EcoRI-digested Genomic DNA Research Articles

2 cloning and expression of mouse deoxycytidine kinase. Pure recombinant mouse and human enzymes show differences in substrate specificity.

A cDNA encoding mouse deoxycytidine kinase (dCK) (EC 2.7.1.74) was cloned from a mouse T-cell lambda ZAP cDNA library. An insert of 2.8 kilobases (kb) contained the entire coding sequence of 780 base pairs. The protein coding sequence was 88% homologous at the nucleotide level with human dCK cDNA (Chottiner, E. G., Shewach, D. S., Datta, N. S., Ashcraft, E., Gribbin, D., Ginsburg, D., Fox, I. H., and Mitchell, B. S. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 1531-1535). At the amino acid level the homology was greater with only 16 of the 260 amino acids being different. Northern blot analyses revealed a size of 3.4 kb for mouse dCK mRNA as compared with 2.8 kb for human dCK. Part of the 3'-untranslated region was conserved between human and mouse dCK cDNA in contrast to the remainder of the 3'-sequence which was unrelated and about 500 nucleotides longer in mouse dCK cDNA. Mouse dCK cDNA showed cross-hybridization with several bands in EcoRI-digested genomic DNA from seven different mammalian species and chicken but not with yeast DNA. Both mouse and human dCK were cloned into the T5 promotor pQE30 vector system, expressed in Escherichia coli and purified to homogeneity. The kinetic constants for dCyd phosphorylation were similar for the human and mouse enzymes and also similar to what previously has been observed for dCK purified from human tissues. Mouse dCK was less efficient with regard to dAdo, dGuo, and ddCyd phosphorylation as compared with human dCK when using ATP as phosphate donor in a phosphoryl transfer assay.

Germline complexity, restriction fragment length polymorphism, and coding region sequences of the human VH7 gene family identified with family-specific FR3 segment oligonucleotides

We have used the most family-specific gene segment, the 5'-end of framework 3 (FR3) to study the germline complexity and coding region sequences of the recently described human VH7 gene family. Because of the high degree of 5' sequence homology between members of the VH7 and VH1 families, full-length coding region probes are unable to distinguish between the two groups. Hybridization with a VH7 coding region probe to EcoRI digested genomic DNA revealed 12 fragments. Many of these hybridizing fragments were also identified with a full length VH1 coding sequence probe. However, examination of the same DNA samples with a VH7 family specific oligonucleotide, encompassing the 5'-end of the FR3 segment, greatly reduced hybridization complexity yielding only four fragments which included one polymorphic band of molecular weight 7.4 kb. The VH7 specific FR3 oligonucleotide was also used under conditions of moderate stringency to isolate VH7 clones from PCR-amplified genomic DNA libraries derived from six unrelated individuals. All clones isolated contained members of the VH7 family. Six sequences were obtained. Gene 7A.4, seen in all individuals, is identical to the previously described germline V 1–4.1b gene other than G-C substitutions at nucleotides 253 and 254. Five distinct pseudogenes were also identified. Stop codons were confined to frameworks 2 and 3. Previously described expressed VH7 genes from cord blood, normal adults and two rheumatoid factors are > 96% homologous to gene 7A.4.

Multiplicity of genes encoding secreted aspartic proteinases in Candida species

The secreted aspartic proteinases (SAP) of Candida sp. are presumed to be potential virulence factors. In the opportunistic pathogen Candida albicans the proteinase genes identified to date, SAP1, SAP2, SAP3 and SAP4, constitute a multigene family. Before addressing the possible role of each proteinase in virulence, we sought to isolate all the members of this multigene family by screening a genomic library with a SAP1 probe for additional C. albicans SAP genes using low-stringency hybridization conditions. Three putative new members, SAP5, SAP6 and SAP7 were isolated and sequenced. The N-terminal segments of the deduced amino acid sequences of SAP5 and SAP6 contained secretion signal sequences similar to those of other Candida SAPs. Upon comparison and alignment with the other reported SAP amino acid sequences, SAP7 is not only the most divergent protein but also exhibits a much longer putative pro-sequence with a single Lys-Lys putative processing site. Using SAP1 to SAP7 as probes, the overall number of SAP genes in C. albicans was tentatively estimated by low-stringency hybridization to EcoRI-digested genomic DNA. While each isolated SAP gene could be assigned to distinct EcoRI bands, the existence of two additional genes not isolated after screening of the C. albicans gene library was inferred. Furthermore, evidence was obtained for the existence of SAP multigene families in other Candida species such as C. tropicalis, C. parapsilosis and C. guillermondii.

