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At least 217 records · Page 12Linked to original sources

Screening cosmid libraries with oligonucleotides corresponding to splice-site consensus sequences.

To facilitate the identification of genes within genomic DNA, we have developed a method based on the use of short oligonucleotides designed from the consensus sequences of splice sites. We describe here the hybridization and washing conditions under which such oligonucleotides can be used to screen cosmid libraries. We confirm the presence of genes within cosmids identified by screening with one oligonucleotide by showing that DNA isolated from such cosmids will hybridize to another splice-site oligonucleotide.

Animals↗

A 3' splice site consensus sequence mutation in the intron 3 of the alpha-galactosidase A gene in a patient with Fabry disease.

Fabry disease is an X-linked disorder accompanied with accumulation of glycosphingolipids resulting from the deficient activity of the lysosomal hydrolase, alpha-galactosidase A (alpha-GalA). In the present study, mRNA for alpha-GalA in fibroblasts from an 11-year-old Japanese patient with Fabry disease was examined using the reverse transcriptase-polymerase chain reaction (PCR). The shorter message of alpha-GalA was demonstrated in this patient when compared with the normal control. The complete deletion of exon 4 in the mRNA for alpha-GalA in the patient was disclosed by analysis of cDNA with restriction enzyme digestion and asymmetrical PCR sequencing. The direct sequencing of the genomic DNA demonstrated a single base substitution (G----A) at the 3' end of the consensus sequence of intron 3. This mutation destroyed a splice site in the alpha-GalA, which produced a mutant allele. It was also shown that the mother of the patient had this mutant as well as normal alleles as a heterozygote.

Child↗

A base-specific recognition signal in the 5' consensus sequence of rotavirus plus-strand RNAs promotes replication of the double-stranded RNA genome segments.

Replication of the segmented double-stranded (ds)RNA genome of rotavirus requires the viral RNA-dependent RNA polymerase (RdRP) to use 11 different (+)RNAs as templates for (-) strand synthesis. Complementary sequences proximal to the 5' and 3' termini are predicted to direct cyclization of the (+)RNAs by forming panhandle structures from which short highly conserved terminal sequences protrude as single-stranded tails. Cell-free replication assays indicate that such structural organization of the 5'- and 3'-ends is required for efficient dsRNA synthesis. Multiple specifically recognized elements exist at the 3'-end that promote dsRNA synthesis including RdRP-recruitment signals and a (-) strand initiation sequence. In contrast to the 3'-end, the role of the 5'-end has been less well defined. In this study, we determined that the 5'-end contains a base-specific recognition signal that plays an important role in the assembly of the RdRP and cofactors into a stable initiation complex for (-) strand synthesis. The 5' recognition signal is associated with the G2 residue of the 5'-consensus sequence, a residue that shows absolute conservation among all rotavirus groups (A, B, and C) examined to date. From our results, we suggest that rotavirus (+)RNA cyclization, although likely initiated by 5'- 3' nucleotide complementarity, may be stabilized by RdRP-dependent bridging. Given that synthesis of the (-) strand on the (+)RNA template will disrupt 5'-3' nucleotide interactions, RdRP-dependent bridging may be the sole mechanism by which the dsRNA product can be held in the necessary cyclized conformation required for efficient multiple rounds of transcription.

Base Sequence↗

Labeling of human centromeres using an alphoid DNA consensus sequence: application to the scoring of chromosome aberrations.

Precise identification of centromeres is required for accurate scoring of asymmetrical chromosome aberrations, such as dicentrics. The centromeric regions of all human chromosomes can be labeled by in situ hybridization of a 30 nucleotide oligomer having the sequence of a conserved region of an alphoid DNA consensus sequence. Fluorescent detection of the hybridized probe allows rapid identification of centromeres and accurate scoring of dicentrics, multicentrics, acentric fragments, and the centromeric content of ring chromosomes. This procedure provides a novel approach for scoring these complex chromosome aberrations, particularly damage induced by radiation or radiomimetic agents.

