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At least 1,117 records · Page 62Linked to original sources
PubMed1997

Cloning of the genes encoding two murine and human cochlear unconventional type I myosins.

Several lines of evidence indicate a crucial role for unconventional myosins in the function of the sensory hair cells of the inner ear. We report here the characterization of the cDNAs encoding two unconventional type I myosins from a mouse cochlear cDNA library. The first cDNA encodes a putative protein named Myo1c, which is likely to be the murine orthologue of the bullfrog myosin I beta and which may be involved in the gating of the mechanotransduction channel of the sensory hair cells. This myosin belongs to the group of short-tailed myosins I, with its tail ending shortly after a polybasic, TH-1-like domain. The second cDNA encodes a novel type I myosin Myo1f which displays three regions: a head domain with the conserved ATP- and actin-binding sites, a neck domain with a single IQ motif, and a tail domain with the tripartite structure initially described in protozoan myosins I. The tail of Myo1f includes (1) a TH-1 region rich in basic residues, which may interact with anionic membrane phospholipids; (2) a TH-2 proline-rich region, expected to contain an ATP-insensitive actin-binding site; and (3) a SH-3 domain found in a variety of cytoskeletal and signaling proteins. Northern blot analysis indicated that the genes encoding Myo1c and Myo1f display a widespread tissue expression in the adult mouse. Myo1c and Myo1f were mapped by in situ hybridization to the chromosomal regions 11D-11E and 17B-17C, respectively. The human orthologuous genes MYO1C and MYO1F were also characterized, and mapped to the human chromosomal regions 17p18 and 19p13.2-19p13.3, respectively.

Amino Acid Sequence↗
PubMed1997

Genetic relationships of the genes encoding the human proteasome beta subunits and the proteasome PA28 complex.

Genomic clones were obtained for the genes encoding the beta subunits of the human proteasome and for the associated proteasome activators PA28alpha and beta (PSME1 and PSME2, respectively). Fluorescence in situ hybridization was used to map the gene encoding the beta subunit PSMB3 (beta3 hs, HsC10-II) to chromosome band 2q35, PSMB2 (beta4 hs, HsC7-I) to band 1p34.2, and PSMB4 (beta7 hs, HSBpros 26) to band 1q21. Genes encoding the alpha and beta subunits of the PA28 complex were found closely linked on chromosome band 14q11.2, within 1 Mb of the beta proteasome locus PSMB5 (beta5 hs, MB1, X). These data complete the mapping of the human proteasome beta subunit loci. With the exception of the genes encoding the PSMB9 and PSMB8 (LMP2 and LMP7, respectively) subunits, the beta genes were not closely linked in the human genome. Both PSMB2 and PSMB4 mapped to a region of chromosome 1 that is proposed to be paralogous to other regions of the human genome where beta proteasome genes map: chromosome 6 containing the major histocompatibility complex (MHC) and chromosome 9. The independent regulation of expression of all of these genes, implied by this study, is consistent with a key role for proteasome assembly in coordination of the complex.

Animals↗
PubMed2002

Functional and structural characterization of the human gene BHLHB5, encoding a basic helix-loop-helix transcription factor.

The genes encoding basic helix-loop-helix (bHLH) transcription factors have been implicated in many aspects of neural development, including cell growth, differentiation, and cell migration. Using both genomic and cDNA mouse and human clones encoding a neural-specific bHLH protein, human BHLHB5 was cloned and mapped to a region on chromosome 8q13 that segregates with Duane syndrome. Genomic sequence analysis of human BHLHB5 and mouse Bhlhb5 revealed that they contain a single exon encoding 381- and 355-amino-acid bHLH proteins, respectively. Multiple amino acid sequence alignments of the Bhlhb5 family members revealed several conserved motifs and an identical 147-amino-acid carboxy-terminal region that contains a 60-amino-acid bHLH domain. A 27-bp trinucleotide repeat (CAG)(9) encoding polyserine was found in human BHLHB5, but only one CAG was found at the corresponding position in the mouse Bhlhb5 and hamster BETA3 genes. Northern blot analysis of human BHLHB5 revealed brain-specific expression with the highest abundance in the cerebellum. Mouse Bhlhb5 can strongly repress a human PAX6 promoter.

