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PubMed2002

Taxonomic position of sugarcane streak mosaic virus in the family Potyviridae.

AcDNA library was generated from purified RNA of sugarcane streak mosaic virus--Andhra Pradesh (SCSMV-AP). Two overlapping clones covering 3160 nucleotides encoding partial CI, complete 6K2, VPg-NIa and NIb genes were sequenced. A comparison of this sequence along with the 3' terminal 1315 nucleotides of SCSMV-AP determined earlier with the other members of the family Potyviridae indicated that it had only 30% identity at the amino acid level for the partial polyprotein open reading frame (ORF) with the members of Ipomovirus and Tritimovirus genera. Further, in the most conserved NIb region also there was only 40% identity with the type members of these genera. Based on this analysis, we suggest the taxonomic affiliation of SCSMV-AP into an undescribed new genus in the family Potyviridae.

Amino Acid Sequence↗

PubMed1992

The complete nucleotide sequence of a feline calicivirus.

We have determined the complete sequence of a feline calicivirus. The virus genome is 7690 bases long and contains two large open reading frames. Proteins specified by these have similarity to those encoded in the corresponding regions of a candidate calicivirus rabbit hemorrhagic disease virus, but are distinctly different from those specified by another such virus, hepatitis E virus. A third, small open reading frame at the 3' end of the genome is present in both feline and rabbit viruses but is absent from hepatitis E. These findings suggest that the calicivirus family, which consists of a single genus, may require subdivision.

Amino Acid Sequence↗

PubMed1996

The unique organization of the rpoB region of Spiroplasma citri: a restriction and modification system gene is adjacent to rpoB.

A 6.5-kb DNA fragment containing the gene (rpoB) encoding the RNA polymerase (RNAP) beta subunit, from the mollicute Spiroplasma citri (Sc), was cloned and sequenced. The classical eubacterial organization, with the genes (rplK, A, J and L) encoding ribosomal proteins L11, L1, L10 and L12 located immediately upstream from rpoB, was not found in the Sc DNA. Instead, an open reading frame (hsdS) potentially encoding a component of a type I restriction and modification system was identified upstream from rpoB, and sequences showing similarities with insertion elements were found between hsdS and rpoB.

Amino Acid Sequence↗

PubMed1999

A Synechococcus leopoliensis SAUG 1402-1 operon harboring the 1-deoxyxylulose 5-phosphate synthase gene and two additional open reading frames is functionally involved in the dimethylallyl diphosphate synthesis.

Experiments have been performed to prove the existence and the functionality of the novel mevalonate independent 1-deoxyxylulose 5-phosphate isoprenoid biosynthesis pathway in cyanobacteria. For this purpose, a segment of the 1-deoxyxylulose 5-phosphate synthase gene (dxs) was amplified from Synechococcus leopoliensis SAUG 1402-1 DNA via PCR using oligonucleotides for conserved regions of dxs. Subsequent hybridization screening of a genomic cosmid library of S. leopoliensis with this segment has led to the identification of an 18.7 kbp segment of the S. leopoliensis genome on which a dxs homologous gene and two adjacent open reading frames organized in one operon could be localized by DNA sequencing. The three genes of the operon were separately expressed in Escherichia coli, proving that the identified cyanobacterial dxs is functionally involved in the formation of dimethylallyl diphosphate, one basic intermediate of isoprenoid biosynthesis.

Amino Acid Sequence↗

PubMed1997

Molecular cloning and expression of a novel Staphylococcus aureus antigen.

A novel gene encoding an antigen from Staphylococcus aureus was isolated from an expression library by screening with antisera from patients with deep Staphylococcus aureus infections. In one positive clone an open reading frame, named ORF-2, was identified. Recombinant ORF-2 protein reacted with human immune serum. ORF-2 was shown to be present in other Staphylococcus aureus strains, but not in related species.

Amino Acid Sequence↗

PubMed2006

Characterization of a novel cAMP-binding, cAMP-specific cyclic nucleotide phosphodiesterase (TcrPDEB1) from Trypanosoma cruzi.

