PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Conserved Sequence”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 343 records · Page 19Linked to original sources
PubMed1991

A conserved sequence element in ribonuclease III processing signals is not required for accurate in vitro enzymatic cleavage.

Ribonuclease III of Escherichia coli is prominently involved in the endoribonucleolytic processing of cell and viral-encoded RNAs. Towards the goal of defining the RNA sequence and structural elements that establish specific catalytic cleavage of RNase III processing signals, this report demonstrates that a 60 nucleotide RNA (R1.1 RNA) containing the bacteriophage T7 R1.1 RNase III processing signal, can be generated by in vitro enzymatic transcription of a synthetic deoxyoligonucleotide and accurately cleaved in vitro by RNase III. Several R1.1 RNA sequence variants were prepared to contain point mutations in the internal loop which, on the basis of a hypothetical 'dsRNA mimicry' structural model of RNase III processing signals, would be predicted to inhibit cleavage by disrupting essential tertiary RNA-RNA interactions. These R1.1 sequence variants are accurately and efficiently cleaved in vitro by RNase III, indicating that the dsRNA mimicry structure, if it does exist, is not important for substrate reactivity. Also, we tested the functional importance of the strongly conserved CUU/GAA base-pair sequence by constructing R1.1 sequence variants containing base-pair changes within this element. These R1.1 variants are accurately cleaved at rates comparable to wild-type R1.1 RNA, indicating the nonessentiality of this conserved sequence element in establishing in vitro processing reactivity and selectivity.

Base Sequence↗
PubMed1989

Conserved sequences in bacterial and viral sialidases.

The genes of the bacterial sialidases from Clostridium sordellii G12, C. perfringens A99, Salmonella typhimurium LT-2 and Vibrio cholerae 395 sequenced so far were examined for homologies and were compared with sequences of viral sialidases. Each of the bacterial sialidases contains a short sequence of twelve amino-acids, which is repeated at four positions in the protein. All these sequences exhibit significant similarities. Comparing the repeated sequences of the four sialidases, five amino-acids were found to be highly conserved at defined positions: Ser-X-Asp-X-Gly-X-Thr-Trp. Additionally, most of the distances between the four repeated regions are also conserved among the different sialidases. The conserved bacterial sequences show similarity with sialidases of influenza A H7N1 and H13N9.

Amino Acid Sequence↗
PubMed1993

Peptide antisera targeted to a conserved sequence in poliovirus capsid VP1 cross-react widely with members of the genus Enterovirus.

Rabbits were immunized with synthetic peptides derived from an immunodominant region of the VP1 capsid protein of enteroviruses. This region shows a high degree of homology among all sequenced members of the genus. Peptide-induced antisera were used for immunoperoxidase staining of cell cultures infected with 41 different serotypes of enterovirus. Specific cytoplasmic staining was readily seen in all but two cases. Echovirus type 22 was previously known to differ genetically from the rest of the enteroviruses, and hence, a negative result was expected. Surprisingly, one of the tested serum samples reacted with echovirus 22-infected cells. Coxsackievirus A7-infected cells could be reliably stained with only one of the tested serum samples. For the remaining 39 serotypes, scattered infected cells resulting from 1 to 2 days of incubation with diluted inocula were easily scored as positive before the cytopathic effect became visible. The same antibodies were also used in a sandwich-type enzyme immunoassay to demonstrate poliovirus antigens in cell extracts as early as 3 h after a high-multiplicity infection. These antibodies are candidates for enterovirus group reagents, being potentially useful in both the laboratory diagnosis of enterovirus infections and research on enterovirus-host interactions.

Amino Acid Sequence↗
PubMed1989

The 1B (NS2), 1C (NS1) and N proteins of human respiratory syncytial virus (RSV) of antigenic subgroups A and B: sequence conservation and divergence within RSV genomic RNA.

