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PubMed1992

Nucleotide sequence of a transactivating Bombyx mori nuclear polyhedrosis virus immediate early gene.

The open reading frame (ORF) of 1572 bp contained in the 3.8 kb ClaI fragment of BmNPV encodes a viral regulatory protein which transactivates the delayed early AcMNPV 39K gene. Transactivation is induced in uninfected cells following transfection with a plasmid containing only the ClaI fragment. Hitherto immediate early gene promoter activity of the included 631 bp leader sequence is evident since no other viral elements are needed for the transcription of the regulatory gene.

Animals↗

PubMed1993

Nucleotide sequences of the Macaca fascicularis apolipoprotein C-III and A-IV genes.

The cynomolgus monkey (Macaca fascicularis) apolipoprotein C-III and apolipoprotein A-IV genes have been isolated from a cynomolgus genomic DNA library and completely sequenced. These genes span 3.1 and 2.8 kilobases (kb), respectively. Apolipoprotein C-III gene is interrupted by three intervening sequences of 613, 135 and 1699 bp, respectively. The open reading frame encodes a protein of 99 amino acids which is 87% similar to the human. The cynomolgus mature protein is 79 residues long. Thr-74 is also present what might allow the formation of O-glycosidic linkage observed in the human protein. Apolipoprotein A-IV gene consist of two intervening sequences of 352 and 774 bp, respectively. The open reading frame encodes a protein of 429 amino acids which is 87% similar to the human. The cynomolgus mature protein is 409 residues long, 33 amino acids longer than the human, due to an insertion of 33 residues in its COOH-terminal region. This insertion is mainly composed of glutamine and glutamic acid, which confers cynomolgus apolipoprotein a higher hydrophilicity.

Amino Acid Sequence↗

PubMed1993

Sequences of tRNA-encoding genes and associated open reading frames of Streptomyces lividans.

A gene library of Streptomyces lividans has been screened for tRNA-encoding genes with labeled Streptomyces tRNA as a probe. By sequence analysis of hybridizing fragments, two single genes have been identified which code for tRNA(Asp) and tRNA(Gly). Associated with the tRNA(Gly) gene, there are three open reading frames (ORFs) which might code for gene products possibly involved in active transport processes through the bacterial membrane. The transcriptional organization of tRNAGly and the following ORFs was examined by high-resolution S1 mapping. A third clone carried a cluster of genes which encode two tRNA(Gln) and three tRNA(Glu). This cluster corresponds to a similar cluster previously described for Streptomyces rimosus [Plohl and Gamulin, Mol. Gen. Genet. 222 (1990) 129-134].

Amino Acid Sequence↗

PubMed1994

A protein involved in stabilization of a large non-symbiotic plasmid of Rhizobium meliloti shows homology to eukaryotic cytoskeletal proteins and DNA-binding proteins.

An open reading frame, denoted ORF2, present in the replication and stabilization region of plasmid pRmeGR4a of Rhizobium meliloti GR4, was identified by sequence analysis. This 1068-bp ORF2 potentially codes for a 356-amino-acid protein that seems to play a role in pRmeGR4a stabilization. Similarities of the ORF2-encoded protein with eukaryotic cytoskeletal proteins and DNA-binding proteins were found.

Amino Acid Sequence↗

PubMed1995

Identification of a region of the alcelaphine herpesvirus-1 genome associated with virulence for rabbits.

The gammaherpesvirus Alcelaphine Herpesvirus 1 (AHV-1) causes the fatal lymphoproliferative disease known as malignant catarrhal fever (MCF), in susceptible hosts. The virulent C500 isolate of AHV-1 became attenuated for the laboratory model, the rabbit, as a result of serial passage in cells of bovine origin. This work describes the identification of a region of the central unique sequence of the C500 genome, located close to the terminal repeat units of the molecule, which is altered on attenuation. The virulent C500 genome contains two copies of a sequence of approximately 2 kbp, contained within a 7 kbp region of the unique DNA located adjacent to the terminal repeats at the left end of the molecule. In the genome of the attenuated virus, there are also two copies of the 2 kbp sequence but they are located at the ends of the attenuated genome unique region, adjacent to the terminally repeated sequences. One open reading frame (ORF), designated putative polypeptide 5, was altered on attenuation such that the 3' sequence was lost. The location of this ORF, coupled with the loss of its 3' sequence, suggests that this ORF may encode a gene involved in the virulent mechanisms of this virus, in a manner similar to that of the transforming proteins of Herpesvirus saimiri (HSV).

