Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “ENCODE”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71Linked to original sources
PubMed1993

The Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content.

Benzene dioxygenase, catalyzing the oxidation of benzene to cis-1,2-dihydroxy-cyclohexa-3,5-diene, comprises four polypeptides that are encoded by plasmid pHMT112 of Pseudomonas putida ML2. In this study, the nucleotide (nt) sequences of four genes encoding this enzyme (bedC1C2BA) were determined, and the amino acid (aa) sequences were deduced. The sequence showed significant homology with the chromosomally encoded benzene dioxygenase and toluene dioxygenase genes (73-77% for nt and 83-99% for aa), but not the plasmid-encoded naphthalene dioxygenase genes (20-26% for nt and 32-36% for aa). A conserved motif (Cys-Xaa-His-15-to-17 aa-Cys-Xaa2-His, where Xaa is any aa), proposed to bind the Rieske-type [2Fe-2S] cluster, was identified in the deduced aa sequence of the iron-sulfur proteins. Three regions were also identified in the flavoprotein which are likely to be involved in FAD and NAD+ binding. The gene order of bedC1C2BA is consistent with most ring-hydroxylating dioxygenases isolated from Pseudomonas. However, the G+C content of 47% is in contrast to the high G+C content of the Pseudomonas chromosome (63%) and other Pseudomonas plasmids (57%), and with its unique codon usage preference this suggests that bedC1C2BA originated from a host derived from a different genus.

Amino Acid Sequence↗
PubMed1993

Sequence of a staphylococcal gene, vat, encoding an acetyltransferase inactivating the A-type compounds of virginiamycin-like antibiotics.

The Staphylococcus aureus plasmids, pIP680 and pIP1156, which confer resistance to A-type compounds of virginiamycin-like antibiotics (Vml: streptogramin A, pristinamycin IIA, virginiamycin M) and to synergistic mixtures of the A and B compounds of Vml antibiotics, were shown to direct the modification of A-type compounds by acetylation. The vat gene, encoding the acetyltransferase modifying A-type compounds, was isolated from plasmid pIP680 and sequenced. This gene potentially encodes a 219-amino-acid (aa) protein, VAT, of 24 330 Da showing at least 38% aa identity with two chloramphenicol acetyltransferases encoded by cat genes isolated from Escherichia coli and Agrobacterium tumefaciens. Resistance to A-type compounds of Vml antibiotics conferred to S. aureus by vat was not expressed in E. coli, although a protein having a M(r) similar to that encoded by this gene was detected in E. coli minicells. The vat gene was detected by the polymerase chain reaction in two chromosomally located staphylococcal conjugative elements and in the conjugative plasmid, pIP1156, conferring resistance to A-type compounds.

Acetyltransferases↗
PubMed1993

Structure of the Paramecium caudatum gene encoding the B-type of the major hemoglobin component.

We have found the gene (Hb) encoding the B-type of the major hemoglobin (Hb) component in the ciliated protist, Paramecium caudatum, stock K33 of syngen 3. Gene Hb, which encodes a protein consisting of 116 amino acids (aa), had the same sequence as the A-type Hb in this species, with the exception of 10 nucleotides (nt) reflecting 5 single-aa differences. The coding region was interrupted at the position between codons 62 and 63 by one short intron, which was comparable with the second intron of plant Hb in position, phase and nt sequence. The maximum alignment of the P. caudatum Hb aa sequence with the other globin sequences from prokaryotes and lower eukaryotes indicates that these globins can be classified into two groups: one consists of protist and cyanobacterial globins of about 120 aa, and the other consists of fungal and other bacterial globins of about 150 aa having a significant homology with higher eukaryotic Hbs. These proteins share more than 25% homology with one another in each group. Our finding of the P. caudatum Hb intron corresponding to the second intron of plant Hb suggests that all of the globin-encoding genes have a common origin, and that at least two groups had already existed in the globin-encoding gene before prokaryote-eukaryote radiation.

Amino Acid Sequence↗
PubMed1993

Isolation and characterization of the genes encoding mouse and human type-5 acid phosphatase.

