scholarly journals Identification and Characterization of IS2404 and IS2606: Two Distinct Repeated Sequences for Detection of Mycobacterium ulcerans by PCR

1999 ◽  
Vol 37 (4) ◽  
pp. 1018-1023 ◽  
Author(s):  
Timothy Stinear ◽  
Bruce C. Ross ◽  
John K. Davies ◽  
Lui Marino ◽  
Roy M. Robins-Browne ◽  
...  
Keyword(s):  
Amino Acid ◽  
Burkholderia Cepacia ◽  
Rhizobium Meliloti ◽  
Amino Acid Identity ◽  
Aeromonas Salmonicida ◽  
Mycobacterium Ulcerans ◽  
Inverted Repeats ◽  
Pcr Screening ◽  
Reading Frame ◽  
Acid Identity

Molecular analysis of Mycobacterium ulcerans has revealed two new insertion sequences (ISs), IS2404 and IS2606. IS2404 was identified by complete sequencing of a previously described repetitive DNA segment fromM. ulcerans. This element is 1,274 bp long, contains 12-bp inverted repeats and a single open reading frame (ORF) potentially encoding a protein of 327 amino acids (aa), and apparently generates 7-bp direct repeats upon transposition. Amino acid similarity was found between the putative transposase and those encoded by ISs in other bacterial sequences from Aeromonas salmonicida(AsIs1), Escherichia coli (H repeat element), Vibrio cholerae (VcIS1), and Porphyromonas gingivalis(PGIS2). The second IS, IS2606, was discovered by sequence analysis of a HaeIII fragment of M. ulcerans genomic DNA containing a repetitive sequence. This element is 1,404 bp long, with 12-bp inverted repeats and a single ORF potentially encoding a protein of 445 aa. Database searches revealed a high degree of amino acid identity (70%) with the putative transposase of IS1554from M. tuberculosis. Significant amino acid identity (40%) was also observed with transposases from several other microorganisms, including Rhizobium meliloti(ISRm3), Burkholderia cepacia(IS1356), Corynebacterium diphtheriae, andYersinia pestis. PCR screening of DNA from 45 other species of mycobacteria with primers for IS2404 confirm that this element is found only in M. ulcerans. However, by PCR, IS2606 was also found in Mycobacterium lentiflavum, another slow-growing member of the genusMycobacterium that is apparently genetically distinct fromM. ulcerans. Testing the sensitivity of PCR based on IS2404 and IS2606 primers demonstrated the ability to detect 0.1 and 1 M. ulcerans genome equivalents, respectively. The ability to detect small numbers of cells by using two gene targets will be particularly useful for analyzing environmental samples, where there may be low concentrations ofM. ulcerans among large numbers of other environmental mycobacteria.

scholarly journals groEL Encodes a Highly Antigenic Protein in Burkholderia pseudomallei

2001 ◽  
Vol 8 (4) ◽  
pp. 832-836 ◽  
Author(s):  
Patrick C. Y. Woo ◽  
Patricia K. L. Leung ◽  
Samson S. Y. Wong ◽  
Pak-Leung Ho ◽  
Kwok-Yung Yuen
Keyword(s):  
Amino Acid ◽  
Recombinant Protein ◽  
Burkholderia Cepacia ◽  
Burkholderia Pseudomallei ◽  
Amino Acid Identity ◽  
Local Alignment ◽  
Amino Acid Residues ◽  
Reading Frame ◽  
Acid Identity ◽  
Burkholderia Vietnamiensis

ABSTRACT No recombinant protein is available for serodiagnosis of melioidosis. In this study, we report the cloning of thegroEL gene, which encodes an immunogenic protein ofBurkholderia pseudomallei. Bidirectional DNA sequencing ofgroEL revealed that the gene contained a single open reading frame encoding 546 amino acid residues with a predicted molecular mass of 57.1 kDa. Basic Local Alignment Search Tool analysis showed that the putative protein encoded by groEL is homologous to the chaperonins encoded by the groEL genes of other bacteria. It has 98% amino acid identity with the GroEL ofBurkholderia cepacia, 98% amino acid identity with the GroEL of Burkholderia vietnamiensis, and 82% amino acid identity with the GroEL of Bordetella pertussis. Furthermore, it was observed that patients with melioidosis develop a strong antibody response against GroEL, suggesting that the recombinant protein and its monoclonal antibody may be useful for serodiagnosis in patients with melioidosis and that the protein may represent a good cell surface target for host humoral immunity. Further studies in these directions would be warranted.

