The making of strand-specific M13 probes

Transcription of a long, interspersed, highly repeated DNA element in Xenopus laevis

We have analyzed the transcription of 1723, a long, repeated DNA element that is interspersed in the genome of Xenopus laevis (B. K. Kay and I. B. Dawid (1983) J. Mol. Biol. 170, 583-596). We have detected RNA homologous to 1723 in total cellular RNA from ovaries, embryos, liver, and cultured kidney cells. Transcripts from both strands of the element are present at similar concentrations in these different RNA preparations. In oocytes, approximately 100 pairs of lampbrush chromosome loops are active in the transcription of 1723 elements. The abundance of 1723 RNA increases during embryogenesis, with the highest level reached at the tadpole stage. From cellular fractionation studies, we conclude that 1723 transcripts are largely limited to the nucleus.

Intermediate filament cDNAs from BHK-21 cells: demonstration of distinct genes for desmin and vimentin in all vertebrate classes

Recombinant cDNA plasmids for the intermediate filament proteins desmin and vimentin were constructed from baby hamster kidney (BHK-21) mRNA. Analysis of four desmin clones gave a sequence of 1574 nucleotides, which is 75% of the total mRNA length. The derived amino acid sequence for hamster desmin shows 92% overall homology with chicken desmin; the homology with hamster vimentin is highest in the alpha-helical middle part (74%). The 3'-noncoding region of desmin mRNA is found to be 677 nucleotides long. With the aid of 5'- and 3'-specific probes, it has been established that there is a single gene for desmin in the hamster genome. This gene expresses a single mRNA species of 2.2 kilobases. Hybridization experiments of a number of DNAs with desmin and vimentin probes show that there are distinct restriction enzyme fragments carrying vimentin and desmin sequences in the genome of representatives of all vertebrate classes.

Isolation and characterization of the RAD2 gene of Saccharomyces cerevisiae

We have cloned the RAD2 gene of Saccharomyces cerevisiae and used it to determine the size and direction of its transcript and to make rad2 deletion mutants. The RAD2 gene encodes a 3.3-kb transcript and the direction of transcription is leftwards, from EcoRI towards Bg/II. Deletions of the RAD2 gene have no effect on viability of vegetative cells or spores, or on sporulation.

Isolation of the dorsal locus of Drosophila

The establishment of embryonic polarity is a crucial step in pattern formation and morphogenesis. In the fruitfly Drosophila melanogaster, embryonic polarity depends primarily on genes expressed in the female during oogenesis. Mutations in these 'maternal effect' genes can lead to major disruptions in normal pattern formation. Two classes of maternal genes essential for the establishment of polarity in the embryo have been identified. Lesions in one class, the 'bicaudal' genes, disrupt the anterior-posterior axis; lesions in the other class disrupt dorsal-ventral polarity, and in the most extreme cases embryos fail to form any ventral or lateral structures. Genetic studies suggest that the anterior-posterior and dorsal-ventral axes may be independent as the defects observed in mutants from each class seem to be restricted to one axis only. The dorsal (dl) locus is one of the maternal effect genes involved in the establishment of dorsal-ventral polarity. Homozygous dl females produce embryos exhibiting the mutant phenotype--complete lack of dorsal-ventral polarity in the strongest alleles--irrespective of the genotype of the father. Although dl is a maternal effect locus and must be expressed during oogenesis, the gene product, or a substance depending on the normal function of the dl gene, seems to be active early in embryogenesis, as the dl phenotype can be partially rescued by injection of cytoplasm from wild-type cleavage-stage embryos. Here we report the molecular cloning of the dorsal locus and a study of its expression.

Fine structure genetic map and complementation analysis of mutations in the dnaA gene of Escherichia coli

A fine structure genetic map of several mutations in the dnaA gene of Escherichia coli was constructed by the use of recombinant lambda and M13 phages. The dnaA508 mutation was found to be the mutation most proximal to the promoter, while the dnaA203 mutation was found to be the most distal one. The order of mutations established in this analysis was: dnaA508, dnaA167, (dnaA5, dnaA46, dnaA211), dnaA205, dnaA204, dnaA203. The mutations dnaA601, dnaA602, dnaA603, dnaA604 and dnaA606 were found to map very close to each other and close to dnaA205 in the middle third of the dnaA gene. In analysing the dominance relationship all 13 dnaA mutations were found to be recessive to the wild type. Characteristic phenotypes of the dnaA(Ts) mutants, like reversibility of the temperature inactivation of the dnaA protein, cold sensitivity of haploid or of merodiploid strains and suppressibility by rpoB mutations, are found to correlate with clusters of mutations within the gene.

