Cloning and sequencing of an endoglucanase (end1) gene from Butyrivibrio fibrisolvens H17c

Summary The nucleotide sequence of a 2.8 kb DNA segment containing an endoglucanase gene (end1) from Butyrivibrio fibrisolvens H17c was determined. The B. fibrisolvens H17c gene was expressed from its own regulatory region in Escherichia coli and three putative consensus promoter sequences were identified upstream of a ribosome binding site and an ATG start codon. The complete amino acid sequence (547 residues) was deduced and homology with the Clostridium thermocellum ME gene product (EGE) was demonstrated. The endoglucanase contained a typical amino-terminal signal sequence and five repeated sequences (PDPTPVD) between amino acids 412–447. The endoglucanase showed relatively high endoglucanase activity against endoglucanase-specific substrates with 1-4 linkages but low activity against xylan and an exoglucanasespecific substrate, p-nitrophenyl--d-cellobioside.Abbreviations CMCase carboxymethylcellulase - DNS dinitrosalicylic acid - end1 gene coding for End1 - End1 endo-1,4--glucanase - nt nucleotide - ORF open reading frame     

Sequence and diversity of rhesus monkey T-cell receptor β chain genes

We have sequenced 23 rearranged T-cell receptor chain (Tcrb) cDNA clones derived from peripheral blood lymphocytes (PBL) of a rhesus monkey. All of the clones have a variable-diversity-joining-constant (V-D-J-C) rearrangement similar to that of humans. Two rhesus constant (C) region genes were found, each closely reasembling human Cb 1 and 2. All of the rhesus J region sequences align well with ten of the 13 reported human J regions. 17 of the 23 rhesus V region sequences could be assigned to families homologous with eight different human families (Vb 1, 2, 6, 7, 8, 9, 13, and 14). The remaining six V region sequences are more distantly related to human Vb 1 and 13. Thus, the organization and sequences of studied rhesus Tcrb chains resemble human homologs. An evolutionary tree analysis revealed paralogous relationships between specific members of the rhesus and human V region families. Analysis of synonymous and nonsynonymous nucleotide sequence differences indicated that the evolution of the presumed major histocompatibility complex (MHC)-contact regions of the Tcrb chains is less constrained than that of the framework regions.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M60529-M60554.     

Structure and evolution of the promoter regions of the DQA genes

HLA-DQ antigens are unique among the class II antigens in that their chains are highly polymorphic. In the present study, we characterized the general structure of the promoter regions of the DQA genes derived from different DR haplotypes and defined their nucleotide sequence polymorphisms. The promoter of each DQA1 allele contains three sequence motifs which are not present in non-DQA related class II genes: one identical to a tumor necrosis factor (TNF) response element, one similar to an NFB binding element, and one similar to a W motif. All DQA alleles lack TATA and CCAAT boxes in the proximal promoter region but carry other sequence elements characteristic of MHC class II genes, including S, X, X2, and Y boxes, and a pyrimidine-rich tract upstream of the X box. Nucleotide sequence polymorphisms among the various DQA1 alleles were noted within the promoter region, with some of the differences mapping within, or close to, regulatory elements that are important for the expression of MHC class II genes. All DQA1 alleles carry an unrearranged, full length, Alu-Sx related repeat immediately upstream of the proximal promoter region. This repeat was not present in the DQA2 (DXA) genes analyzed, confirming that DQ locus duplication probably occurred before integration of the Alu repeat into the primordial DQA1 locus, some 31–43 million years (myr) ago. The DQA2 promoter region is highly conserved between DR4 and DR3 haplotypes, with the degree of conservation exceeding that expected from the neutral mutation rate.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence data base and have been assigned the accession numbers M97 454-M97 464. Correspondence to: E. Morzycka-Wroblewska.     

Genetic differentiation at the 3'UTR of PROS-Ag25: a cDNA homologue of Drosophila melanogaster proteasome subunit PROS-Dm25 in the malaria vector Anopheles gambiae

The Anopheles gambiae cDNA encoding the homologue of the Drosophila melanogaster proteasome PROS-Dm25 was identified and analysed in terms of nucleotide sequence, and chromosomal localisation. In the 3 untranslated region, a GA-rich sequence was mapped which was found to be widely polymorphic among taxa belonging to the A. gambiae complex.     