scholarly journals Molecular cloning and functional characterization of the mouse organic-anion-transporting polypeptide 1 (Oatp1) and mapping of the gene to chromosome X

1999 ◽  
Vol 345 (1) ◽  
pp. 115-120 ◽  
Author(s):  
Bruno HAGENBUCH ◽  
Ilse-Dore ADLER ◽  
Thomas E. SCHMID
Keyword(s):  
Amino Acid ◽  
Organic Anion ◽  
Functional Characterization ◽  
Amino Acid Identity ◽  
Xenopus Laevis Oocytes ◽  
Cdna Insert ◽  
Reading Frame ◽  
Acid Identity ◽  
Organic Anion Transporting Polypeptide ◽  
Cloned Cdna

We have cloned a murine member of the organic-anion-transporting polypeptide (Oatp) family of membrane-transport proteins from mouse liver. The cloned cDNA insert of 2783 bp with an open reading frame of 2011 bp codes for a 12-transmembrane 670-amino-acid protein with highest amino acid identity with the rat Oatp1. When expressed in Xenopus laevis oocytes, the mouse Oatp exhibited the same substrate specificity as the rat Oatp1. Besides the common Oatp substrates bromosulphophthalein, taurocholate, oestrone 3-sulphate and ouabain, the new mouse Oatp also mediates transport of the Oatp1-specific magnetic-resonance-imaging agent gadoxetate. The Oatp2-specific cardiac glycoside digoxin, however, is not transported. Kinetic analyses performed for taurocholate and oestrone 3-sulphate revealed apparent Km values of 12 μM and 5 μM respectively. Northern-blot analysis demonstrated a predominant expression in the liver with an additional moderate expression in the kidney. Taken together, the amino acid identity, the functional characteristics and the tissue distribution suggest that we have isolated the murine orthologue of the rat Oatp1, and consequently the identified protein will be called Oatp1. Using fluorescence in situ hybridization, the murine Oatp1 gene was mapped to chromosome XA3-A5.

scholarly journals Characterization of a DivergentvanD-Type Resistance Element from the First Glycopeptide-Resistant Strain of Enterococcus faeciumIsolated in Brazil

2000 ◽  
Vol 44 (12) ◽  
pp. 3444-3446 ◽  
Author(s):  
Libera M. Dalla Costa ◽  
Peter E. Reynolds ◽  
Helena A. P. H. M. Souza ◽  
Dilair C. Souza ◽  
Marie-France I. Palepou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Resistant Strain ◽  
Enterococcus Faecium ◽  
Amino Acid Identity ◽  
Open Reading Frame ◽  
Glycopeptide Resistance ◽  
Reading Frame ◽  
Acid Identity ◽  
Resistance Phenotype

ABSTRACT Enterococcus faecium 10/96A from Brazil was resistant to vancomycin (MIC, 256 μg/ml) but gave no amplification products with primers specific for known van genotypes. A 2,368-bp fragment of a van cluster contained one open reading frame encoding a peptide with 83% amino acid identity to VanHD, and a second encoding a d-alanine-d-lactate ligase with 83 to 85% identity to VanD. The divergent glycopeptide resistance phenotype was designated VanD4.

scholarly journals Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus

2004 ◽  
Vol 85 (8) ◽  
pp. 2263-2270 ◽  
Author(s):  
J. R. de Miranda ◽  
M. Drebot ◽  
S. Tyler ◽  
M. Shen ◽  
C. E. Cameron ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Identity ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Acid Identity ◽  
Kashmir Bee Virus ◽  
Acute Bee Paralysis Virus ◽  
Bee Virus ◽  
Paralysis Virus

