes. Deletion of both the htx and phn operons of P. stutzeri abolishes all growth on methylphosphonate and aminoethylphosphonate. Both operons individually support growth on methylphosphonate; however, the phn operon supports growth on aminoethylphosphonate and phosphite, as well. The substrate ranges of both C—P lyases are limited, as growth on other phosphonate compounds, including glyphosate and phenylphosphonate, was not observed.

scholarly journals Complete Nucleotide Sequence of Plasmid Rts1: Implications for Evolution of Large Plasmid Genomes

2002 ◽  
Vol 184 (12) ◽  
pp. 3194-3202 ◽  
Author(s):  
Takahiro Murata ◽  
Makoto Ohnishi ◽  
Takeshi Ara ◽  
Jun Kaneko ◽  
Chang-Gyun Han ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Proteus Vulgaris ◽  
Significant Sequence Similarity ◽  
Modular Evolution ◽  
Broad Array ◽  
Reading Frames

ABSTRACT Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300 potential open reading frames (ORFs). Among these, the products of 141 ORFs, including 9 previously identified genes, displayed significant sequence similarity to known proteins. The set of genes responsible for the conjugation function of Rts1 has been identified. A broad array of genes related to diverse processes of DNA metabolism were also identified. Of particular interest was the presence of tus-like genes that could be involved in replication termination. Inspection of the overall genome organization revealed that the Rts1 genome is composed of four large modules, providing an example of modular evolution of plasmid genomes.

Protection against bacteriocin 28b in Serratia matcescens is apparently not related to the expression of an immunity gene

1995 ◽  
Vol 41 (3) ◽  
pp. 217-226 ◽  
Author(s):  
Margarita Beatriz Viejo ◽  
Josefina Enfedaque ◽  
Joan Francesc Guasch ◽  
Santiago Ferrer ◽  
Miguel Regué
Keyword(s):  
Nucleotide Sequence ◽  
Serratia Marcescens ◽  
Structural Gene ◽  
Genomic Library ◽  
Open Reading Frames ◽  
Genetic Determinants ◽  
Gene Encoding ◽  
Immunity Gene ◽  
Release Analysis ◽  
Reading Frames

The gene encoding bacteriocin 28b from Serratia marcescens N28b (bss gene) has been cloned in Escherichia coli and its nucleotide sequence has been determined. The genetic determinants coding for other well-characterized bacteriocins from enterobacteria (colicins) are located in plasmids and they have always been shown to contain a gene responsible for immunity located downstream from the bacteriocin structural gene. In some cases there is another gene located downstream from the immunity gene, which is responsible for bacteriocin release. Analysis of bacteriocin 28b release and the sensitivity to this bacteriocin of E. coli strains harbouring recombinant plasmids containing the bss gene showed that bacteriocin 28b is not released from the cell in these strains and that their phenotypic insensitivity is not associated with any region close to the structural gene. The nucleotide sequence of the region downstream from the bss gene contains two putative open reading frames transcribed in the opposite direction to the bss gene. These open reading frames apparently encode proteins that seem not to be involved in bacteriocin immunity or release. Moreover, a S. marcescens N28b genomic library was screened and no immunity gene was found. Therefore, bacteriocin 28b differs greatly from the bacteriocins from other enterobacteria, and in the following senses it is unique: firstly, the gene encoding bacteriocin 28b seems to be located on the chromosome, and secondly, insensitivity to this bacteriocin in S. marcescens N28b is not associated with the expression of an immunity gene.Key words: bacteriocin, pore-forming colicins, immunity, Serratia marcescens.

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