Two genes for ribosomal protein 51 of Saccharomyces cerevisiae complement and contribute to the ribosomes

We cloned and sequenced the second gene coding for yeast ribosomal protein 51 (RP51B). When the DNA sequence of this gene was compared with the DNA sequence of RP51A (J.L. Teem and M. Rosbash, Proc. Natl. Acad. Sci. U.S.A. 80:4403--4407, 1983), the following conclusions emerged: both genes code for a protein of 135 amino acids; both open reading frames are interrupted by a single intron which occurs directly after the initiating methionine; the open reading frames are 96% homologous and code for the same protein with the exception of the carboxy-terminal amino acid; DNA sequence homology outside of the coding region is extremely limited. The cloned genes, in combination with the one-step gene disruption techniques of Rothstein (R. J. Rothstein, Methods Enzymol. 101:202-211, 1983), were used to generate haploid strains containing mutations in the RP51A or RP51B genes or in both. Strains missing a normal RP51A gene grew poorly (180-min generation time versus 130 min for the wild type), whereas strains carrying a mutant RP51B were relatively normal. Strains carrying mutations in the two genes grew extremely poorly (6 to 9 h), which led us to conclude that RP51A and RP51B were both expressed. The results of Northern blot and primer extension experiments indicate that strains with a wild-type copy of the RP51B gene and a mutant (or deleted) RP51A gene grow slowly because of an insufficient amount of RP51 mRNA. The growth defect was completely rescued with additional copies of RP51B. The data suggest that RP51A contributes more RP51 mRNA (and more RP51 protein) than does RP51B and that intergenic dosage compensation, sufficient to rescue the growth defect of strains missing a wild-type RP51A gene, does not take place.

Evolutionary divergence of genes for ornithine and aspartate carbamoyl-transferases--complete sequence and mode of regulation of the Escherichia coli argF gene; comparison of argF with argI and pyrB

The complete nucleotide sequence of argF is presented, together with that of an operator-constitutive mutant. ArgF is compared with the other gene coding for ornithine carbamoyltransferase (OTCase) in E. coli K-12, argI, and with pyrB, encoding the catalytic monomer of aspartate carbamoyltransferase (ATCase). ArgF and argI appear very closely related having emerged from a relatively recent ancestor gene. The relationship between OTCase and ATCase appears more distant. Nevertheless, the homology observed between the two proteins (mainly in the polar domain) suggests a common origin.

Cell-specified expression of a selectable hybrid gene

We have inserted into a retroviral vector the structural information encoding the selectable bacterial genes neo and gpt linked, respectively, to the promoters of the herpesvirus thymidine kinase gene and the rat preproinsulin II gene. We have used this recombinant retrovirus construction to transduce insulinoma cell lines that are positive or negative for insulin expression. Selection of the transductants for neo yielded resistant colonies from all of the cell lines, while selection for gpt yielded resistant transductants in relatively high frequency only from insulin-producing cells. The 5' end of the gpt transcripts maps to the authentic preproinsulin capping site of the construction.

Conservative replication of double-stranded RNA in Saccharomyces cerevisiae by displacement of progeny single strands

Saccharomyces cerevisiae contains two double-stranded RNA (dsRNA) molecules, L and M, encapsulated in virus-like particles. After cells are transferred from dense (13C 15N) to light (12C 14N) medium, only two density classes of dsRNA are found, fully light (LL) and fully dense (HH). Cells contain single-stranded copies of both dsRNAs and, at least for L dsRNA, greater than 99% of these single strands are the positive protein-encoding strand. Single-stranded copies of L and M dsRNA accumulate rapidly in cells arrested in the G1 phase. These results parallel previous observations on L dsRNA synthesis and are consistent with a role of the positive single strands as intermediates in dsRNA replication. We propose that new positive strands are displaced from parental molecules and subsequently copied to produce the completely new duplexes.