Amino Acid Sequence↗
PubMed2000

The human anti-bullous pemphigoid monoclonal autoantibody P22 is encoded by genes of the IGHV4 and IGLV4 families.

We identified, cloned, and biochemically characterized the full-length cDNAs encoding the heavy and light chains of a human monoclonal antibody (mAb) from the Epstein-Barr virus (EBV)-cell line P22. The cell line P22, which originated from a patient with bullous pemphigoid (an autoimmune disease causing skin blistering) expressed immunoglobulin-G (IgG) with a lambda light chain. Although the variable heavy (IGHV) chain gene family could not be assigned by IGHV repertoire analysis, the determination of its nucleotide sequence demonstrated that the heavy chain of P22 belonged to the IGHV4 family. The limited IGHV4 gene usage by memory IgG, IGA and IgE-expressing cells supports the notion of the autoreactivity-associated IGHV4 genes and stresses the strong selection pressure within germinal centres towards IGHV4 family. Alignment of P22 IGHV4 cDNA sequence to germline sequences from gene databases, revealed a remarkable divergence, suggesting that the heavy chain of the P22 mAb encodes a distinct IGHV4 gene. The variable light chain (IGLV) encodes a IGLV4 gene and is 98% similar to a previously reported IGLV gene. Furthermore, fluorescent staining with the recombinant mAb showed the same reactivity to that of the native antibody. The data reported herein, (a) reveal an autoantibody encoding a distinct IGHV4 gene, (b) confirm the notion that autoantibodies preferentially use IGHV4 genes, and (c) hypothesize that somatic hypermutation within GC may be a mechanism by which autoreactive B lymphocytes escape negative selection.

Amino Acid Sequence↗
PubMed1993

Evidence for a clustered genomic organization of FAX-zinc finger protein encoding transcription units in Xenopus laevis.

Finger associated box-zinc finger proteins (FAX-ZFPs) constitute a subfamily of the many C2H2 type ZFPs in Xenopus laevis. FAX is a highly conserved protein domain connected to variable zinc finger clusters. Three different FAX-ZFPs encoding genomic fragments were isolated and subjected to a detailed structural characterization. All three exhibit a common, highly conserved exon/intron organization, with the variant zinc finger clusters organized in a single exon for each gene analysed. Two of the three genomic fragments contain a second FAX-ZFP encoding (partial) transcription unit each. Further evidence for a clustered organization of FAX-ZFP transcription units is provided by Southern blot analysis of large genomic restriction fragments separated by transverse field gel electrophoresis, and by in situ hybridization on intact chromosomes. Comparative sequence analysis of the genes isolated reveals an exceptional degree of DNA sequence conservation in both exon and intron regions in one part of the FAX encoding region, suggesting that recent gene conversion has led to the combination of these sequence elements with DNA segments including regions encoding variant zinc finger clusters. Overexpression of the FAX domain by itself or of a full-length FAX-ZFP in X. laevis embryos by means of mRNA injection does not interfere with the normal developmental program, suggesting general and not cell specific/regulatory functions for X. laevis FAX-ZFPs.

Amino Acid Sequence↗
PubMed1994

Genes encoding actin-related proteins of Drosophila melanogaster.

Recently, several laboratories have described proteins of yeasts, mammals and Drosophila melanogaster that are 35 to 55% identical to conventional actins, but, as yet, little is known about their functions. We have initiated a systematic study by using degenerate oligonucleotides specifying two highly conserved nucleotide-binding peptides of actin, in conjunction with polymerase chain reaction techniques, to isolate Drosophila genes that encode actin-related proteins. Here we summarize the isolation of four such genes and compare the sequences of the proteins that they encode. Computer searches of databases revealed that three of the encoded proteins are homologs of yeast or mammalian actin-related proteins, implying that the corresponding proteins participate in functions common to many cell types. The fourth gene encodes a novel protein that, apparently is expressed within testes. The four genes are located within the 14D, 53D, 66B and 87C subdivisions of polytene chromosomes.