The gene (mT5AP) encoding murine type-5 acid phosphatase has been isolated and completely sequenced while the gene (hT5AP) encoding human T5AP has been partly sequenced. The murine gene spans 4 kb and contains five exons. Exon 1 is completely non-coding and exon 2 starts with the initiation codon in both mT5AP and hT5AP. The positions of the intron/exon boundaries are completely conserved between mT5AP and hT5AP, but are distinct from the gene encoding the related porcine protein, uteroferrin (Utf). There is strong homology at both the nucleotide (nt) and amino acid (aa) levels between the inferred mouse cDNA and the sequences of rat T5AP and hT5AP, and pig Utf. The mT5AP and hT5AP genes were found to have multiple transcription start points (tsp) by primer extension analysis, consistent with the absence of a consensus TATA box. The sequences for the 5'-flanking regions of mT5AP and hT5AP were determined to -1.6 and -1.0 kb, respectively, relative to the tsp. A 2-kb segment of the mT5AP 5' flanking region linked to a luciferase-encoding reporter gene (Luc) was sufficient to direct tissue-specific transcription in the mouse macrophage cell line, RAW264. Significant sequence similarity between the mT5AP and hT5AP promoters is restricted to the most proximal 200 bp, which also resembles the porcine Utf gene, and a 300-bp segment 700 bp upstream. A progesterone-response element is present only in the mouse promoter and the estrogen- and iron-response elements described previously in the pig gene are absent from both the mouse and human genes. These differences may result in distinctive regulation of T5AP and Utf expression.

Acid Phosphatase↗
PubMed1993

Cloning of a sensory-kinase-encoding gene that belongs to the two-component regulatory family from the cyanobacterium Synechococcus sp. PCC7942.

A screening method employing Escherichia coli was adopted to clone a sensory-kinase (SK)-encoding gene directly from a phylogenetically distant species, the phototrophic cyanobacterium Synechococcus sp. PCC7942. From the Synechococcus chromosomal DNA, we searched for DNA clones which are able to complement phenotypically not only an E. coli envZ mutant for the expression of ompC, but also an E. coli phoR/creC mutant for the expression of alkaline phosphatase. These E. coli genes are known to encode SK. A 0.75-kb DNA fragment was thus cloned under the control of the E. coli lac promoter carried on an E. coli plasmid vector. A larger DNA fragment encompassing an entire open reading frame was then cloned and its complete nucleotide (nt) sequence determined. The nt sequence corresponds to a gene that encodes a 43,280-Da protein of 387 amino acids with a high degree of homology to the bacterial SK. Thus, we succeeded in cloning a SK-encoding gene, which most likely functions in signal transduction in Synechococcus sp. PCC7942. Hence, the gene was designated sasA (Synechococcus adaptive-response SK A). The purified SasA protein was demonstrated in vitro to undergo autophosphorylation.

Adaptation, Physiological↗
PubMed1993

The single group-I intron in the chloroplast rrnL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (I-ChuI).

The single group-I intron (ChLSU.1) in the chloroplast (cp) large subunit rRNA-encoding gene (rrnL) of the green alga Chlamydomonas humicola is located at a position at which no introns have previously been characterized in other systems. In the present study, the nucleotide (nt) sequence of this 1118-bp intron was found to contain an internal open reading frame (ORF) that potentially encodes a basic protein of 218 amino acid residues. The putative C. humicola protein features two copies of the LAGLI-DADG motif and is part of the family of intron-encoded proteins comprising the endonucleases (ENases), I-SceI, I-SceIV and I-CsmI. Expression of the ChLSU.1 intron ORF in vitro in the presence of a 260-bp DNA fragment containing the exon 1-2 junction of an intronless version of the C. humicola rrnL resulted in specific cleavage of the DNA fragment very close to the intron insertion site. This novel intron-encoded ENase, designated I-ChuI, was also shown to generate a staggered cut with 4-nt (CTCG) 3'-OH overhangs 2 bp downstream from the intron insertion site.