Amino Acid Sequence↗

PubMed2002

Arsenical resistance in the IncHI2 plasmids.

The IncHI2 plasmid R478, like other arsenic resistance IncH plasmids, provides increased levels of resistance to sodium arsenate (up to 100mM) and sodium arsenite (up to 10mM) to the host cell. An arsenic resistance fragment of R478 was cloned and sequenced revealing four arsenic resistance associated gene homologues, arsR, arsB, arsC, and arsH. Two other open reading frames in the cloned fragment were found to be homologues of sulphate transport associated genes. Both the four gene arsenic resistance operons and the two gene sulphate transport operons have been previously shown to be transposon associated. However, no evidence of transposability was found associated with these operons in R478. Both the R478 associated arsenic and sulphate transport operons were shown to be common to all arsenic resistance IncH plasmids examined by Southern hybridisation and PCR analysis.

Arsenic↗

PubMed1993

Giardiavirus double-stranded RNA genome encodes a capsid polypeptide and a gag-pol-like fusion protein by a translation frameshift.

Giardiavirus is a small, nonenveloped virus comprising a monopartite double-stranded RNA genome, a major protein of 100 kDa, and a less abundant polypeptide of 190 kDa. It can be isolated from the culture supernatant of Giardia lamblia, a parasitic flagellate in human and other mammals, and efficiently infects other virus-free G. lamblia. A single-stranded copy of the viral RNA can be electroporated into uninfected G. lamblia cells to complete the viral replication cycle. Giardiavirus genomic cDNA of 6100 nt was constructed and its sequence revealed the presence of two large open reading frames that are separated by a -1 frameshift and share an overlap of 220 nt. The 3' open reading frame contains all consensus RNA-dependent RNA polymerase sequence motifs. A heptamer-pseudoknot structure similar to those found at ribosomal slippage sites in retroviruses and yeast killer virus was identified within this overlap. Immunostudies using antisera against synthesized peptides from four regions in the two open reading frames indicated that the 100- and 190-kDa viral proteins share a common domain in the amino-terminal region. But the 190-kDa protein makes a -1 switch of its reading frame beyond the presumed slippage heptamer and is therefore a -1 frameshift fusion protein similar to the gag-pol fusion protein found in retroviruses.

Amino Acid Sequence↗

PubMed1999

CFP, the putative cercosporin transporter of Cercospora kikuchii, is required for wild type cercosporin production, resistance, and virulence on soybean.

Many species of the fungal genus Cercospora, including the soybean pathogen C. kikuchii, produce the phytotoxic polyketide cercosporin. Cercosporin production is induced by light. Previously, we identified several cDNA clones of mRNA transcripts that exhibited light-enhanced accumulation in C. kikuchii. Targeted disruption of the genomic copy of one of these, now designated CFP (cercosporin facilitator protein), results in a drastic reduction in cercosporin production, greatly reduced virulence of the fungus to soybean, and increased sensitivity to exogenous cercosporin. Sequence analysis of CFP reveals an 1,821-bp open reading frame encoding a 65.4-kDa protein similar to several members of the major facilitator superfamily (MFS) of integral membrane transporter proteins known to confer resistance to various antibiotics and toxins in fungi and bacteria. We propose that CFP encodes a cercosporin transporter that contributes resistance to cercosporin by actively exporting cercosporin, thus maintaining low cellular concentrations of the toxin.

Amino Acid Sequence↗

PubMed1992

Identification of replication and stability functions in the complete nucleotide sequence of plasmid pUH24 from the cyanobacterium Synechococcus sp. PCC 7942.

The complete nucleotide sequence is presented for pUH24, the small plasmid of Synechococcus sp. PCC 7942. pUH24 consists of 7835bp and has a G + C content of 59%. The distribution of translation start and stop codons in the sequence allows 36 open reading frames that potentially encode polypeptides of 50 or more amino acids. We postulate that eight of these open reading frames are actual coding sequences. A region has been identified, by experiment, that contains two functions, designated pmaA and pmaB, involved in the segregational stability of the plasmid. The minimal region of pUH24 fully capable of supporting autonomous replication consists of a 3.6kb DNA fragment, which is almost entirely occupied by two overlapping genes most likely coding for essential replication proteins (repA and repB).