Actins↗
PubMed1995

Targeted disruption of 01H1 encoding a particular H1 histone variant causes changes in protein patterns in the DT40 chicken B cell line.

Six members of the chicken H1 gene family, all of which are located in two major histone gene clusters, have been shown to encode six different protein variants. The intracellular mRNA level from one of them, 01H1, encoding the 01H1 variant composed of 218 amino acid residues, constitutes 9.9% of the total H1 mRNA in the DT40 chicken B cell line. To study the specific role of this particular H1 variant, besides its well-known functions as a linker in chromatin maintenance and as a general repressor of transcription, we used targeted integration to construct heterozygous and homozygous DT40 mutants with disruption of one and two 01H1 alleles, respectively. Analyses of the stable transfectants showed that the growth rate of DT40 was unchanged in the absence of two 01H1 alleles. Moreover, the remaining H1 genes were shown to be expressed more in these mutants than in the wild-type cell lines. Two-dimensional polyacrylamide gel electrophoresis showed that within an almost constant background in the homozygous mutants several cellular proteins newly appeared or increased, while some other proteins disappeared or decreased quantitatively. These variable proteins all differed from those that varied in DT40 mutants deprived of one of the eight chicken H2B genes, H2B-V, encoding a particular H2B variant. These results suggest that the 01H1 variant is involved in the regulation of expression of genes that encode the proteins that vary in 01H1-deleted mutants of DT40 cells.

Alleles↗
PubMed1998

An endo-1,4-beta-xylanase-encoding gene from Agaricus bisporus is regulated by compost-specific factors.

Compost is the preferred substrate for growth of the edible fungus Agaricus bisporus. Utilization of compost requires the production of enzymes involved in degradation of lignocellulolytic components. For molecular characterization of these processes we are isolating the encoding genes. By applying heterologous screening techniques, we have cloned such a gene, which is specifically induced on compost encoding an endo-1,4-beta-xylanase (xlnA) belonging to glycosyl hydrolase family 10. The gene encodes a pre-protein of 333 amino acid residues with a predicted molecular mass of 34,946 for the mature protein. The open reading frame is interrupted by ten introns of which introns 5 and 6 are separated by an exon of only two base-pairs. High expression of the xlnA gene was observed in vegetative mycelium grown on sterilized compost while xlnA messengers were not detected in fruit bodies. Addition of glucose or xylose to compost repressed xlnA expression. When glucose-grown colonies were transferred to a medium containing cellulose, xylan or xylose as sole carbon source, the organism responded by expressing xlnA at a high level for a short period. Transfer from glucose to compost yielded a much stronger and constant xlnA induction. A similar pattern of expression was found for the cel3 gene encoding a cellulase, suggesting that these genes are induced by compost-specific factors rather than by the substrates they act upon. Antiserum raised against XLNA protein, which was heterologously expressed in Escherichia coli, detected, when the fungus was grown on compost, an extracellular protein of 33 kDa with endo-xylanase activity.

Agaricus↗
PubMed1999

A second gene encoding the mouse proteasome activator PA28beta subunit is part of a LINE1 element and is driven by a LINE1 promoter.

The PMSE2 gene encodes the beta-subunit of the proteasome activator PA28 and, as shown by genomic Southern blot analysis, there probably exist four copies sharing sequence homology with PMSE2. Here, we report that in the mouse genome there exist two different chromosomal loci for PA28beta, both of which are transcribed and and which encode a functional PA28beta subunit. One of these represents the previously described PMSE2 gene possessing an intron-exon structure and a gamma interferon (IFNgamma)-inducible promoter. The second one, named PMSE2b, which we describe here, exhibits all the characteristics of an expressed retrotransposon. Our data show that the PA28beta retrotransposon is inserted into a transcriptional active LINE1 element and is driven by a LINE1 F-type monomer promoter as revealed by luciferase assays. The resulting PMSE2b mRNA encodes a protein which is indistinguishable from that encoded by the IFNgamma-inducible PMSE2 gene. Since PA28 plays an important role in major histocompatibility complex class I antigen presentation, the implications for the mouse immune system through a constitutively expressed PA28beta subunit and the biological relevance of this finding are discussed.