Molecular Basis of Mucopolysaccharidosis Type IIIB in Emu (Dromaius novaehollandiae): An Avian Model of Sanfilippo Syndrome Type B<

Sanfilippo syndrome type B, or mucopolysaccharidosis (MPS) IIIB, is an autosomal recessive disease caused by a deficiency of lysosomal α-N-acetylglucosaminidase (NAGLU). In Dromaius novaehollandiae (emu), a progressive neurologic disease was recently discovered, which was characterized by NAGLU deficiency and heparan sulfate accumulation. To define the molecular basis, the sequences of the normal emu NAGLU cDNA and gene were determined by PCR-based approaches using primers for highly conserved regions of evolutionarily distant NAGLU homologues. It was observed that the emu NAGLU gene is structurally similar to that of human and mouse, but the introns are considerably shorter. The cDNA had an open reading frame (ORF) of 2259 bp. The deduced amino acid sequence is estimated to share 64% identity with human, 63% with mouse, 41% with Drosophila, 39% with tobacco, and 35% with the Caenorhabditis elegans enzyme. Three normal and two affected emus were studied for nucleotide sequence covering the entire coding region and exon–intron boundaries. Unlike the human gene, emu NAGLU appeared to be highly polymorphic: 19 variations were found in the coding region alone. The two affected emus were found to be homozygous for a 2-bp deletion, 1098-1099delGG, in exon 6. The resulting frameshift predicts a longer ORF of 2370 bp encoding a polypeptide with 37 additional amino acids and 387 altered amino acids. The availability of mutation screening in emus now permits early detection of MPS IIIB in breeding stocks and is an important step in characterizing this unique, naturally occurring avian model for the development of gene transfer studies.     

3-Hydroxy-3-methylglutaryl coenzyme A lyase (HL): cloning and characterization of a mouse liver HL cDNA and subchromosomal mapping of the human and mouse HL genes

3-Hydroxy-3-methylglutaryl coenzyme A lyase (HL) is a homodimeric mitochondrial matrix enzyme that catalyzes the last step of ketogenesis. Using a human HL cDNA as a probe, we isolated a 1.4-kb mouse HL cDNA (HLM) from a mouse liver library and extended the sequence in the 5 direction, using RACE PCR to include the complete coding sequence. The nucleotide sequence of the mouse HL coding region is 85.7% identical to human HL, and 52.6% to Ps. mevalonii HL. Peptide identities of 87.4% and 54.3% respectively were observed. Southern analysis of 29 strains of laboratory mice and of Mus spretus revealed a total of about 25 kb of hybridizing fragments and three polymorphic fragments in both EcoRI and HindIII digestions. The mouse HL locus (Hmgcl) was localized on Chromosome (Chr) 4: Pmv-19-12.6±3.6 cM-Hmgcl-7.3±2.3 cM-Xmv-8-1.5±1.0 cM-Gpd1. The human HL locus (HMGCL) was mapped to distal Chr 1p by analysis of a human-hamster hybrid cell panel and by in situ hybridization.     

Induction of a Streptomyces cacaoi β-lactamase gene cloned in S. lividans

Summary The previously cloned class A -lactamase gene (bla) of Streptomyces cacaoi was shown to be inducible by -lactam compounds in the host organism S. lividans. A regulatory region of 2.75 kb was identified and the nucleotide sequence determined. It contained four open reading frames (ORFs) of which only two were complete and required for induction. ORF1-ORF2 exerted a positive regulatory effect on the expression of bla. Inactivation of ORF1 or of ORF2 resulted not only in the loss of induction, but also in a 30- to 60-fold decrease in the basal (non-induced) level of -lactamase production. ORF1 codes for a DNA-binding protein related to the AmpR repressor/activator, which controls the expression of ampC (class C -lactamase) genes in several Enterobacteria.     