The use of heparin as a simple cost-effective means of controlling background in nucleic acid hybridization procedures

The use of heparin as a simple, effective and cheap substitute for conventional methods of controlling background in hybridization procedures is described and illustrated with reference to the use of DNA probes in filter and in situ hybridization. Possible specific mechanisms for this heparin effect are discussed.

A molecular analysis of fushi tarazu, a gene in Drosophila melanogaster that encodes a product affecting embryonic segment number and cell fate

Mutations at the fushi tarazu locus in Drosophila melanogaster affect both segment number and the pattern of cuticular structures on alternating segments of embryos. The ftz gene has been cloned and characterized. Two mutations, ftzw20 and ftzRpl are associated with lesions in a 3.2 kb fragment of DNA cloned in the Antennepedia Complex (ANT-C) chromosome "walk." The structure of DNA isolated from the ftzw20 and ftzRpl chromosomes indicates that the mutations are associated with a 4.9 kb insertion of DNA and a chromosomal rearrangement breakpoint, respectively. The 3.2 kb genomic DNA fragment hybridizes to a 1.8 kb polyadenylated transcript which accumulates maximally at 2-4 hr of embryonic development. The ftzw20 and ftzRpl mutations have different phenotypic consequences for the developing embryo, although both mutations interrupt the 1.8 kb transcription unit. The genetic and molecular data indicate that the 1.8 kb transcript derives from the ftz locus. The gene products are synthesized and utilized several hours prior to the visibly detectable morphogenetic events which the gene apparently regulates.

Cloning and transcriptional analysis of the segmentation gene fushi tarazu of Drosophila

In the course of studying the Antennapedia (Antp) locus, we found that one of the 3' Antp exons has weak cross-homology to another gene affecting segmentation, fushi tarazu (ftz; meaning "not enough segments"), which is 30 kb to the left of Antp. Homozygous ftz- embryos die before hatching and lack alternate body segments. The reduced number of segments results from the fusion of the anterior portion of one segment with the posterior portion of the next segment. The ftz gene encodes a single 1.9 kb poly(A)+ RNA expressed exclusively from the early blastoderm to gastrula stages of embryonic development. The structure of the ftz gene has been analyzed by S1 nuclease mapping and by restriction mapping of a cDNA clone. The ftz gene consists of two exons, and it is the 3' exon that cross-hybridizes with the 3' exon of Antp. The role of ftz in cell determination is discussed.

Primary structure of the Escherichia coli ribonucleoside diphosphate reductase operon

The nucleotide sequence of the Escherichia coli K-12 DNA comprising the operon for the structural genes of the subunits of ribonucleotide diphosphate reductase has been determined. The DNA sequenced maps at 48.5 minutes on the E. coli chromosome and includes a total length of 8557 nucleotides. An open reading frame between nucleotides 3506 and 5834, encoding a 776-amino acid polypeptide chain with a molecular weight of 87,532, has been identified as the nrdA gene. An open reading frame between nucleotides 6012 and 7139, encoding a 375-amino acid polypeptide with a molecular weight of 43,466, has been identified as the nrdB gene. The sequences reveal not only the primary structures for both subunits, but also some interesting aspects of potential regulatory sites.

The nucleotide sequence of the 16S ribosomal RNA gene of the archaebacterium Halococcus morrhua

The sequence of the 16S rRNA gene from the archaebacterium Halococcus morrhua was determined by the dideoxynucleotide sequencing method. It is 1475 nucleotides long. This is the second archaebacterial sequence to be determined and it provides sequence comparison evidence for the secondary structural elements confined to the RNAs of this kingdom and, also, support for controversial or additional base pairing in the eubacterial RNAs. Six structural features are localized that have varied during the evolution of the archaebacteria, eubacteria and eukaryotes. Moreover, although the secondary structures of both sequenced archaebacterial RNAs strongly resemble those of eubacteria, they contain sufficient eukaryotic-like structural characteristics to reinforce the view that they belong to a separate line of evolutionary descent.