Identification of DNA probes that reveal polymorphisms among closely related Phaseolus vulgaris lines

Analyses of genetic diversity within populations could be of great benefit to plant genetic resources conservation. In order to identify genetic markers that are variable within populations, the genome of Phaseolus vulgaris was screened with several DNA sequences in order to identify hypervariable sequences. Polymorphisms were observed between Middle American and Andean cultivars using the protein III tandem repeat of the M13 phase and the 33.15 human minisatellite. Extensive differences were observed when the DNA of two divergent lines—BAT93 and Jalo EEP558, of Middle American and Andean origin, respectively—were digested with HinfI, TaqI, HaeIII and hybridized with the 33.15 human minisatellite. Similarly, numerous polymorphisms were observed when the M13 protein III tandem repeat region was hybridized with TaqI digests of these cultivars. Polymorphism was also detected among sister lines of two F6 backcross materials involving Middle American and Andean lines when genomic DNA was digested with TaqI and hybridized with M13 tandem repeat region. In addition, polymorphism was observed among Porrillo cultivars that resulted from selection within a single landrace population. Whereas only one isozyme difference had been observed previously among the Porrillo cultivars, eleven restriction fragments detected by the M13 protein III tandem repeat sequence differentiated these cultivars. Ribosomal DNA also hybridized to several polymorphic bands on TaqI and EcoRI genomic Southern blots of the F6 backcross material. Only one polymorphism was observed with EcoRI-digested genomic DNA of BAT93 and Jalo EEP558 was hybridized with microsatellite (GACA)4. This probe might be useful in ascertaining relationships at the species and subspecies level, and as a marker in mapping studies. Our results show that both the human 33.15 minisatellite and M13 should be useful probes to detect within-population variability in common bean.

Limited diversity of the protein D gene (hpd) among encapsulated and nonencapsulated Haemophilus influenzae strains

Protein D is a surface-exposed lipoprotein of the gram-negative bacterium Haemophilus influenzae with affinity for human immunoglobulin D myeloma protein. The gene encoding protein D (hpd) in a serotype b strain of H. influenzae was cloned. Escherichia coli carrying the hpd gene bound human myeloma immunoglobulin D. Nucleotide sequence analysis identified an 1,092-bp open reading frame that was more than 99% identical to the hpd gene from a nontypeable H. influenzae strain. In the deduced amino acid sequences for protein D, only 2 of 364 amino acid residues differed. The restriction fragment length polymorphism of the hpd region in different strains was analyzed by Southern blot analyses of PstI- or EcoRI-digested genomic DNA from 100 H. influenzae strains. The analysis was performed by using isolated fragments of the cloned hpd gene, originating from the nontypeable H. influenzae 772, as probes. All strains tested had DNA sequences with a high degree of homology to the hpd probes. The analysis also showed that restriction endonuclease sites within the gene were more conserved than sites adjacent to the hpd gene. An interesting difference between type b strains and unencapsulated strains was observed. The majority of type b strains seem to have a 1.4-kbp DNA fragment upstream of the hpd gene that is absent in nontypeable strains. On the basis of the high degree of conservation of the hpd gene among H. influenzae strains, we conclude that protein D is a possible vaccine candidate.

