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PubMed2001

Non-autonomous mobile elements in the crenarchaeon Sulfolobus solfataricus.

The genome of the archaeon Sulfolobus solfataricus P2 contains at least four types of short sequence elements lacking open reading frames which are similar to eukaryal non-autonomous mobile elements. The most- conserved elements SM1 (79-80 bp) and SM2 (183-186 bp), with 95 % sequence identity, are present in 40 and 25 copies, respectively. The less-conserved elements SM3 (127-139 bp) and SM4 (160-168 bp), with 75-97 % identity, occur in 44 and 34 copies, respectively. In total, the 143 SM elements constitute about 0.6 % of the genome. The wide distribution of each class of conserved element throughout the genome, and their precise locations, indicate that they are mobile. Direct evidence arises from the presence of SM1 and SM2 in only a fraction of genomic copies of a given class of insertion element, and within copies of open reading frames that are conserved in sequence. SM1 to SM4 are likely to be mobilized by transposases encoded by insertion elements ISC1048, ISC1217, ISC1058 and ISC1173, respectively. Furthermore, the occurrence of clusters of interwoven SM and insertion elements, in potentially mobile units, suggests a mechanism for the transfer of SM elements to other organisms.

Amino Acid Sequence↗

PubMed1992

Cloning of a low-temperature-induced gene lti2 from the cyanobacterium Anabaena variabilis M3 that is homologous to alpha-amylases.

A gene called lti2 which is induced by a shift to a low temperature was isolated from the cyanobacterium Anabaena variabilis strain M3. This gene contained an open reading frame of 552 amino acid residues which exhibited homology to known alpha-amylases. The level of lti2 transcript increased 40-fold within an hour after a temperature shift from 38 to 22 degrees C and then slowly decreased to a low steady-state level. A less extensive expression of the lti2 gene is also induced by a temperature shift from 22 to 38 degrees C.

Amino Acid Sequence↗

PubMed1993

The gene and the RNA for the precursor to the plastid-located glycerol-3-phosphate acyltransferase of Arabidopsis thaliana.

The gene and the RNA from Arabidopsis thaliana for the plastid-located glycerol-3-phosphate acyltransferase (GPAT; EC 2.3.1.15) and their encoded product have been studied. The gene (designated ATS1) was isolated by screening a lambda DASH genomic library for cross-hybridization with a radiolabeled probe prepared from cDNA for GPAT from squash. cDNA clones representing the mRNA were isolated by screening a lambda ZAPII cDNA library for hybridization with a radiolabeled probe prepared from a DNA fragment of ATS1. The nucleotide sequences of the gene and the cDNA were determined, and the 5' end of the RNA was mapped by primer extension. Sequences similar to the TATA box, polyadenylation sequences and intron-splicing sequences were found at the expected locations. The pre-mRNA was 3288 nucleotides long and contained 5' and 3'-untranslated sequences of 57 and 442 nucleotides, respectively. The coding sequence of 1377 nucleotides was interrupted by 11 introns of 1412 nucleotides in total and the 3'-untranslated sequence contained another intron of 94 nucleotides. The open-reading frame encoded a polypeptide of 459 amino acid residues, the amino acid sequence of which was highly homologous to those of precursors to plastid-located GPATs from squash and pea. The enzymatic activity of a gene product that was over-produced in Escherichia coli confirmed the identity of the gene.

Amino Acid Sequence↗

PubMed1994

Sequence of the sor-operon for L-sorbose utilization from Klebsiella pneumoniae KAY2026.

We have sequenced the complete sor-operon of Klebsiella pneumoniae KAY2026. The operon has been mapped at 91 min on the Klebsiella gene-map. It comprises seven open reading frames for the genes sorCDFBAME, which are expressed from the single promotor sorCP. The gene sorC codes for a regulator protein that positively and negatively regulates the expression of the operon; sorD encodes a D-glucitol-6-phosphate dehydrogenase, the genes sorFBAM encode four proteins of a phosphoenolpyruvate-dependent L-sorbose-phosphotransferase system and sorE, finally, an L-sorbose-1-phosphate-reductase.

Amino Acid Sequence↗

PubMed1994

The sequence of a human mitochondrial glycerol-3-phosphate dehydrogenase-encoding cDNA.

