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PubMed1988

Nucleotide sequence and expression of the human skeletal alpha-actin gene: evolution of functional regulatory domains.

Regulation of the actin multigene family involves the recognition of regulatory sequences that specify the tissue type and developmental program of expression for each actin isotype. In order to investigate the underlying regulatory mechanisms, the human skeletal alpha-actin gene and its 5' regulatory region have been cloned and sequenced. This actin gene has seven exons; there is one large intron in the 5' untranslated region which is characteristic of the actins and many muscle-specific genes. The 5' flanking sequences are sufficient to direct tissue-specific and differentiation-regulated expression when transfected into the heterologous rat L8 myogenic cells, indicating a highly conserved regulatory system. The DNA sequence was compared to that of other actin genes, and several regions of sequence similarity were identified, particularly within regions known to be important for gene expression. Most notable among the conserved sequences are the CC(A/T rich)6GG (CArG box) motifs which have demonstrated interactions with trans-acting transcriptional factors. This same motif has been identified in several other genes and in some also serves as a binding site for transcription regulatory factors.

Actins↗
PubMed2005

PAP IB, a new member of the Reg gene family: cloning, expression, structural properties, and evolution by gene duplication.

Reg proteins are expressed in various organs and are involved in cancers and neurodegenerative diseases. They display a typical C-type lectin-like domain but possess additional highly conserved amino acids. By studying human databases and Expressed Sequence Tags library, we identified a new member called PAP IB. Using probabilistic approaches, we established a phylogenetic tree of eighteen Reg proteins. The dendogram showed that they constitute a superfamily composed of three distinct families (FI to FIII) of paralogues that resulted from duplication. We therefore focused on two proteins, REG Ialpha and PAP IB, belonging to the more closely related FI and FII families, respectively. REG Ialpha and PAP IB share 50% sequence identity. After cloning PAP IB, however, we found that it was expressed almost only in pancreas, unlike REG Ialpha, whose expression is ubiquitous. In addition, by building a model of the structure of PAP IB based on the X-ray structure of REG Ialpha, we observed that the two proteins displayed distinctive surface charge distribution, which may lead to different ligands binding. In spite of their common fold that should result in closely related functions, REG Ialpha and PAP IB are a good example of duplication and divergence, probably with the acquisition of new functions, thus participating in the evolution of the protein repertoire.

Amino Acid Sequence↗
PubMed1989

Apolipoprotein E*3-Leiden allele results from a partial gene duplication in exon 4.

The apolipoprotein E3-Leiden variant has been shown to be associated with familial dysbetalipoproteinemia (FD) in a dominant manner (Havekes et al., Hum Genet 1986;73:157-163). Applying the polymerase chain reaction technique, we have cloned and sequenced relevant parts of both APOE alleles of the original proband. In exon 4 of the E*3-Leiden allele a partial gene duplication encompassing 21 nucleotides was found, leading to a tandem repeat of the codons 120-126 or 121-127. Using an E3-Leiden mutation specific oligonucleotide probe, the same mutation was found in two additional independently ascertained FD patients with an E3E3 phenotype based on isoelectric focusing. The E*3-Leiden mutation will be useful in the elucidation of the etiology of dominantly inherited forms of FD.

Amino Acid Sequence↗
PubMed2000

Effects of S100A1 and S100B on microtubule stability. An in vitro study using triton-cytoskeletons from astrocyte and myoblast cell lines.