The human factor H-related gene 2 (FHR2): structure and linkage to the coagulation factor XIIIb gene

The human factor H-related gene 2 (FHR2) encodes a serum protein structurally and immunologically related to complement factor H. We describe the isolation and genomic organization of the human FHR2 gene from a yeast artificial chromosome library. The FHR2 gene is organized in five exosn and span about 7 kilobases (kb) of human genomic DNA. A comparison with the corresponding cDNA sequence (clone DDESK59) shows that the analyzed FHR2 gene has a deleted region within exon 4. A new splice acceptor site created in the truncated exon indicates that the analyzed gene could be translated to a truncated protein. Further, we demonstrate that the genes for FHR2 and subunit of coagulation factor XIII are located in the same 165 kb YAC DNA. Thus, the three structurally related genes FXIIIb, FHR2, and factor H are linked on human chromosome 1 in the regulators of complement activiation (RCA) gene cluster. The physical linkage of the FHR2 and the factor H genes provides additional evidence for a close relatedness of complement factor H and the factor H-related proteins. The linkage and the almost exclusive organization in short consensus repeat-containing domains indicates a close evolutionary relationship of the FXIIIb, FHR2, and factor H genes.The nucleotide sequence data reported in this paper have been submitted to the EMBL and GenBank nucleotide sequence databases and have been assigned the accession number X86564 (exon 1), X86565 (exon 2), X86566 (exon 3 and 4), and X86567 (exon 5)     

Molecular cloning and sequence analysis of bovine T-cell receptor γ and δ chain genes

Nine bovine T-cell receptor (Tcr) chain (Tcrg) and three Tcr chain (Tcrd) cDNA clones were isolated from the cDNA libraries constructed from peripheral blood lymphocytes and thymocytes. Of nine Tcrg cDNA clones, only four were rearranged and contained specific V, J, and C gene segments, but the remaining five contained specific J and C or only C gene segments without the V gene segment. Three kinds of Tcrg-C, which were highly related at the nucleotide and amino acid levels, were found and designated as Tcrg-C1, Tcrg-C2, and Tcrg-C3. Compared with human and mouse Tcrg-C, bovine Tcrg-C sequences are much longer, with about 27–55 amino acids corresponding to the hinge and connector regions, where the characteristic repetitive 5-amino acid motif (TTEPP or TTKPP) exists in sheep Tcrg-C as previously reported. From three Tcrd cDNA clones, two Tcrd-V and three Tcrd-J segments were isolated. The nucleotide and deduced amino acid sequences of bovine Tcrd-C, especially the transmembrane and cytoplasmic domains, are well conserved among species. As in bovine Tcrg-C, diversity of amino acid residues in the Tcrd-C region is concentrated in the hinge regions. Southern blot analysis showed that there are at least three Tcrg-C genes and one Tcrd-C gene in the bovine genome. The analysis also revealed the presence of Tcrg-C- and Tcrd-C-associated restriction fragment length polymorphisms among bovine breeds.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers D90409-20.     

Cloning and characterization of a novel NK cell-specific serine protease gene and its functional 5′-flanking sequences

Rat natural killer cell Met-ase-1 (RNK-Met-1) is a 30 000 M _r serine protease (granzyme) found in the cytolytic granules of CD3- large granular lymphocytes (LGL) with natural killer (NK) activity. To characterize the genomic sequences responsible for the CD3- LGL-restricted expression of this gene, we screened a rat genomic library with RNK-Met-1 cDNA, and obtained bacteriophage clones that contained the RNK-Met-1 gene. The RNK-Met-1 gene comprises 5 exons and spans approximately 5.2 kilobases (kb), exhibiting a similar structural organization to a class of CTL-serine proteases with protease catalytic residues encoded near the borders of exons 2, 3, and 5. The 5-flanking region of the RNK-Met-1 gene contains a number of putative promoter and enhancer regulatory elements and shares several regions of homology with the 5-flanking region of the mouse perforin gene. We have prepared nested deletions from approximately 3.3 kb of the 5-flanking region of the RNK-Met-1 gene, and inserted these upstream of the chloramphenicol acetyltransferase (CAT) reporter gene. These 5-flanking RNK-Met-1-CAT constructs were transiently transfected into rat LGL leukemia, T-lymphoma, and basophilic leukemia cell lines.The nucleotide sequence data reported in this Papershave been submitted to the EMBL/GenBank nucleotide sequence database and have been assigned the accession number L38482.     

