The making of strand-specific M13 probes

Structure of a human histone cDNA: evidence that basally expressed histone genes have intervening sequences and encode polyadenylylated mRNAs

We have isolated and sequenced full-length cDNA clones encoding the human basally expressed H3.3 histone from a human fibroblast cDNA library. Several features of this atypical cDNA distinguish it and its gene from the well-characterized cell-cycle regulated histone genes and their RNA transcripts. The H3.3 mRNA is approximately equal to 1200 bases long, contains unusually long 5' and 3' untranslated regions, and has a 3' polyadenylylated terminus. In addition, we have isolated and characterized a cDNA clone that is a precursor to the H3.3 mRNA and contains an intervening sequence interrupting its 5' untranslated region. Hybridization of subsegments of the cDNA to human genomic DNA reveals a complex multigene family. The differences in the structures of basal and cell-cycle histone genes suggest a model to explain the differences in their expression.

A complex of single-strand binding protein and M13 DNA as hybridization probe

Single-stranded DNA was complexed to the single-strand binding protein (SSB) of Escherichia coli in a mass ratio of 30:1. The protein moiety of this complex can be labelled by a number of methods of which we have chosen radio-iodination and biotinylation as examples. The SSB-M13 DNA complexes, labelled to high specific activities, were used as probes in hybridization experiments in which 1.6 X 10(-18) moles of immobilized target DNA were detected. The stability of the hybrids was not severely decreased by the binding of SSB. Analysis of hybrids by electron microscopy showed that complexing of DNA with SSB could be used to allow its subsequent identification in the hybrids.

Characterization of the rat gamma-crystallin gene family and its expression in the eye lens

Rat genomic clones, which together contain all of the rat genomic gamma-crystallin sequences, have been characterized. Five gamma-crystallin genes are located on a contiguous DNA region, 63 X 10(3) base-pairs long. These genes, named (5') gamma 1-1, gamma 1-2, gamma 2-2 and gamma 3-1 (3'), are all oriented head to tail. A sixth gamma-crystallin gene, named the gamma 4-1 gene, could not be linked to the gamma-crystallin gene cluster with our present set of genomic clones. Mapping experiments using single copy sequences which form the extreme 5' or 3' region of the gene cluster showed that, if the gamma 4-1 gene is located on the same chromosome, then it must be separated from the gene cluster by at least 25 X 10(3) base-pairs of DNA. All gamma-crystallin genes have a similar mosaic structure. They contain a large (0.9 X 10(3) to 1.88 X 10(3) base-pairs) intron in the middle of the gene and are further interrupted close to the 5' end of the gene. The length of the first exon varies from about 40 to about 50 base-pairs. The complementary DNA clone pRL-gamma-3 used in this study is a copy of the transcript of the gamma 3-1 gene, while the second complementary DNA clone, pRL-gamma-2, is most likely a copy of the transcript of the gamma 2-1 gene. It is further shown that rat lens messenger RNA protects fragments from the 3' ends of the four other gamma-crystallin genes against degradation by S1 nuclease, hence all six gamma-crystallin genes present in the rat genome must be transcribed in the lens. Repetitive sequences were found to be present between and around the gamma-crystallin genes. Mapping with cloned repetitive sequences showed that three different repeats, designated A, B and C, occur more than once in the gamma-crystallin gene cluster. Repeat C is also found in the gamma 4-1 region. A repetitive region 3' to the gamma 3-1 gene contains members of all three repeat families.

Evidence that two mutations, wDZL and z1, affecting synapsis-dependent genetic behavior of white are transcriptional regulatory mutations

Both the white mutant allele, wDZL, and the zeste mutant allele, z1, reduce white transcript levels in adult head tissues, but have no effect on these levels in other tested adult tissues. wDZL results from insertion of a complex transposon approximately 5.0 kb 5' to white. Juxtaposition of this transposon to white produces a novel transcription unit beginning in the transposon and producing a mature transcript containing both white and transposon sequences. Head-specific expression of this novel transcription unit correlates with the observed repression of wild-type white transcript levels. wDZL and z1 are known to cause synapsis-dependent repression of w+ expression in trans as assessed by eye pigment deposition. Collectively, these results suggest an unexpected and informative correspondence between cis and synapsis-dependent trans regulatory effects. We discuss the implied mechanistic relationship between regulation of transcription and transvection effects in Drosophila.