A 2618-bp cDNA that encodes the human mitochondrial glycerol-3-phosphate dehydrogenase has been isolated from a HeLa cell cDNA library and the nucleotide sequence determined. An open reading frame encodes a protein of 727 amino acids that is 96% similar to the rat protein and, like the rat protein, contains sites homologous to the Ca(2+)-binding sites of calmodulin, as well as FAD- and putative glycerol-phosphate-binding sites.

Amino Acid Sequence↗

PubMedDate not supplied

Phase variation of lipopolysaccharide in Haemophilus influenzae.

Lipopolysaccharide (LPS) structures on Haemophilus influenzae, defined by monoclonal antibodies, can show phase variation from generation to generation. Several genetic loci are involved in LPS biosynthesis by H. influenzae. In this paper, we describe three loci which play a role in LPS phase variation: the lic loci; lic1 and lic3 have been sequenced and lic2 has been partially sequenced. Each locus consists of multiple open reading frames (ORF), and each contains a repetitive sequence within the 5' end of the first ORF which may be involved in the phase variability. Genes within lic1 and lic2 are directly involved in the expression of phase-variable epitopes, but the role of genes within lic3 is at a more complex level.

Amino Acid Sequence↗

PubMed2005

Molecular cloning of mRNA from toad granular gland secretion and lyophilized skin: identification of Bo8--a novel prokineticin from Bombina orientalis.

Prokineticins are small (approximately 8 kDa), biologically active secretory proteins whose primary structures have been highly conserved throughout the Animal Kingdom. Representatives have been identified in the defensive skin secretions of several amphibians reflecting the immense structural/functional diversity of polypeptides in such. Here we describe the identification of a prokineticin homolog (designated Bo8) from the skin secretion of the Oriental fire-bellied toad (Bombina orientalis). Full primary structural characterization was achieved using a combination of direct Edman microsequencing, mass spectrometry and cloning of encoding skin cDNA. The latter approach employed a recently described technique that we developed for the cloning of secretory peptide cDNAs from lyophilized skin secretion, and this was further extended to employ lyophilized skin as the starting material for cDNA library construction. The Bo8 precursor was found to consist of an open-reading frame of 96 amino acid residues consisting of a putative 19-residue signal peptide followed by a single 77-residue prokineticin (Mr=7990 Da). Amino acid substitutions in skin prokineticins from the skin secretions of bombinid toads are confined to discrete sites affording the necessary information for structure/activity studies and analog design.

Amino Acid Sequence↗

PubMed1998

Characterisation of an Arabidopsis cDNA encoding a thylakoid lumen protein related to a novel 'pentapeptide repeat' family of proteins.

We have cloned an Arabidopsis cDNA encoding a novel thylakoid lumen protein, P17.4, that has been previously isolated from lumen extracts of spinach chloroplasts. The protein is synthesised with a bipartite presequence containing a Sec-type lumen-targeting signal peptide and the precursor protein is imported into the lumen of pea chloroplasts. The encoded protein is homologous to an Anabaena protein that is essential for correct glycolipid localisation, and is also related to at least 16 unassigned open reading frames in Synechocystis. This family of proteins is characterised by the presence of numerous pentapeptide repeats with the consensus structure AXLXX, and its members are predicted to be located in the cytosol, plasma membrane and periplasm/lumen. P17.4 is therefore the first higher plant member of an extended family of putative cyanobacterial proteins that may serve important roles in lipid transport or assembly.

Amino Acid Sequence↗

PubMed1997

Molecular cloning of rat G-protein-coupled receptor kinase 6 (GRK6) from brain tissue, and its mRNA expression in different brain regions and peripheral tissues.

The rat G-protein-coupled receptor kinase 6 (GRK6) cDNA was cloned from rat brain tissue by a combination of reverse-transcription polymerase chain reactions (RT-PCR), based on homology to the cloned human GRK6, and rapid amplification of cDNA ends (RACE-PCR). We obtained a clone of 2817 bp with an open reading frame of 1731 bp encoding for a protein of 576 amino acids that is 96.7% identical and 97.9% similar to its human counterpart. mRNA was detectable in all brain areas examined. In addition, GRK6 was expressed in skeletal muscle, small intestine, aorta, liver, heart, lung, thymus, stomach, uterus and kidney.

Amino Acid Sequence↗

PubMed2001

Identification of an internal gene to the human Galectin-3 gene with two different overlapping reading frames that do not encode Galectin-3.

