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PubMed1992

IS231D, E and F, three new insertion sequences in Bacillus thuringiensis: extension of the IS231 family.

IS231 constitutes a family of insertion sequences widespread among Bacillus thuringiensis subspecies. Three new IS231 variants have been isolated from B. thuringiensis subspecies finitimus (IS231 D and E) and israelensis (IS231F). Like the previously described IS231A, B and C, these 1.7 kb elements display single open reading frames encoding 477/478-amino-acid proteins which share between 72% and 88% identity with those of the other members of the family. Sequence comparisons also reveal that all the iso-IS231 terminal inverted repeats are strongly conserved 20 bp sequences. A region susceptible to forming a stable hairpin structure is found just upstream of the open reading frame. Nucleotide substitutions occurring on one strand of the hairpin stems are compensated for by complementary changes at facing positions, giving credence to the hypothesis that this secondary structure plays a role in the regulation of transposition. Examination of IS231 D, E and F flanking sequences reveals that IS231F is bordered by a 12 bp direct repeat. No direct repeats were found flanking IS231D or IS231E.

Amino Acid Sequence↗

PubMed2001

Characterization of a hypervariable region in the genome of Chlamydophila pneumoniae.

Chlamydophila pneumoniae displays surprisingly little genomic variation, as seen by comparisons of the published genomes from three different isolates and sequencing of four different genes from different isolates. We have in the present study, however, demonstrated genomic variation between 10 C. pneumoniae isolates in the 11690-bp region between the two outer membrane protein genes pmp1 and pmp2. This region of the C. pneumoniae CWL-029 isolate contains seven C. pneumoniae-specific open reading frames (hb1-7, encoding hydrophobic beta-sheet-containing proteins). We identified additionally 12 open reading frames in the C. pneumoniae CWL-029 genome encoding hypothetical proteins with similarity to the seven hypothetical Hb-proteins. Compared to other isolates, genomic variation is seen to cause frame-shifting of three of the 19 hb-open reading frames, which are proposed to be three full-length genes and eight frame-shifted pseudogenes. The hypothetical proteins encoded by these proposed genes contain an N-terminally located highly hydrophobic stretch of 50-60 residues. A similar motif is found in all identified Chlamydia inclusion membrane proteins and therefore the Hb-proteins are candidate inclusion proteins.

Bacterial Outer Membrane Proteins↗

PubMed2001

A cryptic plasmid, pAO1, from a compost bacterium, Bacillus sp.

The complete nucleotide sequence of a new cryptic plasmid, pAO1 isolated from a compost bacterium Bacillus sp., has been analyzed. Analysis of the PCR-based 16S rRNA sequence showed the bacterium harboring pAO1 was closely related to Bacillus pallidus. The plasmid pAO1 was 3,325 bp in size. Two open reading frames, ORF1 and ORF2, encoding putative polypeptides of 248 and 290 amino acids, respectively, were identified within the sequence. The ORF1 has a limited sequence similarity to an integrase/recombinase, while the ORF2 has high similarity with the replication protein of pBC1 from Bacillus coagulans. A putative origin sequence for a plus-strand was located between ORFs. Southern blot analysis indicates this plasmid replicates via a rolling circle-type mechanism.

Bacillus↗

PubMed1991

Nucleotide sequence of a cDNA coding for the mitochondrial precursor protein of cytochrome c oxidase subunit IV from the slime mold Dictyostelium discoideum.

Subunit-specific polyclonal antibodies were used to isolate cDNA clones encoding subunit IV of Dictyostelium discoideum cytochrome c oxidase. DNA sequence analysis reveals an open reading frame of 149 amino acids. As shown by sequencing of the protein N-terminus, the subunit is synthesized with a 24 residue cleavable presequence which leads to a mature polypeptide of 14305 Da. The slime mold subunit exhibits a low but significant degree of similarity with subunit Va of human and subunit VI of yeast cytochrome c oxidase.

Amino Acid Sequence↗

PubMed1994

An African swine fever virus gene with similarity to the T-lymphocyte surface antigen CD2 mediates hemadsorption.