Synthesis of single-stranded hybridization probes from reusable DNA templates bound to solid support

A convenient and rapid technique for preparing radiolabeled single-stranded DNA hybridization probes has been developed. Single-stranded recombinant M13 phage DNA containing the mRNA strand of a cloned cDNA is bound to diazobenzyloxymethyl-cellulose in a manner that permits the synthesis of a complementary DNA using reverse transcriptase and primed with either oligo(dT) or the M13 single-stranded primer. A procedural advantage is that after synthesis the unincorporated radiolabeled nucleotides are washed away easily, and the radiolabeled single-stranded DNA probe is eluted with formamide, ready for use. To limit the DNA copy to the insert, a preliminary synthesis reaction is performed with unlabeled nucleotides, primer, and enzyme, followed by digestion of the reaction mix with a restriction endonuclease that recognizes a unique site in the recombinant immediately upstream of the cDNA insert. After elution of the unlabeled synthesized complementary DNA, a second synthesis reaction yields highly radiolabeled single-stranded DNA that extends only the length of the mRNA insert. A major advantage is that the restriction enzyme-cleaved, cellulose-bound template can be stored and reused repeatedly.

Nicotiana chloroplast genome : 8. Localization of genes for subunits of ATP synthase, the cytochrome b-f complex and the 32 kD protein

Using the existing restriction map and probes from wheat and pea ct-DNA, seven protein genes have been localized in the chloroplast genome of N. tabacum. On the clock-like map, the location of each gene is indicated by its time zone: the 15.2 kD polypeptide of the cytochrome b/f complex at 3∶15, cytochrome f at 4∶30, LS of RuBPCase at 4∶50, both β and ɛ subunits of ATP synthase at or near 5∶00, proton-translocating subunit of ATP synthase at 8∶20, α subunit of ATP synthase at 8∶40 and the 32 kD protein at 9∶30. The genome organization of Nicotiana chloroplast DNA is similar to spinach.

Isolation and characterisation of a cDNA encoding the precursor for human apolipoprotein AII

cDNA clones encoding human apolipoprotein AII have been isolated from an adult liver cDNA library. Apo AII mRNA was shown to be approximately 600 bases in length by RNA blot hybridisation. The intracellular precursor of apo AII was inferred from the cDNA sequence to be a 100 amino acid polypeptide consisting of the 77 residue mature protein and an additional 23 amino terminal residues. The amino terminal extension, divisible into an 18 residue signal peptide and a 5 residue propeptide, is separated from the first amino acid of mature apo AII by dibasic residues. The 5' untranslated region of the message is 61 bases in length and the 3' untranslated region 113 bases. A polyadenylation signal is situated 14 bases 3' of the poly(A) tail.

Gene transfer, expression, and molecular cloning of the human transferrin receptor gene

We describe the molecular cloning of the human transferrin receptor gene by a gene transfer approach. Mouse Ltk- cells were cotransformed with the herpes simplex thymidine kinase gene and total human DNA. Transformants expressing human transferrin receptor were isolated by selection on hypoxanthine/aminopterin/thymidine (HAT) medium and fluorescence-activated cell sorting of HAT-resistant cells. Thirty-four kilobases of human DNA was isolated by screening a genomic library constructed from the DNA of a secondary transformant. Gene transfer of the cloned DNA established that 31 kb of DNA was sufficient to encode the receptor. A probe from the 5' end of the gene was used to isolate a cDNA clone with an insert of 4.9 kb. Hybridization of the cDNA to the cloned genomic DNA revealed a minimum of 12 exons. They extend over the entire 31 kb of expressing DNA and over 2 kb of adjacent 3' untranslated sequences that are not required for receptor expression in L cells.

Nucleotide sequence analysis of a zein genomic clone with a short open reading frame

The nucleotide sequence of the zein genomic clone (W22)Z7 and its flanking sequences from the W22 inbred line of maize is reported. The sequence is 1587 bp long and contains 444 bp of 5' noncoding sequence and 342 bp of 3' noncoding sequence. The Z7 sequence belongs to a large complex multigene family and is a member of the B49 subfamily. It is 86% homologous to other known sequences from the same subfamily, but contains four in-frame termination codons caused by single base changes. Its flanking regions contain the usual eukaryotic transcriptional signals.