The primary structure of the imported mitochondrial protein, ornithine transcarbamylase from rat liver: mRNA levels during ontogeny

Ornithine transcarbamylase, one of the enzymes of the urea cycle in ureotelic organisms, is synthesized in the cytoplasm of hepatocytes as a precursor larger than the mature form found in the mitochondrial matrix. We deduced the amino acid sequence of the precursor of ornithine transcarbamylase from rat liver from the nucleotide sequence of overlapping cDNA clones spanning the complete coding region, 3' untranslated region, and most of the 5' untranslated region of the mRNA. The mature enzyme consists of 322 amino acids and is derived from the larger precursor by proteolytic removal of 32 amino acids from the amino-terminus. The amino-terminal extension contains eight basic and no acidic residues. This highly basic character appears to be a feature of presequences on cytoplasmically synthesized mitochondrial proteins. Comparison of the amino acid sequence determined for the enzyme from rat with that from human liver (Horwich et al., 1984) shows that there is a high degree of homology between the sequences of the mature protein (93%) and relatively less homology between the sequences of the amino-terminal extension (72%). The ornithine transcarbamylase from rat liver also shows a considerable degree of amino acid homology (44%) with the enzyme from Escherichia coli (Van Vliet et al., 1984) and leads to suggestions about residues involved in substrate binding and catalysis. An analysis of levels of RNA in fetal and neonatal liver shows that ornithine transcarbamylase mRNA levels increase from about 40% of adult levels at day 14 of gestation to a peak at day 20 of gestation, and, after a drop around the time of birth, rises to adult levels during the second week after birth.

Localization of the upstream regulatory sites of yeast iso2-cytochrome c gene

In order to study the regulation of expression of the iso2-cytochrome c gene, we have constructed a fused gene between the 5'flanking region of the gene coding for the yeast iso2-cytochrome c and the coding region of the E. coli beta-galactosidase lacZ gene. When introduced in yeast cells this hybrid gene is expressed and regulated like the production of iso2-cytochrome c: it is under the control of the general catabolic repression and of the unlinked trans-acting CYP1 gene whose CYP1-18 allele causes an overproduction of iso2-cytochrome c. The expression of hybrid genes whose upstream region has been progressively shortened or altered by internal deletions was studied either in wild-type CYP1+ cells or in cells carrying the CYP1-18 allele grown either on glucose or on glycerol. It appears that the expression and the regulation of the iso2-cytochrome c gene is controlled by an upstream regulatory site composed of a positive and a negative element. This site is the target of regulation by the CYP1 gene product and, directly or through this gene, of the control by the general catabolic repression.

Molecular evidence for partial inactivation of Y loops in T(X:Y)56 males from D. hydei

Using loop-specific DNA clones, we established that the T(X:Y)56 (Hackstein and Hennig 1982) chromosome, formerly thought to be deleted for the Yshort arm and the associated 'nooses' loops is actually an XYS X YL combination. It carries, adjacent to the translocation junction, the complete and uninterrupted set of the two dysfunctional 'nooses' domains. The morphologically altered and functionally defective loops are transcribed at about 50% of the normal rate. Transcripts in one of the two 'nooses' domains are preferentially underrepresented and their distribution in the spermatocyte nucleus is distorted, presumably as a consequence of a spreading effect. No alteration in transcript size or in the correct strand selection, and no variegation of transcription on the single spermatocyte level, were observed. In another translocation T(X:Y)97, in which 'tubular ribbons' were reported to be inactivated (Hess 1970), complete elimination of DNA sequences is observed. A possible mechanism for the position effect inactivation of Y loops in X:Y translocations is discussed briefly.