Centromere↗

Transcriptional activation of the Escherichia coli adaptive response gene aidB is mediated by binding of methylated Ada protein. Evidence for a new consensus sequence for Ada-binding sites.

The Escherichia coli aidB gene is part of the adaptive response to DNA methylation damage. Genes belonging to the adaptive response are positively regulated by the ada gene; the Ada protein acts as a transcriptional activator when methylated in one of its cysteine residues at position 69. Through DNaseI protection assays, we show that methylated Ada (meAda) is able to bind a DNA sequence between 40 and 60 base pairs upstream of the aidB transcriptional startpoint. Binding of meAda is necessary to activate transcription of the adaptive response genes; accordingly, in vitro transcription of aidB is dependent on the presence of meAda. Unmethylated Ada protein shows no protection against DNaseI digestion in the aidB promoter region nor does it promote aidB in vitro transcription. The aidB Ada-binding site shows only weak homology to the proposed consensus sequences for Ada-binding sites in E. coli (AAANNAA and AAAGCGCA) but shares a higher degree of similarity with the Ada-binding regions from other bacterial species, such as Salmonella typhimurium and Bacillus subtilis. Based on the comparison of five different Ada-dependent promoter regions, we suggest that a possible recognition sequence for meAda might be AATnnnnnnG-CAA. Higher concentrations of Ada are required for the binding of aidB than for the ada promoter, suggesting lower affinity of the protein for the aidB Ada-binding site. Common features in the Ada-binding regions of ada and aidB are a high A/T content, the presence of an inverted repeat structure, and their position relative to the transcriptional start site. We propose that these elements, in addition to the proposed recognition sequence, are important for binding of the Ada protein.

Adaptation, Physiological↗

The 3' flanking region of the human erythropoietin-encoding gene contains nitrogen-regulatory/oxygen-sensing consensus sequences and tissue-specific transcriptional regulatory elements.

We have reported the identification of a classical canonical CAAT box, TATA boxes and other transcriptional regulatory elements in the 5' flanking region of the human erythropoietin (hEp)-encoding gene [Lee-Huang et al., Gene 128 (1993) 227-236]. These elements were not found in the hEp genomic clones reported by others. Our genomic clone extends in both directions beyond any reported clones, by 3.9 kb on the 5' side and by 1.8 kb on the 3' side. Many important regulatory elements are found in these extended flanking regions. We report here the genomic structure of the extended 3' flanking region of hEp. This region contains the following regulatory elements: nitrogen-regulatory/oxygen-sensing consensus sequences, 5'-TTTTGCA and 5'-CCCTGCA; tissue-specific regulatory elements, including binding sites for A-activator, 5'-GTGGTGCAA; for DBP, 5'-TGATTTTGT; for HNF, 5'-T(A/G)TTTGT; and for C/EBP, 5'-T(T/G) (T/G)TGCAAT; a lymphokine-responsive element, 5'-GTGAAACCCC (Rev), as well as binding sites for AP and Sp1. In addition, the nucleotide (nt) sequence in this region is rich in inverted repeats (palindromes) that allow the formation of hairpin loops. A total of 14 potential stem loops with a maximum loop size of 20 nt are found. The identification of these regulatory elements in hEp should provide further insight into the tissue-specific and inducible expression of hEp. Such knowledge should be useful in the clinical modulation of erythropoiesis under physiologic and pathologic conditions.

Base Sequence↗

Consensus sequence of transcription factor SF-1 binding site and putative binding site in the 5' flanking regions of genes encoding mouse steroidogenic enzymes 3betaHSDI and Cyp17.

