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Results for “Conserved Sequence”

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PubMed1991

Highly conserved sequences in the 3'-untranslated region of the COL1A1 gene bind cell-specific nuclear proteins.

Sequencing of the 3' untranslated region (3'-UTR) of the human COL1A1 gene revealed numerous putative regulatory motifs and two highly conserved regions flanking the two polyadenylation sites. The conserved regions were separated by about 700 bp of less conserved sequences. The first region consists of almost all the 3'-UTR of the shorter (4.8 kbp) COL1A1 transcript. The second conserved domain includes a motif shared with several collagen genes. Both conserved domains bind cell-specific nuclear proteins suggesting that the 3'-UTR is important for cell specific expression of the COL1A1 gene.

Amino Acid Sequence↗

PubMed1987

Nuclear pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe strictly requires an intron-contained, conserved sequence element.

It has recently been argued that pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe may be more similar to splicing in metazoan species than in the budding yeast Saccharomyces cerevisiae. In this report we show that, contrary to this assumption, the conserved sequence element 5'-CTPu APy-3' found in all S. pombe introns 6-18 nucleotides upstream of the 3' splice site is, like the TACTAAC box in S. cerevisiae, indispensable for efficient splicing. The conserved adenine residue of this sequence is used for branch formation and point mutations introduced into the CTPuAPy sequence abolish splicing and seem not to result in the recruitment of cryptic branch sites. We also show that an S. cerevisiae intron is correctly excised in S. pombe whereby the TACTAAC box is used in branch formation.

Base Sequence↗

PubMedDate not supplied

A conserved sequence in the immunoglobulin J kappa-C kappa intron: possible enhancer element.

Several functionally important genetic elements (such as the TATA box, mRNA splice sequences, poly(A) addition signal) were first detected as short segments of unexplained sequence homology within non-coding regions of different genes. A short region of unknown sequence in the intron between the human J kappa and C kappa immunoglobulin coding regions was found to be sufficiently homologous to the corresponding segment of the mouse gene to form stable heteroduplexes. Although no specific function has yet been definitely ascribed to this region (which we call the kappa intron conserved region, or KICR), some functional significance has been inferred from the findings that (1) activation of B lymphocytes induces a DNase hypersensitivity site in this region and (2) deletions including this region reduce expression of kappa genes introduced into lymphoid cells. To delineate the KICR more precisely and to test the generality of the sequence conservation in a third species, we have sequenced this region of the human and mouse genes and have examined the corresponding region of a recently cloned rabbit kappa gene. We find a segment of about 130 base pairs (bp) that shows striking conservation in all three species, demonstrating homology significantly higher than within the C kappa coding region itself. Two short sequences from the J kappa-C kappa intron that were noted by other investigators to be homologous to proposed 'enhancer' sequences both lie within the conserved region.

Animals↗

PubMed1998

Genetic analysis of a conserved sequence in the HoxD complex: regulatory redundancy or limitations of the transgenic approach?

Extensive sequencing in the HoxD complex of several vertebrate species has revealed a set of conserved DNA sequences interspersed between neighboring Hox genes. Their high degree of conservation strongly suggested that they are used for regulatory purposes, a hypothesis that was largely confirmed by using "classical transgenesis" or in vivo mutagenesis through the embryonic stem (ES) cell technology. Here, we show that this is not always the case. We report that the deletion of a conserved regulatory sequence located in the HoxD complex gives different results, depending on the transgenic approach that was used. In "conventional" transgenesis, this sequence was necessary for proper expression in a subdomain of the developing limb. However, a deletion of this sequence in complexo did not confirm this effect, thereby creating an important discrepancy between the classical transgenic and the ES cell-based, targeted mutagenesis. This unexpected observation may show the limitations of the former technology. Alternatively, it could illustrate a redundancy in regulatory circuits and, thus, justify the combination of parallel strategies.

Alleles↗

PubMed1995

Complex genetic organization of junB: multiple blocks of flanking evolutionarily conserved sequence at the murine and human junB loci.

