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Role for the Wilms tumor gene in genital development?

Detailed molecular definition of the WAGR region at chromosome 11p13 has been achieved by chromosome breakpoint analysis and long-range restriction mapping. Here we describe the molecular detection of a cytogenetically invisible 1-megabase deletion in an individual with aniridia, cryptorchidism, and hypospadias but no Wilms tumor (WT). The region of overlap between this deletion and one associated with WT and similar genital anomalies but no aniridia covers a region of 350-400 kilobases, which is coincident with the extent of homozygous deletion detected in tumor tissue from a sporadic WT. A candidate WT gene located within this region has recently been isolated, suggesting nonpenetrance for tumor expression in the first individual. The inclusion within the overlap region of a gene for WT predisposition and a gene for the best-documented WT-associated genitourinary malformations leads us to suggest that both of these anomalies result from a loss-of-function mutation at the same locus. This in turn implies that the WT gene exerts pleiotropic effect on both kidney and genitourinary development, a possibility supported by the observed expression pattern of the WT candidate gene in developing kidney and gonads.

Aniridia↗

Stability and asymmetric replication of the Bacillus subtilis 168 chromosome structure.

Chromosomal DNAs from a number of strains derived from Bacillus subtilis 168 were digested with restriction endonucleases NotI or SfiI, and the locations of chromosomal alterations were compared with the recently constructed standard NotI-SfiI restriction map (M. Itaya and T. Tanaka, J. Mol. Biol. 220:631-648, 1991). In general, the chromosome structure of B. subtilis 168 was found to be stable, as expected from the genetic stability of this species. DNA alterations, typically deletions, are formed in three limited loci on the chromosome. One of these alterations was characterized as a spontaneous deletion formed between rrn operons, and another occurred as a result of prophage SP beta excision. I found that oriC and terC are not located on precisely opposite sides of the chromosome. Replication in the counter clockwise direction was 196 kb longer than replication in the clockwise direction. The characteristic of length difference is not changed by deletion formation.

Bacillus Phages↗

Physical linkage of the human growth hormone gene cluster and the skeletal muscle sodium channel alpha-subunit gene (SCN4A) on chromosome 17.

The human growth hormone (GH) locus, a cluster of five genes, spans 47 kb on chromosome 17q22-q24. The skeletal muscle sodium channel alpha-subunit locus (SCN4A), a 32.5-kb gene, has previously been mapped to 17q23.1-q25.3. We demonstrate that both the GH gene cluster and the SCN4A gene colocalize to a single 525-kb yeast artificial chromosome (YAC) containing DNA derived from human chromosome 17. Restriction maps of two cosmids encompassing the 5' terminus of the GH locus and including up to 40 kb of 5'-flanking sequences demonstrate a perfect 20-kb overlap with previously published maps of the SCN4A gene. A 720-bp DNA segment, encompassing sequences 32.3 to 31.6 kb 5' to GH, was sequenced and found to be identical to exon 14 of SCN4A. These data demonstrate that the SCN4A gene and the entire GH gene cluster are contained within 100 kb on chromosome 17 and are separated by only 21.5 kb. Remarkably, this physical linkage between GH and SCN4A also reveals that multiple elements critical to tissue-specific transcriptional activation of the GH gene lie within the SCN4A gene.

Base Sequence↗

Characterization of phi GA1, an inducible phage particle from Brevibacterium flavum.

Eighteen related strains of Arthrobacter, Brevibacterium and Corynebacterium were used as indicator strains in an attempt to isolate corynephages from a large number of soils and from waste-water samples. Although no phages capable of producing plaques were isolated, one of the indicator strains used, Brevibacterium flavum ATCC 14067, was lysogenic for the inducible phage phi GA1. This phage was not observed to form plaques on any of the strains tested. phi GA1 is of B1-morphotype with a linear double-stranded DNA genome of 48.1 kb with cohesive ends; a restriction map is presented.

Arthrobacter↗

The unstable region of Streptomyces ambofaciens includes 210 kb terminal inverted repeats flanking the extremities of the linear chromosomal DNA.