Using 42 nucleotide sequences extracted from the Transcription Regulatory Regions Database (TRRD) containing SF-1 transcription factor binding site, we have determined the decanucleotide (GTCAAGGTCA) consensus sequence for SF-1 binding. In the frequency matrix of this sequence nucleotides between the 3rd and the 7th position had the highest frequency and guanine nucleotides at the 6th and the 7th positions were recognized in all nucleotide sequences. The latter suggests a crucial role of these guanines for the interaction of DNA with SF-1 protein. The determined consensus and frequency matrix were used for search of putative SF-1 binding sites in regulatory regions of two genes, encoding mouse Cyp17 (17alpha-hydroxylase/17-20-lyase) and 3betaHSDI (3beta-hydroxysteroid dehydrogenase/4delta-5delta-isomerase I), the microsomal enzymes involved in steroidogenesis. 5;-Flanking regions of genes encoding Cyp17 and 3betaHSDI were shown to contain six and five such binding sites, respectively. The presence of the putative SF-1 binding sites in the regulatory regions of mouse Cyp17 and 3betaHSDI suggests that gene SF-1 could represent one of the putative genes which (as we predicted earlier) determine coordinated inheritable variability of hormonal activity in mouse Leydig cells.

3-Hydroxysteroid Dehydrogenases↗

Interferon consensus sequence binding protein-deficient mice display impaired resistance to intracellular infection due to a primary defect in interleukin 12 p40 induction.

Mice lacking the transcription factor interferon consensus sequence binding protein (ICSBP), a member of the interferon regulatory factor family of transcription proteins, were infected with the intracellular protozoan, Toxoplasma gondii. ICSBP-deficient mice exhibited unchecked parasite replication in vivo and rapidly succumbed within 14 d after inoculation with an avirulent Toxoplasma strain. In contrast, few intracellular parasites were observed in wild-type littermates and these animals survived for at least 60 d after infection. Analysis of cytokine synthesis in vitro and in vivo revealed a major deficiency in the expression of both interferon (IFN)-gamma and interleukin (IL)-12 p40 in the T. gondii exposed ICSBP-/- animals. In related experiments, macrophages from uninfected ICSBP-/- mice were shown to display a selective impairment in the mRNA expression of IL-12 p40 but not IL-1alpha, IL-1beta, IL-1Ra, IL-6, IL-10, or TNF-alpha in response to live parasites, parasite antigen, lipopolysaccharide, or Staphylococcus aureus. This selective defect in IL-12 p40 production was observed regardless of whether the macrophages had been primed with IFN-gamma. We hypothesize that the impaired synthesis of IL-12 p40 in ICSBP-/- animals is the primary lesion responsible for the loss in resistance to T. gondii because IFN-gamma-induced parasite killing was unimpaired in vitro and, more importantly, administration of exogenous IL-12 in vivo significantly prolonged survival of the infected mice. Together these findings implicate ICSBP as a major transcription factor which directly or indirectly regulates IL-12 p40 gene activation and, as a consequence, IFN-gamma-dependent host resistance.

Acute Disease↗

A gene, han1A, encoding an archaeal histone-like protein from the Thermococcus species AN1: homology with eukaryal histone consensus sequences and the implications for delineation of the histone fold.

The han1A gene, encoding a subunit of the histone-like protein HAN1 from the Thermococcus species AN1, has been cloned and sequenced. Sequence analysis of the translation product of the gene demonstrates homology with other archaeal histone-like proteins of the 'HMf family' and eukaryal consensus sequences, particularly H4. The region of highest homology between the AN1 histone subunit, termed the HAN1A1 subunit, and the H4 consensus is suggested, by the 3-dimensional structure of the histone octamer, to interact with the minor groove of DNA. The results presented add further weight to the notion that the 'archaeal histones' and the eukaryal histones are indeed related and that the approximate 65 amino acid residue length of the archaeal histones represents the archaeal equivalent of the histone fold structural building block common to all eukaryal histones.

Amino Acid Sequence↗

The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element.