Amino Acid Sequence↗
PubMed1995

Three genes hrdB, hrdD and hrdT of Streptomyces griseus IMRU 3570, encoding sigma factor-like proteins, are differentially expressed under specific nutritional conditions.

Three genes (hrd) homologous to the rpoD gene of Escherichia coli, that encode sigma factor-like proteins, have been cloned from DNA of the candicidin-producing strain Streptomyces griseus IMRU 3570. They are located in different regions of the chromosome. Sequence analysis showed that the first one is analogous to the hrdB gene of S. coelicolor. The second showed high similarity to the hrdD gene of S. coelicolor and S. aureofaciens and is linked, as in S. coelicolor, to a N-acetyltransferase-encoding gene (nat) distantly related to the pat and bar genes that encode resistance to bialafos. The third showed no close homology with other known hrd genes from actinomycetes and has been named hrdT. Functional domains in the three S. griseus Hrd proteins are highly conserved in relation to those of the sigma 70 protein family. Northern analysis showed that hrdB is expressed as a 1.9-kb transcript during active growth in phosphate-rich medium, but it is less efficiently transcribed under sporulation conditions (phosphate-starved) or after a heat-shock treatment. Two other shorter transcripts of 1.2 and 0.7 kb were also detected with the same probe. The hrdD gene is transcribed as a single 1.1-kb transcript under sporulation conditions following nutritional shiftdown and, to a lower extent, during growth conditions in phosphate-rich medium. The hrdT gene is weakly transcribed (1.5-kb RNA) under all conditions tested. The hrd-encoded sigma factors probably recognize actinomycetes promoters (SEP type) with E. coli-like consensus sequences.

Amino Acid Sequence↗
PubMed1995

Genes encoding RubisCO in Pseudomonas hydrogenothermophila are followed by a novel cbbQ gene similar to nirQ of the denitrification gene cluster from Pseudomonas species.

The cbbL and cbbS genes, encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), were cloned and sequenced from a thermophilic hydrogen-oxidizing bacterium, Pseudomonas hydrogenothermophila strain TH-1. The cbbL gene encoded a 474-amino-acid (aa) protein (53,285 Da); cbbS encoded a 124-aa protein (14,656 Da). An ORF found downstream from the cbbLS genes encoded a 267-aa protein (29,565 Da) which had no similarity to cbbX located downstream from cbbLS from Alcaligenes eutrophus and Xanthobacter flavus. This gene, called cbbQ, was highly similar to the nirQ gene of the denitrification gene cluster from P. aeruginosa and P. stutzeri.

Alcaligenes↗
PubMed1995

Sequence and arrangement of genes encoding sigma factors in Clostridium acetobutylicum ATCC 824.

The nucleotide sequence of a 2.7-kb region of Clostridium acetobutylicum ATCC 824 DNA containing three open reading frames was determined. They encoded homologs of three proteins of Bacillus subtilis, and the gene arrangement in both organisms was identical. The first gene, orfA, was 801-bp long; the 31-kDa (266 aa) product it encoded exhibited homology with the putative sigma E-processing enzyme. The second gene, sigE, was 708-bp long encoding a 27-kDa (235 aa) product; the third gene, sigG, was 774-bp long encoding a 30-kDa (257 aa) product. These two proteins showed high homology with sigma E and sigma G, two sporulation-specific sigma factors.

Amino Acid Sequence↗
PubMed1995

The eighth Cct gene, Cctq, encoding the theta subunit of the cytosolic chaperonin containing TCP-1.