We previously reported that alternative transcripts were initiated within the second intron of the human Galectin-3 gene (LGALS3). We now demonstrate that these transcripts arise from an internal gene embedded within LGALS3 and named galig (Galectin-3 internal gene). Tissue-specific expression of galig was assayed by screening of several human tissues. Contrary to LGALS3, galig appears to be tightly regulated and principally activated in leukocytes from peripheral blood. Cloning and characterization of galig transcripts revealed that they contain two out-of-frame overlapping open-reading frames (ORFs). Transfection of expression vectors encoding enhanced green fluorescent protein (EGFP) chimeras indicated that both ORFs could be translated in proteins unrelated to Galectin-3. The ORF1 polypeptide targets EGFP to cytosol and nucleus whereas ORF2 targets EGFP to mitochondria. These results revealed the exceptional genetic organization of the LGALS3 locus.

Amino Acid Sequence↗

PubMed2005

In vitro read-through polysome/ribosome display of full-length protein ORF and it's applications.

Combination of nonsense suppression and protein-ribosome-mRNA (PRM) complexation techniques leads to a new strategy "read-through polysome/ribosome display", which is designed to display full-length open reading frame (ORF) domain of the protein on the natural mRNA templates. The optimised conditions are to use the anticodon-adjusted tRNA for Leu as a nonsense suppressor in a reconstituted translation system containing diminished amounts of release factors (RFs). When applied to pseudo-natural mRNAs of Escherichia coli dihydrofolate reductase (E. coli DHFR), the input mRNA was recovered as a polysome complex displaying full-length DHFR.

3' Untranslated Regions↗

PubMed2003

Characterization of Cestrum yellow leaf curling virus: a new member of the family Caulimoviridae.

Cestrum yellow leaf curling virus (CmYLCV) has been characterized as the aetiological agent of the Cestrum parqui mosaic disease. The virus genome was cloned and the clone was proven to be infectious to C. parqui. The presence of typical viroplasms in virus-infected plant tissue and the information obtained from the complete genomic sequence confirmed CmYLCV as a member of the Caulimoviridae family. All characteristic domains conserved in plant pararetroviruses were found in CmYLCV. Its genome is 8253 bp long and contains seven open reading frames (ORFs). Phylogenetic analysis of the relationships with other members of the Caulimoviridae revealed that CmYLCV is closely related to the Soybean chlorotic mottle virus (SbCMV)-like genus and particularly to SbCMV. However, in contrast to the other members of this genus, the primer-binding site is located in the intercistronic region following ORF Ib rather than within this ORF, and an ORF corresponding to ORF VII is missing.

Amino Acid Sequence↗

PubMed1994

Positive and negative regulation of sequences upstream of the form II cbb CO2 fixation operon of Rhodobacter sphaeroides.

The unlinked form I and form II Calvin cycle CO2 fixation (cbb) operons of the photosynthetic bacterium Rhodobacter sphaeroides are located on different genetic elements, yet both operons are positively regulated by the transcription activator protein CbbR, the product of the cbbR gene located immediately upstream of the form I operon. By employing deletion mutagenesis, and a newly constructed promoter probe vector, the form II operon promoter (cbbFIIp) and three other promoters (Up, Vp, and Wp) were localized within 2.1 kb upstream of the form II operon. Mutations in both cbbR and the first gene of the form I operon (cbbFI) elicited both positive and negative responses when transcriptional fusions controlled by these four promoters were examined. With the exception of Wp, all these upstream promoters were repressed by oxygen. In addition, these promoters were associated with open reading frames of unknown function whose deduced amino acid sequences showed no significant relationship to proteins in current databases. The results of these experiments suggest that the promoter sequences and genes upstream of the form II cbb operon may be intimately involved with control of the cbb regulon of this photosynthetic organism.

Amino Acid Sequence↗

PubMed1995

The bovine herpesvirus 1 maturational proteinase and scaffold proteins can substitute for the homologous herpes simplex virus type 1 proteins in the formation of hybrid type B capsids.