Cloning and characterization of the Methylobacterium extorquens polyhydroxyalkanoic-acid-synthase structural gene

A cosmid gene bank of partially EcoRI-digested genomic DNA from Methylobacterium extorquens IBT no. 6 was screened for DNA fragments restoring polyhydroxyalkanoic-acid (PHA) accumulation in the PHA-negative mutant Alkaligenes eutrophus H16 PHB-4. The M. extorquens PHA-synthase structural gene phaCMex was mapped on a 23-kbp EcoRI fragment by complementation studies, by hybridization experiments with heterologous DNA probes from A. eutrophus H16 encoding for phaA, phaB and phaC and by nucleic acid sequence analysis. Evidence for the presence of genes for a beta-ketothiolase or an acetoacetyl-coenzyme A reductase on this fragment was not obtained. The nucleotide sequence of a 3.7-kbp region was obtained. It contained the entire 1.815-kbp phaCMex plus approximately each 900-bp upstream and downstream of phaCMex.PhaCMex encoded a protein of 605 amino acids with a relative molecular mass (M(r)) of 66742, which exhibited 38.1% amino acid identity with the A. eutrophus PHA synthase. Determination of the N-terminal amino acid sequence of an M(r) 65,000 protein, which was enriched concomitantly with the purification of PHA granules in sucrose gradients, revealed a sequence that was identical with the amino acid sequence deduced from the most probable translation start codon except for a valine, which was obviously removed post-translationally. Enzyme analysis, which was done with the native gene and a phaCMex'-'lacZ fusion gene, gave no evidence for expression of phaCMex in Escherichia coli.

A 2359-base pair DNA fragment from Cryptosporidium parvum encoding a repetitive oocyst protein

A Cryptosporidium parvum λgt11 expression library was constructed using EcoRI-digested genomic DNA extracted from in vitro-excysted oocysts. Screening of this library with rat anti- Cryptosporidium antiserum led to the isolation of a clone containing a 2359-bp EcoRI fragment. When this fragment was ligated into the EcoRI site of plasmid vector pMS1S, the resulting clone expressed a 200-kDa β-galactosidase fusion protein. Western blot analysis using serum raised against this fusion protein indicated that the EcoRI fragment represented part of a gene encoding a 190-kDa oocyst wall protein of C. parvum. Sequencing of the fragment revealed a continuous open reading frame encoding 786 amino acids. The DNA sequence is relatively low in G + C (39.1%), and the third codon position contains only 17.9% G + C. The deduced peptide sequence has unusually high proportions of cysteine, proline, glutamine and histidine. Another striking feature of the amino acid sequence is the presence of distinctly repetitive regions based on conserved cysteine residues.

Genetic variability in a family of satellite DNAs from tilapia (Pisces: Cichlidae).

We have cloned and sequenced members of a family of satellite DNAs from three genera of the tilapiine tribe of fishes: Oreochromis, Sarotherodon, and Tilapia. The satellite DNAs, visualized as intensely staining bands following electrophoretic separation of EcoRI-digested genomic DNA, consist of three size variants differentially distributed in the various tilapiine species. The sizes of the monomers are approximately 237 bp (type I), 230 bp (type II), and 209 bp (type III). Several cloned monomers were sequenced from Oreochromis niloticus (type III), Oreochromis placidus (types I and II), Sarotherodon galilaeus (type I), Tilapia zillii (type I), and Tilapia rendalli (type I). Comparison of derived consensus sequences for the monomer units of the satellite DNAs revealed sequence identities within and between species that ranged from 89 to 96%. The type II and type III size variants appear to have arisen by deletions of 9 and 29 bp, respectively, within different regions of the type I satellite. Hybridization of a cloned monomer satellite from O. niloticus (type III) to PalI digests of genomic DNA from all three genera detected polymorphic, high molecular weight restriction fragments that produced fingerprint-like patterns. The complexity of these DNA fingerprints varied from one species to another, suggesting a markedly different genomic organization for these polymorphic satellite DNAs.

