[DNA "fingerprinting" of individual yeast chromosomes].
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Bacteriophages↗
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Candidate disease resistance genes in sunflower cloned using conserved nucleotide-binding site motifs: genetic mapping and linkage to the downy mildew resistance gene Pl1.
Disease resistance gene candidates (RGCs) belonging to the nucleotide-binding site (NBS) superfamily have been cloned from numerous crop plants using highly conserved DNA sequence motifs. The aims of this research were to (i) isolate genomic DNA clones for RGCs in cultivated sunflower (Helianthus annuus L.) and (ii) map RGC markers and Pl1, a gene for resistance to downy mildew (Plasmopara halstedii (Farl.) Berl. & de Toni) race 1. Degenerate oligonucleotide primers targeted to conserved NBS DNA sequence motifs were used to amplify RGC fragments from sunflower genomic DNA. PCR products were cloned, sequenced, and assigned to 11 groups. RFLP analyses mapped six RGC loci to three linkage groups. One of the RGCs (Ha-4W2) was linked to Pl1, a downy mildew resistance gene. A cleaved amplified polymorphic sequence (CAPS) marker was developed for Ha-4W2 using gene-specific oligonucleotide primers. Downy mildew susceptible lines (HA89 and HA372) lacked a 276-bp Tsp5091 restriction fragment that was present in downy mildew resistant lines (HA370, 335, 336, 337, 338, and 339). HA370 x HA372 F2 progeny were genotyped for the Ha-4W2 CAPS marker and phenotyped for resistance to downy mildew race 1. The CAPS marker was linked to but did not completely cosegregate with Pl1 on linkage group 8. Ha-4W2 was found to comprise a gene family with at least five members. Although genetic markers for Ha-4W2 have utility for marker-assisted selection, the RGC detected by the CAPS marker has been ruled out as a candidate gene for Pl1. Three of the RGC probes were monomorphic between HA370 and HA372 and still need to be mapped and screened for linkage to disease resistance loci.
Base Sequence↗
The myxoma virus thymidine kinase gene: sequence and transcriptional mapping.
The myxoma virus thymidine kinase (TK) gene is encoded on a 1.6 kb SacI-SalI restriction fragment located between 57.7 and 59.3 kb on the 163 kb genomic map. The nucleotide sequence of this fragment as well as 228 bp from the adjacent SalI-AA2 fragment was determined and found to encode four major open reading frames (ORFs). Three of these ORFs are similar in nucleotide sequence to ORFs L5R and J1R, and the TK gene of vaccinia virus (VV). The fourth ORF, MF8a, shows similarity to the ORFs found in the same position relative to the TK genes of Shope fibroma virus, Kenya sheep-1 virus and swine-pox virus. A search of the complete VV nucleotide sequence for regions of similarity to MF8a identified the host specificity gene C7L. Northern blot analysis of early viral RNA identified transcripts of approximately 700 nucleotides for both the TK gene and ORF MF8a. The 5' ends of the TK gene and ORF MF8a early mRNAs were mapped by primer extension to initiation sites 13 nucleotides downstream of sequences with similarity to the VV early promoter consensus. The sizes of the TK and MF8a mRNAs are consistent with transcription termination and polyadenylation occurring downstream of the sequence TTTTTNT, which is identical to the consensus sequence for the VV transcription termination signal.
Amino Acid Sequence↗
Conformationally variable Rab protein surface regions mapped by limited proteolysis and homology modelling.