A 2330 nucleotide sequence spanning the 1B (NS2), IC (NS1) and N genes and intergenic regions of human respiratory syncytial virus strain 18537, representing antigenic subgroup B, was determined by sequencing cloned cDNAs of intracellular mRNAs. Comparison with the previously reported sequences for strain A2 of subgroup A showed that 1B, 1C and N were highly conserved at the nucleotide level (78, 78 and 86% identity, respectively) and at the amino acid level (92, 87 and 96% identity, respectively). The gene-start signals were exactly conserved between subgroups, and the gene-end signals contained only a single nucleotide substitution each in 1B and N. In most cases intergenic and non-coding gene sequences that were not part of presumed transcriptive signals were much less well conserved (generally 50 to 71%) than sequences that were part of translational open reading frames (82 to 86%). The nucleotide and deduced amino acid sequences of the N gene and protein of the Long strain of subgroup A were determined by sequencing cDNA clones of intracellular mRNA; the nucleotide sequence (representing all but the first 10 nucleotides of the gene) contained 15 differences from that of the A2 strain, but the deduced amino acid sequences were identical.

Amino Acid Sequence↗
PubMed1994

Mouse erythroid cells express multiple putative RNA helicase genes exhibiting high sequence conservation from yeast to mammals.

RNA secondary structure is a critical determinant of RNA function in ribosome assembly, pre-mRNA splicing, mRNA translation and RNA stability. The 'DEAD/H' family of putative RNA helicases may help regulate these processes by utilizing intrinsic RNA-dependent ATPase activity to catalyze conformational changes in RNA secondary structure. To investigate the repertoire of DEAD/H box proteins expressed in mammals, we used PCR techniques to clone from mouse erythroleukemia (MEL) cells three new DEAD box cDNAs with high similarity to known yeast (Saccharomyces cerevisiae) genes. mDEAD2 and mDEAD3 (mouse DEAD box proteins) are > 95% identical to mouse PL10 but exhibit differential tissue-specific expression patterns; mDEAD2 and mDEAD3 are also approx. 70% identical (at the aa level) to yeast DED1 and DBP1 proteins. Members of this DEAD box subclass contain C-terminal domains with high content of Arg, Ser, Gly and Phe, reminiscent of the RS domain in several Drosophila and mammalian splicing factors. mDEAD5 belongs to a second class related to translation initiation factors from yeast (TIF1/TIF2) and mammals (eIF-4A); this class contains a novel conserved peptide motif not found in other DEAD box proteins. Northern blotting shows that mDEAD5 is differentially expressed in testis vs. somatic tissues. Thus, mouse erythroid cells produce two highly conserved families of putative RNA helicases likely to play important roles in RNA metabolism and gene expression.

Amino Acid Sequence↗
PubMed1996

Genomic organization and sequence conservation in type I Trichomonas vaginalis viruses.

To reveal the genetic conservation of type I Trichomonas vaginalis viruses (TVV) we cloned and sequenced the 4.6-kb ds RNA of a TVV-T5 isolate for comparison with the cDNA sequence of a related TVV-T1 ds RNA. Analogous to TVV-T1, the TVV-T5 ds RNA also contains an upstream capsid protein gene overlapped with a downstream RNA-dependent RNA polymerase (RDRP) gene by a +1 reading frame shift. A conserved ribosomal slippage heptamer (C CUU UUU) was found within the consensus 14-nt overlap, and the context of the sequence surrounding the heptamer suggests a potential ribosomal frameshifting in the biosynthesis of RDRP from the initiation of capsid protein either through two consecutive -1 shifts or a +1 shift.

Animals↗
PubMed2000

Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene.

The recently raised awareness of the threat of a new influenza pandemic has stimulated interest in the detection of influenza A viruses in human as well as animal secretions. Virus isolation alone is unsatisfactory for this purpose because of its inherent limited sensitivity and the lack of host cells that are universally permissive to all influenza A viruses. Previously described PCR methods are more sensitive but are targeted predominantly at virus strains currently circulating in humans, since the sequences of the primer sets display considerable numbers of mismatches to the sequences of animal influenza A viruses. Therefore, a new set of primers, based on highly conserved regions of the matrix gene, was designed for single-tube reverse transcription-PCR for the detection of influenza A viruses from multiple species. This PCR proved to be fully reactive with a panel of 25 genetically diverse virus isolates that were obtained from birds, humans, pigs, horses, and seals and that included all known subtypes of influenza A virus. It was not reactive with the 11 other RNA viruses tested. Comparative tests with throat swab samples from humans and fecal and cloacal swab samples from birds confirmed that the new PCR is faster and up to 100-fold more sensitive than classical virus isolation procedures.

