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PubMed1985

Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli.

DNA polymerase I of Escherichia coli provides an excellent model for the study of template-directed enzymatic synthesis of DNA because it is a single subunit enzyme, it can be obtained in large quantities and the three-dimensional structure of the polymerizing domain (the Klenow fragment) has recently been determined (Ollis et al., 1985). One approach to assigning functions to particular portions of the structure is to correlate the altered enzymatic behavior of mutant forms of DNA polymerase I with the change in the primary sequence of the protein. Towards this end we have developed a rapid procedure for mapping any polA mutation to a region no larger than 300 base-pairs within the polA gene. Two series of polA deletion mutants with defined end-points were constructed in vitro and cloned into bacteriophage lambda. These phages can then be used to map precisely E. coli polA mutants. Twelve polA- alleles have been mapped in this way and for nine of them the nature of the mutational change has been determined by DNA sequence analysis. Two of the mutations, polA5 and polA6, which affect the enzyme-DNA interaction, provide evidence for the location of the DNA binding region on the polymerase three-dimensional structure.

Base Sequence↗
PubMed1990

A physical-genetic map of the lipid-containing bacteriophage PR4.

A physical map of the bacteriophage PR4 genome was constructed which includes 59 sites for 10 restriction endonucleases. The average size of the phage PR4 genome estimated from the sum of DNA fragments generated with the restriction endonucleases Hphl, Mnll, Bgll, AlwNl, and BstXl is 15,170 +/- 240 bp. A collection of recombinant plasmids containing restriction fragments of PR4 DNA generated with Bgll, Hphl, Mnll, and Xmnl inserted into either the low copy number plasmid vector pHSG575 or the high copy number plasmid vector pUC19 was constructed. This collection of recombinant plasmids represents roughly 93% of the PR4 genome. We also constructed a bank of 136 recombinant plasmids containing PR4 DNA fragments resulting from Hpall partial digestion. We have localized 13 genes on the phage PR4 genome through marker rescue with these phage DNA clones. These genes include the structural genes for the major capsid protein (P2) and a nonstructural protein (P6A) implicated in virus assembly.

Alleles↗
PubMed1992

Nucleotide sequence and genetic map of cowpea severe mosaic virus RNA 2 and comparisons with RNA 2 of other comoviruses.

We report the nucleotide sequence of cowpea severe mosaic comovirus (CPSMV) genomic RNA 2. The molecule is composed of 3732 nucleotide (nt) residues, exclusive of the polyadenylate at the 3' end. Only one of the six reading frame registers has a long open reading frame, from nt 255 to nt 3260 in the polarity of encapsidated RNA and corresponding to a polyprotein of 1002 amino acid residues (aa). As has been reported for other comoviruses, a second in-frame AUG, at nt position 531, apparently also initiates translation, at least in vitro. Multiple alignments of the deduced CPSMV polyprotein aa sequence with those of bean pod mottle comovirus (BPMV), cowpea mosaic comovirus (CPMV), and red clover mottle comovirus (RCMV) were consistent with a similar size for each of the three genes: the putative movement protein, beginning at the second in-frame AUG, the large coat protein (L), and the small coat protein. Identical nucleotide sequences in the terminal noncoding regions of RNA 2 of the four viruses are limited to 9 nt at the 5' end and the 3' polyadenylate. However, extensive similarities in sequence and potential structure were found. For all three genes and the 5' untranslated region, CPSMV and BPMV are more similar to each other than either is to CPMV or RCMV, the last two being similar to each other. Observed similarities predict that both cleavage sites in the CPSMV RNA 2 polyprotein are at glutamine-serine dipeptides. A sequence of 16 aa at the amino terminus of L, determined by automated Edman degradation, matched a region of the deduced aa sequence in the polyprotein and is consistent with cleavage at the predicted glutamine-serine dipeptide.

Amino Acid Sequence↗
PubMed1980

The genome-linked protein of picornaviruses. VII. Genetic mapping of poliovirus VPg by protein and RNA sequence studies.

The poliovirus genome-linked protein (VPg) has been subjected to radiochemical microsequence analysis. Sequence studies of virion RNA by a modification of Sanger's dideoxy method have revealed a base sequence corresponding to the amino acid analysis. This result proves that VPg is virus-encoded. The RNA sequence has allowed us to predict the total amino acid sequence of VPg and part of its precursor. VPg is, at most, 27 amino acids long. It maps within the 3' terminal segment of the viral genome that encodes the precursor polypeptide NCVP1b for the virus-specific RNA polymerase NCVP4.

Amino Acid Sequence↗
PubMed1982

The use of unideterminant fragments of ferredoxin in the genetic mapping of determinant specificity of the immune response.

The ferredoxin (Fd) molecule is a small non-mammalian immunogenic protein containing 55 amino acid residues with only two major antigenic determinants located with the NH2-terminal heptapeptide and the COOH-terminal pentapeptide. Selective enzyme cleavages of Fd with either trypsin or carboxypeptidase A result in the inactivation of the antigenic determinants by the removal of a tripeptide at the NH2-terminal and two amino acid residues at the COOH-terminal, effectively leaving 52 and 53 amino acid fragments respectively, each containing a single antigenic determinant. Fd digested with both enzymes yielded a 50 amino acid peptide with both determinants inactivated. Purity of these digests was assessed using monoclonal antibodies in standard and antigen-blocking ELISAs. The doubly digested peptide had virtually no reactivity with anti-Fd sera, reconfirming that the central cysteine-rich region is serologically silent. It was found that the sum of the reactivities of the N- and C-determinant-bearing peptides as equal to that of the native Fd and that the ratio of the reactivities could be used to assess determinant selectivity in the response to Fd in congenic recombinant strains of mice. This method was used in mapping the determinant selectivity in the antibody response to the MHC of mice to the left of the I-B subregion. Use of the B10.HTT strain indicated that separate genes mapping to the same subregion code for the magnitude of the antibody response and the determinant selectivity of the response.

