Partial Nucleotide Sequence Analysis Research Articles

Gene-scrambling mutagenesis: generation and analysis of insertional mutations in the alginate regulatory region of Pseudomonas aeruginosa

A novel method for random mutagenesis of targeted chromosomal regions in Pseudomona aeruginosa was developed. This method can be used with a cloned DNA fragment of indefinite size that contains a putative gene of interest. Cloned DNA is digested to produce small fragments that are then randomly reassembled into long DNA inserts by using cosmid vectors and lambda packaging reaction. This DNA is then transferred into P. aeruginosa and forced into the chromosome via homologous recombination, producing in a single step a random set of insertional mutants along a desired region of the chromosome. Application of this method to extend the analysis of the alginate regulatory region, using a cloned 6.2-kb fragment with the algR gene and the previously uncharacterized flanking regions, produced several insertional mutations. One mutation was obtained in algR, a known transcriptional regulatory of mucoidy in P. aeruginosa. The null mutation of algR was generated in a mucoid derivative of the standard genetic strain PAO responsive to different environmental factors. This mutation was used to demonstrate that the algR gene product was not essential for the regulation of its promoters. Additional insertions were obtained in regions downstream and upstream of algR. A mutation that did not affect mucoidy was generated in a gene located 1 kb upstream of algR. This gene was transcribed in the direction opposite that of algR transcription and encoded a polypeptide of 47 kDa. Partial nucleotide sequence analysis revealed strong homology of its predicted gene product with the human and yeast argininosuccinate lyases. An insertion downstream of algR produced a strain showing reduced induction of mucoidy in response to growth on nitrate as the nitrogen source.

Identification of a 66 KDa protein associated with yeast mitochondrial ATP synthase as heat shock protein hsp60

A 66 kDa protein, denoted P66, not hitherto classified as an integral component of yeast mitochondrial ATPase, is often observed in preparations of this enzyme complex. A physical association exists between P66 and the assembled ATPase complex since both components are coimmunoprecipitated by anti-F 1β monoclonal antibody. Two recombinant clones expressing proteins immunologically similar to P66 were isolated from a yeast genomic library in λgt11 by screening with a polyclonal anti-holo-ATPase antibody. Based on restriction site mapping and partial nucleotide sequence analysis, both clones encompass the gene encoding the yeast heat shock protein hsp60. The identification of P66 with hsp60, taken together with its demonstrated association with the mitochondrial ATPase complex, is consistent with recent suggestions that hsp60 is involved in assembly of the ATP synthase complex.

Vasopressin mRNA in the neurolobe of the rat pituitary

Pro-vasopressin-neurophysin mRNA (AVP mRNA) was assayed in the pituitary gland of rats from different strains, using a specific cRNA probe corresponding to exon C of the vasopressin gene. Northern blot analysis revealed the presence of an about 650 base pair (bp) AVP mRNA in the neurolobe of all strains. No signal was found in the anterior or intermediate lobes. Partial nucleotide sequence analysis suggested identity with the genuine AVP mRNA. Osmotic stimulation with 2% saline or water deprivation increased AVP mRNA levels in a fashion that paralleled changes seen in the hypothalamus. The origin of the AVP mRNA in the neurolobe is uncertain but is likely to be the pituicytes. Transport of the mRNA into the nerve endings of hypothalamic supraoptic and paraventricular neurons is an alternative possibility.

Human Papillomavirus Type 56: a New Virus Detected in Cervical Cancers

A new human papillomavirus type (HPV-56) was identified by low stringency Southern blot analysis with an HPV-31 DNA probe, in a cervical intraepithelial neoplasm (CIN). The DNA of this virus was molecularly cloned and shown to be a new HPV type based on the absence of cross-reactivity to HPV types 1 to 55 under high-stringency hybridization conditions. At low stringency, HPV-56 was most related to HPV types 30 and 45. The deduced organization of the open reading frames of HPV-56, from hybridization and partial nucleotide sequence analyses, reveals a typical HPV genome. HPV-56 was detected in two of 464 normal cervical tissues, in five of 227 cervical condylomas and CIN, and in two of 84 invasive cancers of the cervix.