Inducible expression of amplified human beta interferon genes in CHO cells

Plasmid DNA containing the human beta-interferon (IFN-beta) gene and mouse dihydrofolate reductase cDNA was transfected into dihydrofolate reductase-negative Chinese hamster ovary cells. Dihydrofolate reductase-positive transformants were obtained, and cells containing amplified copies of mouse dihydrofolate reductase were selected by exposure to increasing methotrexate concentrations. These cells were found to express high levels of human IFN-beta after polyriboinosinic acid-polyribocytidylic acid superinduction or NDV infection; this was a result of coamplification of the IFN-beta gene. Levels of expression of 1 U/cell per day were achieved on superinduction, giving corresponding titers of up to 10(10) U/liter medium in culture supernatants. Constitutive production of IFN-beta rates of about 0.5% of superinduced rates was observed; cells producing these levels of IFN-beta had acquired resistance to cytotoxic antiviral effects of IFN-beta. Two forms of human IFN-beta were produced; a major glycosylated 23,000-dalton form and an unglycosylated 18,500-dalton form. The latter had greatly reduced antiviral activity. IFN-beta production was very sensitive to cellular growth rate; the highest levels were produced by density-arrested cultures. Regulation of IFN-beta production by polyriboinosinic acid-polyribocytidylic acid or by cell density effects required the presence of DNA sequences 5' to the IFN-beta-coding sequences; replacement of these sequences with the simian virus 40 early promoter resulted in uninducible, density-independent production of IFN-beta.

Transcriptional and genetic analyses of the herpes simplex virus type 1 genome: coordinates 0.29 to 0.45

We have constructed a map of the genes encoded by a 23,000-nucleotide-pair region of herpes simplex virus type 1. This region, defined by the three adjacent EcoRI fragments N (map coordinates 0.298 to 0.315), F (0.315 to 0.421), and M (0.421 to 0.448), has previously been shown by genetic analysis to contain the genes for thymidine kinase, nucleocapsid protein p40, glycoprotein B, DNA-binding protein, and DNA polymerase. We report the identification and mapping of RNAs defining 13 viral genes encoded by the region 0.298 to 0.448. The transcriptional pattern shows families of overlapping messages, similar to those observed in other regions of the viral genome. We also isolated mutants representing four distinct complementation groups and physically mapped several of the mutations to regions within EcoRI fragment F by marker rescue. Mutations representing complementation groups 1-9 (glycoprotein B), 1-1 (DNA-binding protein), and 1-3 (DNA polymerase) were mapped to coordinates 0.361 to 0.368 to 0.411, and 0.411 to 0.421, respectively. A fourth previously undefined complementation group was mapped to the region between glycoprotein B and DNA-binding protein. Comparing the transcription mapping with marker rescue data suggests that the genes for glycoprotein B, DNA-binding protein, DNA polymerase, and nucleocapsid protein p40 are expressed as 3.3-, 4.2-, 4.3- or 4.2- or both, and 2.4-kilobase mRNAs, respectively.

Transcripts of human HLA gene fragments lacking the 5'-terminal region in transfected mouse cells

Clones of mouse L cells transfected with a human HLA-B7 gene fragment lacking the 5' segment of exon 2 and all upstream sequences express HLA-specific transcripts of various lengths. These include species that correspond in size to full-length HLA-B7 mRNA. The level of these transcripts is increased in cells treated with interferon. It is probable that the full-length transcripts arise as a result of the linkage of the HLA-B7 gene fragments with DNA segments providing transcription initiation or polyadenylylation signals.

Cloning and sequencing of the ribosomal RNA genes in maize: the 17S region

The maize genes for the 17S, 5.8S, and 26S ribosomal RNAs (rRNAs) are located on chromosome 6 and consist of 9-kb sequences repeated about 5,000-10,000 times per 2C. One of these sequences was isolated from a lambda library containing maize Eco RI genomic segments. The sequence of the small-subunit (17S) RNA was determined using the M13 shotgun-dideoxy sequencing approach. The maize sequence was compared with nuclear rRNAs from yeast, Xenopus, and rat. Using these sequences, it is possible to identify tentatively the start and the end points of the sequence of the maize nuclear small subunit rRNA. This RNA has a length of 1809 nucleotides. The alignment of all four sequences for maximal homology allows us to identify regions within the rRNA that have been conserved during eukaryotic evolution.