Physical maps of the chromosomes of three strains of Streptomyces ambofaciens were constructed by ordering Asel fragments generated from the genomic DNA as a single linear chromosome of about 8 Mb. The physical maps of the three strains were very similar. For strain DSM40697, a Dral map was obtained by positioning the Dral sites relative to the Asel map. Eighteen genetic markers as well as the deletable and amplifiable region were assigned to the Asel and Dral fragments in this strain. The resulting genetic map resembled that of Streptomyces coelicolor A3(2). The two terminal Asel fragments exhibited retarded pulsed-field gel electrophoresis mobility, demonstrating that proteins are covalently bound at this position. A restriction map of this region was made using four additional endonucleases. Repeated sequences present at both ends of the chromosome were mapped as long terminal inverted repeats stretching over 210 kb. This corresponds to the longest terminal inverted repeats so far characterized. The deletable region of S. ambofaciens was localized at the chromosomal extremities.

Chromosomes, Bacterial↗

Orthopoxvirus DNA: a comparison of restriction profiles and maps.

Characteristic DNA endonuclease digest fragment electropherograms and restriction site maps permitted differentiation and genome structure analysis of 38 orthopoxviruses that included isolates of monkeypox virus from humans and animals, monkeypox white variants, variola, vaccinia, ectromelia, Tatera (gerbil) and raccoon poxviruses, and cowpox and camelpox viruses. HindIII cleavage sites mapped on the 38 virus genome DNAs plus SmaI, BglI, SacI, KpnI, XhoI, and SalI maps for variola (Harvey) and monkeypox (Copenhagen) virus DNAs were derived essentially by cross-hybridizations with monkeypox, vaccinia, and variola virus-cloned DNA restriction fragments, thus digest fragments could be assigned homologous regions on previously established genome maps. Salient of our observations, the DNA HindIII maps correlated to a high degree, but variations in middle and especially terminal DNA region cleavage sites provided a basis for discerning species, strains and variants. The extent of the inverted terminal repetitions (ITRs) for 37 DNAs were determined with HindIII, PvuI, SalI, and ClaI, plus nine more restriction enzymes for Bangladesh variola virus DNA by hybridizations with either the terminal tandemly repeated 70-bp segment or an EcoRI-PvuI near hairpin-end 75-bp segment from WR vaccinia virus. The opposite terminal regions of variola DNA were considerably asymmetrical compared to the large symmetrical ITRs of the other species examined. An apparent DNA inversion and concurrent deletion (1 kbp) with subsequent repair of DNA to original structure was suggested from right terminal region maps of four viruses chosen from a variola virus passage series in monkeys. Correlative with virus geographic distribution, two strains of monkeypox virus, each containing two variants, were differentiated by DNA profiles of isolates from smallpox-like disease (SLD) patients of the African rainforest region. The DNAs of five monkeypox viruses isolated from laboratory and zoo animals resembled most DNAs from SLD monkeypox viruses from Sierra Leone. A poxvirus from an American raccoon contained 40% DNA that did not cross-hybridize with orthopoxvirus DNA probes. The DNAs of recent isolates from a gerbil and from a camel each mapped as unique African orthopoxvirus species and differed from variola virus.

Animals↗

Molecular and phenotypic variation of the Zw locus region in Drosophila melanogaster.

Restriction map polymorphism in a 13-kb region of the Zw locus in Drosophila melanogaster was investigated for 64 X chromosome lines with seven 6-cutter and ten 4-cutter restriction enzymes. A total of 203 restriction sites were scored, of which 20 were found to be polymorphic. The estimated nucleotide variation for this region for overall data (pi = 0.003 and 0.001, and theta = 0.003 and 0.002, for 4-cutter and 6-cutter studies, respectively) was smaller than that reported for most regions studied in D. melanogaster. It was found that the Slow allozyme has a larger nucleotide variation and haplotype diversity than the Fast allozyme. Results suggest the relatively recent divergence of the Fast allozyme from the Slow allozyme. Glucose 6-phosphate dehydrogenase (G6PD) activity was measured as a phenotype of the Zw locus. A significant difference in G6PD activity between allozymes was detected. The between-line effect was highly significant within the Slow allozyme, but was not significant within the Fast allozyme. Although a direct causative link could not be established, these results suggest an association between the amounts of quantitative and molecular genetic variation at the Zw locus region.