The chaperonin containing t-complex polypeptide 1 (TCP-1), as one of its subunits, CCT, is a cytosolic heterooligomeric molecular chaperone assisting in the folding of proteins in eukaryotic cytosol. We have isolated a Tcp-1-related 119-bp cDNA fragment from a human cDNA library by polymerase chain reaction, and cloned full-length mouse cDNAs orthologous to the human cDNA by hybridization. The nucleotide (nt) sequence of the longest mouse clone (1844 bp) shows an open reading frame (ORF) encoding a TCP-1-related polypeptide of 548 amino acids (aa) (59,562 Da). This gene is different from Tcp-1 and the six Tcp-1-related genes reported previously, Tcp-1 (Ccta), Cctb, Cctg, Cctd, Ccte, Cctz and Ccth, which encode subunits of CCT. The product of the novel gene was analysed using an antibody raised against the C terminus of the polypeptide deduced from the nt sequence. We found that this gene encodes a subunit of CCT (polypeptide S1; 62 kDa and pI 6.25 by two-dimensional gel analysis). We have named it Cctq, encoding the theta subunit of CCT (CCT theta). The aa sequence of CCT theta shows 23-29% identity to the other CCT subunits, alpha, beta, gamma, delta, epsilon, zeta and eta, and 29% identity to the archaebacterial chaperonin TF55. CCT theta also contains the motifs common to all the other subunits of CCT which are postulated to be involved in ATPase activity.

Amino Acid Sequence↗
PubMed1995

Characterization of the succinate dehydrogenase-encoding gene cluster (sdh) from the rickettsia Coxiella burnetii.

We have identified and sequenced four genes that encode the protein subunits comprising the succinate dehydrogenase enzyme complex (Sdh) of the rickettsia Coxiella burnetii. The Sdh-encoding gene cluster (sdhCDAB) begins 3326 bp upstream from the citrate synthase-encoding gene (gltA) start codon and is read with opposite polarity. An open reading frame encoding the N-terminal 280 amino acids (aa) of 2-oxoglutarate dehydrogenase (SucA) begins 24 bp downstream from the stop codon of the gene specifying the iron-sulfur subunit (sdhB) of Sdh. The deduced aa sequence of Sdh subunits and the N-terminal portion of SucA revealed significant aa identity with the Esherichia coli homologues ranging from a low of 36.6% for SdhD to a high of 61.2% for SdhA and SdhB. Primer extension identified transcription start points (tsp) for sdh and sucA. The region upstream from the sdh tsp, but not the sucA tsp, displayed homology to promoter consensus sequences of E. coli. Further evidence that sucA transcription can occur independent of sdh transcription was provided by demonstrating that a TnphoA insertion disrupting sdhB had no effect on the production of SucA by an E. coli cell-extract-directed in vitro transcription/translation system. The plasmid clone pLPM60, which carries the C. burnetii sdhCDAB coding and upstream regulatory regions, rescued an E. coli sdhA mutant (MOB252), indicating functional expression of the rickettsial locus. A cell extract of MOB252 transformed with pLPM60 showed a sixfold greater level of Sdh enzyme activity over the E. coli wild type. A plasmid clone lacking the sdh upstream regulatory region did not complement nor produce sdh mRNA by dot blot analysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Potato (Solanum tuberosum) invertase-encoding cDNAs and their differential expression.

A full-length cDNA clone encoding a potato invertase (Inv) has been isolated. It is highly related (77% nucleotide identity) to a previously characterised potato cDNA clone encoding a putative extracellular Inv. These Inv genes encode a subfamily of apoplastic enzymes which are shown to be distinct, on the basis of sequence similarity, from the related subfamily of vacuolar enzymes. In order to differentiate between the expression of the two potato genes encoding apoplastic Inv, a single-stranded conformational polymorphism (SSCP) assay was developed for products generated by reverse transcription-polymerase chain reaction (RT-PCR) utilising primers designed to amplify both potato sequences. Using this approach, we have shown that these two identified Inv from potato are expressed in a tissue-specific and developmentally regulated manner.

Amino Acid Sequence↗
PubMed1994

Characterization of cDNAs encoding the murine A+U-rich RNA-binding protein AUF1.