Alu repeats are interspersed repetitive DNA elements specific to primates that are present in 500,000 to 1 million copies. We show here that an Alu sequence encodes functional binding sites for retinoic acid receptors, which are members of the nuclear receptor family of transcription factors. The consensus sequences for the evolutionarily recent Alu subclasses contain three hexamer half sites, related to the consensus AGGTCA, arranged as direct repeats with a spacing of 2 bp, which is consistent with the binding specificities of retinoic acid receptors. An analysis was made of the DNA binding and transactivation potential of these sites from an Alu sequence that has been previously implicated in the regulation of the keratin K18 gene. These Alu double half sites are shown to bind bacterially synthesized retinoic acid receptors as assayed by electrophoretic mobility shift assays. These sites are further shown to function as a retinoic acid response element in transiently transfected CV-1 cells, increasing transcription of a reporter gene by a factor of approximately 35-fold. This transactivation requires cotransfection with vectors expressing retinoic acid receptors, as well as the presence of all-trans-retinoic acid, which is consistent with the known function of retinoic acid receptors as ligand-inducible transcription factors. The random insertion of potentially thousands of Alu repeats containing retinoic acid response elements throughout the primate genome is likely to have altered the expression of numerous genes, thereby contributing to evolutionary potential.

Animals↗

The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae.

Replication origins have been mapped to positions that coincide, within experimental error (several hundred base pairs), with ARS elements. To determine whether the DNA sequences required for ARS function on plasmids are required for chromosomal origin function, the chromosomal copy of ARS306 was deleted and the chromosomal copy of ARS307 was replaced with mutant derivatives of ARS307 containing single point mutations in domain A within the ARS core consensus sequence. The chromosomal origin function of these derivatives was assayed by two-dimensional agarose gel electrophoresis. Deletion of ARS306 deleted the associated replication origin. The effects on chromosomal origin function of mutations in domain A paralleled their effects on ARS function, as measured by plasmid stability. These results demonstrate that chromosomal origin function is a property of the ARS element itself.

Base Sequence↗

[Antibody responses to consensus sequence of hypervariable region 1 from hepatitis C virus protein E2 in relation to the phase of infection].

Three overlapping peptides containing linear B-cell epitopes and corresponding to the consensus sequence of hypervariable region 1 (HVR1) from protein E2 were studied for their capacity to interact with the sera from patients with acute and chronic hepatitis C. Antibodies to these peptides are detectable with the comparable frequency in both acute and chronic hepatitis C viral infection, other than after viral elimination. A relationship of the outcome of acute Infection to the presence or absence of antibodies to the test peptides has not been established. The level of antibodies against protein E2 HVR1 C-terminus is significantly higher in chronic hepatitis C.

Adolescent↗

Identification of calmodulin-binding peptide consensus sequences from a phage-displayed random peptide library.

The calcium-binding protein, calmodulin (CaM), was used to screen a phage library displaying random peptides 26 amino acids (aa) in length. Twenty CaM-binding peptides were identified, 17 of which contained one of three consensus sequence motifs: + W-OlambdaR, WRAAV or WRXXAAAL, where +, -, O, lambda and X are positively charged, negatively charged, hydrophobic, leucine or valine, and any residue, respectively. The Trp residue in these motifs is located within 14 aa of the N-terminus of the displayed peptide. Previous studies [Dedman et al., J. Biol. Chem. 268 (1993) 23025-23030] using a library displaying random peptides 15 aa in length identified CaM-binding peptides which contained a Trp-Pro dipeptide motif. These results suggest that the type of CaM-binding motif identified can vary between different types of combinatorial peptides.

Amino Acid Sequence↗

Expression of interferon consensus sequence binding protein induces potent immunity against BCR/ABL-induced leukemia.

Mice deficient in the interferon consensus sequence binding protein (ICSBP) develop a disease resembling chronic myeloid leukemia (CML), which in humans is caused by the BCR/ABL oncoprotein. Interferon-alpha (IFN-alpha) induces ICSBP expression and is an effective therapy for CML. This study examined whether enforced expression of ICSBP might antagonize BCR/ABL-induced leukemia; results demonstrated that ICSBP-modified cells generated a protective CD8(+) cytotoxic T-cell response against BCR/ABL-transformed BaF3 cells in a murine leukemia model. ICSBP expression represents a novel means of stimulating a host immune response to BCR/ABL(+) leukemia cells and a potential strategy for immunotherapy of CML. (Blood. 2001;97:3491-3497)

Animals↗

Interferon-induced early changes in nuclear protein interactions with the interferon consensus sequence.