Amino Acid Sequence↗
PubMed1980

Genetic mapping of the hemochromatosis locus on chromosome six.

The purpose of this paper is to report a pedigree with hereditary hemochromatosis in which a recombination between the HLA-A and B loci occurred. Both the maternal and paternal HLA-A3, B7 haplotypes were carrying an allele for hemochromatosis. The A3, B12 haplotype of the proband was a recombinant of the maternal A3, B7 and A28, B12 haplotypes. The hemochromatosis locus segregated with the HLA-A locus and not with the HLA-B locus. Thus, the hemochromatosis locus maps in close proximity to the HLA-A locus.

Adult↗
PubMed1992

Physical and genetic mapping of cloned ribosomal DNA from Toxoplasma gondii: primary and secondary structure of the 5S gene.

The ribosomal DNA (rDNA encoding rRNA) of the obligately intracellular protozoan parasite, Toxoplasma gondii, was identified, cloned, physically mapped, its copy number determined, and the 5S gene sequenced. Using total RNA as a probe, a collection of recombinant lambda phages containing copies of rDNA were isolated from a lambda 2001 tachyzoite genomic library. Northern gel hybridization confirmed specific homology of the 7.5-kb rDNA unit, subcloned into pTZ18R, to T. gondii rRNA. The mapped rDNA found in pTOX1 contained small ribosomal subunit (SS; 18S)- and large ribosomal subunit (LS; 26S)-encoding genes localized using intragenic heterologous probes from the conserved sequences of the SS (18S) and LS (28S) Xenopus laevis genes. the physical mapping data, together with partial digestion experiments and Southern gel hybridization, confirmed a 7.5-kb rDNA unit arranged in a simple head-to-tail fashion that is tandemly repeated. We estimated the rDNA repeat copy number in T. gondii to be 110 copies per haploid tachyzoite genome. Parts of the SS gene and the complete 5S gene were sequenced. The 5S gene was found to be within the rDNA locus, a rare occurrence found only in some fungi and protozoa. Secondary-structure analysis revealed an organization remarkably similar to the 5S RNA of eukaryotes.

Animals↗
PubMed1990

Identification and genetic mapping of proteins encoded in the fimbrial subunit gene region of Bacteroides nodosus.

The fimbriae produced by the anaerobic bacterium Bacteroides nodosus are important in the pathogenesis of ovine foot rot. Studies on other microorganisms have shown that the genes coding for the production and assembly of fimbriae are often clustered. By the use of maxicells, transposon mutagenesis and expression vectors, we have identified several genes which are located in the fimbrial subunit gene region. Antiserum was prepared against one of the proteins (88 kDa) which we were able to overproduce in Escherichia coli. In Western blots, these antibodies reacted with an 88 kDa protein located in the B. nodosus cell membrane. However, they did not react with the putative basal protein which is found in fimbrial preparations. We concluded that in B. nodosus the genes involved in fimbrial assembly are not all localised to one small region of the genome. In addition, our studies showed that although the fimbrial subunits are not assembled into intact fimbriae, an N-terminal sequence is processed in E. coli.

Animals↗
PubMed1987

A new method for the physical and genetic mapping of large plasmids: application to the localisation of the virulence determinants on the 90 kb plasmid of Salmonella typhimurium.

A new method based on transposon-promoted deletions was used to generate a set of deletions in the 90 kb virulence plasmid of Salmonella typhimurium. The analysis of 16 deletion mutants allowed: (1) construction of the restriction map of the plasmid for HindIII, BamHI and BglII; (2) localisation of the plasmid region involved in virulence; (3) identification of two functional replicons on the plasmid.

DNA Mutational Analysis↗
PubMed1995

Refined genetic mapping of a gene for familial juvenile nephronophthisis (NPH1) and physical mapping of linked markers. APN Study Group.

We have recently assigned a gene for familial juvenile nephronophthisis (NPH1) to chromosome 2q between microsatellite markers at loci D2S135 and D2S110. Here we have extended and refined our previous linkage analysis by studying five additional NPH families and by testing five additional markers. By haplotype analysis in a large family yielding proof of linkage, D2S135 and D2S283 were defined with certainty as flanking the NPH1 critical region within a 14-cM interval. These data now allow cytogenetic assignment of the NPH1 critical region to 2q11.1-q21.1. Furthermore, haplotype analysis in 12 small families helped to define as flanking markers D2S293 and D2S363, which span an 8-cM interval. Multipoint linkage analysis by the location score method resulted in a maximum multipoint lod score of 10.30. The Zmax-1 support interval spans 6.9 cM and is flanked by marker loci D2S293 and D2S363. Since IL1A maps to this region and has been cytogenetically mapped to 2q13 in the literature, NPH1 can be assigned more closely to 2q13 or adjacent bands. Contigs of CEPH mega-YAC clones in the region were established by screening the clones with microsatellite markers, adding marker IL1A to the physical map as a novel assignment. We conclude that the NPH1 gene most probably localizes to an interval of 6.9 cM between marker loci D2S293 and D2S363 in the vicinity of 2q13. This contig mapping provides the basis for cloning of this interval and for isolation of the NPH1 gene.

Chromosome Mapping↗