Analysis of Variance↗

A YAC contig encompassing the Treacher Collins syndrome critical region at 5q31.3-32.

Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development the features of which include conductive hearing loss and cleft palate. Previous studies have localized the TCOF1 locus between D5S519 (proximal) and SPARC (distal), a region of 22 centirays as estimated by radiation hybrid mapping. In the current investigation we have created a contig across the TCOF1 critical region, using YAC clones. Isolation of a novel short tandem repeat polymorphism corresponding to the end of one of the YACs has allowed us to reduce the size of the critical region to approximately 840 kb, which has been covered with three nonchimeric YACs. Restriction mapping has revealed that the region contains a high density of clustered rare-cutter restriction sites, suggesting that it may contain a number of different genes. The results of the present investigation have further allowed us to confirm that the RPS14 locus lies proximal to the critical region and can thereby be excluded from a role in the pathogenesis of TCOF1, while ANX6 lies within the TCOF1 critical region and remains a potential candidate for the mutated gene.

Annexin A6↗

The 5' part of the mouse immunoglobulin kappa locus.

The 5' region of the mouse kappa locus comprises 63 Vkappa genes in six contigs of together 1.5 Mb, including one which links the region to the central part of the locus. The structures of the contigs were established by detailed restriction mapping of cosmid clones prepared from libraries of mouse C57BL/6 DNA and of yeast and bacterial artificial chromosomes (YACs, BACs with mouse DNA inserts). Pulsed-field gel electrophoresis of yeast artificial chromosome digests indicated that the gaps between the contigs were 10 to 60 kb, comprising together about 160 kb. The region of the kappa locus described here contains Vkappa1, Vkappa2, Vkappa9/10, Vkappa11, Vkappa12/13, Vkappa20, Vkappa24, Vkappa32, Vkappa33/34 and Vkappa38C genes as well as the VkappaRF gene and, towards the center of the locus, a number of Vkappa4/5 genes. Near the 5' end of the locus interspersed alpha-tubulin gene-like sequences were found. At its 3' side the region borders on the Vkappa4/5 contigs of the central region of the locus which is described in the accompanying report (Eur. J. Immunol. 1999. 29: 2057-2064). Structural details are to be found in the Internet at http://www.med.uni-muenchen.de/biochemie/zach au/kappa.htm. In a concluding section the main features of the structure of the mouse kappa locus are summarized.

Animals↗

Characterization of a multigene family encoding an endopolygalacturonase in Sclerotinia sclerotiorum.

Sclerotinia sclerotiorum produces several polygalacturonases which together with other pectinolytic enzymes are involved in the degradation of pectin. A number of different genomic clones were isolated by screening a genomic DNA library in phage EMBL3. Southern-blot and restriction mapping indicate that seven genes constitute two subfamilies of a multigene family encoding endopolygalactutonase. Using pulsed-field gel electrophoresis to separate S. sclerotiorum chromosomes each subfamily was found to hybridize to a different chromosome. A comparison of the nucleotide sequence for the coding region of three members of the gene family reveals surprisingly few base substitutions suggesting that this gene family arose from recent multiple duplication events.

Amino Acids↗

Cloning and comparison of A alpha mating-type alleles of the Basidiomycete Schizophyllum commune.

An A alpha mating-type allele (A alpha 4) was isolated by walking the chromosome from the closely linked PAB1 gene. A cosmid clone containing the A alpha 4 allele isolated from the walk was used as a probe to recover the A alpha 1 allele from another cosmid library. Cosmids encoding mating-type activity were identified by transforming Schizophyllum cells and screening for activation of A-regulated development. Putative mating-type transformants were confirmed in mating tests and genetic analyses of progeny. The identity of the specific alleles isolated was demonstrated by showing that their effectiveness in transforming for mating type is limited to recipient strains possessing an A alpha allele different from the one encoded by the cloned sequences. Transforming DNA is active in trans, suggesting that A alpha encodes a diffusible product. Restriction mapping shows that A alpha 1 and A alpha 4 are coded in the same physical region of the genome, but within a subregion that contains extensive sequence divergence. In addition, Southern analyses show that there is only one copy of A alpha 1 or A alpha 4 per haploid genome, and that they do not cross-hybridize to one another or to any of the other A alpha alleles. A alpha 1 and A alpha 4 were subcloned as 2.8 and 1.2 kb fragments, respectively, retaining in transformation all the mating-type activity demonstrated of the original cosmids.