Isolation and chromosomal localization of the human En-2 gene

By low stringency hybridization we have isolated from a human cosmid genomic library sequences homologous with a probe from the Drosophila engrailed gene. Partial nucleotide sequence analysis shows a consensus splice acceptor site followed by an open reading frame (ORF) that can encode 104 amino acids; the first 94 amino acids have 71% identity with the Drosophila engrailed protein. The shared region contains a homeo domain and is within the region of engrailed shared with the Drosophila invected gene and the mouse En-1 and En-2 genes. At the amino acid level, the human sequence is 85% identical with the mouse En-1 gene and 100% identical with the mouse En-2 gene. Hybridization against a panel of human-hamster somatic cell hybrids maps this human En-2 gene to chromosome 7, and regional mapping by in situ hybridization to human chromosomes localizes it to region 7q36 at the end of the long arm.

Recombination in hamster cell nuclear extracts between adenovirus type 12 DNA and two hamster preinsertion sequences.

A cell-free system of nuclear extracts from BHK21 cells has been developed to catalyse recombination in vitro between the DNA of adenovirus type 12 (Ad12) and two different hamster preinsertion sequences. The pBR322 cloned 1768 bp fragment p7 and the 3.1 kbp fragment p16 from BHK21 hamster DNA had previously been identified as the preinsertion sites corresponding to the junctions between Ad12 DNA and hamster DNA in cell line CLAC1 and in the Ad12-induced tumour T1111(2), respectively. Preinsertion sequences, which had recombined previously with foreign (Ad12) DNA, might again be recognized by the recombination system even in a cell-free system. PstI cleaved Ad12 DNA and the circular or the EcoRI linearized p7 or p16 preinsertion sequences were incubated with nuclear extracts. Recombinants were isolated by transfecting the DNA into recA- Escherichia coli strains and by screening for Ad12 DNA-positive colonies. Without a selectable eukaryotic marker, all Ad12 DNA positive recombinants were registered. Out of a total of greater than 90 p7-Ad12 DNA recombinants, 21 were studied by restriction-hybridization, and four by partial nucleotide sequence analyses. Among the p16-Ad12 DNA recombinants, four were analysed. The sites of linkage between Ad12 DNA and p7 or p16 hamster DNA were all different and distinct from the original CLAC1 or T1111(2) junction site between Ad12 and hamster DNA. The in vitro recombinants were not generated by simple end-to-end joining of the DNA fragments used in the reaction but by genetic exchange. Thirteen of the 25 recombinants were derived from the 61-71 map unit fragment of Ad12 DNA. Recombination experiments between Ad12 DNA and four randomly selected unique or repetitive hamster DNA sequences of 1.5-6.2 kbp in length did not yield recombinants. Apparently, the p7 and p16 hamster preinsertion sequences recombined with Ad12 DNA with a certain preference.

Gene conversion-like events cause steroid 21-hydroxylase deficiency in congenital adrenal hyperplasia.

Genomic DNAs from twelve Japanese patients with steroid 21-hydroxylase [21-OHase; steroid 21-monooxygenase; steroid, hydrogen-donor:oxygen oxidoreductase (21-hydroxylating); EC 1.14.99.10] deficiency were analyzed by Southern blot hybridization. A 3.7-kilobase (kb) Taq I and a 1.7-kb Pvu II restriction endonuclease fragment that correspond to a 21-OHase B gene were absent from the DNA of two unrelated patients with the salt-wasting form of the disease. However, a 10.5-kb Bgl II fragment corresponding to the region encompassing the 21-OHase B gene was still present in these two patients. The genes encoding 21-OHase were cloned from one of these two patients, who was homozygous by descent for HLA-A26;B39;C4A3;C4B1;DR4. Restriction endonuclease mapping as well as partial nucleotide sequencing analysis revealed that the 21-OHase B gene of the patient has been converted to the pseudogene, 21-OHase A, as far as the critical 0.5-kb sequence was concerned. Thus, the defect was due to both chromosomes each carrying two copies of 21-OHase A pseudogene and lacking functional 21-OHase B gene.

Type XII collagen: distinct extracellular matrix component discovered by cDNA cloning.