A+U-rich elements (ARE) serve to control the degradation of some proto-oncogene and lymphokine mRNAs. The protein, AUF1, which consists of two polypeptides of 37 and 40 kDa (p37 and p40, respectively) when purified from cytosol, has been implicated in ARE-directed mRNA turnover due to its binding to ARE. Molecular cloning of a cDNA (p37AUF1) corresponding to human p37 predicted a polypeptide containing two non-identical RNA recognition motifs (RRM) and a C-terminal Gln-rich domain [Zhang et al. Mol. Cell. Biol. 13 (1993) 7652-7665]. Two cDNAs, designated muAUF1-3 and muAUF1-7, were isolated from a murine fetal cDNA library, using as a probe, a fragment of the p37AUF1 cDNA encoding RRM1 and approximately half of RRM2. The muAUF1-3 open reading frame (ORF) was very homologous to human p37AUF1 with the greatest homology between the corresponding RRMs and the C-terminal Gln-rich motif. Clone muAUF1-7 was highly homologous to muAUF1-3, but was truncated within the region encoding the RNP-1 box in RRM2. Clone muAUF1-3 encoded 19 amino acids in RRM1 not encoded by either muAUF1-7 or human p37AUF1. Such alterations in sequence could modify the RNA-binding properties of these proteins and have concomitant effects on ARE-directed posttranscriptional processes.

Adenine↗
PubMed1994

The biphenyl/polychlorinated biphenyl-degradation locus (bph) of Pseudomonas sp. LB400 encodes four additional metabolic enzymes.

The bph locus of Pseudomonas sp. LB400, encoding biphenyl/polychlorinated biphenyl (PCB) degradation, contains a region of about 3.5 kb of hitherto unknown function, between bphC and bphD. This DNA segment has now been characterized. Four structural genes have been located and identified by a combination of expression cloning, enzyme activity tests and DNA sequencing. The region contains four closely spaced cistrons (bphKHJI) encoding a glutathione S-transferase (GST), a 2-hydroxypenta-2,4-dienoate hydratase, an acetaldehyde dehydrogenase (acylating) and a 4-hydroxy-2-oxovalerate aldolase, respectively. The latter three are enzymes required for conversion of the aliphatic end product of bphABCD-encoded catabolism of biphenyls to Krebs cycle intermediates. The discovery of these genes provides a rationale for growth of the strain on chlorinated biphenyls which yield chlorinated benzoates as dead-end metabolites. The sequences of the enzymes involved are 54-71% identical to those of homologous enzymes encoded by the dmp and xyl operons. The role of the GST in the degradation of biphenyls is less clear, but since it was found to contain, in the putative xenobiotic substrate-binding domain, a region which shares about 29% of identical amino acids with a bacterial tetrachlorohydroquinone dehalogenase, it may be involved in dehalogenation of PCB-degradative intermediates.

Aldehyde Oxidoreductases↗
PubMed1994

Sequence and genetic analysis of multiple flagellin-encoding genes from Proteus mirabilis.

Surface-induced overproduction of flagellin is one of the hallmarks of Proteus mirabilis swarmer cell differentiation. In this study, we analyzed the nucleotide (nt) and amino acid (aa) sequences, and expression of the P. mirabilis flagellin-encoding gene (fliC) region. The nt sequence analysis of a 3567-bp region reveals three ORFs, each with homology to known Escherichia coli flagellar genes. The first ORF corresponds to fliD, the gene encoding the flagellar filament capping protein, FliD (HAP2). The second and third ORFs are highly homologous to each other and to fliC genes from many other Gram- bacteria. To distinguish between the two alleles, we have designated these genes fliC1 and fliC2. Sequences highly homologous to promoter sites for the alternate sigma factor of RNA polymerase, sigma 28, are found 5' to the start of each gene. Additionally, both fliC1 and fliC2 have a conserved direct tandem repeat (DTR) sequence upstream from the sigma 28 promoter that may have functional significance in the transcriptional control of fliC expression during swarmer cell differentiation. Both FliC1 and FliC2 were produced in E. coli, but only FliC1 could complement FliC- mutants of E. coli. Southern hybridization data indicate the presence of fliC1 and fliC2 in six distinct P. mirabilis strains, indicating that multiple flagellin-encoding genes are common in P. mirabilis. Hybridization data also suggest the presence of a third flagellin-encoding gene, fliC3, in all isolates. The possible significance of multiple fliC in swarmer cell differentiation is discussed.