Animals↗
PubMed2006

Identification of cDNAs encoding viper venom hyaluronidases: cross-generic sequence conservation of full-length and unusually short variant transcripts.

The immobilisation of prey by snakes is most efficiently achieved by the rapid dissemination of venom from its site of injection into the blood stream. Hyaluronidase is a common component of snake venoms and has been termed the "venom spreading factor". In the absence of nucleotide or protein sequence data to confirm the functional identity of this venom component, we interrogated a venom gland EST database for the saw-scaled viper, Echis ocellatus (Nigeria), using the gene ontology (GO) term "carbohydrate metabolism". A single hyalurononglucosaminadase-activity matching sequence (EOC00242) was found and used to design PCR primers to acquire the full-length cDNA sequence. Although very different from the bee venom and mammalian hyaluronidase sequences, the E. ocellatus sequence retained all the catalytic, positional and structural residues that characterise this class of carbohydrate metabolising hydrolases. An extraordinarily high level of sequence identity (>95%) was observed in analogous venom gland cDNA sequences isolated (by PCR) from another saw-scaled viper species, E. pyramidum leakeyi (Kenya), and from the sahara horned viper, Cerastes cerastes cerastes (Egypt) and the puff adder, Bitis arietans (Nigeria). Smaller amplicons, lacking hyaluronidase catalytic residues because of 768 bp or 855 bp central deletions, appear to encode either truncated peptides without hyaluronidase activity, or are non-translated transcripts because they lack consensus translation initiating motifs.

Amino Acid Sequence↗
PubMed1996

The gene promoter for a bean abscission cellulase is ethylene-induced in transgenic tomato and shows high sequence conservation with a soybean abscission cellulase.

Bean leaf abscission (organ separation) correlates with the de novo accumulation of a pI9.5 cellulase and its mRNA. Overlapping genomic clones encoding the bean abscission cellulase (BAC) were isolated and partially sequenced. In addition, a genomic clone for a soybean abscission cellulase (SAC) was identified and the sequence compared to the BAC genomic sequence. Two 5'-upstream regions are particularly well conserved in the two sequences. Of special interest here is the region between -1 and -200 in the BAC promoter which is highly conserved in the SAC gene. Particle gun bombardment with a BAC promoter construct containing 210 bp of BAC sequence 5' to the transcription start site was sufficient to drive abscission-specific and ethylene and auxin-regulated transient expression in bean. In addition to the transient expression assay, expression was examined in stably transformed tomato. A similar -210 bp BAC promoter construct supported a low level of ethylene-inducible reporter gene expression in tomato leaf abscission zones and adjacent petioles but not in ethylene-treated stem tissue or fruit. Expression from the -210 promoter in tomato abscission zones was inhibited by silver thiosulfate, an ethylene action inhibitor, and was partially inhibited by treatment with auxin.

Base Sequence↗
PubMed1992

The 5' ends of LINE1 repeats in rabbit DNA define subfamilies and reveal a short sequence conserved between rabbits and humans.

The 5' ends of five full-length LINE1 (L1) repeats from the rabbit genome (L1Oc) were mapped and their nucleotide sequences determined. Computer-generated alignments showed that these five L1Oc repeats can be divided into subfamilies, each of which has a characteristic sequence upstream of the first open reading frame (ORF1). These five L1Ocs range in size from 6.5 to 7.3 kb, with 5' ends located 76 to 1125 bp upstream of ORF1. Two of these subfamilies appear to have diverged from a common ancestor at least 66 million years ago. Comparisons of the 5' ends of L1s from rabbit, human, mouse, and rat show no common sequence 5' to ORF1, except for a 22-bp sequence that is found near the beginning of all characterized full-length L1s from rabbit and human. A statistical analysis indicates that this 22-bp aligned block is highly significant. Part of this 22-bp sequence matches the microE1 binding site in immunoglobulin gene enhancers. This strong conservation suggests that the microE1 binding site may be part of a transcriptional regulatory element at the 5' ends of rabbit and human L1 repeats.