Two Oryza sativa Genomic DNA Clones Encoding 16.9-Kilodalton Heat-Shock Proteins

When all living organisms are exposed to elevated temperatures, they exhibit induced synthesis of a set of proteins known as HSPs.Y Using rice heat-shock cDNA pTSS.1 (5) as a probe, we isolated two 16.9-kD HSP genes from a rice genomic library (Table I). The rice genomic library was constructed in a XgtlO vector using EcoRI-digested rice genomic DNA fragments (size between 2.0 and 4.0 kb) as inserts that were eluted from agarose gel pieces by a NA 45 DEAE membrane (Schleicher and Schuell). The heat-shock cDNA pTS1 hybridized to 2.5and 3.4-kb EcoRI-digested rice genomic DNA fragments in Southern hybridization. The DNA sequences of the two rice genomic HSP genes, Oshspl6.9A and Oshspl6.9B, were determined and analyzed as shown in Figure 1. Oshspl6.9A contained the sequence of cDNA pTS1. Comparison of Oshspl6.9A and Oshspl6.9B genes reveals that they share 98.8% homology in terms of the nucleotide sequence in the coding regions and 99.3% homology at the level of the deduced amino acid sequence. Multiple copies of the HSE-like sequence, similar to the Drosophila heat-shock consensus sequence (4), can be identified upstream from the putative TATA box, TATAAATA. The initiation site of the transcription of Oshspl6.9A and Oshspl6.9B, which was identified by the primer extension method (1), is located 131 bases upstream from the coding region and 26 bases downstream from the TATA-like region. The deduced polypeptide sequence of the Oshspl6.9A gene exhibits 73 and 84% homology to Gmhspl7.5E from soybean (2) and c5-8 from wheat (3), respectively. Table I. Characteristics of Two 16.9-kD Heat-Shock Genes from Oryza sativa

Expression of the Polymorphic Human DNA Repair Gene XRCC1 Does Not Correlate with Radiosensitivity in the Cells of Human Head and Neck Tumor Cell Lines

The human X-ray repair cross-complementing gene 1 (XRCC1) is highly polymorphic in the cells of human head and neck squamous cell carcinoma lines and in a variety of other human cell lines. We describe six patterns seen in Southern analysis of EcoRI-digested genomic DNA. Levels of XRCC1 mRNA vary in cells of human head and neck cell lines as seen in northern blots. Expression of this gene in cell culture does not correlate with radiobiological parameters, clinical outcome, or the DNA restriction fragment length polymorphisms.

Identification of Mycobacterium kansasii by DNA hybridization

A DNA probe specific for Mycobacterium kansasii was obtained from a plasmid clone library of EcoRI-digested genomic DNA. The probe specifically identified culture-confirmed isolates of M. kansasii and isolates in cultures of environmental water samples. In an attempt to distinguish between isolates of M. kansasii, we used two methods to demonstrate restriction fragment length polymorphisms in the genomic DNA. Both of these methods failed to detect any differences between the isolates. These isolates included the type strain TMC 1201, environmental isolates, and clinical isolates from Australia and the Solomon Islands. This result suggests that the genome of M. kansasii is highly conserved and that genetic divergence within this species in insignificant.

Molecular fingerprinting of isolates of the genus Peptostreptococcus using rRNA genes from Escherichia coli and P. anaerobius

Restriction fragment length polymorphisms (RFLPs) of rRNA genes were evaluated as a tool for intra- and interspecies differentiation of Peptostreptococcus isolates. RFLPs from a collection of 20 clinical isolates and five ATCC strains representing five Peptostreptococcus spp. (P. anaerobius, P. asaccharolyticus, P. magnus, P. micros and P. prevotii) were obtained by hybridization of Southern blots of HindIII- or EcoRI-digested genomic DNA with three probes: probe A, a 0.98 kb HindIII fragment with a partial 16S rRNA gene sequence from P. anaerobius ATCC 27337; probe B, cloned Escherichia coli rrnB operon in plasmid pKK3535; and probe C, E. coli 16S and 23S rRNA. The hybridization patterns varied, but all yielded RFLPs useful for both intra- and inter-species differentiation. RFLPs of P. asaccharolyticus clinical isolates were closely related to each other and differed significantly from those of the ATCC type strains. The profiles of P. prevotii differed from those of the other four species studied, and based on the HindIII- and EcoRI-generated RFLPs, the strains in this species are more heterogeneous than the other four species studied.