Amino Acid Sequence↗
PubMed1994

The pectin lyase-encoding gene (pnl) family from Glomerella cingulata: characterization of pnlA and its expression in yeast.

Oligodeoxyribonucleotide primers were designed from conserved amino acid (aa) sequences between pectin lyase D (PNLD) from Aspergillus niger and pectate lyases A and E (PELA/E) from Erwinia chrysanthemi. The polymerase chain reaction (PCR) was used with these primers to amplify genomic DNA from the plant pathogenic fungus Glomerella cingulata. Three different 220-bp fragments with homology to PNL-encoding genes from A. niger, and a 320-bp fragment with homology to PEL-encoding genes from Nicotiana tabacum and E. carotovora were cloned. One of the 220-bp PCR products (designated pnlA) was used as a probe to isolate a PNL-encoding gene from a lambda genomic DNA library prepared from G. cingulata. Nucleotide (nt) sequence data revealed that this gene has seven exons and codes for a putative 380-aa protein. The nt sequence of a cDNA clone, prepared using PCR, confirmed the presence of the six introns. The positions of the introns were different from the sites of the five introns present in the three PNL-encoding genes previously sequenced from A. niger. PNLA was synthesised in yeast by cloning the cDNA into the expression vector, pEMBLYex-4, and enzymatically active protein was secreted into the culture medium. Significantly higher expression was achieved when the context of the start codon, CACCATG, was mutated to CAAAATG, a consensus sequence commonly found in highly expressed yeast genes. The produced protein had an isoelectric point (pI) of 9.4, the same as that for the G. cingulata pnlA product.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Characterization of the Streptomyces peucetius ATCC 29050 genes encoding doxorubicin polyketide synthase.

The dps genes of Streptomyces peucetius, encoding daunorubicin (DNR)-doxorubicin (DXR) polyketide synthase (PKS), are largely within an 8.7-kb region of DNA that has been characterized by Southern analysis, and gene sequencing, mutagenesis and expression experiments. This region contains nine ORFs, many of whose predicted products are homologous to known PKS enzymes. Surprisingly, the gene encoding the DXR PKS acyl carrier protein is not in this region, but is located about 10 kb distant from the position it usually occupies in other gene clusters encoding type-II PKS. An in-frame deletion in the dpsB gene, encoding a putative subunit of the DXR PKS, resulted in loss of production of DXR and the known intermediates of its biosynthetic pathway, confirming that this gene and, by implication, the adjacent dps genes are required for DXR biosynthesis. This was verified by expression of the dps genes in the heterologous host, Streptomyces lividans, which resulted in the production of aklanonic acid, an early intermediate of DXR biosynthesis.

Amino Acid Sequence↗
PubMed1994

The Schizosaccharomyces pombe pka1 gene, encoding a homolog of cAMP-dependent protein kinase.

We have isolated 16 independent Schizosaccharomyces pombe cDNA clones that suppress the temperature-sensitive (ts) phenotype of a Saccharomyces cerevisiae strain containing the dominant-negative RAS2val19ala22 allele. Fourteen of these cDNAs encode Sz. pombe Ras1. The other two clones encode the C-terminal region of a protein we have named Pka1. We have cloned the pka1 gene from a Sz. pombe genomic library. It contains an uninterrupted open reading frame encoding a 512-amino-acid (aa) protein. The C-terminal region (aa 200-512) of Pka1 is 51-63% identical to cAMP-dependent protein kinase (Pka) catalytic subunits from other eukaryotes. Production of Pka1 suppresses the ts phenotypes exhibited by Sa. cerevisiae ras1-ras2ts or cyr1ts strains. Furthermore, overproduction of Pka1 in Sz. pombe results in a sterile phenotype and an abnormal morphology similar to that exhibited by cells in which the cAMP pathway is constitutively activated. These observations suggest that pka1 encodes the Sz. pombe Pka catalytic subunit.

Amino Acid Sequence↗