We have screened a cDNA library constructed from tendon fibroblast mRNA for the presence of collagenous coding sequences. Nucleotide sequence analysis of one isolated clone, pMG377, reveals that the clone encodes a polypeptide that is homologous to, yet distinctly different from, type IX short-chain collagen polypeptides. The structure of the conceptual translation product of the cDNA is also different from that of all other collagen types. Therefore, we have given the type IX-like collagen chain encoded by pMG377 the designation alpha 1(XII). Ribonuclease protection assays with single-stranded cRNA probes demonstrate that alpha 1(XII) mRNA is present in several tissues such as calvaria, tendon, and sternal cartilage of 17-day-old chicken embryo and in cornea from 6-day-old embryos. Using pMG377 as the hybridization probe, we isolated a fragment of the corresponding gene from a chicken genomic library. Partial nucleotide sequence analysis of the genomic clone DG12 shows that the exon/intron structure of the alpha 1(XII) collagen gene appears to be homologous to that of the alpha 1(IX) and alpha 2(IX) collagen genes. Our data demonstrate that types IX and XII collagen are two homologous members of a family of unique collagenous proteins that show tissue-specific patterns of expression. Based on their structure and the properties of their genes, we conclude that this family of collagens is distinctly different from that of fibrillar collagens.

En-1 and En-2, two mouse genes with sequence homology to the Drosophila engrailed gene: expression during embryogenesis.

Two mouse genes, En-1 and En-2, have sequence homology to the engrailed (en) and invected (inv) genes of Drosophila (Joyner et al. 1985). Partial nucleotide sequence analyses of genomic and cDNA clones show that the homologous sequences can encode a stretch of 107 amino acids, including a centrally located, 60-amino-acid homeo box. Within the homologous regions of the mouse and Drosophila genes, 78 (73%) of the amino acids are identical. Such extensive conservation of sequence outside the homeo box between vertebrate and Drosophila homeo box-containing genes is thus far unique. En-1 and En-2 are expressed during mouse embryogenesis. Transcripts from both genes were detected in RNA samples from teratocarcinoma cells, which serve as in vitro models for the early embryo, and from embryos at 9.5 through 17.5 days of development. For each gene we observed a unique pattern of changes in the number and relative intensities of transcripts detectable during embryonic development. Transcripts from both genes are represented abundantly in RNA extracted from the posterior portion of the fetal brain, and are much less abundant in RNA from other fetal tissues, including the anterior portion of the brain and the spinal cord. The chromosome map positions of En-1 and En-2 were determined by recombinant inbred strain analyses. Unlike their Drosophila counterparts, they are unlinked: En-1 is in the central portion of the mouse chromosome 1 and En-2 is in the proximal portion of mouse chromosome 5. Both genes map in the vicinity of mutations that are known to cause abnormalities during development.

Rat ceruloplasmin. Molecular cloning and gene expression in liver, choroid plexus, yolk sac, placenta, and testis.

A rat ceruloplasmin cDNA clone was isolated from a rat liver cDNA library and identified by partial nucleotide sequence analysis. Rat liver ceruloplasmin mRNA levels were measured during the acute phase response to inflammation by cytoplasmic dot hybridization to ceruloplasmin cDNA. Regulation of ceruloplasmin synthesis appeared to be at the mRNA level, with the concentration of ceruloplasmin mRNA increasing significantly 12 h after induction of inflammation, reaching a maximum of 350% of normal at 36 h and returning to normal levels within 60 h. Using Northern blot analysis, extrahepatic ceruloplasmin gene expression was observed in choroid plexus, yolk sac, placenta, and testis. All these tissues are at the interface between, and possibly involved in maintaining homeostasis in, adjacent extracellular compartments. No ceruloplasmin mRNA was detected in RNA from stomach and small intestine.

Characterization of 5'-flanking region of heart myosin light chain 2A gene. Structural and functional evidence for promoter activity.

Two recombinant clones, lambda LC5 and lambda LC13, encompassing the entire regulatory myosin light chain 2 (MLC2A) gene of chicken heart muscle were isolated. Of these, lambda LC5 which contains a large 5'-flanking sequence of about 7.0 kb, was characterized by a partial nucleotide sequence analysis. A TATA-like sequence (TATTTTTA) and a CAAT-box (CAAAAGT) are located at positions -32 and -59, respectively, which most likely constitute the functional promoter region in the gene. Based on primer extension reaction with a synthetic 20-mer corresponding to the 5'-leader sequence and total poly(A+) RNA, the probable transcription initiation site in the gene was located. The gene promoter activity was demonstrated following transient expression of recombinant genomes containing the chicken upstream sequence fused to the bacterial chloramphenicol acetyltransferase (CAT) or to the rat preproinsulin II genes. The extracts from a Quail fibroblast cell line (QT35) transfected with the construct (pLCo5.2iCat) containing the putative chicken promoter, and the CAT gene promoted the formation of 3'-acetate chloramphenicol. Another construct (pBC12LC5.2f) contains the rat preproinsulin II gene placed under the control of chicken promoter and a simian virus 40 origin of replication. Transfection of COS cell line with pBC12LC5.2f DNA resulted in an efficient expression of rat preproinsulin mRNA initiating from the chicken promoter. The transfection assay also allowed detection of chicken MLC2A gene transcripts by S1-nuclease protection of end-labeled DNA probes. A comparison of the MLC2A upstream gene sequence with those available for skeletal myosin light chains revealed no common sequence elements, suggesting that cardiac MLC2A gene promoter region has diverged considerably from its counterparts in skeletal muscle.