Alleles↗

Identification of EcoRV fragments spanning the N alpha-tubulin gene of Physarum.

The N alpha-tubulin gene of Physarum polycephalum has an EcoRV site at codons 252/253. EcoRV digestion of physarum DNA generated two EcoRV fragments per gene copy comprising both coding and flanking sequences. Hybridisation probes which included coding sequences upstream from the central EcoRV site cross-hybridised with another alpha-tubulin gene. Probes derived from either 5'- or 3'-flanking regions were gene-specific. These probes identified two EcoRV fragments in the haploid strain CLdAXE viz 5.4 kb (5'-fragment) and 6.2 kb (3'-fragment). The same two fragments were identified in EcoRV digests of DNA of the diploid strain M3CVIII, and a second form of the gene was also identified comprising two fragments viz 5.0 kb (5'-end) and 5.5 kb (3'-end). Both forms gave rise to an identical 4.65 kb HindIII fragment as judged by restriction mapping.

Deoxyribonucleases, Type II Site-Specific↗

Molecular and biological characterization of cottontail rabbit papillomavirus variant DNA sequences integrated in the VX7 carcinoma.

The transplantable VX7 carcinoma was derived from a tumor induced by a recoverable strain of cottontail rabbit papillomavirus (CRPV) able to replicate in domestic rabbits. Low levels of late viral gene expression have been retained through serial propagation in rabbits. We have cloned and characterized the three major types of CRPV sequences integrated in this tumor, a genome-length 8-kb DNA molecule and two rearranged 9- and 3.8-kb molecules. The VX7 8-kb DNA displays only a few differences in its restriction map, when compared to the wild-type (wt) CRPV DNA. The VX7 9- and 3.8-kb DNAs derive from the VX7 8-kb DNA since they share the same restriction site polymorphism. The VX7 9-kb DNA contains a duplication of the E6 open reading frame. The VX7 3.8-kb DNA results from the deletion of most of the E region and the insertion, between the borders of the deletion, of 174-nucleotide-long segment of the long control region potentially driving the expression of a truncated L2 protein. Both VX7 9- and 3.8-kb species potentially allow the expression of abnormal E6 fusion proteins. Nineteen point mutations were detected in the 3.8-kb DNA, compared to the wt CRPV DNA. None of these molecules were able to induce warts in domestic rabbits, in contrast to wt CRPV DNA. Furthermore, when cloned VX7 DNAs were inoculated together with wt CRPV DNA, none of the VX7 CRPV sequences, as identifiable by their specific restriction enzyme cleavage patterns, could be detected in the resulting warts. This suggests that CRPV sequences integrated in the VX7 carcinoma are no longer able to replicate as episomes, which might be a prerequisite for the production of warts.

Amino Acid Sequence↗

The human ASM (adult skeletal muscle) gene: expression and chromosomal assignment to 11p15.

A rat adult skeletal muscle probe (Asm15) originated from a rhabdomyosarcoma was used to isolate the human homologous sequence from a placenta cDNA library. Among several positive clones the longest EcoRI-EcoRI insert (ASM1) obtained was 1875 bp long with 72% homology with rat Asm15 cDNA sequence. Important variations of ASM1 RNA level were observed in different adult skeletal muscles. Expression of a 29kD ASM1 protein was demonstrated in human adult skeletal muscle lysates using an antiserum (PB1579) raised against the C terminal region of the rat Asm15 protein. The human ASM gene was assigned by somatic cell analysis with human (ASM1) and rat (Asm15) probes to chromosome 11, and by in situ hybridization with the human probe to 11p15, a chromosome region involved in human embryonal rhabdomyosarcomas. Except for the presence of a HindII restriction site, the results obtained for the restriction map and the sequence of ASM1 cDNA (data not shown) exhibited extensive homology with the human H19 DNA sequence which have been mapped with a mouse probe also in 11p15. This suggests that ASM/Asm and H19 may represent the same sequence (in this hypothesis the presence of the supplementary HindII site in our ASM1 probe is explained by polymorphic variability). However it was reported that human and mouse H19 mRNA did not encode for a protein but acted as an RNA molecule whereas in our present study ASM protein was detected in human adult skeletal muscle. This could be explained by important regulation of ASM protein expression during development and cell differentiation. However we cannot exclude for the different species studied (mouse, rat, and man) the hypothesis that H19 and ASM/Asm mRNA may represent two distinct messengers from the same gene or even from duplicated genes.