The complete nucleotide sequence of a novel virus is presented here together with serological evidence that it belongs to Kashmir bee virus (KBV). Analysis reveals that KBV is a cricket paralysis-like virus (family Dicistroviridae: genus Cripavirus), with a non-structural polyprotein open reading frame in the 5′ portion of the genome separated by an intergenic region from a structural polyprotein open reading frame in the 3′ part of the genome. The genome also has a polyadenylated tail at the 3′ terminus. KBV is one of several related viruses that also includes acute bee paralysis virus (ABPV). Although KBV and ABPV are about 70 % identical over the entire genome, there are considerable differences between them in significant areas of the genome, such as the 5′ non-translated region (42 % nucleotide identity), between the helicase and 3C-protease domains of the non-structural polyprotein (57 % amino acid identity) and in a 90 aa stretch of the structural polyprotein (33 % amino acid identity). Phylogenetic analyses show that KBV and ABPV isolates fall into clearly separated clades with moderate evolutionary distance between them. Whether these genomic and evolutionary differences are sufficient to classify KBV and ABPV as separate species remains to be determined.

scholarly journals Molecular cloning and overexpression of a glutathione transferase gene from Proteus mirabilis

1996 ◽  
Vol 318 (1) ◽  
pp. 157-162 ◽  
Author(s):  
Brunella PERITO ◽  
Nerino ALLOCATI ◽  
Enrico CASALONE ◽  
Michele MASULLI ◽  
Beatrice DRAGANI ◽  
...  
Keyword(s):  
Amino Acid ◽  
Proteus Mirabilis ◽  
Burkholderia Cepacia ◽  
Glutathione Transferase ◽  
Amino Acid Identity ◽  
Amino Acid Residues ◽  
Reading Frame ◽  
Promoter Sequences ◽  
E Coli ◽  
Cloned Gene

The structural gene of the Proteus mirabilis glutathione transferase GSTB1-1 (gstB) has been isolated from genomic DNA. A nucleotide sequence determination of gstB predicted a translational product of 203 amino acid residues, perfectly matching the sequence of the previously purified protein [Mignogna, Allocati, Aceto, Piccolomini, Di Ilio, Barra and Martini (1993) Eur. J. Biochem. 211, 421–425]. The P. mirabilis GST sequence revealed 56% identity with the Escherichia coli GST at DNA level and 54% amino acid identity. Similarity has been revealed also with the translation products of the recently cloned gene bphH from Haemophilus influenzae (28% identity) and ORF3 of Burkholderia cepacia (27% identity). Putative promoter sequences with high similarity to the E. coli σ70 consensus promoter and to promoters of P. mirabiliscat and glnA genes preceded the ATG of the gstB open reading frame (ORF). gstB was brought under control of the tac promoter and overexpressed in E. coli by induction with isopropyl-β-d-thiogalactopyranoside and growth at 37 °C. The physicochemical and catalytic properties of overexpressed protein were indistinguishable from those of the enzyme purified from P. mirabilis extract. Unlike the GST belonging to Mu and Theta classes, GSTB1-1 was unable to metabolize dichloromethane. The study of the interaction of cloned GSTB1-1 with a number of antibiotics indicates that this enzyme actively participates in the binding of tetracyclines and rifamycin.

scholarly journals Genetic Diversity of Carbapenem-Hydrolyzing Metallo-β-Lactamases from Chryseobacterium(Flavobacterium) indologenes

2000 ◽  
Vol 44 (11) ◽  
pp. 3028-3034 ◽  
Author(s):  
Samuel Bellais ◽  
Laurent Poirel ◽  
Sophie Leotard ◽  
Thierry Naas ◽  
Patrice Nordmann
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Inverse Pcr ◽  
Related Gene ◽  
Reading Frame ◽  
Acid Identity ◽  
Broad Spectrum Resistance ◽  
Class B ◽  
Pcr Techniques