A comparison of the murine and human junB loci reveals nine regions of distal 5'- and 3'-flanking DNA that exhibit greater than 72% sequence identity. A large fraction (over 50%) of the junB locus is contained in these flanking evolutionarily conserved sequences (FECS), which may be required for effecting the proper transcriptional regulation of this gene. Comparative sequence analyses involving kilobases of distal flanking DNAs have been performed for only a small number of vertebrate genes. The available data and the results presented here suggest that FECS may emerge as common yet important functional components of genes, a hypothesis with significant implications for characterizing genes involved in human disease.

Animals↗

PubMed2000

The ftsZ gene of Haloferax mediterranei: sequence, conserved gene order, and visualization of the FtsZ ring.

We sequenced the ftsZ gene region of the halophilic archaeon Haloferax mediterranei and mapped the transcription start sites for the ftsZ gene. The gene encoded a 363-amino-acid long FtsZ protein with a predicted molecular mass of 38 kDa and an isoelectric point of 4.2. A high level of similarity to the FtsZ protein of Haloferax volcanii was apparent, with 97 and 90% identity at the amino acid and nucleotide levels, respectively. Structural conservation at the protein level was shown by visualization of the FtsZ ring structure in H. mediterranei cells using an antiserum raised against FtsZ of H. volcanii. FtsZ rings were observed in cells in different stages of division, including cells with pleomorphic shapes and cells that appeared to be undergoing asymmetric division. Cells were also observed that displayed constriction-like invaginations in the absence of an FtsZ ring, indicating that morphological data are not sufficient to determine whether pleomorphic Haloferax cells are undergoing cell division. Both the upstream and downstream gene order in the ftsZ region was found to be conserved within the genus Haloferax. Furthermore, the downstream gene order, which includes the secE and nusG genes, is conserved in almost all euryarchaea sequenced to date. The secE and nusG genes are likely to be transcriptionally and translationally coupled in Haloferax, and this co-expression may have been a selective force that has contributed to keeping the gene cluster intact.

Amino Acid Sequence↗

PubMed1986

Role of conserved sequence elements 9L and 2 in self-splicing of the Tetrahymena ribosomal RNA precursor.

Oligonucleotide-directed mutagenesis has been used to alter highly conserved sequences within the intervening sequence (IVS) of the Tetrahymena large ribosomal RNA precursor. Mutations within either sequence element 9L or element 2 eliminate splicing activity under standard in vitro splicing conditions. A double mutant with compensatory base changes in elements 9L and 2 has accurate splicing activity restored. Thus, the targeted nucleotides of elements 9L and 2 base-pair with one another in the IVS RNA, and pairing is important for self-splicing. Mutant splicing activities are restored by increased magnesium ion concentrations, supporting the conclusion that the role of the targeted bases in splicing is primarily structural. Based on the temperature dependence, we propose that a conformational switch involving pairing and unpairing of elements 9L and 2 is required for splicing.

Animals↗

PubMed2005

Conserved sequences and the evolution of gene regulatory signals.

Studies of evolutionary conservation of gene regulatory signals have led to a paradox: extensive sequence similarity implies functional conservation in non-coding regions across mammalian species; however, this stands in contrast to our understanding of transcriptional regulatory sites composed of degenerate recognition sequences for transcription factors that can maintain functional equivalence despite considerable sequence divergence. The latter observation provides an explanation for the rapid evolution of new traits through the gain and loss of transcription factor binding sites that bring new genes under the control of an existing genetic regulatory network. The former observation might point to novel mechanisms of gene regulation and/or chromosome function that are currently unappreciated. Recent comparative genome analysis has highlighted extensive conserved sequences in mammalian genomes that are beginning to be functionally characterized.

Animals↗

PubMed1979

Sequence of inverted terminal repetitions from different adenoviruses: demonstration of conserved sequences and homology between SA7 termini and SV40 DNA.