Trypanosoma cruzi, the causative agent of Chagas disease, encodes a number of different cAMP-specific PDE (phosphodiesterase) families. Here we report the identification and characterization of TcrPDEB1 and its comparison with the previously identified TcrPDEB2 (formerly known as TcPDE1). These are two different PDE enzymes of the TcrPDEB family, named in accordance with the recent recommendations of the Nomenclature Committee for Kinetoplast PDEs [Kunz, Beavo, D'Angelo, Flawia, Francis, Johner, Laxman, Oberholzer, Rascon, Shakur et al. (2006) Mol. Biochem. Parasitol. 145, 133-135]. Both enzymes show resistance to inhibition by many mammalian PDE inhibitors, and those that do inhibit do so with appreciable differences in their inhibitor profiles for the two enzymes. Both enzymes contain two GAF (cGMP-specific and -stimulated phosphodiesterases, Anabaena adenylate cyclases and Escherichia coli FhlA) domains and a catalytic domain highly homologous with that of the T. brucei TbPDE2/TbrPDEB2 family. The N-terminus+GAF-A domains of both enzymes showed significant differences in their affinities for cyclic nucleotide binding. Using a calorimetric technique that allows accurate measurements of low-affinity binding sites, the TcrPDEB2 N-terminus+GAF-A domain was found to bind cAMP with an affinity of approximately 500 nM. The TcrPDEB1 N-terminus+GAF-A domain bound cAMP with a slightly lower affinity of approximately 1 muM. The N-terminus+GAF-A domain of TcrPDEB1 did not bind cGMP, whereas the N-terminus+GAF-A domain of TcrPDEB2 bound cGMP with a low affinity of approximately 3 muM. GAF domains homologous with those found in these proteins were also identified in related trypanosomatid parasites. Finally, a fluorescent cAMP analogue, MANT-cAMP [2'-O-(N-methylanthraniloyl)adenosine-3',5'-cyclic monophosphate], was found to be a substrate for the TcPDEB1 catalytic domain, opening the possibility of using this molecule as a substrate in non-radioactive, fluorescence-based PDE assays, including screening for trypanosome PDE inhibitors.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed1998

On the presence and organization of open reading frames of the nonmotile pathogen Brucella abortus similar to class II, III, and IV flagellar genes and to LcrD virulence superfamily.

Brucellae are pathogenic, nonmotile bacteria that are facultative intracellular parasites. Little is known about the genetics of these bacteria. Open reading frames from Brucella abortus with similarity to the flagellin, M-ring, and hook of related bacteria were discovered. The open reading frames encode proteins of three of the four flagellum gene classes, namely II, III, and IV. A homolog of the LcrD virulence superfamily was also found. This superfamily is involved in type III protein secretion. B. abortus has the potential for motility and type III secretion.

Amino Acid Sequence↗

PubMed1994

Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria.

We have characterized a new family of proteins (the ROK family) which includes six transcriptional repressors for sugar catabolic operons, three sugar kinases, and three unidentified open reading frames. Analysis of the aligned sequences and phylogenetic tree construction allow predictions regarding the functional nature of conserved domains and residues within these proteins as well as the pathway of evolutionary divergence that gave rise to the family.

Amino Acid Sequence↗

PubMed2000

The polyester polyurethanase gene (pueA) from Pseudomonas chlororaphis encodes a lipase.

A gene (pueA, polyurethane esterase A) encoding an extracellular polyurethanase (PueA) was cloned from Pseudomonas chlororaphis into Escherichia coli. The enzyme secreted from E. coli showed esterase activity when assayed with p-nitrophenyl acetate. Subcloning of a 3. 2-kb SalI-EcoRI fragment into a T7 RNA polymerase expression vector (pT7-6) produced a (35)S-labeled protein of 65 kDa. Nucleotide sequencing of pueA showed an open reading frame encoding a 65-kDa protein of 617 amino acid residues, with the serine hydrolase consensus sequence GXSXG. PueA was over-expressed using the pT7-6 vector transformed into E. coli BL21(DE3) and was purified in one step using Sephadex G-75.

Amino Acid Sequence↗

PubMed1995

A stationary-phase-dependent viability block governed by two different polypeptides from the RhsA genetic element of Escherichia coli K-12.

Multicopy plasmids bearing a small internal portion of the RhsA genetic element of Escherichia coli K-12 imparted a viability block on cultures grown to stationary phase in broth. Inclusion of the last 25 codons of the RhsA core open reading frame (called core-ORF) in the plasmid insert was crucial for eliciting this toxic effect. The toxic effect could be suppressed by including the adjacent Rhs component, dsORF-a1, on the multicopy plasmid. The toxic effect was enhanced in RpoS- strains.