A number of genes are transcriptionally regulated by interferons via a cis acting regulatory element (interferon consensus sequence). After incubation with HeLa cell nuclear extracts, a synthetic 29 mers probe representing the consensus was retarded as a single band whose amount increased after the addition of IFN to the cells. DNase I footprinting showed that a region of the non coding strand was protected differentially upon interferon treatment. After nuclear protein blotting and probing with the oligonucleotide, two proteins (114 and 50 kDa) of the desired specificity were revealed. Their absolute and relative amounts do not appear to be dependent of the IFN treatment.

Cell Nucleus↗

The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification.

SUMO-1 is an ubiquitin-related protein that is covalently conjugated to a diverse assortment of proteins. The consequences of SUMO-1 modification include the regulation of protein-protein interactions, protein-DNA interactions, and protein subcellular localization. At present, very little is understood about the specific mechanisms that govern the recognition of proteins as substrates for SUMO-1 modification. However, many of the proteins that are modified by SUMO-1 interact directly with the SUMO-1 conjugating enzyme, Ubc9. These interactions suggest that Ubc9 binding may play an important role in substrate recognition as well as in substrate modification. The SUMO-1 consensus sequence (SUMO-1-CS) is a motif of conserved residues surrounding the modified lysine residue of most SUMO-1 substrates. This motif conforms to the sequence "PsiKXE," where Psi is a large hydrophobic residue, K is the lysine to which SUMO-1 is conjugated, X is any amino acid, and E is glutamic acid. In this study, we demonstrate that the SUMO-1-CS is a major determinant of Ubc9 binding and SUMO-1 modification. Mutating residues in the SUMO-1-CS abolishes both Ubc9 binding and substrate modification. These findings have important implications for how SUMO-1 substrates are recognized and for how SUMO-1 is ultimately transferred to specific lysine residues on these substrates.

Amino Acid Sequence↗

The intracellular antibody capture technology (IACT): towards a consensus sequence for intracellular antibodies.

We describe the application of an intracellular antibody capture technology (IACT) as a generic in vivo selection procedure for isolating intracellular antibodies or ICAbs. IACT was applied to the de novo selection of functional ICAbs against the microtubule-associated protein TAU, found in neurofibrillary lesions of Alzheimer's disease brains. A panel of 17 different ICAbs was created which bind TAU inside cells and the epitopes recognized by the selected ICAbs have been determined by an in vivo epitope mapping procedure. Finally, sequence analysis showed that the IACT-derived ICAbs are characterized by a common signature of conserved amino acid residues, suggesting that the IACT naturally selects a sort of "captured consensus sequence" for intracellular antibodies. The development of IACT, together with the possibility of scaling up in a high throughput and automated format, makes IACT a new enabling tool for target validation in functional genomics and global proteomics.

Alzheimer Disease↗

Conformational study based on simulated annealing and 1H NMR of peptides comprising the consensus sequence Arg5-Asp-Val-Arg-Gly9: effects of the substitution Ser 12 by Ala 12 or of 3 residues deletion at the N-terminus.

A conformational search by simulated annealing has been performed on two peptides derivated from the tetradecapeptide used to isolate the Xenopus laevis skin maturation RXVRG-endoprotease. The Ala 12 derivative, obtained by substitution in the hydrophobic C terminal fragment and the undecapeptide 4-14, obtained by deletion of an acidic rich tripeptide, were studied. No unique structure has been found for the tetradecapeptide Ala 12. This structural disorganization could explain the loss of activity of the endoprotease towards the substituted peptide. For the undecapeptide, two different models in accordance with the NMR data were found. The conformational differences between these two models are located in the consensus sequence and in each case an hairpin-like conformation is observed. These results could be related to the enhanced cleavage activity of the maturation enzyme. The obtained structures are also compared with those of the original tetradecapeptide.

Alanine↗