We have established the nucleotide sequence for the inverted terminal repetition of human adenovirus type 3, a subgroup B adenovirus. The repetition, which is 136 bp long, shows a high degree of homology with the known sequence for the inverted repetition of adenovirus type 5 (Steenbergh et al., 1977) a subgroup C adenovirus. Partial sequence information convering 120 bp of the inverted terminal repetitions of human serotype 12, a subgroup A member, and of simian adenovirus type 7 has also been obtained. A comparison of the established sequences shows that the terminal repetitions, in particular the first 50 bp from the ends, contain sequences that have been well conserved in adenovirus evolution. For instance, only six mismatched base pairs were detected among the first 50 bp in the repetitions of simian adenovirus type 7 and human adenovirus type 5, although the homology between simian adenovirus 7 and human subgroup C adenoviruses was estimated to be only 30%. A 14 bp sequence located 9-22 nucleotides from the ends is present in DNAs from all the human serotypes examined as well as in simian adenovirus 7 DNA. Furthermore, the simian adenovirus 7 repetition contains a 21 bp sequence which is present in SV40 DNA, close to the origin of DNA replication.

Adenoviridae↗

PubMed1990

Sequence conservation and divergence of hepatitis delta virus RNA.

The complete RNA sequence of the hepatitis delta virus (HDV) obtained from the Nauru Island in the Pacific was determined by cDNA cloning and amplification by polymerase chain reaction (PCR). The sequence showed 14-17% divergence from the two known HDV RNA sequences. There are three highly conserved domains: the region around the autocatalytic cleavage site of the genomic RNA (nucleotides 659 to 772), the region around the autocatalytic cleavage site of the antigenomic-sense RNA (nucleotides 847 to 966), and the region around the middle one-third domain of the open reading frame (ORF) encoding the hepatitis delta antigen on the antigenomic RNA (nucleotides 1267 to 1347). The two autocatalytic activities are required for the cleavage and ligation of HDV RNA during RNA replication. The third conserved domain codes for the RNA-binding domain of HDAg, which specifically interacts with HDV RNA. Three nucleotide changes within the genomic catalytic sequence are present but did not alter the catalytic cleavage activity of the HDV RNA. Microheterogeneity of the RNA sequences was also detected. One of these occurred within the coding region of the delta antigen, creating an amber termination codon in some of the RNA species. Thus, this HDV strain contains two different RNA species, one of which encodes a delta antigen of 214 amino acids and the other 195 amino acids. These two protein species were detected by immunoblotting of the patient's plasma. In contrast to other HDV strains, only three ORFs capable of encoding more than 100 amino acids each are present in this HDV RNA. We recommend that oligonucleotides complementary to the highly conserved sequences should be used as primers for PCR in clinical detection assays of hepatitis delta virus infection.

Adult↗

PubMed1986

Deletion analysis of the Klebsiella pneumoniae nitrogenase promoter: importance of spacing between conserved sequences around positions -12 and -24 for activation by the nifA and ntrC (glnG) products.

The nitrogen fixation promoters of Klebsiella pneumoniae are atypical procaryotic promoters lacking the usual -10 and -35 elements, requiring instead conserved sequences around -12 and -24 for transcriptional activation. By constructing a set of five deletions between the -12 and -24 elements in the nifH promoter, the spacing between the conserved GC and GG motifs at -12 and -24, respectively, has been reduced from the wild-type 10 bases to 9, 8, 6, 5, and 4 bases. The deletion of a single nonconserved nucleotide was sufficient to eliminate transcriptional activation by either nifA or ntrC (glnG). All deletions relieved the multicopy inhibition of chromosomal nif expression normally shown by the nifH promoter. These results demonstrate a stringent requirement for the 10-base spacing found in ntr-activated promoters. In addition, specific sequences around the invariant GG at -24 were shown to be necessary for activation by either nifA or ntrC, with a minimal requirement for nucleotides through to position -27 for this activation.

Bacterial Proteins↗

PubMed1996

Identification and functional characterization of a highly conserved sequence in the intron of the kappa light chain gene.