Expression of human alpha-tubulin genes: interspecies conservation of 3' untranslated regions

To examine the sequence complexity and differential expression of human alpha-tubulin genes, we constructed cDNA libraries from two unrelated tissue types (epidermis and fetal brain). The complete sequence of a positively hybridizing alpha-tubulin clone from each library is described. Each is shown to represent an abundantly expressed gene from fetal brain and keratinocytes, respectively. Although the coding regions are extensively homologous (97%), the 3' untranslated regions are totally dissimilar. This property has been used to dissect the human alpha-tubulin multigene family into members bearing sequence relatedness in this region. Surprisingly, each of these noncoding regions shares very high (65 to 80%) interspecies homology with the 3' untranslated region of one of the two rat alpha-tubulin genes of known sequence. These unexpected homologies imply the existence of selective pressure on the 3' untranslated regions of some cytoskeletal genes which maintains sequence fidelity during the course of evolution, perhaps as a consequence of an as yet unidentified functional requirement.

Transcription of the immediate early genes of human cytomegalovirus strain AD169

Cloned sub-genomic fragments of human cytomegalovirus strain AD169 were used to analyse immediate-early (IE) transcription in virus-infected cells. Transcriptionally active regions of the HCMV genome were identified by hybridising cytoplasmic IE poly(A)+-RNA with dot blots and Southern transfers of restriction endonuclease digests of recombinant plasmids. The size, number and, in some cases, the orientation of transcription of IE RNA species were determined. The most abundant IE mRNA (IE-1.95) was mapped at 0.0764-0.0865 map units. The transcription of two middle abundant (1.7 and 2.15 kb) IE RNAs was initiated immediately downstream, and in the same orientation as the IE-1.95 gene. A second transcriptionally active area was identified at 0.593-0.619 map units. Three mRNA species (IE-1.75, IE-3.8 and IE-4.8) were derived from this region. Additional minor IE transcription was also observed from other regions of the HCMV genome. Hybrid-selected translation was used to identify the polypeptides encoded by the major IE RNA species.

Amounts, synthesis, and some properties of intracisternal A particle-related RNA in early mouse embryos

Early mouse embryos express two morphological subtypes of intracisternal A-type particles, one resembling those occurring in mouse tumors (referred to as IAP) and the other apparently specific for early embryos [referred to as IAP(epsilon)]. Using cloned fragments of IAP genes as labeled probes in dot-hybridization experiments, we detected IAP-related RNA sequences in mouse oocytes and preimplantation embryos. IAP RNA is relatively abundant in ovarian oocytes, is reduced in amount to approximately equal to 1/10th in the ovulated egg, and increases approximately equal to 100 times (from approximately equal to 1.3 X 10(3) to approximately equal to 1.5 X 10(5) molecules per embryo) between the one-cell stage and late blastocyst stage. Most of the IAP RNA consists of a single size class of about 5.4 kilobases, and a major fraction of this RNA is polyadenylylated. Quantitative considerations suggest that only a few percent of the IAP RNA in embryos are associated with particles. In two-cell embryos, the number of IAP RNA molecules is less than 1/10th the number of IAP(epsilon) particles, suggesting that IAP(epsilon) is genetically distinct from IAP and presumably represents a family of as yet unidentified retrovirus-like elements.

Screening recombinant phage M13 plaques with RNA probes; a one-step procedure which identifies clones containing either of the complementary DNA strands

We describe a method for detecting specific DNA sequences cloned in M13 phage vectors, based on the procedure of Woo (in Wu, R., Methods in Enzymology, Vol. 68, Academic Press, New York, 1979, pp. 389-395). M13 plaques are adsorbed to a nitrocellulose filter that has been pre-saturated with bacteria. The filter is incubated on an agar plate to amplify the phage; the DNA is alkali-denatured and then hybridized with a radioactive RNA probe. Unlike standard procedures, this method detects and distinguishes M13 plaques containing phage particles which harbor either the coding or non-coding (RNA-like) DNA strand, when single-stranded RNA is used as probe. We have optimized this procedure with M13 clones containing mouse histidine tRNA gene sequences and have used it to determine the sequence of both strands of a mouse glycine tRNA gene.