Nucleotide sequence of murine ornithine decarboxylase mRNA

Ornithine decarboxylase (OrnDCase; L-ornithine carboxy-lyase, EC 4.1.1.17) is the first and rate-limiting enzyme in the biosynthesis of polyamines in mammalian cells. During cell growth the enzyme is regulated by rapid changes in the level of its mRNA and protein. To explore the molecular basis of these changes, we cloned a full-length cDNA copy of the major 2.4-kilobase OrnDCase mRNA from mouse cells and determined its sequence. The cDNA contains 2465 nucleotides derived from OrnDCase mRNA, consisting of a 737-nucleotide-long 5' noncoding segment, a coding segment of 1383 nucleotides terminated by a TAG triplet, and a 342-nucleotide 3' noncoding segment. The encoded protein of 461-amino acid residues has a molecular weight of 51,105 and has a potential site for phosphorylation by casein kinase II. In the unusually long 5' leader sequence, there are four ATG triplets, each of which is followed by an in-phase termination signal; the presence of these upstream ATGs could explain the low in vitro translational activity of OrnDCase mRNA reported earlier. A restriction digest of mouse genomic DNA was probed with a defined OrnDCase coding sequence, revealing a multimembered family of OrnDCase-related genes.

Independent control elements that determine yolk protein gene expression in alternative Drosophila tissues

The adjacent and divergently transcribed yp1 and yp2 genes of Drosophila were separated at a site that is 342 base pairs upstream of yp2 and 883 base pairs upstream of yp1. Each gene was separately used to transform Drosophila germ-line-producing flies with a single copy of the introduced gene. Transcripts from the introduced genes were found only in adult females. Thus, the introduced genes maintain the sex- and time-specific expression pattern of the endogenous yp genes. However, the pattern of tissue-specific expression differed among the two introduced genes and the endogenous genes. Transcripts from both of the endogenous genes are found in fat bodies and ovaries. In contrast, transcripts from the introduced yp1 gene are found only in fat bodies, and those from the introduced yp2 gene are found only in ovaries. Thus, each introduced DNA segment lacks at least one of the cis-acting elements required for the normal pattern of tissue-specific expression. These results indicate that the expression of a yp gene in different tissues is determined by different cis-acting elements.

Ty elements transpose through an RNA intermediate

We have followed Ty transposition with a donor Ty element, TyH3, whose expression is under the control of the GAL1 promoter. Sequence analysis reveals dramatic structural differences in TyH3 before and after transposition. If the donor TyH3 is marked with an intron-containing fragment, the intron is correctly spliced out of the Ty during transposition, suggesting that the Ty RNA is the intermediate for transposition. Furthermore, the pattern of sequence inheritance in progeny Ty insertions derived from the marked Ty follows the predictions of the model of retroviral reverse transcription. Comparison of marked Ty elements before and after movement shows that transposition is highly mutagenic to the Ty element. These results demonstrate that during transposition, Ty sequence information flows from DNA to RNA to DNA.

Amino acid sequence of the non-collagenous globular domain (NC1) of the alpha 1(IV) chain of basement membrane collagen as derived from complementary DNA

NC1, the C-terminal non-collagenous globular domain of collagen IV, represents one of the two end regions responsible for the assembly and cross-linking of the extracellular network of basement membrane collagen. Several cDNA clones for the NC1 domain of the alpha 1(IV) collagen chain of mouse have been isolated by using synthetic oligonucleotides as screening probes for mouse libraries. The oligonucleotides were synthesized according to known stretches of the corresponding protein sequence. Sequencing of the overlapping cDNA clones allowed the complete amino acid sequence of the NC1 domain to be deduced as well as the C-terminal 165 amino acid residues of the triple helix. It consists of 229 amino acid residues which comprise two homologous regions with a high content of cysteine. These DNA and protein sequences are compared to the corresponding sequences of other collagens and discussed with respect to their structural and biological significance.