An open reading frame, LMW8-DR, in the African swine fever virus (ASFV) genome possesses striking similarity to the lymphocyte membrane antigen CD2. All characterized CD2 domains, including the amino-terminal signal sequence, IgV, hinge, IgC2, stalk, transmembrane, and proline-rich carboxy cytoplasmic domains, are highly conserved in the ASFV gene. Critical residues for the binding of the lymphocyte function-associated antigen (LFA-3) and CD59 and for T-cell activation are also partially conserved. LMW8-DR is actively transcribed in ASFV-infected swine macrophages and Vero cells at late times in the infection cycle and Vero and COS cells transiently expressing the LMW8-DR open reading frame hemadsorbed swine red blood cells. The structural and functional similarities of LMW8-DR to CD2, a protein that is involved in cell-cell adhesion and immune response modulation, suggest a possible role in the pathogenesis of ASFV infection.

African Swine Fever Virus↗

PubMed1992

Complete nucleotide sequence of a Selenomonas ruminantium plasmid and definition of a region necessary for its replication in Escherichia coli.

A plasmid from Selenomonas ruminantium subspecies lactilytica has been subcloned in Escherichia coli K-12 and completely sequenced. Three open reading frames (ORFs) of 909, 801, and 549 bp were identified and the complete sequence was analyzed by comparison with DNA and protein databases. No significant deoxynucleotide or amino acid sequence homology with other published genes or proteins was detected. The plasmid was shown to replicate independently in E. coli K-12 by a DNA polymerase I-dependent mechanism and deletion analysis defined the DNA sequence responsible for this phenotype.

Amino Acid Sequence↗

PubMed1995

Identification of the major capsid protein gene of human herpesvirus 7.

Two human herpesvirus 6 (HHV-6) open reading frames were identified with significant amino acid similarity to UL86 (major capsid protein, MCP) and UL85 of human cytomegalovirus (HCMV) in human herpesvirus 7 (HHV-7) genes. The predicted lengths of the complete HHV-7 MCP and the HCMV-UL85 open reading frames were 1344 and 293 amino acids with estimated molecular weights of approximately 153 and 33 kDa, respectively. Computer analysis showed that the amino acid of HHV-7 MCP was 61% identical to the MCP of HHV-6 variants A and B, 28% to HCMV. These results suggest that HHV-7 is more closely related to HHV-6 than to HCMV.

Adult↗

PubMed1991

cDNA encoding murine FK506-binding protein (FKBP): nucleotide and deduced amino acid sequence.

A FKBP cDNA encoding murine FK506 binding protein (FKBP) has been cloned, and its complete nucleotide sequence has been determined. The open reading frame within the 1556-bp cDNA segment encodes an 108 amino acid (aa) protein that differs from the human FKBP by three aa and from the bovine FKBP by five aa. Molecular modeling of the protein places the aa substitutions at positions not directly involved in drug binding or interaction with the potential drug target protein, calcineurin A.

Amino Acid Sequence↗

PubMed1995

Cloning and sequencing of the Bordetella pertussis cpn10/cpn60 (groESL) homolog.

The nucleotide sequence downstream from the Bordetella resistance to killing (brk) locus in Bordetella pertussis was determined. Analysis of the sequence revealed an operon consisting of two highly predicted open reading frames (ORFs). The deduced amino-acid sequence of each ORF has strong homologies to the heat-shock proteins/chaperonins Cpn60 and Cpn10. The promoter contains consensus sequences for both sigma 32 and sigma 70 binding, and it possesses the CIRCE regulatory inverted repeat. A potential Rho-independent terminator was identified and appears to be shared with the brkA gene.

Amino Acid Sequence↗

PubMed2005

Full genome sequence of peste des petits ruminants virus, a member of the Morbillivirus genus.

Peste des petits ruminants virus (PPRV) causes an acute febrile illness in small ruminant species, mostly sheep and goats. PPRV is a member of the Morbillivirus genus which includes measles, rinderpest (cattle plague), canine distemper, phocine distemper and the morbilliviruses found in whales, porpoises and dolphins. Full length genome sequences for these morbilliviruses are available and reverse genetic rescue systems have been developed for the viruses of terrestrial mammals, with the exception of PPRV. This paper presents the first published full length genome sequence for PPRV. The genome was found to be consistent with the rule-of-six and open reading frames (ORFs) were identified that encoded the eight proteins characteristic of morbilliviruses. At the nucleotide (nt) level, the full length genome of PPRV was most similar to that of rinderpest, the other ruminant morbillivirus. However, at the protein level five of the six structural proteins and the V protein showed a greater similarity to the dolphin morbillivirus (DMV) while only the C and L proteins showed a high relationship to rinderpest.