Animals↗
PubMed2000

Four genes encode acetylcholinesterases in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. cDNA sequences, genomic structures, mutations and in vivo expression.

We report the full coding sequences and the genomic organization of the four genes encoding acetylcholinesterase (AChE) in Caenorhabditis elegans and Caenorhabditis briggsae, in relation to the properties of the encoded enzymes. ace-1 and ace-2, located on chromosome X and I, respectively, encode two AChEs (ACE-1 and ACE-2) that present 35% identity. The C-terminal end of ACE-1 is homologous to the C terminus of T subunits of vertebrate AChEs. ACE-1 oligomerizes into amphiphilic tetramers. ACE-2 has a hydrophobic C terminus of H type. It associates into glycolipid-anchored dimers. In C. elegans and C. briggsae, ace-3 and ace-4 are organized in tandem on chromosome II, with only 356 nt and 369 nt, respectively, between the stop codon of ace-4 (upstream gene) and the ATG of ace-3. ace-3 produces only 5 % of the total AChE activity. It encodes an H subunit that associates into dimers of glycolipid-anchored catalytic subunits, which are highly resistant to the usual AChE inhibitors, and which hydrolyze butyrylthiocholine faster than acetylthiocholine. ACE-4 is closer to ACE-3 (54 % identity) than to ACE-1 or ACE-2. The usual sequence FGESAG surrounding the active serine residue in cholinesterases is changed to FGQSAG in ace-4. ACE-4 was not detected by our current biochemical methods, although the gene is transcribed in vivo. However the level of ace-4 mRNAs is far lower than those of ace-1, ace-2 and ace-3. The ace-2, ace-3 and ace-4 transcripts were found to be trans-spliced by both SL1 and SL2, although these genes are not included in typical operons. The molecular bases of null mutations g72 (ace-2), p1304 and dc2 (ace-3) have been identified.

Acetylcholinesterase↗
PubMed1999

1H NMR imaging of residual dipolar couplings in cross-linked elastomers: dipolar-encoded longitudinal magnetization, double-quantum, and triple-quantum filters.

Contrastfilters for NMR imaging of residual 1H dipolar couplings of elastomers are introduced based on dipolar-encoded longitudinal magnetization, as well as double- and triple-quantum coherences. The spin response is discussed in the initial excitation time regime for methylene, methyl, and methine protons applicable to poly(isoprene) and other elastomers, taking into account the hierarchy of dipolar couplings and the associated editing features of multiple-quantum experiments. The efficiency of these filters is investigated for a series of cross-linked poly(isoprene) samples. Spatially resolved dipolar-encoded longitudinal magnetization decays and double-quantum and triple-quantum buildup curves are presented for a phantom made of poly(isoprene) with different cross-link densities. Two-dimensional images representing residual dipolar couplings are presented using dipolar-encoded longitudinal magnetization, double-quantum, and triple-quantum contrast filters. Images from dipolar-encoded longitudinal magnetization and triple-quantum coherences show the highest resolution and contrast, respectively.

Algorithms↗
PubMed2001

MR imaging with phase encoding of intermolecular multiple quantum coherences.

Novel 2D and 3D pulse sequences producing images through the phase encoding of intermolecular multiple quantum coherences (i-MQCs) are presented. The signal acquired with these sequences is free from intermolecular zero quantum coherences (i-ZQCs) which are not phase encoded and additional phase cycling eliminates artifacts. Phase encoding during the n-quantum evolution period provides n times the resolution expected from equivalent phase encoding of the reconverted single quantum coherences. These sequences have potential applications for producing i-MQC images of biological tissues as well as nonbiological materials with substantial amounts of water.

Magnetic Resonance Imaging↗
PubMed1999

Tumor necrosis factor receptors encoded by poxviruses.