S100A1 and S100B are members of a multigenic family of Ca(2+)-binding proteins of the EF-hand type highly abundant in astrocyte and striated muscle cells that have been implicated in the Ca(2+)-dependent regulation of several intracellular activities including the assembly and disassembly of microtubules and type III intermediate filaments. In the present work we tested S100A1 and S100B for their ability to cause microtubule and/or intermediate filament disassembly in situ using triton-cytoskeletons obtained from U251 glioma cells and rat L6 myoblasts. Our results indicate that: (i) both proteins cause a Ca(2+)-dependent disassembly of cytoplasmic microtubules in a dose-dependent manner; (ii) the S100A1- and S100B-inhibitory peptide, TRTK-12, blocks the S100A1 and S100B effects on microtubules; (iii) S100A1Delta88-93, an S100A1 mutant lacking the C-terminal extension, does not affect microtubule stability; and (iv) no obvious S100A1- or S100B-dependent intermediate filament disassembly could be observed under the experimental conditions used in the present study, but S100A1- and S100B-dependent microtubule disassembly results in a tendency of vimentin intermediate filaments to aggregate into bundles and/or to condense. Together, these results suggest that S100A1 and S100B probably cause microtubule disassembly by interacting with the microtubule wall, and that the two proteins do not affect intermediate filament stability via interaction with preformed intermediate filaments, in agreement with previous biochemical investigation. Our present data lend support to the possibility that S100A1 and S100B might have a role in the in vivo regulation of the state of assembly of microtubules in a Ca(2+)-regulated manner and, potentially, on microtubule-based activities in astrocytes and myoblasts. Also, these data suggest that the both S100 proteins use their C-terminal extension for interacting with microtubules.

Animals↗
PubMed2002

A survey of gene expression and diversity in the venom glands of the pitviper snake Bothrops insularis through the generation of expressed sequence tags (ESTs).

In order to produce a global panorama of the transcriptional activity of snake venom glands and to correlate with its venom composition, we constructed a DNA complementary to RNA library from the venom glands of the Viperidae snake Bothrops insularis for the generation of expressed sequence tags (ESTs). Sequences from 610 independent clones were grouped in 297 clusters, revealing the putative identification of 210 distinct gene products. Toxin sequences correspond to 56% of all transcripts (85 clusters), being the metalloproteinases (23%) and the bradykinin-potentiating peptides (11%) the major components. This approach revealed a new highly expressed toxin similar to vascular endothelial growth factor, which was recently reported (J. Biol. Chem. 276 (2001) 39836). Among the 125 clusters matching cellular proteins, the major part represents molecules involved in gene and protein expression, notably in disulfide bond assembly, reflecting a high specialization of this tissue for toxin synthesis. An unusual representation of retrotransposon-like sequences was also found and could be related to the occurrence and diversity of many paralogous forms of toxins in the venom gland. Our B. insularis dbEST allowed the identification of the most common classes of toxins present in Viperidae venoms, which parallels the complex hemorrhagic effects evoked by the venom on the prey. In addition, it provides the first comprehensive set of reptilian gene sequences described so far.

Amino Acid Sequence↗
PubMed2001

Genetic and functional relationships between MHC and NK receptor genes.

HLA class I and NK receptors are encoded within dense clusters of immune loci. The MHC, at 6p21.3, and the complex containing the KIR loci, at 19q13.4, both feature variation in the number of genes, as well as sequence polymorphism. In addition to T cell receptors, several variable class I-related molecules interact with polymorphic NK receptors. Some of the lectin-related NK receptor genes, at 12p13.1, also have ligands belonging to the extended class I family. The expanding clusters of class I-related sequences and their receptors, some of which evolved recently, reveal further complexity in immune recognition of disease.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2002

Subcellular localization of S100A11 (S100C, calgizzarin) in developing and adult avian skeletal muscles.

S100A11 is a member of a multigenic family of Ca(2+)-modulated proteins of the EF-hand type. We studied the subcellular localization of S100A11 in developing and adult avian skeletal muscle cells by confocal laser scanning microscopy and immunogold cytochemistry to get information about possible functional roles of this protein. Analyses of alpha-actinin, S100A1 and S100B were done in parallel for comparison. Low levels of S100A11 were found in skeletal muscle cells at embryonic day (E) 8. At E12, S100A11 was found in myotubes in the form of fine dots located between Z-discs, and on the sarcolemma and its invaginations. At E15, S100A11 was found on the sarcolemma and internal membranes, likely longitudinal tubules, where the protein was co-localized in part with S100A1 and S100B. At E18 and afterwards, co-localization of the three S100 proteins on internal membranes was almost complete. No evidence for association of S100A11 with the contractile elements of the sarcomeres was obtained. Our data suggests that, like S100A1 and S100B, S100A11 might have a role in the regulation of membrane activities, probably in relation to Ca(2+) fluxes in skeletal muscle cells.