Animals↗
PubMed2002

Identifying a folding nucleus for the lysozyme/alpha-lactalbumin family from sequence conservation clusters.

Four subfamilies of c-type lysozyme and one subfamily of alpha-lactalbumin are defined from 78 sequences, and their folding nucleus is identified with a method based on conserved residues and native structural contacts between pairs of conserved residues. One large cluster of 19 conserved residues is found which is mostly nonpolar, buried, and nonfunctional. It can be subdivided into three subclusters: (1) conserved residues in four helices; (2) conserved residues that stabilize the connector between the alpha and the beta domains; and (3) a beta-turn, sitting in the middle of a bowl of alpha-helix residues. It is proposed that this folding nucleus initiates four helices, A, B, C, and D, three beta sheets, and the connector, which corresponds closely to the nucleation of the so-called fast folding track pathway. As the secondary structures propagate, nonconserved residues and functionally conserved residues would form additional contacts. The conserved residues are selected with a phylogenetic scheme in which single members of subfamilies are selected. Subfamilies are then equally weighted to obtain the consensus conservation.

Amino Acid Sequence↗
PubMed2004

Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation.

In nature, 1 out of every 10 proteins has an (alpha/beta)(8) (TIM)-barrel fold, and in most cases, pairwise comparisons show no sequence similarity between them. Hence, delineating the key residues that induce very different sequences to share a common fold is important for understanding the folding and stability of TIM-barrel domains. In this work, we propose a new consensus approach for locating these stabilizing residues based on long-range interactions, hydrophobicity, and conservation of amino acid residues. We have identified 957 stabilizing residues in 63 proteins from a nonredundant set of 71 TIM-barrel domains. Most of these residues are located in the 8-stranded beta-sheet, with nearly one half of them oriented toward the interior of the barrel and the other half oriented toward the surrounding alpha-helices. Several stabilizing residues are found in the N- and C-terminal loops, whereas very few appear in the alpha-helices that surround the internal beta-sheet. Further, these 957 residues are placed in 434 stabilizing segments of various sizes, and each domain contains 1-10 of these segments. We found that 8 segments per domain is the most abundant one, and two thirds of the proteins have 7-9 stabilizing segments. Finally, we verified the identified residues with experimental temperature factors and found that these residues are among the ones with less mobility in the considered proteins. We suggest that our new protocol serves as a powerful tool to identify the stabilizing residues in TIM-barrel domains, which can be used as potential candidates for studying protein folding and stability by means of protein engineering experiments.

Conserved Sequence↗
PubMed2006

A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes.

The 3' untranslated regions (3' UTR) of eukaryotic genes can contain motifs involved in regulation of gene expression or localization at the post-transcriptional level. This study concerns the identification of novel, conserved elements in 3' UTRs of many ribosomal protein mRNAs in Caenorhabditis elegans and Caenorhabditis briggsae. Analysis of the region around the polyadenylation signal in many ribosomal protein mRNAs indicates the conservation of a sequence motif UUGUU occurring both before and immediately after the polyadenylation signal. Building a statistical model of this motif and searching a database of C. elegans 3' UTRs reveals that this motif is also present in the 3' UTR of some genes involved in translation and ribosome maturation, among others. We suggest that this signal may be involved in translation or other message-level regulation of ribosomal genes in C. elegans.

3' Untranslated Regions↗
PubMed1984

A conserved sequence element is present around the transcription initiation site for RNA polymerase A in Saccharomycetoideae.