A highly conserved 225 bp sequence was identified within the J-C intron of the murine kappa light-chain immunoglobulin gene and its nuclear protein-binding and regulatory function were examined. The binding of nuclear proteins to this fragment was found to reflect the differentiation state of the cell used to prepare the nuclear extracts and three different complexes are seen with this fragment: CI, CII and CIII. CIII is present in all cell types. CI is present in fibroblasts, T cells and early B cells, but not mature B cells. Moreover, nuclear extracts prepared from the early pre-B cell line, 70Z/3, that was treated with agents which activate kappa gene transcription have a reduced ability to form CI. Therefore, the presence of CI correlates with the absence of kappa gene transcription. CII is present in all stages of B cell development, however its composition changes with B cell maturation. Contained within the 225 bp element is the ets family-binding motif GGAA and the B-cell-and-macrophage-specific family member, PU.1 binds this sequence and participates in CII formation. The 225 bp fragment showed modest augmentation of expression in CAT reporter constructs containing the heavy chain enhancer (HCE) and a light chain promoter in the plasmacytoma, S194, and uninduced 70Z/3 cells and mediated a small but reproducible response to IFN-gamma in 70Z/3 cells. Thus, the 225 bp sequence contained within the J-C intron may function as a regulatory element for kappa light chain gene expression.

Animals↗

PubMed1987

Formation of a type I collagen RNA dimer by intermolecular base-pairing of a conserved sequence around the translation initiation site.

A symmetrical sequence around the translation initiation site of several collagen genes is highly conserved. Deletions in this sequence increase translational efficiency of an alpha 2(I) collagen - CAT chimeric gene after DNA transfection of NIH 3T3 fibroblasts (Schmidt, Rossi and de Crombrugghe, submitted). The secondary structure, predicted by the sequence of this segment, was shown to exist in solution in 200 mM NaCl at 37 degrees C. Cell-free translation of the corresponding RNA using a reticulocyte lysate is inhibited 2 to 4-fold by preincubation with a 0.5 M NaCl extract of an NIH 3T3 ribosomal eluate. Cell-free translation of two mutant RNAs, with partial deletions of the conserved sequence, is not inhibited by such preincubation. This inhibition is not due to degradation of the RNA and requires a protein component of the ribosomal eluate, which, however, is not required after the preincubation step. Preincubation of the RNA with the ribosomal eluate from NIH 3T3 fibroblasts causes the reversible formation of an intermolecular dimer in which the conserved symmetrical sequences hybridize to each other. This results in an increase in the degree of secondary structure of the conserved segment around the translation initiation site. We speculate that translational efficiency could be modulated by influencing the equilibrium between monomer and dimer.

Base Composition↗

PubMed1992

Antibody from hen's eggs against a conserved sequence of the gametophytic self-incompatibility proteins of plants.

A convenient way of producing effective antibodies to plant proteins is presented. It takes into account the following facts: (1) many plant proteins are highly glycosylated, thus giving rise to nonspecific antibodies which cross-react with other glycoproteins, (2) it is more common nowadays to know the DNA sequence of a protein coding gene than to have significant amounts of that protein well purified as antigen, and (3) eggs from immunized hens are very convenient sources of large amounts of antibodies. An antibody which specifically detects self-incompatibility proteins (S-proteins) in Solanaceae was isolated. The published cDNA sequences and deduced amino acid sequences of Nicotiana alata (an ornamental tobacco) S-proteins were computer analyzed in order to recognize a peptide with a conserved sequence which would effectively give rise to antibodies. An adequate amount of this peptide was synthesized and part of it was coupled to a macromolecular carrier (bovine serum albumin). Antibodies to this peptide-carrier complex were recovered from egg yolks of immunized hen in amounts corresponding to 300 ml of antiserum per month. From the total immunoglobulin fraction isolated, the antibody specific for S-proteins was affinity purified over 100-fold on a peptide-coupled column. The antibody showed high levels of specificity for putative S-specific sequences in N. alata and in petunia. Also the size, polymorphy, and quantity of the detected antigens were in very good accordance with previously published data. In addition to the present application, this procedure should be useful for a wide variety of proteins.