ABSTRACT The class B carbapenem-hydrolyzing β-lactamase IND-1 has been characterized for Chryseobacterium indologenes strain 001. With internal primers for the bla gene for IND-1 (bla IND-1) and an internalbla IND-1 probe, PCR amplifications failed, while hybridization results were positive when DNA from anotherC. indologenes isolate, strain CIP101026, was used as a template. Thus, a bla IND-related gene was cloned from this C. indologenes reference strain. Sequencing of the insert of a recombinant plasmid conferring resistance to carbapenems revealed an open reading frame with a G + C content of 39.9% and coding for a 243-amino-acid preprotein named IND-2. IND-2 shared 80% amino acid identity with IND-1 and had a similar broad-spectrum resistance profile, including resistance to carbapenems. It was classified in functional subgroup 3a of class B carbapenem-hydrolyzing β-lactamases. IND-1 and IND-2, despite their genetic diversity, possessed similar kinetic parameters, except that ceftazidime was hydrolyzed less by IND-2. To obtain the entirebla IND-related gene sequences of eight otherC. indologenes isolates, PCR was performed using internal and external primers, followed by inverse PCR techniques. The likely chromosome-mediated metallo-β-lactamases of the 10 C. indologenes isolates were divided into several groups and subgroups. IND-1, IND-2, IND-2a, IND-3, and IND-4 shared 77 to 99% amino acid identity.

A sea urchin homologue of the chordate Brachyury (T) gene is expressed in the secondary mesenchyme founder cells

Development ◽  
1995 ◽  
Vol 121 (9) ◽  
pp. 2747-2754 ◽  
Author(s):  
Y. Harada ◽  
H. Yasuo ◽  
N. Satoh
Keyword(s):  
Amino Acid ◽  
Sea Urchin ◽  
Larval Stage ◽  
Single Copy ◽  
Amino Acid Identity ◽  
Molecular Probe ◽  
Reading Frame ◽  
Acid Identity ◽  
Origin And Evolution ◽  
Founder Cells

Chordates are thought to have emerged from some common ancestor of deuterostomes by organizing shared anatomical and embryological features including a notochord, a dorsal nerve cord and pharyngeal gill slits. Because the notochord is the most prominent feature of chordates and because the Brachyury (T) gene is essential for notochord formation, the T gene is a key molecular probe with which to explore the origin and evolution of chordates. We investigated whether the sea urchin (echinoderm) conserves the T gene and, if so, where the sea urchin T gene is expressed. A cDNA clone for the sea urchin T (HpTa) gene contained a long open reading frame that encodes a polypeptide of 434 amino acids. Although the overall degree of amino acid identity was not very high (52%, sea urchin/mouse), in the T domain of the N terminus the amino acid identity was 73% (sea urchin/mouse). The HpTa gene is present as a single copy per haploid genome. As with the chordate T gene, the expression of HpTa is transient, being first detected in the swimming blastula, maximally transcribed in the gastrula, decreasing at the prism larval stage and barely detectable at the pluteus larval stage. HpTa transcripts were found in the secondary mesenchyme founder cells, vegetal plate of the mesenchyme blastula, extending tip of the invaginating archenteron and, finally, the secondary mesenchyme cells at the late-gastrula stage.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Genome Sequence of Hardyhisp2, a Gammapleolipovirus Infecting Haloarcula hispanica

2021 ◽  
Vol 10 (19) ◽  
Author(s):  
Mike Dyall-Smith ◽  
Friedhelm Pfeiffer ◽  
Pei-Wen Chiang ◽  
Sen-Lin Tang
Keyword(s):  
Amino Acid ◽  
Viral Genome ◽  
Amino Acid Identity ◽  
Spike Protein ◽  
Inverted Repeats ◽  
Halophilic Archaeon ◽  
Content Type ◽  
Terminal Inverted Repeats ◽  
Acid Identity ◽  
Haloarcula Hispanica

ABSTRACT Hardyhisp2 virus infects the halophilic archaeon Haloarcula hispanica DSM 4426T and is closely related to His2 (Pleolipoviridae family). The viral genome is 16,133 bp long, with terminal inverted repeats of 599 bp. The predicted spike protein is only weakly similar (32% amino acid identity) to that of His2.

scholarly journals A50 Whole-genome sequencing of African swine fever isolates from Sardinia

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
C Torresi ◽  
F Granberg ◽  
L Bertolotti ◽  
A Oggiano ◽  
B Colitti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Temporal Distribution ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Genotype I ◽  
Acid Identity ◽  
Wide Range ◽  
Intergenic Sequences ◽  
Genes Encoding

Abstract In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.

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