Base Sequence↗

PubMed1997

Cloning and sequence of a type I pullulanase from an extremely thermophilic anaerobic bacterium, Caldicellulosiruptor saccharolyticus.

A gene coding for a pullulanase from the obligately anaerobic, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus has been cloned in Escherichia coli. It consists of an open reading frame (pulA) of 2478 bp which codes for an enzyme of 95,732 Da and is flanked by two other open reading frames. A truncated version of the gene which lacks 381 bp of 5'-sequence also has pullulanase activity and it appears that the amino-terminal portion of the gene is not essential for either activity or thermostability. Amino acid sequence comparisons with other published amylases and pullulanases showed that it possesses homology to the four key regions common to these enzymes.

Amino Acid Sequence↗

PubMed2002

Protective efficacy of a tandemly linked, multi-subunit recombinant leishmanial vaccine (Leish-111f) formulated in MPL adjuvant.

Three immunodominant leishmanial antigens (TSA, LmSTI1 and LeIF) previously identified in the context of host response to infection in infected donors and BALB/c mice, as well as their ability to elicit at least partial protection against Leishmania major infection in the BALB/c mouse model, were selected for inclusion into a subunit based vaccine. This is based on the premise that an effective vaccine against leishmaniasis (a complex parasitic infection) would require a multivalent cocktail of several antigens containing a broader range of protective epitopes that would cover a wide range of MHC types in a heterogeneous population. For practical considerations of vaccine development, we report on the generation of a single recombinant polyprotein comprising the sequences of all three open reading frames genetically linked in tandem. The resulting molecule, Leish-111f, comprises an open reading frame that codes for a 111kDa polypeptide. Evaluation of the immunogenicity and protective efficacy of Leish-111f formulated with IL-12 revealed that the immune responses to the individual components were maintained and as well, rLeish-111f protected BALB/c mice against L. major infection to a magnitude equal or superior to those seen with any of the individual components of the vaccine construct or SLA, a soluble Leishmania lysate. But because rIL-12 is expensive and difficult to manufacture and its efficacy and safety as an adjuvant for human use is questionable, we screened for other adjuvants that could potentially substitute for IL-12. We report that monophosphoryl lipid A (MPL) plus squalene (MPL-SE) formulated with rLeish-111f elicited protective immunity against L. major infection. The demonstrated feasibility to manufacture a single recombinant vaccine comprising multiple protective open reading frames and the potential use of MPL-SE as a substitute for IL-12, takes us closer to the realization of an affordable and safe Leishmania vaccine.

Adjuvants, Immunologic↗

PubMed1997

Molecular cloning and characterization of a cDNA encoding the third putative mammalian hyaluronan synthase.

We report the isolation of a cDNA encoding the third putative hyaluronan synthase, HAS3. Partial cDNAs and genomic fragments of mouse Has3 were obtained using a degenerate polymerase chain reaction approach. Partial clones facilitated the isolation of genomic and cDNA clones representing the mouse Has3 open reading frame. The open reading frame of 554 amino acids predicted a protein of 63.3 kDa with multiple transmembrane domains and several consensus HA binding motifs. Sequence comparisons indicated that mouse Has3 is most closely related to Has2 (71% amino acid identity) and also related to Has1 (57% identity), Xenopus laevis DG42 (56% identity), and Streptococcus pyogenes HasA (28% identity). Isolation of a genomic fragment of human HAS3 indicated high conservation between mouse and human sequences, similar to those observed for HAS1 and HAS2. Expression of the mouse Has3 open reading frame in transfected COS-1 cells led to high levels of hyaluronan synthesis, as determined through a classical particle exclusion assay, and by in vitro HA synthase assays. These results suggest that there are three putative mammalian hyaluronan synthases encoded by three separate but related genes which comprise a mammalian hyaluronan synthase (HAS) gene family.

Amino Acid Sequence↗

PubMed1999

Molecular analysis of the genome of Chuzan virus, a member of the Palyam serogroup viruses, and its phylogenetic relationships to other orbiviruses.