Amino Acid Sequence↗

PubMed1998

Putative heat shock protein 70 gene from Actinobacillus actinomycetemcomitans: molecular cloning and sequence analysis of its gene.

We have cloned and sequenced two overlapping fragments of chromosomal DNA from Actinobacillus actinomycetemcomitans. The nucleotide sequence contained two open reading frames. The deduced amino acid sequences of the two open reading frames showed significant homology with the heat shock proteins hsp70 and hsp40 of other organisms respectively. The upstream open reading frame consisted of 1902 bp, corresponding to 634-amino-acid residues. The CAA codon for glutamines was frequently seen in hsp70, i.e., in 30 of 32 glutamines (93.8%). The spacing region between the two open reading frames was unusually long compared with other prokaryotic organisms. A number of unique and distinguishing features of the sequences in the hsp70 family were verified, and it was found that a particular spacing sequence between the hsp70 and hsp40 gene loci can be used to identify A. actinomycetemcomitans from the periodontal pocket.

Aggregatibacter actinomycetemcomitans↗

PubMed2002

The genome organization of pea stem necrosis virus and its assignment to the genus Carmovirus.

The complete sequence of the single-stranded, positive-sense RNA genome of pea stem necrosis virus (PSNV) has been determined. The 4,048-nucleotide genome contains five open reading frames (ORFs). The 5'-proximal ORF encodes a 25-kD protein (p25). If the amber termination codon is read through, the ORF produces a read-through protein of 84 kD (p84). Two small, centrally located ORFs encoded a 7-kD protein (p7) and a 6-kD protein (p6), respectively. The 38-proximal ORF encodes a 38-kD (p38) capsid protein. Comparison of the genome organization with that of other viruses justifies the assignment of PSNV to the genus Carmovirus.

Carmovirus↗

PubMed1990

Reconstitution of nucleotide excision nuclease with UvrA and UvrB proteins from Escherichia coli and UvrC protein from Bacillus subtilis.

Recently, an open reading frame which has a deduced amino acid sequence that shows 38% homology to Escherichia coli UvrC protein was found upstream of the aspartokinase II gene (ask) in Bacillus subtilis (Chen, N.-Y., Zhang, J.-J., and Paulus, H. (1989) J. Gen. Microbiol. 135, 2931-2940). We found that plasmids containing this open reading frame complement the uvrC mutations in E. coli. We joined the open reading frame to a tac promoter to amplify the gene product in E. coli and purified the protein to near homogeneity. The apparent molecular weight of the gene product is 69,000, which is consistent with the calculated molecular weight of 69,378 fro the deduced gene product of the open reading frame. The purified gene product causes the nicking of DNA at the 8th phosphodiester bond 5' and the 5th phosphodiester bond 3' to a thymine dimer when mixed with E. coli UvrA and UvrB proteins and a DNA substrate containing a uniquely located thymine dimer. We conclude that the gene product of the open reading frame is the B. subtilis UvrC protein. Our results suggest that the B. subtilis nucleotide excision repair system is quite similar to that of E. coli. Furthermore, complementation of the UvrA and UvrB proteins from a Gram-negative bacterium with the UvrC protein of Gram-positive B. subtilis indicates a significant evolutionary conservation of the nucleotide excision repair system.

Amino Acid Sequence↗

PubMed1989

Isolation of the rat s-myc gene having tumor suppressing activity.

We have isolated a myc related gene, called s-myc, from a rat genomic library using a 32P-labeled fragment of exon 3 of v-myc as a probe. Nucleotide sequencing showed that the s-myc gene contains an open reading frame of 1,287 bp without introns. The s-Myc protein predicted from the DNA sequence has approximately 60% amino acid sequence homology with that of the mouse N-Myc protein. Transfection of the s-myc gene into rat RT4-AC tumor cells induced morphological changes of the cells and suppressed their tumorigenicity in nude mice.

Amino Acid Sequence↗

PubMed1994

Transcription of multiple exogenous mouse mammary tumor viruses in a single mammary tumor of an SHN mouse.