Poxviruses encode several cytokine response modifying (Crm) proteins. The Crm proteins possess sequence homology to several human proteins important in immunity. This homology and the conservation of Crm proteins among poxvirus strains suggest an immunomodulatory function that provides a survival advantage to the virus. Cowpox virus encodes several tumor necrosis factor (TNF) receptor family homologues: CrmB, CrmC, and CrmD. CrmB and CrmD encode a similar approximately 155 amino acid COOH-terminus region distal to their TNF ligand-binding portions. These C-terminus regions contain no significant homology with sequences in public databases. It is not known whether the C-terminus regions have a complementary function to the TNF ligand-binding domains, or an unrelated function. Myxoma virus, a rabbit poxvirus, encodes a protein termed T2 which is homologous to CrmB and CrmD. Deletion of the T2 gene results in decreased pathogenicity of myxoma in rabbits. T2 has also been shown to interfere with TNF-induced apoptosis in vitro. Understanding the role viral TNF receptor homologues play in altering host immune responses may suggest ways to develop specific anti-inflammatory therapeutics.

Animals↗
PubMed1997

Cloning and nucleotide sequence analysis of a Brucella abortus gene encoding an 18 kDa immunoreactive protein.

A DNA fragment encoding an approximately 18 kDa protein from Brucella abortus strain 2308 was cloned and expressed in Escherichia coli. This recombinant protein, designated BA18K, reacted in Western blot analysis with sera obtained from experimentally and naturally infected animals including mice, goats, dogs and humans. Restriction enzyme analysis of the plasmid (pBA28) encoding BA18K revealed the presence of an approximately 8.7 kbp Sau3A genomic DNA fragment within the vector and subsequent subcloning and Western blot analysis limited the region encoding BA18K to an approximately 3.0 kbp Pst 1 DNA fragment. DNA sequence analysis of this region identified an open reading frame capable of encoding a protein of 177 amino acids with a predicted relative molecular mass of 17529. Comparison of the deduced amino acid sequence of BA18K with those in the protein sequence databases yielded no homology with previously described proteins from other bacterial genera. These searches did, however, indicate that BA18K is identical to the previously described outer membrane protein (OMP) from B. abortus strain 544 designated Omp 19.

Amino Acid Sequence↗
PubMed1993

Analysis of proteins encoded by IE regions 1 and 2 of human cytomegalovirus using monoclonal antibodies generated against recombinant antigens.

The genomic region of human cytomegalovirus (HCMV) encoding the major immediate-early (IE) proteins was cloned as overlapping fragments into a prokaryotic expression vector. Three recombinant polypeptides were used as antigens to generate monoclonal antibodies specifically reactive with the proteins encoded by IE region 1 and IE region 2. At least 10 different antigenic regions were identified on the IE proteins of HCMV. One monoclonal generated against an IE-2 polypeptide of 156 amino acids (termed SMX) was found to react with a viral pentapeptide, which was also a constituent of the beta-chain of human HLA-DR. This peptide was contained in the 40-kDa (p40) protein encoded by IE region 2. This protein appeared to be an abundant product of the major IE region in infected cells at late times after infection. The putative translation initiation site for p40 was mapped to position 3348 of the IE2 sequence using monoclonal antibody SMX. It is therefore proposed that p40 consists of amino acids 242-580 encoded by the IE2 gene of HCMV (strain AD169). Neither this late protein nor any other of the IE1/IE2-encoded proteins was detectable in extracellular virions.

Amino Acid Sequence↗
PubMed1993

DNA sequence and transcriptional analyses of the region of the equine herpesvirus type 1 Kentucky A strain genome encoding glycoprotein C.