We determined the nucleotide sequence of a 3.5-kb region of the bovine herpesvirus 1 (BHV-1) genome which contained the complete BHV-1 homologs of the herpes simplex virus type 1 (HSV-1) UL26 and UL26.5 genes. In HSV-1, the UL26 and UL26.5 open reading frames encode scaffold proteins upon which viral capsids are assembled. The UL26-encoded protein is also a proteinase and specifically cleaves both itself and the UL26.5-encoded protein. The overall BHV-1-encoded amino acid sequence showed only 41% identity to the HSV-1 sequences and was most divergent in the regions defined to be involved in the scaffolding function. We substituted the proteins encoded by the BHV-1 homologs of the UL26 and UL26.5 open reading frames, expressed in baculovirus, for the corresponding HSV-1 proteins in an in vitro HSV-1 capsid assembly system. The proteins expressed from the BHV-1 UL26 and UL26.5 homologs facilitated the formation of hybrid type B capsids indistinguishable from those formed entirely with HSV-1-encoded proteins.

Amino Acid Sequence↗

PubMed1998

Inhibition of human cytomegalovirus DNA maturation by a benzimidazole ribonucleoside is mediated through the UL89 gene product.

2-Bromo-5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole (BDCRB) is a member of a new class of benzimidazole ribonucleosides which inhibit human cytomegalovirus (HCMV) late in the replication cycle without inhibiting viral DNA synthesis. We show here that polygenomic concatemeric HCMV DNA does not mature to unit genome length in the presence of BDCRB. To discover the locus of action, virus resistant to BDCRB was selected by serial passage in the presence of the compound. Genetic mapping experiments with BDCRB-resistant virus demonstrated that the resistance phenotype mapped to one amino acid (Asp344Glu; low resistance) or two amino acids (Asp344Glu and Ala355Thr; high resistance) within the product of exon 2 of the HCMV U(L)89 open reading frame. The HCMV U(L)89 open reading frame and its homologs are among the most conserved open reading frames in the herpesviruses, and their products have sequence similarities to a known ATP-dependent endonuclease from the double-stranded DNA bacteriophage T4. These findings strongly suggest that BDCRB prevents viral DNA maturation by interacting with a U(L)89 gene product and that the U(L)89 open reading frame may encode an endonucleolytic subunit of the putative HCMV terminase. Further, since mammalian cell DNA replication does not involve a DNA maturation step, compounds which inhibit viral DNA maturation should be selective and safe.

Amino Acid Sequence↗

PubMed2004

Multiple groups of endogenous betaretroviruses in mice, rats, and other mammals.

Betaretroviruses exist in endogenous and exogenous forms in hosts that are widely distributed and evolutionarily distantly related. Here we report the discovery and characterization of several previously unknown betaretrovirus groups in the genomes of Mus musculus and Rattus norvegicus. Each group contains both mouse and rat elements, and several of the groups are more closely related to previously known betaretroviruses from nonmurine hosts. Some of the groups also include members from hosts which were not previously known to harbor betaretroviruses, such as the gray mouse lemur (Microcebus murinus) and Seba's short-tailed bat (Carollia perspicillata). Some of the mouse and rat elements possess intact open reading frames for gag, pro, pol, and/or env genes and display characteristics of having retrotransposed recently. We propose a model whereby betaretroviruses have been evolving within the genomes of murid rodents for at least the last 20 million years and, subsequent to (or concomitant with) the global spread of their murid hosts, have occasionally been transmitted to other species.

Amino Acid Sequence↗

PubMed1994

Nucleotide sequence of the pectate lyase gene from alkali-tolerant Bacillus sp. YA-14.

The nucleotide sequence of the pectate lyase gene (pe lK) from alkali-tolerant Bacillus sp. was identified and analyzed. A 1,260-base pair open reading frame for the pe lK gene was observed and encoded for a protein of 420 amino acids. The signal peptide was composed of 21 amino acid residues. In the deduced primary structure of this enzyme, the three conserved regions of several pectate lyases were found and showed high homologies.

Alkalies↗

PubMed1990

Nucleotide sequence and expression of the gutQ gene within the glucitol operon of Escherichia coli.

The glucitol operon in Escherichia coli is known to consist of five structural genes with the order: gut O P A B D M R. We have sequenced downstream from gutR and have identified an open reading frame encoding a water-soluble protein (223 amino acids; molecular weight = 23,562) with a putative ATP binding site. Expression of this protein in a maxicell system has been demonstrated. A repetitive extragenic palindromic (REP) sequence capable of forming stem-loop structures follows gutQ in the downstream, presumptive intercistronic region. The function of the Gut Q protein is not known.

Amino Acid Sequence↗