Bacterial Proteins↗

PubMed1995

Analysis of the open reading frames of the main capsid proteins of actinophage VWB.

The nucleotide sequence of a 6 kb fragment encoding the main late proteins (p14, p38 and p24) of actinophage VWB was obtained. Sequence comparison of the encoded proteins with those filed in databases indicated that the phage VWB main late proteins were all novel. A search for special motifs revealed that p14 (13.3 kDa) has a P-loop sequence commonly found in ATP- and GTP-binding proteins. This observation might indicate that p14 is important for ATP-driven DNA translocation during encapsidation of VWB phage DNA into the phage head. Furthermore, the polypeptide ORF2 (26.9 kDa) has an unusual primary structure consisting of 3 stretches of acidic amino acid residues and a glycine/arginine rich C-terminal end. From comparison with other proteins including the bacteriophage T4 prohead core component and from the data of special motif analysis the ORF2 gene product is probably involved in prohead core formation.

Amino Acid Sequence↗

PubMed2001

Expression and functional properties of proteins encoded in the x-II ORF of HTLV-I.

With the aim of identifying viral proteins that contribute to the distinctive properties of HTLV-I biology and pathogenicity, several laboratories have investigated the coding potential of the X region of the genome, which includes five partially overlapping open reading frames (ORFs). We and others have shown that, in addition to the essential regulatory proteins Rex and Tax, a number of accessory proteins encoded in the X region can be produced by alternative splicing and multicistronic translation. One X region ORF, termed X-II, produces two protein isoforms named Tof/p30II and p13II, which are expressed from a doubly- and singly-spliced mRNA, respectively. Initial functional analyses demonstrated that Tof/p30II is a nucleolar/nuclear protein that possesses a region capable of binding to RNA, and p13II is a mitochondrial protein that alters the morphology and function of this organelle. Together with data from other laboratories demonstrating the production of antibodies and CTL against x-II ORF products in HTLV-I infected subjects and the requirement of this ORF for efficient viral replication in vivo, these findings suggest that further characterization of Tof/p30II and p13II will yield insight into remaining undefined aspects of HTLV-I pathogenicity and replication.

Amino Acid Sequence↗

PubMed1992

The complete sequence of K3B, a 7.9 kb fragment between PGK1 and CRY1 on chromosome III, reveals the presence of seven open reading frames.

We have determined the nucleotide sequence of a segment from chromosome III of Saccharomyces cerevisiae extending over 7.9 kb between the PGK1 and CRY1 loci. The fragment contains seven open reading frames, YCR241, YCR242, YCR243, YCR244, YCR245, YCR246 and YCR247, of more than 70 codons. The study of the effects of a global disruption of YCR242, YCR243, YCR244, YCR245 and YCR247 shows that they are not essential for growth and division.

Amino Acid Sequence↗

PubMed1992

The region essential for efficient autonomous replication of pSa in Escherichia coli.

Comparative analyses were made between plasmid pSa17, a deletion derivative of pSa that is capable of replicating efficiently in Escherichia coli and plasmid pSa3, a derivative that is defective for replication. By comparing the restriction maps of these two derivatives, the regions essential for replication and for stable maintenance of the plasmid were determined. A 2.5 kb DNA segment bearing the origin of DNA replication of pSa17 was sequenced. A 36 kDa RepA protein was encoded in the region essential for replication. Downstream of the RepA coding region was a characteristic sequence including six 17 bp direct repeats, the possible binding sites of RepA protein, followed by AT-rich and GC-rich sequences. Furthermore, an 8 bp incomplete copy of the 17 bp repeat was found in the promoter region of the repA gene. Based on the hypothesis that RepA protein binds to this partial sequence as well as to intact 17 bp sequences, an autoregulatory system for the synthesis of RepA protein may be operative. Another open reading frame (ORF) was found in the region required for the stability of the plasmid. The putative protein encoded in this ORF showed significant homology to several site-specific recombination proteins. A possible role of this putative protein in stable maintenance of the plasmid is discussed.

Amino Acid Sequence↗

PubMed1996

The gag coding region of the Drosophila telomeric retrotransposon, HeT-A, has an internal frame shift and a length polymorphic region.