Tryptic proteolysis of the small GTPases Rab4 and Rab5 is a multi-step, nucleotide-dependent process. Using N-terminal peptide sequencing, matrix-assisted laser desorption ionization-time-of-flight MS and molecular modelling, we identified the three initial sites of proteolysis in Rab5 as Arg-4, Arg-81 and Arg-197. Arg-4 and Arg-81 lie within regions previously implicated in Rab5 endocytic function, and Arg-197 lies in a region involved in membrane targeting. Topologically, Arg-81 lies within the conformationally variable Switch II region shown to be important for protein-protein interactions of other GTPases. Homology modelling studies on Rab5 indicate that the Arg-81 side chain is buried in the Rab5 GTP conformation, but is solvent-accessible in the GDP conformation, explaining the dependence of proteolysis on nucleotides. Peptide mapping of Rab4 was performed to take advantage of additional scissile bonds within Switch II to determine more precisely the limits of the nucleotide-dependent protease-accessible region. The Rab4 cleavage sites corresponded to Arg-81 and Pro-87 of Rab5, and taken together with the finding that Rab5 was not cleaved at Arg-91 this analysis defines an eight-residue surface-exposed conformationally variable region lying in the centre of Switch II. A sequence comparison of Rab proteins shows these eight residues to have a loosely conserved motif that we term Switch II(v) for its relative variability. C-terminal to Switch II(v) is a highly conserved Rab-specific YYRGA motif that we term Switch II(c) for its constant sequence. N-terminal to Switch II(v) is a sequence-invariant G-domain involved in nucleotide binding and hydrolysis. We propose that the Rab Switch II(v) region imparts specificity to nucleotide-dependent protein-protein interactions.
Amino Acid Sequence↗
Long-range correlations in nucleotide sequences.
DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations. We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term a 'DNA walk'. We then use the mapping to provide a quantitative measure of the correlation between nucleotides over long distances along the DNA chain. Thus we uncover in the nucleotide sequence a remarkably long-range power law correlation that implies a new scale-invariant property of DNA. We find such long-range correlations in intron-containing genes and in nontranscribed regulatory DNA sequences, but not in complementary DNA sequences or intron-less genes.
Animals↗
DNA damage induced in vivo by 7-methoxy-2-nitronaphtho[2,1-b]-furan (R7000) in the lacI gene of Escherichia coli.
DNA adducts that block replication, induced in vivo by the 5-nitrofuran derivative R7000 (7-methoxy-2-nitronaphtho[2, 1-b]-furan) were mapped, at nucleotide resolution, in a region of the lacI gene of Escherichia coli, using a reiterative primer extension assay [D. Chandrasekhar, B. Van Houten, High resolution mapping of UV-induced photoproducts in the Escherichia coli lacI gene: inefficient repair of the non-transcribed strand correlates with high mutation frequency, J. Mol. Biol., 1994, Vol. 238, pp. 319-332]. It was found that R7000 induced a broad spectrum of low frequency replication blocks rather than particular hot spots in a limited number of particular targets. Most of these replication blocks were observed at G nucleotides, and most of G nucleotides present in the DNA sequence, if not all, constituted a possible target for the chemical attack of the compound. In addition, a large part of replication blocks observed at A, C or T could also reflect a replication block at the 3' or 5' nucleotide flanking a guanosine-DNA adduct. Only a very small number of replication blocks could be observed at A, C or T nucleotides non-adjacent to a G. These results show that, guanosine-DNA adducts are the main DNA lesions that block replication induced by R7000 in E. coli and suggests a strong reactivity of the genotoxic species generated in vivo by R7000 with the G nucleotidic targets. From 26 R7000-induced mutations previously mapped in this region [E. Touati, E. Krin, P. Quillardet, M. Hofnung, 7-methoxy-2-nitronaphto[2,1-b]furan (R7000)-induced mutation spectrum in the lacI gene of Escherichia coli: influence of SOS mutagenesis, Carcinogenesis, 1996, Vol. 17, pp. 2543-2550.], 22 (85%) occurred at GC base pairs at which termination products were observed. The other mutagenic events involved AT base pairs adjacent to a G nucleotide forming a replication block. Thus all mutagenic events occurred at, or adjacent to, a G nucleotide forming a replication block. Although it could not be excluded that some mutagenic events are due to undetected DNA lesions that do not block replication, these results strongly suggest that guanosine-DNA adducts that block DNA replication are responsive for a large part of the mutagenic events generated by R7000. The powerful capacity of R7000 to form adducts at most of the guanosine residues in a DNA sequence may account for at least part of its very potent genotoxic properties.
Bacterial Proteins↗
Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS.