Animals↗
PubMed2003

Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: potential of predicting functional gene domains.

Recent evidence adds support to a traditional concept according to which the eukaryotic nucleus is organized into functional domains by scaffold or matrix attachment regions (S/MARs). These regions have previously been predicted to have a high potential for stress-induced duplex destabilization (SIDD). Here we report the parallel results of binding (reassociation) and computational SIDD analyses for regions within the human interferon gene cluster on the short arm of chromosome 9 (9p22). To verify and further refine the biomathematical methods, we focus on a 10 kb region in the cluster with the pseudogene IFNWP18 and the interferon alpha genes IFNA10 and IFNA7. In a series of S/MAR binding assays, we investigate the promoter and termination regions and additional attachment sequences that were detected in the SIDD profile. The promoters of the IFNA10 and the IFNA7 genes have a moderate approximately 20% binding affinity to the nuclear matrix; the termination sequences show stronger association (70-80%) under our standardized conditions. No comparable destabilized elements were detected flanking the IFNWP18 pseudogene, suggesting that selective pressure acts on the physicochemical properties detected here. In extended, noncoding regions a striking periodicity is found of rather restricted SIDD minima with scaffold binding potential. By various criteria, the underlying sequences represent a new class of S/MARs, thought to be involved in a higher level organization of the genome. Together, these data emphasize the relevance of SIDD calculations as a valid approach for the localization of structural, regulatory, and coding regions in the eukaryotic genome.

Animals↗
PubMed1998

Hydropathic analysis and mutagenesis of the catalytic domain of the cGMP-binding cGMP-specific phosphodiesterase (PDE5). cGMP versus cAMP substrate selectivity.

The mechanism of discrimination between cGMP and cAMP in the catalytic site of the cGMP-binding cGMP-specific phosphodiesterase (BTPDE5A1 or PDE5) has been investigated. A hydropathy analysis of the catalytic domains of different families of PDEs suggests that substrate selectivity of PDEs could result from the pattern of hydrophobic/hydrophilic residues in a short segment surrounding a conserved Glu that has been shown to be critical for cGMP binding in the catalytic domain of PDE5. This implies that the substrate selectivity of PDE5 could be altered by replacing the residues within this segment that are conserved in cGMP-specific PDEs with the conserved residues in the corresponding positions of cAMP-specific PDEs. The A769T/L771R, W762L/Q765Y, and W762L/Q765Y/A769T/L771R mutant PDE5s were expressed in High Five cells, and their substrate selectivities were compared with that of wild-type PDE5. The results indicate that the substrate-binding site of PDE5 contains positive elements for accommodating cGMP, as well as negative elements that discriminate against binding of cAMP, and that the cGMP/cAMP selectivity of PDE5 can be shifted 106-fold by substituting four residues of PDE5 with the residues in the corresponding positions of PDE4.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed1993

Molecular cloning, expression, and chromosomal localization of the human earliest lymphocyte activation antigen AIM/CD69, a new member of the C-type animal lectin superfamily of signal-transmitting receptors.