Identification of a telomeric fragment from the right arm of chromosome III of Aspergillus nidulans

A minimum of 11 bands hybridising to an oligonucleotide complementary to the putative telomeric repeat sequence (TTAGGG)n was visible in a Southern blot of EcoRI-digested Aspergillus nidulans genomic DNA. All 11 were sensitive to BAL 31 exonuclease digestion, consistent with telomeric locations. Blots of DNA from aneuploid strains deleted for a dispensable, extreme distal region on the right arm of chromosome III lack a 1.3-kb EcoRI band, indicating that this fragment is located at or near the chromosome III right arm telomere.

Identification of a telomeric fragment from the right arm of chromosome III ofAspergillus nidulans

A minimum of 11 bands hybridising to an oligonucleotide complementary to the putative telomeric repeat sequence (TTAGGG)n was visible in a Southern blot of EcoRI-digested Aspergillus nidulans genomic DNA. All 11 were sensitive to BAL 31 exonuclease digestion, consistent with telomeric locations. Blots of DNA from aneuploid strains deleted for a dispensable, extreme distal region on the right arm of chromosome III lack a 1.3-kb EcoRI band, indicating that this fragment is located at or near the chromosome III right arm telomere.

A single oligonucleotide can be used to rapidly isolate DNA sequences flanking a transposon Tn5 insertion by the polymerase chain reaction

We have developed a strategy to rapidly construct DNA hybridization probes for the isolation of genes disrupted by transposon Tn5 insertions. A single oligonucleotide complementary to and extending outward from the ends of the inverted repeat of Tn5 was used to prime DNA synthesis in the polymerase chain reaction. The amplified product consisted of DNA sequences adjacent to both ends of the transposon insertion. The general feasibility of the approach was tested by amplifying pBR322 sequences from a derivative of pBR322 containing a Tn5 insertion. To amplify genomic DNA sequences flanking a Tn5 insertion in the chromosome of a Pseudomonas syringae strain, circular substrates were generated by ligating EcoRI-digested genomic DNA. Tn5 was contained intact within one such circular molecule, as the transposon does not contain sites for cleavage by EcoRI. The amplified product (approximately 2.5 kb) was used as a DNA hybridization probe to isolate the homologous fragment from a cosmid library of wild-type Pseudomonas syringae genomic DNA. This approach may be applied to the efficient isolation of sequences flanking any Tn5 insertion.

Molecular cloning and expression of antigens from Actinobacillus actinomycetemcomitans in Escherichia coli

In order to study the role of membrane proteins in mucosal colonization by Actinobacillus actinomycetemcomitans, a plasmid library was constructed by ligating EcoRI-digested genomic DNA from A. actinomycetemcomitans strain Y4 into EcoRI-digested and dephosphorylated pUC13 DNA. A second library was constructed by ligating Sau3A-digested and size-fractionated A. actinomycetemcomitans strain Y4 DNA into BamHI-cleaved and dephosphorylated pUC13 DNA. The DNA was transformed into Escherichia coli strain MC1022 and plated onto Luria-Bertani agar containing 100 μg/ml ampicillin and X-gal. Recombinant colonies were examined for the expression of A. actinomycetemcomitans antigens by colony immunoscreening using rabbit antiserum to strain Y4. Nine positive clones were isolated. Three of these clones produced proteins that reacted with rabbit antiserum to strain Y4 on a Western transfer, and seven of these clones reacted with rabbit antiserum to strain Y4 as measured by indirect immunofluorescence. One reactive clone contained an 8.4 kb plasmid, which directed the synthesis of a peptide with an M r of 20,000 as measured by SDS-PAGE. Partial DNA sequence analysis revealed the presence of a signal-peptide leader sequence at the amino terminus suggesting that the native protein is a membrane component of A. actinomycetemcomitans. Thus A. actinomycetemcomitans antigens can be expressed in E. coli, and some of these proteins may be expressed on the E. coli cell surface.