In a study of genetic variation in the AIDS virus, HTLV-III/LAV, sequential virus isolates from persistently infected individuals were examined by Southern blot genomic analysis, molecular cloning, and nucleotide sequencing. Four to six virus isolates were obtained from each of three individuals over a 1-year or 2-year period. Changes were detected throughout the viral genomes and consisted of isolated and clustered nucleotide point mutations as well as short deletions or insertions. Results from genomic restriction mapping and nucleotide sequence comparisons indicated that viruses isolated sequentially had evolved in parallel from a common progenitor virus. The rate of evolution of HTLV-III/LAV was estimated to be at least 10(-3) nucleotide substitutions per site per year for the env gene and 10(-4) for the gag gene, values a millionfold greater than for most DNA genomes. Despite this relatively rapid rate of sequence divergence, virus isolates from any one patient were all much more related to each other than to viruses from other individuals. In view of the substantial heterogeneity among most independent HTLV-III/LAV isolates, the repeated isolation from a given individual of only highly related viruses raises the possibility that some type of interference mechanism may prevent simultaneous infection by more than one major genotypic form of the virus.
Acquired Immunodeficiency Syndrome↗
Heterogeneous nuclear ribonucleoprotein a1 binds to the 3'-untranslated region and mediates potential 5'-3'-end cross talks of mouse hepatitis virus RNA.
The 3'-untranslated region (3'-UTR) of mouse hepatitis virus (MHV) RNA regulates the replication of and transcription from the viral RNA. Several host cell proteins have previously been shown to interact with this regulatory region. By immunoprecipitation of UV-cross-linked cellular proteins and in vitro binding of the recombinant protein, we have identified the major RNA-binding protein species as heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1). A strong hnRNP A1-binding site was located 90 to 170 nucleotides from the 3' end of MHV RNA, and a weak binding site was mapped at nucleotides 260 to 350 from the 3' end. These binding sites are complementary to the sites on the negative-strand RNA that bind another cellular protein, polypyrimidine tract-binding protein (PTB). Mutations that affect PTB binding to the negative strand of the 3'-UTR also inhibited hnRNP A1 binding on the positive strand, indicating a possible relationship between these two proteins. Defective-interfering RNAs containing a mutated hnRNP A1-binding site have reduced RNA transcription and replication activities. Furthermore, hnRNP A1 and PTB, both of which also bind to the complementary strands at the 5' end of MHV RNA, together mediate the formation of an RNP complex involving the 5'- and 3'-end fragments of MHV RNA in vitro. These studies suggest that hnRNP A1-PTB interactions provide a molecular mechanism for potential 5'-3' cross talks in MHV RNA, which may be important for RNA replication and transcription.
3' Untranslated Regions↗
Development and characterization of genome-wide single nucleotide polymorphism markers in the green alga Chlamydomonas reinhardtii.
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Animals↗
Conserved organization of the murine immunoglobulin epsilon gene region: restriction endonuclease maps and switch-region nucleotide sequence.
Various inbred mouse strains showed remarkable conservation of organization in the epsilon germline region as determined by restriction mapping. Restriction fragment length polymorphisms (RFLP) were seen in the epsilon gene region for only two of eight restriction enzymes tested. Furthermore, the RFLP did not correlate with the IgE-response phenotype for the murine strains SJL, SJA, C57BL/6, BALB/c, A/ST, and A/J. The IgE class-switch region (S epsilon) DNA from an SJL genomic clone was sequenced and was compared with S epsilon sequences from BALB/c mice. These S epsilon sequences were at least 95% homologous. Most of the S epsilon sequence differences observed between the two strains were single base pair substitutions, deletions, or insertions. The largest difference between the S epsilon sequences resulted from an insertion of seven contiguous bases seen in the SJL S epsilon region.
Animals↗
Poly-3-hydroxybutyrate degradation in Rhizobium (Sinorhizobium) meliloti: isolation and characterization of a gene encoding 3-hydroxybutyrate dehydrogenase.