The SHN mouse strain, established in Japan independently from other mammary tumor-prone strains, is known to have a very high incidence of early-onset mammary tumors. In this study, we demonstrate that exogenous mouse mammary tumor virus (MMTV) plays a crucial role in early-onset mammary tumorigenesis in this strain. We subsequently isolated MMTV RNA from a mammary tumor of an SHN female mouse, reverse transcribed it, and amplified a 1.2-kb coding region of the long terminal repeat (LTR) by use of the polymerase chain reaction. The products were then subcloned into a pUC18 vector. Six clones were obtained, and their nucleotide sequences were determined. Nucleotide sequences of the six cloned LTRs indicated that two MMTVs are transcribed in the tumor. Both of them had point mutations and were different from known LTR sequences. Both LTRs had a potential open reading frame encoding 320 amino acids. The amino acid variabilities were predominantly between positions 280 and 320 codons when compared with deduced open reading frames. In contrast, only a few point mutations were detected in the regulatory area that contains five glucocorticoid elements, the nuclear factor-1 binding sites, the octamer consensus sequence, and the TATA box. Because point mutations occur more predominantly between positions 280 and 320, it is possible that mutations in this area endow MMTV with beneficial functions for propagation through mutational selection during tumorigenesis.

Animals↗

PubMed1996

The DNA sequence of cosmid 14-5 from chromosome XIV reveals 21 open reading frames including a novel gene encoding a globin-like domain.

In this paper is described the DNA sequence of cosmid 14-5 from chromosome XIV of Saccharomyces cerevisiae. The sequence is 38 855 bases long and contains 21 open reading frames (ORFs) plus three internal ORFs. Six ORFs correspond to known yeast genes (SLA2, ZWF1, BLH1, KEX2, SIN4 and URE2); two other ORFs had already been sequenced because they are adjacent to known genes; the remaining 12 ORFs are novel genes. Of these, one ORF (NII42) is particularly interesting since it shows a significant similarity to mammalian globin. Another ORF (N1254) displays two zinc finger motifs as well as a DNAJ motif.

Animals↗

PubMed1997

Sequencing of a 9.9 kb segment on the right arm of yeast chromosome VII reveals four open reading frames, including PFK1, the gene coding for succinyl-CoA synthetase (beta-chain) and two ORFs sharing homology with ORFs of the yeast chromosome VIII.

A 9.9 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains four open reading frames (ORFs) longer than 100 amino acids. One gene, PFK1, has already been cloned and sequenced and the other one is the probable yeast gene coding for the beta-subunit of the succinyl-CoA synthetase. The two remaining ORFs share homology with the deduced amino acid sequence (and their physical arrangement is similar to that) of the YHR161c and YHR162w ORFs from chromosome VIII.

Amino Acid Sequence↗

PubMed1994

Sporulation regulatory protein SpoIIID from Bacillus subtilis activates and represses transcription by both mother-cell-specific forms of RNA polymerase.

Mother-cell-specific gene expression during sporulation of Bacillus subtilis is controlled by sigma E and sigma K RNA polymerases. sigma E is required for the expression of genes during stage III (engulfment of the forespore), while sigma K is required for the expression of genes during stage IV (formation of the spore cortex) and stage V (formation of the spore coat). Previous studies indicated that SpoIIID could influence transcription by sigma K RNA polymerase in vitro. We demonstrate here that SpoIIID is a DNA-binding protein that recognizes specific sequences in the promoter regions and open reading frames of both sigma E- and sigma K-dependent genes. We also show that SpoIIID can activate or repress transcription by both forms of RNA polymerase. These results support the idea that the appearance and subsequent disappearance of SpoIIID plays a major role in controlling the mother-cell pattern fo gene expression during stages III to V of sporulation.

Bacillus subtilis↗

PubMed2001

Sequence and gene expression analyses of plasmid pHPM8 from Helicobacter pylori reveal the presence of two operons with putative roles in plasmid replication and antibiotic activity.

The DNA sequence of a 7.8-kb Helicobacter pylori plasmid, pHPM8, was determined. Six open reading frames (ORFs) were present. Ribonuclease protection studies showed that ORF1/ORF2 and ORF3/ORF4 genes are organized in operons possibly involved in plasmid replication and in production of a peptide with antibiotic activity, respectively. Finding areas of pHPM8 with a high level of identity to H. pylori chromosomal DNA supported the hypothesis that recombination occurs between plasmids and the chromosome of H. pylori.

Amino Acid Sequence↗