The nucleotide sequence of the entire genome of Chuzan virus, which belongs to the Palyam serogroup orbiviruses and causes congenital abnormalities of cattle, has been completed by analysis of the genes encoding minor core proteins (VP1, VP4 and VP6) and non-structural proteins (NS1, NS2 and NS3). The genome of Chuzan virus is 18,915 bp in length and the coding capacity of its open reading frames is 6071 aa. Comparative sequence analysis with other serogroups of the genus Orbivirus indicated that the outer capsid protein VP2, which is the neutralizing antigen, appears to be the most variable and the major core protein VP3 is the most conserved. Overall, the structural proteins, with the exception of VP2, are more conserved than the non-structural proteins among orbiviruses. Chuzan virus is phylogenetically most related to African horsesickness virus.

Base Sequence↗

PubMed1993

The glpP and glpF genes of the glycerol regulon in Bacillus subtilis.

The Bacillus subtilis glpPFKD region contains genes essential for growth on glycerol or glycerol 3-phosphate (G3P). The nucleotide sequence of glpP encoding a regulatory protein and the previously unidentified glpF encoding the glycerol uptake facilitator was determined. glpF is located immediately upstream of glpK and the two genes were shown to constitute one operon which is transcribed separately from glpP. A sigma A-type promoter and the transcriptional start point for glpFK were identified. In the 5' untranslated leader sequence (UTL) of glpFK mRNA a conserved inverted repeat is found. The repeat is believed to be involved in the control of expression of glpFK by termination/antitermination of transcription, a control mechanism previously suggested for the regulation of glpD encoding G3P dehydrogenase. Expression of glpFK and glpD requires the inducer G3P and the glpP gene product. A 2.9 kb B. subtilis chromosomal DNA fragment containing the glpP open reading frame was cloned to give plasmid pLUM7. pLUM7 contains a functional glpP gene as shown by its ability to complement various glpP mutants. Immediately upstream of glpP an open reading frame is found (ORF1). Disrupting ORF1 by plasmid integration in the B. subtilis chromosome does not affect the ability to grow on glycerol as sole carbon and energy source. With the present report all B. subtilis glp genes located at 75 degrees on the chromosomal map have been identified.

Amino Acid Sequence↗

PubMed1991

Molecular analysis of the virulence locus of the Salmonella dublin plasmid pSDL2.

The virulence properties of various non-typhoid Salmonella serotypes depend on the presence of large plasmids 60-100 kb in size. We have shown previously that the virulence region on the 80 kb plasmid pSDL2 of Salmonella dublin Lane maps within a 14kb SalI fragment. In this report we show that an 8.2 kb region within this fragment is sufficient to express lethal disease in BALB/c mice. Sequence analysis of this segment revealed six sequential open reading frames designated vsdA-F, which encode putative proteins of 13-65kDa. Deletion analysis and location of Tn5-oriT inserts which abolish virulence suggest that vsdA, vsdC, vsdD and vsdE are essential for virulence expression. Downstream of vsdF we discovered a locus involved in stable plasmid maintenance. Deletion of that region resulted in plasmid multimerization and instability.

Amino Acid Sequence↗

PubMed1997

Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid.

Sphingomonas sp. strain HV3 (formerly Pseudomonas sp. HV3), which degrades aromatics and chloroaromatics, harbors a mega-plasmid, pSKY4. A sequenced 4 kb fragment of the plasmid reveals a novel gene organization for catechol meta-pathway genes. The putative meta operon starts with the cmpF gene encoding a 2-hydroxymuconic semialdehyde hydrolase. The gene has a 6 bp overlap with the previously characterized ring-cleavage gene, catechol 2,3-dioxygenase, cmpE. Downstream of cmpE is a 429 bp open reading frame of unknown function. Gene cmpC, encoding a 2-hydroxymuconic semialdehyde dehydrogenase, starts 44 bp further downstream. It has the highest homology to 2-hydroxymuconic semialdehyde dehydrogenases of dmp and xyl pathways and to XylC from the marine oligotroph Cycloclasticus oligotrophus. The gene organization is different from other known meta pathways. This is the first report of organization of plasmid-encoded meta-pathway genes in the genus Sphingomonas.

Amino Acid Sequence↗

PubMed2003

Chromosomal arm replacement in Streptomyces griseus.

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.

Base Sequence↗