We have cloned and sequenced the 3-hydroxybutyrate dehydrogenase-encoding gene (bdhA) from Rhizobium (Sinorhizobium) meliloti. The gene has an open reading frame of 777 bp that encodes a polypeptide of 258 amino acid residues (molecular weight 27,177, pI 6.07). The R. meliloti Bdh protein exhibits features common to members of the short-chain alcohol dehydrogenase superfamily. bdhA is the first gene transcribed in an operon that also includes xdhA, encoding xanthine oxidase/dehydrogenase. Transcriptional start site analysis by primer extension identified two transcription starts. S1, a minor start site, was located 46 to 47 nucleotides upstream of the predicted ATG start codon, while S2, the major start site, was mapped 148 nucleotides from the start codon. Analysis of the sequence immediately upstream of either S1 or S2 failed to reveal the presence of any known consensus promoter sequences. Although a sigma54 consensus sequence was identified in the region between S1 and S2, a corresponding transcript was not detected, and a rpoN mutant of R. meliloti was able to utilize 3-hydroxybutyrate as a sole carbon source. The R. meliloti bdhA gene is able to confer upon Escherichia coli the ability to utilize 3-hydroxybutyrate as a sole carbon source. An R. meliloti bdhA mutant accumulates poly-3-hydroxybutyrate to the same extent as the wild type and shows no symbiotic defects. Studies with a strain carrying a lacZ transcriptional fusion to bdhA demonstrated that gene expression is growth phase associated.
Amino Acid Sequence↗
The human genome: the nature of the enterprise.
The development of methods of cloning and sequencing DNA has liberated genetics from the constraints of breeding experiments, and all organisms are now accessible to genetical analysis by the new methods. The analysis of the human genome is likely to produce a revolution in biomedical science, and it is argued that high priority should be given to gene identification. The strategy advocated is one which identifies the expressed genes and pursues mapping in parallel.
Genome, Human↗
Avian endogenous provirus (ev-3) env gene sequencing: implication for pathogenic retrovirus origination.
The avian endogenous env gene product blocks the surface receptor and, as a result, cells become immune to related exogenous retroviruses. On the other hand, the same sequence can be included in the pathogenic retrovirus genome, as shown by oligonucleotide mapping. However, since the complete env gene sequence was not known, the comparison of genomic nucleotide sequences was not possible. Therefore an avian endogenous provirus with an intact env gene was cloned from a chicken gene bank and the regions coding for the C terminus of the gp85 and gp37 proteins were sequenced. Comparison of this sequence with those of other retroviruses proved that one of the pathogenic viruses associated with osteopetrosis is a cross between avian endogenous virus and Rous sarcoma virus. Retroviruses and, especially, endogenous retroviruses are traditionally of the most developed models of viral carcinogenesis. Many endogenous retroviruses are implicated in neoplastic transformation of the cell. For instance, endogenous mouse mammary tumor virus of some inbred lines appears to be the only causative agent in these mammary cancers. Other even nonpathogenic murine endogenous retroviruses are involved in the origination of MCF-type recombinant acute leukosis viruses. Some endogenous retroviruses are implicated in the transduction or activation of cellular protooncogenes. Our interest in endogenous viruses is based on their ability to make cells resistant to exogenous retroviruses. Expression of their major envelope glycoprotein leads to cellular surface receptor blockage and imparts immunity to infection by the related leukemia retroviruses. This problem is quite elaborated for chicken endogenous virus RAV-O (7-9).(ABSTRACT TRUNCATED AT 250 WORDS)
Animals↗
Structure and characterization of the Sorghum vulgare gene encoding NADP-malate dehydrogenase.
A genomic clone encoding the NADP-malate dehydrogenase precursor has been isolated from a Sorghum vulgare lambda EMBL4 library using a cDNA probe. The entire structure of this nuclear gene (4.6 kb) encoding the 429-amino acid precursor is reported, as well as 602 bp of the 5'-flanking and 695 bp of the 3'-flanking regions. The gene is interrupted by 13 introns from 79 to 495 bp in length. S1 nuclease mapping showed the S. vulgare gene transcript to contain an untranslated leader sequence of 44 nucleotides. In the 5'-flanking region, several short sequences similar to the consensus motifs involved in the light-regulation process of other plant genes were found.
Amino Acid Sequence↗
Sequence analysis of a mosquito ribosomal protein rpL8 gene and its upstream regulatory region.