DNA sequence and transcriptional analyses were performed on the region of the equine herpesvirus type 1 (EHV-1) genome (KyA strain) (map units 0.129 to 0.152) encoding open reading frames (ORFs) 15 and 16. ORF16 encodes a homolog of glycoprotein C of HSV-1 (herpes simplex virus type 1), while ORF15 corresponds in position to HSV-1 UL45 but exhibits no significant homology at the amino acid level. Sequence analyses revealed that the EHV-1 gC ORF of 468 amino acids and ORF15 of 227 amino acids mapped at nucleotides (nt) 716 to 2119 and 2397 to 3077, respectively (relative to the 5' end of the BamHI recognition site at map unit 0.152). ORF15 exhibited significant homology (69% identity) at the amino acid level to the EHV-4 gene located 3' of the EHV-4 gC homolog. Sequence analyses identified potential CAAT and TATA boxes for the EHV-1 gC ORF and a TATA box for ORF15. While no consensus polyadenylation signal was detected between ORFs 15 and 16, two polyadenylation signals were detected 3' of ORF15. Northern blot and S1 nuclease analyses were used to map and characterize the gC and ORF15 mRNAs, and metabolic inhibitors were used to identify the kinetic class of these two genes. The results revealed that gC is a gamma-1 gene which encodes a 2.8-kb mRNA, while ORF15 is a gamma-2 gene encoding a 0.9-kb mRNA which is 3' coterminal with the gC transcript. The gC and ORF15 mRNAs were shown by S1 nuclease analyses to initiate approximately 34 and 26 nucleotides downstream of their respective TATA boxes and to have a common termination site 18 to 20 nucleotides downstream of a consensus polyadenylation signal. Comparative sequence analysis revealed that the KyA strain gC protein differs in only three amino acid residues from the gC protein of the EHV-1 Ab4 and T431 strains, and one of the three amino acid differences occurred within a segment of six contiguous amino acids showing high degree of hydrophilicity in the gC molecule. Further comparative sequence analysis revealed that KyA strain genome has a major deletion in the region of ORF17 which lies 5' of gC in the Ab4 strain. This finding that 1038 base pairs (bp) of the 1203-bp ORF17 is deleted indicates that ORF17 is nonessential for EHV-1 replication in cell culture. To examine the regulation of the EHV-1 gC gene, transient transfection assays using CAT (chloramphenicol acetyltransferase) reporter gene constructs of gC were performed.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1994

Cloning sequencing and expression of the gene encoding the VP2 protein of the human group B rotavirus, ADRV.

Adult diarrheal rotavirus, ADRV, is a noncultivable human group B rotavirus. A complete cDNA copy of ADRV gene segment 2 has been cloned and sequenced. Gene segment 2 contains 2844 bases and encodes one long open reading frame beginning at base 14 and terminating at base 2812. Gene 2 encodes a protein containing 933 amino acids with a calculated molecular weight of 105.6 kDa and a pl of 5.5. The gene 2 polypeptide contains significant homology with the VP2 protein which comprises the core of group A rotavirus strains. The gene 2 protein has been expressed in a rabbit reticulocyte lysate in vitro and is identical in molecular mass with a protein previously demonstrated to be present on iodinated EDTA-treated virions and from in vitro translations of total ADRV mRNA. A recombinant baculovirus containing gene segment 2 has been constructed and used to express the encoded VP2 equivalent protein. The expressed VP2 protein is immunoprecipitable by hyperimmune anti-ADRV serum, porcine group B infection serum, and human convalescent serum but not by hyperimmune serum to group A rotavirus. Our results suggest that ADRV gene segment 2 encodes the VP2 protein equivalent to group A rotavirus strains present in the core of the group B virion.

Amino Acid Sequence↗
PubMed1995

Varicella-zoster virus open reading frame 1 encodes a membrane protein that is dispensable for growth of VZV in vitro.

Varicella-zoster virus (VZV) encodes 69 unique open reading frames, 5 of which do not have herpes simplex virus type 1 (HSV-1) homologs. One of the 5, ORF1, is predicted to encode a protein of 108 amino acids. We identified a 470-base RNA corresponding to ORF1. To determine whether ORF1 encodes a protein, an 11-amino-acid epitope was inserted in frame after the ninth codon of the ORF1 open reading frame. A recombinant virus carrying this epitope expressed a protein that was immunoprecipitated with monoclonal antibody to the epitope. The ORF1 protein was detected in the membrane of infected cells. The size of ORF1 protein expressed in VZV-infected cells was slightly larger than the size expressed by translation in vitro, suggesting that the protein may undergo post-translational modification in infected cells. Insertion of stop codons immediately before the epitope in the ORF1 gene resulted in a recombinant virus that did not express ORF1 protein and that was not growth impaired in cell culture. Thus, ORF1 encodes a protein that localizes to the membrane of VZV-infected cells and that is dispensable for virus growth in vitro.

Antibodies, Monoclonal↗