Inducible expression of amplified human beta interferon genes in CHO cells

Plasmid DNA containing the human beta-interferon (IFN-beta) gene and mouse dihydrofolate reductase cDNA was transfected into dihydrofolate reductase-negative Chinese hamster ovary cells. Dihydrofolate reductase-positive transformants were obtained, and cells containing amplified copies of mouse dihydrofolate reductase were selected by exposure to increasing methotrexate concentrations. These cells were found to express high levels of human IFN-beta after polyriboinosinic acid-polyribocytidylic acid superinduction or NDV infection; this was a result of coamplification of the IFN-beta gene. Levels of expression of 1 U/cell per day were achieved on superinduction, giving corresponding titers of up to 10(10) U/liter medium in culture supernatants. Constitutive production of IFN-beta rates of about 0.5% of superinduced rates was observed; cells producing these levels of IFN-beta had acquired resistance to cytotoxic antiviral effects of IFN-beta. Two forms of human IFN-beta were produced; a major glycosylated 23,000-dalton form and an unglycosylated 18,500-dalton form. The latter had greatly reduced antiviral activity. IFN-beta production was very sensitive to cellular growth rate; the highest levels were produced by density-arrested cultures. Regulation of IFN-beta production by polyriboinosinic acid-polyribocytidylic acid or by cell density effects required the presence of DNA sequences 5' to the IFN-beta-coding sequences; replacement of these sequences with the simian virus 40 early promoter resulted in uninducible, density-independent production of IFN-beta.

Genes for gentamicin-(3)-N-acetyltransferases III and IV: I. Nucleotide sequence of the AAC(3)-IV gene and possible involvement of an IS140 element in its expression

Genes for gentamicin-3-acetyltransferases [ACC(3)] of types III and IV have been cloned from various R-plasmids. In two R-plasmids, pWP14a (AAC(3)-III) and pWP7b [AAC(3)-IV], resistance genes have been found directly adjacent to a single copy of an IS element, IS140. Nucleotide sequence determination of the AAC(3)-IV gene from plasmid pWP7b and of part of IS140 from three different sources suggested that the -35 region of the AAC(3)-IV promoter was part of the IS element. A similarly built-up promoter was found in pWP14a. It was found also, that a hygromycin B phosphotransferase was expressed from a locus neighbouring the AAC(3)-IV gene in pWP7b which was under the control of the same promoter. In two other R-plasmids, pWP113a and pWP116a, the AAC(3)-III gene was found in different genetic environments, namely close to Tn3-like structures.

Cloning and sequencing of a full length cDNA coding for a human apoferritin H chain: evidence for a multigene family

We have cloned a segment of cDNA from human liver coding for an apoferritin subunit, probably an H chain. Sequence comparison with the available protein sequence shows that our clone corresponds to a ferritin subunit present as a minor species in human spleen and placenta, but as major species in HeLa cells. Northern blot analysis shows the existence of only one band of similar size in human liver, HeLa cells, Daudi lymphoma and Hep3B hepatoma cell lines. In contrast, Southern blot analysis provides evidence for a multigene family.

Characterization of the mRNA coding for ribonucleoside diphosphate reductase in Escherichia coli

Total Escherichia coli RNA was separated by electrophoresis on methyl mercury agarose gels, transferred to diazobenzyloxymethyl-paper, and hybridized to various DNA probes containing different segments of the nrd genes to determine the organization of these genes. A 3.2-kilobase polycistronic mRNA transcript which hybridizes to both the nrdA and nrdB genes indicated that the nrdA and nrdB genes are organized in an operon. The polycistronic transcript contained the nrdA gene at the 5' end and the nrdB gene at the 3' end. The size of the polycistronic mRNA was sufficient to code for the 80,000-molecular-weight B1 protein and the 40,000-molecular-weight B2 protein. The results also indicated that the nrdA and nrdB genes are the only genes in E. coli that code for ribonucleoside diphosphate reductase. Two smaller RNA species that hybridized to nrd DNA were observed and probably overlap with the 3.2-kilobase nrd mRNA.