Tissue-specific expression of rat aldolase A mRNAs. Three molecular species differing only in the 5'-terminal sequences.

Three species of aldolase A mRNA (mRNAs I, II, and III) only differing in the structure of the 5'-terminal noncoding region were detected in rat tissues. The cDNA clones for mRNAs II and III were prepared from ascites hepatoma AH60C and sequenced. The mRNA II is 1393 nucleotides long excluding poly(A) tail, while the mRNA III is 1440 nucleotides long, some 50 nucleotides longer than the mRNA II. The mRNAs II and III differ in the sequence between -25 and the 5' termini from the previously reported skeletal muscle aldolase A mRNA (mRNA I, 1343 nucleotides long). By contrast, the residual 5' noncoding sequence (-24 to -1) and the coding and 3' noncoding sequences are common to all the mRNAs. By dot spot hybridization and S1 mapping the distribution of these mRNAs in the various tissues was determined. The mRNA I appears exclusively in a skeletal muscle and some in heart and hepatoma AH60C, whereas the mRNAs II and III appear more or less in all the tissues examined, implying that their appearances are under tissue-specific control. Furthermore, partial nucleotide sequence analysis of the fetal liver aldolase A mRNA supports that aldolase A mRNA that reappeared in hepatoma is really a resurgence of the gene product expressed in the fetus.

Molecular analysis of the human class I alcohol dehydrogenase gene family and nucleotide sequence of the gene encoding the beta subunit.

Human alcohol dehydrogenase (ADH) exists as a heterogeneous group of isozymes capable of oxidizing a wide variety of aliphatic and aromatic alcohols. The five distinct human ADH subunits, each encoded by a separate gene, are differentially expressed during development and are subject to tissue-specific regulation. To analyze the organization and regulation of human ADH genes we first isolated a cDNA clone (pADH12) encoding the 3' portion of the beta ADH gene. In the current study pADH12 was used to screen a human genomic library, and several overlapping and nonoverlapping clones were selected. Hybridization and partial nucleotide sequence analyses of the clones indicated that three full-length human ADH genes encoding the alpha, beta, and gamma subunits were isolated. Human genomic DNA hybridization results indicate that the alpha, beta, and gamma ADH genes form a closely related gene family and suggest that the other known human ADH genes (i.e. those encoding the pi and chi subunits) share a more distant evolutionary relationship. Nucleotide sequence analysis of the beta ADH gene reveals that the coding region is interrupted by eight introns and spans approximately 15 kilobases. A presumptive transcription initiation site for the beta ADH gene was located by S1 nuclease mapping at a position 70 base pairs upstream of the start codon. The 5' flanking region possesses a TATA box promoter element as well as two tandem DNA sequences which display homology to previously examined glucocorticoid-responsive elements.

A v-erbB-related protooncogene, c-erbB-2, is distinct from the c-erbB-1/epidermal growth factor-receptor gene and is amplified in a human salivary gland adenocarcinoma.

From a human genomic library, we obtained six v-erbB-related DNA clones. A DNA probe prepared from one of the clones, lambda 107, hybridized to EcoRI fragments of 6.4 and 13 kilobase pairs of human DNA. Neither of these fragments was amplified in A431 vulva carcinoma cells, in which the gene encoding the epidermal growth factor receptor is amplified. In addition, the probe from lambda 107 hybridized with a single, 4.8-kilobase poly(A)+ RNA species and did not react with EGF receptor mRNA. Thus, we conclude that clone lambda 107 represents a v-erbB-related gene (c-erbB-2) that is distinct from the EGF receptor gene. In contrast, the other five clones were shown to represent the EGF receptor gene (c-erbB-1). Partial nucleotide sequence analysis of the lambda 107 insert showed that this clone contained at least seven putative exons and that six of them could encode the kinase domain characteristic of protein products of the src oncogene family. Southern blot analysis showed close similarity of the restriction patterns of the rat c-erbB-2 gene and the rat neu oncogene, suggesting possible involvement of c-erbB-2 in human cancer. In fact, approximately 30-fold amplification of c-erbB-2 was observed in a human adenocarcinoma of the salivary gland.