Adult↗

Characterization of an erythromycin resistance (erm) plasmid in Streptococcus pyogenes.

Three erythromyxin-resistant Swedish isolates of Streptococcus pyogenes, representing different T-types, were studied. Two of the strains showed constitutive high-level (MIC > 200 micrograms/ml) and one showed moderate (MIC 6.4 micrograms/ml) resistance; the latter strain was sensitive to lincosamide and clindamycin, and resistance was not induced by erythromycin. In each of the strains, a plasmid with an estimated Mw of 17.6 +/- 0.9 x 10(6) was isolated in addition to smaller cryptic plasmids. The three plasmids pSE701, pSE702, and pSE703 had very similar restriction enzyme cleavage patterns. Novobiocin curing of the high-level resistance strain ER559 showed the resistance to be linked to its 17.6 x 10(6) plasmid, pSE703. Furthermore, by electroporation this rather large plasmid was reintroduced into an erythromycin-sensitive cured derivative, acquiring resistance, and the plasmid was again recovered from the transconjugant. One of the plasmids, pSE702, was shown by filter mating to be conjugative within S. pyogenes. DNA-DNA hybridization showed that the resistance determinant of the present three isolates was related to the erm gene on plasmid pAM beta 1 of Enterococcus faecalis but not to that of plasmid pE194 of Staphylococcus aureus. The copy numbers of pSE702 and pSE703, derived from the two high-level resistant strains, were 11 +/- 3 and 17 +/- 5 compared to 2 +/- 1 for pSE701, derived from the moderately resistant strain, possibly accounting for the phenotypic variation observed. The plasmids pSE702 and pAM beta 1 showed about 80% homology in DNA-DNA hybridization tests and high similarity in their restriction maps.

Drug Resistance, Microbial↗

Characterization of RAD4 gene required for ultraviolet-induced excision repair of Saccharomyces cerevisiae propagated in Escherichia coli without inactivation.

The previously isolated RAD4 gene designated as pPC1 from the genomic library of Saccharomyces cerevisiae (Yoon et al., 1985, Korean J. Genetics 7, 97-104) appeared to propagate in Escherichia coli and yet retained its complementing activity to rad4 mutants without inactivation. The subcloned RAD4 gene was found to be localized within a 2.5 kb DNA fragment flanking Bg1II and BamHI sites in the insert DNA, and was shown to have the same restriction map as a yeast chromosomal DNA, as determined by Southern hybridization. Tetrad analysis and pulse-field chromosome mapping have revealed that the cloned RAD4 gene can be mapped and integrated into the yeast chromosome V, the actual site of this gene. DNA-tRNA hybridization has shown that the isolated RAD4 gene did not contain a suppressor tRNA gene. These results have indicated that the pPC1 is a functional RAD4 gene playing a unique role involved in the nucleotide excision repair of yeast without any genetic change during amplification in E. coli.

Chromosome Mapping↗

Identity of the 17-kilodalton protein, a DNA-binding protein from Escherichia coli, and the firA gene product.

The 17-kilodalton protein, a DNA-binding protein encoded by the skp gene of Escherichia coli, was found to be identical to histonelike protein I, the product of the firA gene. This conclusion was reached after chromosomal localization, using the recently constructed high- and low-resolution E. coli restriction maps, and by direct comparison of the N-terminal amino acid sequence of histonelike protein I and the 17-kilodalton protein.

Chromosome Mapping↗

Physical mapping of the genomic DNA of the Oryctes rhinoceros baculovirus, KI.

A non-occluded baculovirus, OBV-KI has been isolated from the insect pest, Oryctes rhinoceros. The viral genome is estimated to be 123 kb, with a G + C content of 43 mol% and no detectible methylated bases. A restriction map of the OBV-KI genome for BamHI, EcoRI, HindIII, PstI, SalI and XbaI has been constructed.

Animals↗