New versatile cloning and sequencing vectors based on bacteriophage M13

A new pair of cloning and sequencing vectors based on bacteriophage M13mp7 has been developed. These vectors (M13tg130 and M13tg131) contain, in addition to the EcoRI, BamHI, HindIII, SmaI, SalI and PstI sites present in other vectors [cf., M13mp8 and M13mp9, Messing and Vieira, Gene 19 (1982) 269-276], unique restriction recognition sequences for the enzymes EcoRV, KpnI, SphI, SstI and XbaI. A restriction site for the enzyme BglII has been incorporated into the polylinker region of one of the vector pair to permit rapid discrimination between the two vectors.

Molecular cloning and characterization of the RAD1 gene of Saccharomyces cerevisiae

We have cloned the RAD1 gene of Saccharomyces cerevisiae and physically mapped it to a 4.0-kb DNA fragment from chromosome XVI. The RAD1 gene determines a transcript of 3.1 kb, and the direction of transcription was found to be leftwards, from EcoRI towards Bg/II (Fig. 1). Deletions of the RAD1 gene were made and were found to have no effect on viability of vegetative cells or spores, or on sporulation.

ampC beta-lactamase hyperproduction in Escherichia coli: natural ampicillin resistance generated by horizontal chromosomal DNA transfer from Shigella

Six ampicillin-resistant clinical isolates of Escherichia coli that hyperproduced the chromosomal ampC beta-lactamase were studied. By DNA sequence analysis, we found that five of them were identical over an entire 449-base-pair sequence and carried a novel strong ampC promoter [Olsson, O., Bergström, S. & Normark, S. (1982) EMBO J. 1, 1411-1416]. Except for one base pair this sequence was identical to that of a low beta-lactamase-producing clinical isolate of Shigella sonnei. Spontaneous one-step mutants of S. sonnei that overproduced the ampC beta-lactamase by 45-fold were characterized and found to be mutated at the single base that distinguishes S. sonnei from the five E. coli hyperproducers. The most likely explanation for this result is that chromosomal DNA was transferred in vivo from Shigella to E. coli across the species barrier.

The molecular organization of the Antennapedia locus of Drosophila

The Antennapedia complex (ANT-C) of Drosophila is a cluster of genes involved in the regulation of morphogenesis, including at least three homoeotic loci (Antp, Scr, and pb), in which mutations cause switches of cell fates from one developmental pathway to another. We have isolated DNA clones containing most of the ANT-C, a region of about 300 kb. Antp mutations are distributed across more than 100 kb of the ANT-C. Dominant Antp mutations are associated with certain chromosome rearrangements and insertions that interrupt the 100 kb region; other chromosome breaks within the region cause recessive lethality and have no dominant effects. Two prominent transcripts (3.5 and 5.0 kb) are derived from exons within and at the two ends of the 100 kb region.

The complete nucleotide sequence of the Neurospora crassa am (NADP-specific glutamate dehydrogenase) gene

The complete nucleotide sequence of a 2.7-kb genomic fragment, containing the Neurospora crassa am [NADP-specific glutamate dehydrogenase (GDH)] gene, has been determined. The transcription initiation and polyadenylation sites have been defined by S1 mapping. There are at least four initiation sites between 35 and 60 bases downstream of a TATAAA sequence. The single polyadenylation site is immediately downstream of a six-nucleotide sequence which is present in the corresponding position in the N. crassa gene (pl) coding for the imported proteolipid component of mitochondrial ATP synthase [Viebrock et al. Embo J. 1 (1982) 565-571] the initiation sites also show some sequence similarity between am and pl. There are two introns, of 66 and 61 bases respectively; they interrupt sequences that are conserved (highly so in the case of the second intron) between Neurospora and Escherichia coli. As well as showing typical consensus splicing sequences, the two introns show some striking internal similarities to each other. The am gene resembles the pl gene in its strongly selective use of codons (pyrimidines preferred to purines and guanine to adenine in third positions). The coding sequence here reported requires four corrections to be made in the previously published amino acid sequence of Neurospora GDH.

Cloning and sequencing of a full length cDNA coding for human retinol-binding protein

We have isolated and sequenced a cDNA clone coding for human Retinol Binding Protein. The sequence indicates that Retinol Binding Protein is synthesized as a single polypeptide chain precursor which is then matured to the secreted protein by removal of a leader peptide. Southern and Northern blot analysis suggest that the gene is present in one or few copies per haploid genome and is transcribed in a single mRNA species.