The activation of T lymphocytes, both in vivo and in vitro, induces the expression of CD69. This molecule, which appears to be the earliest inducible cell surface glycoprotein acquired during lymphoid activation, is involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. To determine the structural basis for CD69 function, the cDNA coding for CD69 was isolated by a polymerase chain reaction-based strategy using oligonucleotides deduced from peptide sequences of the purified protein. The isolated cDNA exhibited a single open reading frame of 597 bp coding for CD69, and predicted a 199-amino acid protein of type II membrane topology, with extracellular (COOH-terminal), transmembrane, and intracellular domains. The CD69 clone hybridized to a 1.7-kb mRNA species, which was rapidly induced and degraded after lymphocyte stimulation, consistent with the presence of rapid degradation signals at the 3' untranslated region. Transient expression of the polypeptide encoded by CD69 cDNA in COS-7 cells demonstrated that it presented properties comparable to native CD69 protein. The CD69 gene was regionally mapped to chromosome 12 p13-p12 by both somatic cell hybrid DNA analysis and fluorescence in situ hybridization coupled with GTG banding (G bands by trypsin using Giemsa). Protein sequence homology search revealed that CD69 is a new member of the Ca(2+)-dependent (C-type) lectin superfamily of type II transmembrane receptors, which includes the human NKG2, the rat NKR-P1, and the mouse NKR-P1 families of NK cell-specific genes. CD69 also has a structural homology with other type II lectin cell surface receptors, such as the T cell antigen Ly49, the low avidity immunoglobulin E receptor (CD23), and the hepatic asialoglycoprotein receptors. The CD69 protein also shares functional characteristics with most members of this superfamily, which act as transmembrane signaling receptors in early phases of cellular activation.

Amino Acid Sequence↗
PubMed2004

Diversity and relatedness among the type I interferons.

Type I interferons (IFNs) include the IFN-alpha family of subtypes, IFN-beta, IFN-omega, IFN-tau, IFN-kappa, IFN-lambda, and IFN-zeta. IFN genes lack introns and encode secretory signal peptide sequences that are proteolytically cleaved prior to secretion from the cell. In contrast to the approximately 50% amino acid sequence identity among the human IFN-alpha subtypes, human IFN-alphas share approximately 22% identity with human IFN-beta and 37% identity with human IFN-omega. Many of the conserved residues among the type I IFNs are implicated in receptor recognition and structural integrity. This report provides an update on the gene annotations for the mouse and human IFN gene clusters on chromosome 4 and 9, respectively, with accompanying amino acid sequence alignments. Based on sequence identities, a phylogenic tree analysis for the different mammalian Type I IFNs is also presented, showing the high degree of relatedness among these IFNs. Notably, sequence alignment of the different human and mouse IFN promoter regions reveals different signature patterns for transcription factor binding sites, implying different inducers might differentially activate the transcription of the different IFNs.

Amino Acid Sequence↗
PubMed1989

Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae.

We have investigated HO endonuclease-induced double-strand break (DSB) recombination and repair in a LACZ duplication plasmid in yeast. A 117-bp MATa fragment, embedded in one copy of LACZ, served as a site for initiation of a DSB when HO endonuclease was expressed. The DSB could be repaired using wild-type sequences located on a second, promoterless, copy of LACZ on the same plasmid. In contrast to normal mating-type switching, crossing-over associated with gene conversion occurred at least 50% of the time. The proportion of conversion events accompanied by exchange was greater when the two copies of LACZ were in direct orientation (80%), than when inverted (50%). In addition, the fraction of plasmids lost was significantly greater in the inverted orientation. The kinetics of appearance of intermediates and final products were also monitored. The repair of the DSB is slow, requiring at least an hour from the detection of the HO-cut fragments to completion of repair. Surprisingly, the appearance of the two reciprocal products of crossing over did not occur with the same kinetics. For example, when the two LACZ sequences were in the direct orientation, the HO-induced formation of a large circular deletion product was not accompanied by the appearance of a small circular reciprocal product. We suggest that these differences may reflect two kinetically separable processes, one involving only one cut end and the other resulting from the concerted participation of both ends of the DSB.

DNA Repair↗
PubMed1993

A gene with specific and global effects on recombination of sequences from tandemly repeated genes in Saccharomyces cerevisiae.

The preservation of sequence homogeneity and copy number of tandemly repeated genes may require specific mechanisms or regulation of recombination. We have identified mutations that specifically affect recombination among natural repetitions in the yeast Saccharomyces cerevisiae. The rrm3 mutation stimulates mitotic recombination in the naturally occurring tandem repeats of the rDNA and copper chelatin (CUP1) genes. This mutation does not affect recombination of several other types of repeated genes tested including Ty elements, mating type information and duplications created by transformation. In addition to stimulating exchange among the multiple CUP1 repeats at their natural chromosomal location, rrm3 also increases recombination of a duplication of CUP1 units present at his4. This suggests that the RRM3 gene may encode a sequence-specific factor that contributes to a global suppression of mitotic exchange in sequences that can be maintained as tandem arrays.