A major component of Drosophila telomeres is the retrotransposon HeT-A, which is clearly related to other retrotransposons and retroviruses. This retrotransposon is distinguished by its exclusively telomeric location, and by the fact that, unlike other retrotransposons, it does not encode its own reverse transcriptase. HeT-A coding sequences diverge significantly, even between elements within the same genome. Such rapid divergence has been noted previously in studies of gag genes from other retroelements. Sequence comparisons indicate that the entire HeT-A coding region codes for gag protein, with regions of similarity to other insect retrotransposon gag proteins found throughout the open reading frame (ORF). Similarity is most striking in the zinc knuckle region, a region characteristic of gag genes of most replication-competent retroelements. We identify a subgroup of insect non-LTR retrotransposons with three zinc knuckles of the form: (1) CX2CX4HX4C, (2) CX2CX3HX4C, (3) CX2CX3HX6C. The first and third knuckles are invariant, but the second shows some differences between members of this subgroup. This subgroup includes HeT-A and a second Drosophila telomeric retrotransposon, TART. Unlike other gag regions, HeT-A requires a -1 frameshift for complete translation. Such frameshifts are common between the gag and pol sequences of retroviruses but have not before been seen within a gag sequence. The frameshift allows HeT-A to encode two polypeptides; this mechanism may substitute for the post-translational cleavage that creates multiple gag polypeptides in retroviruses. D. melanogaster HeT-A coding sequences have a polymorphic region with insertions/deletions of 1-31 codons and many nucleotide changes. None of these changes interrupt the open reading frame, arguing that only elements with translatable ORFs can be incorporated into the chromosomes. Perhaps HeT-A translation products act in cis to target the RNA to chromosome ends.

Amino Acid Sequence↗

PubMed1991

A bacterial homolog to the mitochondrial enoyl-CoA hydratase.

A 257-amino acid (aa) open reading frame in the photosynthetic bacterium, Rhodobacter capsulatus, shows significant homology to the mitochondrial enoyl-CoA hydratase (290 aa). This similarity in size and sequence suggests that R. capsulatus oxidizes fatty acids using specific components, more like the mitochondrial system than the multifunctional component system of Escherichia coli.

Amino Acid Sequence↗

PubMed2005

Drosophila molting neurohormone bursicon is a heterodimer and the natural agonist of the orphan receptor DLGR2.

Bursicon is a neurohumoral agent responsible for tanning and hardening of the cuticle and expansion of the wings during the final phase of insect metamorphosis. Although the hormonal activity was described more than 40 years ago, the molecular nature of bursicon has remained elusive. We identify here Drosophila bioactive bursicon as a heterodimer made of two cystine knot polypeptides. This conclusion was reached in part from the unexpected observation that in the genome of the honey bee, the orthologs of the two Drosophila proteins are predicted to be fused in a single open reading frame. The heterodimeric Drosophila protein displays bursicon bioactivity in freshly enclosed neck-ligated flies and is the natural agonist of the orphan G protein-coupled receptor DLGR2.

Amino Acid Sequence↗

PubMed2001

A 11.7-kb deletion triggers intersexuality and polledness in goats.

Mammalian sex determination is governed by the presence of the sex determining region Y gene (SRY) on the Y chromosome. Familial cases of SRY-negative XX sex reversal are rare in humans, often hampering the discovery of new sex-determining genes. The mouse model is also insufficient to correctly apprehend the sex-determination cascade, as the human pathway is much more sensitive to gene dosage. Other species might therefore be considered in this respect. In goats, the polled intersex syndrome (PIS) mutation associates polledness and intersexuality. The sex reversal affects exclusively the XX individuals in a recessive manner, whereas the absence of horns is dominant in both sexes. The syndrome is caused by an autosomal gene located at chromosome band 1q43 (ref. 9), shown to be homologous to human chromosome band 3q23 (ref. 10). Through a positional cloning approach, we demonstrate that the mutation underlying PIS is the deletion of a critical 11.7-kb DNA element containing mainly repetitive sequences. This deletion affects the transcription of at least two genes: PISRT1, encoding a 1.5-kb mRNA devoid of open reading frame (ORF), and FOXL2, recently shown to be responsible for blepharophimosis ptosis epicanthus inversus syndrome (BPES) in humans. These two genes are located 20 and 200 kb telomeric from the deletion, respectively.

Animals↗