Relationship among selected Leptospira interrogans serogroups as determined by nucleic acid hybridization.

Leptospiral DNAs from a variety of Leptospira interrogans serogroups of veterinary significance, as well as a nonpathogenic leptospira, were compared by Southern blot hybridization of EcoRI-digested genomic DNA. The serogroups examined could be assigned to one of three groups on the basis of the degree of cross-hybridization between genomic DNAs. Only a few restriction fragments hybridized between the three groups, and most of these were shown to contain ribosomal DNA. The restriction fragment length polymorphism observed among the intergroup hybridizations allowed differentiation among serogroups and, in some cases, serovars. Under the hybridization conditions used, no hybridization was observed between leptospiral DNA and Leptonema, Escherichia coli, or porcine DNA.

Kappa/lambda immunoglobulin distribution in Graves' thyroid-stimulating antibodies. Simultaneous analysis of C lambda gene polymorphisms.

From patients with untreated Graves' disease 11 sera showing high cAMP release in the FRTL-5 cell assay were studied for relative proportions of kappa or lambda Ig molecules showing cAMP releasing activity. Immunoabsorption of gamma-globulins was performed using monoclonal murine anti-kappa or anti-lambda antibodies linked to cyanogen bromide-activated sepharose. Specific kappa- or lambda-adsorbed fractions were also eluted from immunoabsorbents using chaotrophic thiocyanate buffers and equilibrated with pH 7.4 low salt buffer by dialysis. Immunoabsorption and elution experiments showed that five Graves' sera contained predominant cAMP-releasing activity within lambda Ig fractions, whereas two Graves' sera showed predominant cAMP-releasing activity in kappa Ig fractions. Four sera showed cAMP release approximately equally divided between kappa and lambda Ig both after immunoabsorption and specific anti-kappa or anti-lambda eluates were studied. C lambda genotypes were examined by Southern blotting and restriction fragment length polymorphism analysis of Eco RI-digested genomic DNA from 158 patients with Graves' disease in parallel with 112 normal controls and 29 patients with autoimmune hypothyroidism. Notable shifts in proportions of 8/8 and 18/18 genotypes were present when Graves' patients were compared with normal controls. Allelic frequencies and ratios of genotype 8 to 18 were significantly different (P less than 0.05) when Graves' patients were compared either to normal controls or to patients with autoimmune hypothyroidism.

A novel centromeric repetitive DNA from human chromosome 22.

A recombinant DNA clone localized in the centromeric region of chromosome 22 was isolated from a flow-sorted human chromosome 22 DNA library. When the original insert of about 1.9 kb was used to probe Southern blots of EcoRI-digested genomic DNA it revealed at least 40 fragments. A comparable pattern was obtained with each of the three subclones (800, 700, and 380 bp). In situ hybridization showed signals clustered in the region 22cen. DNA sequence analysis using the 380 bp fragment subcloned in pTZ18/19 (p22hom48.4) revealed eight copies of a 48 bp repeat and the size of hybridizing restriction fragments indicated that this tandemly repeated sequence is spread over a region of a few hundred kilobases. Whereas this novel DNA, termed D22Z3, displayed no sequence homology to rodent and monkey genomes cross-homology was discernible for DNA from two great ape species.

Cloning of a cDNA for steroid sulfatase: frequent occurrence of gene deletions in patients with recessive X chromosome-linked ichthyosis.

A human steroid sulfatase (steryl-sulfatase; steryl-sulfate sulfohydrolase, EC 3.1.6.2) cDNA 2.4 kilobases long was isolated from a human placental lambda gt11 cDNA expression library. The library was screened with monospecific rabbit antibodies elicited by injection of steroid sulfatase protein purified from human placentas. Hybridization of the cDNA with EcoRI-digested genomic DNA indicated that patients from 14 of 15 apparently unrelated families have gross deletions of the gene for steroid sulfatase. One patient had genomic DNA fragments that were identical to those from normal individuals, indicating the absence of any major deletions as the cause of his lack of steroid sulfatase enzyme activity.