Amino Acid Sequence↗

PubMed1991

Primary structure of the merozoite surface antigen 1 of Plasmodium vivax reveals sequences conserved between different Plasmodium species.

Merozoite surface antigen 1 (MSA1) of several species of plasmodia has been shown to be a promising candidate for a vaccine directed against the asexual blood stages of malaria. We report the cloning and characterization of the MSA1 gene of the human malaria parasite Plasmodium vivax. This gene, which we call Pv200, encodes a polypeptide of 1726 amino acids and displays features described for MSA1 genes of other species, such as signal peptide and anchoring sequences, conserved cysteine residues, number of potential N-glycosylation sites, and repeats consisting here of 23 glutamine residues in a row. When the nucleotide and deduced amino acid sequences of the MSA1 of P. vivax are compared to those of another human malaria parasite, Plasmodium falciparum, and to those of the rodent parasite Plasmodium yoelii, 10 regions of high amino acid similarity are observed despite the very different dG + dC contents of the corresponding genes. All of the interspecies conserved regions reside within the conserved or semiconserved blocks delimited by the sequences of different alleles of the MSA1 gene of P. falciparum.

Amino Acid Sequence↗

PubMed1997

Conserved sequences in the fibers of epidemic keratoconjunctivitis associated human adenoviruses.

The fiber gene sequences of the human adenovirus types 19 and 37 were determined. The predicted polypeptides exposed a high homology. Ad8, Ad19, and Ad37 can cause epidemic keratoconjunctivitis (EKC), whereas Ad9 only infrequently causes acute follicular conjunctivitis. Comparison of the fiber knobs of Ad8, Ad9, Ad19, Ad37, and other previously published fiber sequences revealed that only two amino acid residues were conserved in the fiber knobs of Ad8, Ad19, and Ad37. Since the knob is responsible for interaction with the cell receptor, these two amino acid residues could play an important role in the pathogenicity of EKC causing adenoviruses.

Adenoviridae↗

PubMed1996

Similarities in Restriction Fragment Patterns of Mitochondrial DNAs of PhytophthoraSpecies Strongly Depend on the Restriction Enzyme Used Due to Heterogeneous Base Distribution and Sequence Conservation

Mitochondrial DNAs of six morphologically different Phytophthora species were digested with 15 restriction enzymes. The numbers of restriction fragments obtained differed considerably from those theoretically expected for random base distribution. Enzymes with relatively many G and C in their recognition sequences produced significantly larger numbers of fragments. Moreover, fragments generated by most of these enzymes were more often shared by two or more species than those from enzymes with more A and T in their recognition sequence. It is concluded that base distribution in mitochondrial DNA of Phytophthora is heterogeneous,AT-rich stretches occurring scattered over the mitochondrial genome and GC-rich regions present in conserved sequences, presumably genes. A practical consequence for taxonomic RFLP studies is that optimal enzymes can be selected, depending on the desired level of resolution.

Journal Article↗

PubMed1998

Polyadenylation of influenza virus mRNA transcribed in vitro from model virion RNA templates: requirement for 5' conserved sequences.

Here we report the development of two independent assays which demonstrate for the first time that exogenous model RNA templates based on influenza virus virion RNA (vRNA) are transcribed in vitro to produce polyadenylated mRNA. We investigated the activities of mutated templates with known polymerase binding properties to test our model that polyadenylation occurs when a polymerase complex, which is bound to conserved 5' sequences of vRNA, prevents read-through of the U track at which polyadenylation subsequently occurs by reiterative copying. Mutated templates with perturbed polymerase binding sites (i.e., a deletion mutant lacking the first 4 5' residues and a U-->A point mutant at the third residue) initiated transcription in the in vitro assay but failed to produce polyadenylated transcripts, whereas an A-->U point mutant at the fourth residue, which retained polymerase binding properties similar to those of the wild type, produced polyadenylated transcripts. Our results show that nucleotides within the conserved 5' sequence are required for polyadenylation and support the hypothesis that polymerase binding to 5' sequences of the template is required for mRNA synthesis.

Base Sequence↗