Biological Evolution↗
PubMed2002

High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants.

We present a method for high-resolution genetic mapping that takes advantage of the ordered set of viable gene deletion mutants, which form a set of colinear markers covering almost every centimorgan of the Saccharomyces cerevisiae genome, and of the synthetic genetic array (SGA) system, which automates the construction of double mutants formed by mating and meiotic recombination. The Cbk1 kinase signaling pathway, which consists minimally of CBK1, MOB2, KIC1, HYM1, and TAO3 (PAG1), controls polarized morphogenesis and activation of the Ace2 transcription factor. Deletion mutations in the Cbk1 pathway genes are tolerated differently by common laboratory strains of S. cerevisiae, being viable in the W303 background but dead in the S288C background. Genetic analysis indicated that the lethality of Cbk1 pathway deletions in the S288C background was suppressed by a single allele specific to the W303 background. SGA mapping (SGAM) was used to locate this W303-specific suppressor to the SSD1 locus, which contains a known polymorphism that appears to compromise SSD1 function. This procedure should map any mutation, dominant or recessive, whose phenotype is epistatic to wild type, that is, a phenotype that can be scored from a mixed population of cells obtained by germination of both mutant and wild-type spores. In principle, SGAM should be applicable to the analysis of multigenic traits. Large-scale construction of ordered mutations in other model organisms would broaden the application of this approach.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Genetic dissection of anxiety in autoimmune disease.

Systemic lupus erythematosus (SLE), a complex multigenic disease, is characterized by hypergammaglobulinemia, autoantibody production and immune complex-type lupus nephritis. In addition to these signs and symptoms in SLE, there can be symptoms of neurological disorders, including anxiety. To clarify mechanisms governing the anxiety seen in lupus, we carried out genome-wide scans, and found that the region including interferon-alpha (IFN-alpha) on NZB chromosome 4 is significantly linked to the anxiety-like behavior seen in SLE-prone New Zealand Black (NZB) x New Zealand White (NZW) F(1) (B/W F(1)) mice. This finding was confirmed by anxiety-like performances of mice with heterozygous NZB/NZW alleles in the susceptibility region onto the NZW background. In B/W F(1) mice, neuronal IFN-alpha levels were elevated, and blockade of the micro (1) opioid receptor or corticotropin-releasing hormone receptor 1, possible downstream effectors for IFN-alpha in the brain partially overcame the anxiety-like behavior seen in the B/W F(1) mice. Consistently, neuronal corticotropin-releasing hormone levels were higher in B/W F(1) than NZW mice. Furthermore, pretreatment of micro (1) opioid receptor antagonist abolished anxiety-like behaviour seen in IFN-alpha-treated NZW mice. Anxiety is shown to be mediated by multiple mediators. Our data suggest that a genetically determined endogenous excess amount of IFN-alpha in the brain may form one aspect of anxiety-like behavior seen in SLE-prone mice.

Alleles↗
PubMed1989

Genetic factors influencing lignin peroxidase activity in Phanerochaete chrysosporium ME446.

Haploid recombinant progeny of Phanerochaete chrysosporium ME446, genome compositions of which had been defined by RFLP-mapping, vary in their idiophasic behaviour. This allowed us to formulate a model of the sequence of idiophasic activities. One component of this variation, the amount of lignin peroxidase activity, is independent of the allele distributions of the lignin peroxidase gene clusters, but correlates with the allele distribution of another locus. This locus appears to control the spread of the lignin peroxidase-active state within the idiophasic mycelial mat and may be the mating-type locus. The successful determination of linkage relied on analysis of chromosome intervals rather than linkage to single markers; this approach should be generally useful for analysing quantitative characters by RFLP mapping.

Alleles↗