Structure of the mouse 3-Methyladenine DNA Glycosylase gene and exact localization upstream of the α-globin gene cluster on Chromosome 11

In this paper we describe the genomic organization of the mouse 3-Methyladenine DNA Glycosylase (MPG) gene and localize three putative regulatory elements around this gene. The MPG gene plays a key role in the excision repair of methylated adenine residues and has been localized upstream of the -globin gene cluster in human and mouse. The human MPG gene has been fully characterized, whereas up to now only the cDNA sequence of the mouse MPG gene had been published. Here, we describe a detailed restriction map, the intron/exon structure, the CpG-rich putative promoter sequence, and the exact localization of the mouse MPG gene with respect to the murine -globin gene cluster. Our analysis reveals a remarkable different exon/intron structure of the mouse MPG gene compared with its human homolog. Two prominent DNase hypersensitive sites (HSS) were found 0.1 and 1.5 kb upstream of the coding sequence. In addition to these elements, an erythroid prominent HSS was mapped at the intron/exon boundary of the last exon. The characterization and localization of the MPG gene in mouse makes it now possible to carry out transgenic and gene targeting experiments and are essential to understand the control of gene expression of the MPG gene in particular and of the whole region in general.The nucleotide sequence data reported in this paper will be submitted to Genbank.     

Sequence and diversity of bovine T-cell receptor β-chain genes

The nucleotide sequences of 38 T-cell receptor (Tcr) -chain cDNA clones which were isolated from a cDNA library (2 × 10⁶ plaques) constructed from bovine peripheral blood lymphocytes were determined. Of 38 cDNA clones, 22 were rearranged and contained the functional variable (V) gene segments. These clones were tentatively divided into nine Tcrb-V gene families which correspond to the human Tcrb-V family. Among them, a Tcrb-V12 gene segment was isolated from 9 out of 22 clones, suggesting that this Tcrb-V family was expressed in the bovine peripheral blood lymphocytes. Two different constant (C) geen segments were found, and both C regions were composed of 178 amino residues. The amino acid sequences of bovine Tcrb-C regions are approximately 80%–82%, 78%, and 78% similar to those from human, mouse, and rabbit, respectively. To estimate Tcrb-V-associated restriction fragment length polymorphisms (RFLPs), Southern blot analysis was performed using liver DNAs from four bovine breeds, Holstein, Angus, Hereford, and Japanese Black. However, no significant difference was observed among genomic DNAs of Tcrb-V loci from these four breeds.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers D90121-40. Address correspondence and offprint requests to: N. Ishiguro.     

Structure of tumor necrosis factor-alpha haploblocks in European populations

DNA variants in the tumor necrosis factor-α (TNF) and linked lymphotoxin-α genes, and specific alleles of the highly polymorphic human leukocyte antigen B (HLA-B) gene have been implicated in a plethora of immune and infectious diseases. However, the tight linkage disequilibrium characterizing the central region of the human major histocompatibility complex (MHC) containing these gene loci has made difficult the unequivocal interpretation of genetic association data. To alleviate these difficulties and facilitate the design of more focused follow-up studies, we investigated the structure and distribution of HLA-B-specific MHC haplotypes reconstructed in a European population from unphased genotypes at a set of 25 single nucleotide polymorphism sites spanning a 66-kilobase long region across TNF. Consistent with the published data, we found limited genetic diversity across the so-called TNF block, with the emergence of seven common MHC haplotypes, termed TNF block super-haplotypes. We also found that the ancestral haplotype 8.1 shares a TNF block haplotype with HLA-B*4402. HLA-B*5701, a known protective allele in HIV-1 pathogenesis, occurred in a unique TNF block haplotype.     

Molecular analysis of the gene cluster involved in cephalosporin biosynthesis from Lysobacter lactamgenus YK90

Determination of the nucleotide sequence downstream from the Lysobacter lactamgenus pcbC gene encoding isopenicillin N synthase revealed that five open-reading frames (ORF) including the pcbC gene were tightly linked in the same orientation. Each ORF has the remarkable feature of the protein-coding frame in the DNA sequence with a high G + C content. Expression in Escherichia coli and a comparison of the deduced amino acid sequences with published sequences showed that the gene cluster contained a deacetoxycephalosporin C synthetase (DAOCS) gene (cefE), an ORF having homology with the Cephalosporium acremonium DAOCS/deacetylcephalosporin C synthetase gene (cefEF), an isopenicillin N epimerase gene(cefD), and a -lactamase gene. The gene order was pcbC-cefE-ORF3-cefD--lactamase.