Isolation and expression of the Escherichia coli gene encoding malate dehydrogenase.

An oligodeoxynucleotide specific for a pentapeptide sequence corresponding to amino acid residues 32 through 36 of Escherichia coli malate dehydrogenase was chemically synthesized and used to identify the mdh gene on plasmid pLC32-38 from the Clarke-Carbon recombinant library. Cells transformed with this plasmid exhibited a 10-fold increase in malate dehydrogenase activity. A 1.2-kilobase PvuII fragment which hybridized with the oligodeoxynucleotide probe was subcloned, and the identity of the mdh structural gene was confirmed by partial nucleotide sequence analysis. The expression of the mdh gene, as measured by both Northern blotting and enzyme assays, was found to vary over a 20-fold range with different culture conditions.

Expression of a biologically active fragment of human IgE epsilon chain in Escherichia coli.

cDNA corresponding to human IgE heavy (epsilon) chain mRNA was cloned from human IgE-secreting myeloma U266 cells. Partial nucleotide sequence analysis demonstrated that the cloned cDNA contained the coding region for about two-thirds of the CH2 and all of the CH3 and CH4 domains as well as the 3'-untranslated region. This epsilon cDNA was inserted into expression vector pUC7 and expression of an epsilon-chain fragment in Escherichia coli was demonstrated by protein blot analysis using 125I-labeled goat anti-human IgE as probe. The expression product was purified on a column of goat anti-human IgE-conjugated Sepharose 4B and the polypeptide was found to retain binding activity to human basophils.

A cDNA clone for protein Z, a major barley endosperm albumin

An 18 residue amino terminal sequence of the barley endosperm protein Z polypeptide is presented. In vitro translation of barley endosperm mRNA and subsequent immunoaffinity isolation using protein Z antibodies identified two major protein Z precursor polypeptides of M.W.44,000 and 46,000 among the translation products. Partial nucleotide sequence analysis identified a cDNA clone to encode the amino terminal portion of protein Z. Messenger RNA sequences 1,800 nucleotides in length, sufficient to code for the protein Z precursor polypeptides, were detected by hybridization to the protein Z cDNA probe. Hybridization of the probe to restriction endonuclease fragments of barley nuclear DNA suggests, that protein Z is encoded by a small multigene family.

Isolation of a cDNA clone for the type I regulatory subunit of bovine cAMP-dependent protein kinase.

A cDNA clone for the type I regulatory subunit (RI) of cAMP-dependent protein kinase (ATP:protein phosphotransferase, EC 2.7.1.37) was isolated from bovine testis by a differential screening method. mRNA coding for RI was enriched 50- to 100-fold by polysome immunoadsorption chromatography with affinity-purified rabbit anti-RI and protein A-Sepharose. Poly(A)+ RNA from these polysomes was utilized to construct a cDNA library in pBR322, and this library was screened for hybridization to 32P-labeled cDNAs synthesized from either total or RI-enriched poly(A)+ RNA. Plasmids isolated from colonies showing preferential hybridization to the latter probe were further characterized by hybrid selection and DNA sequence analysis. One of these plasmids (designated 62C12) contains a 1,350-nucleotide insert that hybridized to RI mRNA; partial nucleotide sequence analysis confirmed its identity and indicated that it may contain the entire RI coding region. We also have identified a recombinant plasmid with a 1,550-nucleotide insert that selected through hybridization a mRNA coding for a 55,000-dalton protein that crossreacts with anti-RI antibodies. The function of this latter protein is unknown.

Rat gastrin's amino acid sequence determined from the nucleotide sequence of the mRNA

Gastrin cDNA was synthesized using a synthetic oligodeoxynucleotide to specifically prime rat mRNA preparations for reverse transcription. Hybridization analysis using this cDNA indicated that rat gastrin mRNA is the same size as that which codes for hog gastrin. The amino acid sequence for rat gastrin 34 was determined from a partial nucleotide sequence analysis of the cDNA and indicates that in rat, as in other species, gastrin is synthesized as a larger precursor which is processed following two consecutive basic amino acids to yield molecules of 34 and 17 amino acids (gastrin-34 and gastrin-17).