To identify DNA elements involved in the initiation of rRNA transcription in yeast we located the start site of the rRNA operon of Kluyveromyces lactis and Hansenula wingei, both members of the Saccharomycetoideae, by S1 nuclease analysis and determined the surrounding nucleotide sequences. Comparison of these sequences with those of Saccharomyces carlsbergensis, S. cerevisiae and S. rosei (all belonging to the same yeast subfamily) reveals an identical sequence at the site of transcription initiation from position +1 to +7 which is part of a larger conserved region extending from position -9 to +23; the conserved heptanucleotide sequence is supposed to constitute an important part of the promoter for yeast RNA polymerase A. The non-transcribed spacers (NTS) upstream of position -9 have diverged strongly with the exception of two short elements around positions -75 and -135. The external transcribed spacer (ETS) downstream of position +23 is largely conserved between K. lactis, S. rosei and S. carlsbergensis except for a divergent region around position +75. On the other hand, the ETS of H. wingei has diverged significantly.

Ascomycota↗
PubMed2000

Low molecular weight serine protease inhibitors from insects are proteins with highly conserved sequences.

A low molecular weight protease inhibitor peptide found in ovaries of the desert locust Schistocerca gregaria (SGPI-2), was purified from plasma of the same locust and sequenced. It was named SGCI. It was found active towards chymotrypsin and human leukocyte elastase. SGCI was synthesized using a solid-phase procedure and the sequence of its reactive site for chymotrypsin was determined. Compared with an inhibitor purified earlier from another locust species, the total sequence of SGCI showed 88% identity. In particular, the sequence of the reactive site of these inhibitors was identical. Our search for a closely related peptide in an insect species far removed from locusts, the lepidopteran Spodoptera littoralis, was unfruitful but a different chymotrypsin inhibitor, belonging to the Kazal family, was found whose mass is greater than that of SGCI (20 vs 3.6 kDa). Its N-terminal sequence shares 80% identity with that of a chymotrypsin inhibitor purified earlier from the haemolymph of another lepidopteran. Conservation of the amino acid sequence in the reactive site seems to be an exception among protease inhibitors.

Amino Acid Sequence↗
PubMed1996

A bovine mtDNA-binding protein to a conserved sequence adjacent to the termination associated sequence in the vertebrate mitochondrial displacement loop region.

We have found a sequence-specific mitochondrial (mt) DNA-binding protein in bovine mitochondria. The binding site designated Mt5 is adjacent to the termination associated sequence in the vertebrate mt displacement loop region and is interspecifically conserved. An UV-crosslinking and gel filtration demonstrated that a Mt5-binding protein (designated Mt5BP) exists in the mitochondria as a homodimer of an approximately 97-kDa polypeptide. The nucleotide sequence of Mt5 is homologous to that of the binding site for the recently reported mt pause-region binding protein (mtPBP) 1 from sea urchin embryo mitochondria. Gel mobility shift competition experiments indicated that Mt5BP can recognize human sequence couterparts for the mtPBP1-binding site. These results suggest that Mt5BP is related to mtPBP1 with respect to discontinuance of heavy-strand synthesis.

Animals↗
PubMed1984

A sequence conserved in both the chicken and mouse alpha 2(I) collagen promoter contains sites sensitive to S1 nuclease.

We have examined the S1 nuclease sensitivity in the promoter of both the chicken and mouse alpha 2(I) collagen genes. When these DNAs are introduced into supercoiled plasmids and digested with S1 nuclease, a discrete region containing one or more cleavages is found in each promoter. These S1 cleavage sites were mapped by the distance of the S1 site from known restriction enzyme cleavage sites. In the chicken gene, the S1-sensitive segment is located 180 to 200 base pairs preceding the start site of transcription, whereas in the mouse promoter it is between -145 to -165 base pairs. This site in the chicken promoter maps to the segment that has previously been shown to be S1 and DNase I hypersensitive in chromatin. Although these S1 sites are found at different distances from the start site of transcription in the two promoters, the sequences at these sites are strongly conserved between the two species. Each sequence consists of an identical tandem repeat containing a short palindrome within each repeat. Since the DNA sequence does not exhibit the features that would favor either a left-handed Z-DNA configuration or a cruciform structure, an alternative model is discussed that could account for the S1 sensitivity of these sequences. The conservation of these sequences and their S1 sensitivity suggests they play a role in the activation or regulation of the alpha 2(I) collagen gene promoters.

Animals↗