The gene encoding Aedes albopictus ribosomal protein L8 was isolated using a cDNA probe. Based on the deduced amino acid sequence, rpL8 has a mass of 28,605 Da, a pI of 11.97, and contains 9.6% Arg and 11.9% Lys. The rpL8 gene spans 1229 nucleotides, and contains three exons measuring 73, 150, and 648 nucleotides. The first intron is 293 nucleotides long and interrupts an 85-nucleotide untranslated leader sequence. The AUG codon is located 12 nucleotides downstream of the 5'-end of the second exon. Separating the second and third exon is a 65-nucleotide intron. The major transcription initiation site, identified by primer extension and polymerase stop reactions, mapped 378 nucleotides upstream from the AUG start codon; minor initiation sites were also detected. The DNA sequence upstream of the rpL8 gene was T-rich, but conventional TATA and CAAT boxes were absent. This is the first molecular analysis of a mosquito ribosomal protein gene.
Aedes↗
Parvovirus genome: nucleotide sequence of H-1 and mapping of its genes by hybrid-arrested translation.
The nucleotide sequence of the parvovirus H-1 has been determined by the chain-terminating method of Sanger. The sequence is 5,176 nucleotides long. Two large open reading frames (1 and 2) and two smaller open reading frames (3 and 4) of potential importance were identified in the plus-strand sequence. Promoter sequences are located at map positions 4 and 38 when map positions are expressed as percent of genome length from the 3' end of the virion minus strand. The locations for the genes for the parvovirus capsid proteins and a 76,000-dalton noncapsid protein (NCVP1) were mapped by hybrid-arrested translation. The gene for the capsid proteins VP1 and VP2' is located in the 5' half of the virus genome. The gene for NCVP1 is located in the 3' half of the viral DNA.
Amino Acids↗
Temporal usage of multiple promoters during the life cycle of human papillomavirus type 31b.
The life cycles of human papillomaviruses (HPVs) are dependent upon the differentiation of the epithelial cells they infect. HPV type 31b (HPV31b) virions can be purified following the growth of a latently HPV-infected cell line (CIN-612 9E) in the organotypic or raft system. Treatment of the CIN-612 9E raft tissues with protein kinase C (PKC) activators is required for upregulation of late gene expression and efficient production of virions. We employed the raft culture system to study the temporal usage of HPV31b promoters during the viral life cycle. We compared monolayer cultures of CIN-612 9E cells, untreated CIN-612 9E raft tissues, and PKC-induced CIN-612 9E raft tissues harvested at various time points during epithelial differentiation. We found that the HPV31b major early promoter precisely maps to nucleotide (nt) 99 (P99). A transcriptional start site for both early and late gene transcripts mapped upstream of P99 at nt 77 (P77). The P77 and P99 promoters were used constitutively throughout the HPV31b life cycle; however, initiation from P99 was much stronger than from P77. Mapping of the differentiation-induced P742 promoter revealed multiple start sites. These start sites were difficult to detect in monolayer cultures, were induced in untreated rafts, and were greatest in PKC-induced raft tissues at 8 to 12 days. A constitutively active promoter, P3320, was also defined and is responsible for the transcription of unspliced and spliced RNAs containing E5a, E5b, L2, and L1 open reading frames.
Base Sequence↗
Beta-lactamase expression in Streptomyces cacaoi.
Plasmids were prepared by inserting genomic DNA fragments from Streptomyces cacaoi within the mel gene of plasmid pIJ702. The inserted DNA fragments contain the beta-lactamase-encoding bla gene and upstream nucleotide sequences of various lengths. The transcription start point of bla was identified by nuclease S1 mapping. Upstream nucleotide sequences of sufficient lengths had an enhancing effect on beta-lactamase production by the Streptomyces host. The dot blot hybridization assay revealed that this effect was exerted at the transcriptional level. Experimental evidence strongly suggests that the underlying mechanism involves, at least in part, one or several trans-acting elements. In one of the constructs, in which the upstream nucleotide sequence was reduced to 0.3 kb, the bla promoter was present but the bla gene was expressed by readthrough from a promoter, possibly the mel promoter, of the pIJ702 vector.
Amino Acid Sequence↗