Developmental and tissue-specific expression of a family of transcripts related to rat insulin-like growth factor II mRNA

We have constructed a cDNA library from the mRNA of a rat liver cell line (BRL-3A) and characterized cDNA clones encoding the protein precursor of the rat insulin-like growth factor II (pre-pro-rIGF-II). This precursor, inferred from the nucleotide sequence, consists of a signal peptide, the rIGF-II sequence, and a trailer polypeptide of unknown significance. The characterized cDNA sequence (1016 nt) is part of a 3.4 kb mRNA species. Northern analysis reveals that a probe containing the extreme 5' noncoding region hybridizes to a second RNA (1.6 kb), while a probe corresponding to the 5' noncoding region proximal to the coding region hybridizes to two other RNA species (1.75 and 1.1 kb). All four RNAs are differentially expressed in all of the neonatal tissues that were examined, while the 3.4 kb pre-pro-rIGF-II mRNA and the 1.1 kb transcript are absent from adult tissues.

Dot-blot procedure with [32P]DNA probes for the sensitive detection of avocado sunblotch and other viroids in plants

Avocado sunblotch viroid (ASBV) has been detected down to a level of about 20 pg per gram fresh weight of leaves by the use of a dot-blot hybridization procedure and partially purified nucleic acid extracts. Three [32P]DNA probes were compared, two prepared from full-length ASBV clones in the single-strand M13mp93 vector and the other by primer extension on purified ASBV. All three probes gave the same sensitivity of detection of ASBV. The methods developed have also been used successfully for the routine detection of potato spindle tuber viroid, citrus exocortis viroid, and coconut cadang cadang viroid.

"Transactivation" control signals in the promoter of the herpesvirus thymidine kinase gene

The herpes simplex virus thymidine kinase (TK) gene is transcriptionally activated in trans ("transactivated") by virus-encoded proteins during the infectious cycle. We show that TK plasmids introduced into a HeLa cell transient transcription assay system are also transactivated after infection with a TK- virus. Several aspects of this response are similar to regulation during the normal infectious cycle. Assay of TK promoter deletion and 5- to 10-base-pair substitution mutants in this system reveals that the transactivation response depends on the intactness of 109 base pairs of 5' gene flanking sequence. Differences between these results and analogous assays in the Xenopus oocyte system are discussed. A model for the putative binding of transactivator(s) to the promoter region is presented.

Molecular cloning and characterization of the glucoamylase gene of Aspergillus awamori

The filamentous ascomycete Aspergillus awamori secretes large amounts of glucoamylase upon growth in medium containing starch, glucose, or a variety of hexose sugars and sugar polymers. We examined the mechanism of this carbon source-dependent regulation of glucoamylase accumulation and found a several hundredfold increase in glucoamylase mRNA in cells grown on an inducing substrate, starch, relative to cells grown on a noninducing substrate, xylose. We postulate that induction of glucoamylase synthesis is regulated transcriptionally. Comparing total mRNA from cells grown on starch and xylose, we were able to identify an inducible 2.3-kilobase mRNA-encoding glucoamylase. The glucoamylase mRNA was purified and used to identify a molecularly cloned 3.4-kilobase EcoRI fragment containing the A. awamori glucoamylase gene. Comparison of the nucleotide sequence of the 3.4-kilobase EcoRI fragment with that of the glucoamylase I mRNA (as determined from molecularly cloned cDNA) revealed the existence of four intervening sequences within the glucoamylase gene. The 5' end of the glucoamylase mRNA was mapped to several locations within a region -52 to -73 nucleotides from the translational start. Sequence and structural features of the glucoamylase gene of the filamentous ascomycete A. awamori were examined and compared with those reported in genes of other eucaryotes.

Nucleotide sequence of yeast gene CP A1 encoding the small subunit of arginine-pathway carbamoyl-phosphate synthetase. Homology of the deduced amino acid sequence to other glutamine amidotransferases

A yeast DNA fragment carrying the gene CP A1 encoding the small subunit of the arginine pathway carbamoyl-phosphate synthetase has been sequenced. Only one continuous coding sequence on this fragment was long enough to account for the presumed molecular mass of CP A1 protein product. It codes for a polypeptide of 411 amino acids having a relative molecular mass, Mr, of 45 358 and showing extensive homology with the product of carA, the homologous Escherichia coli gene. CP A1 and carA products are glutamine amidotransferases which bind glutamine and transfer its amide group to the large subunits where it is used for the synthesis of carbamoyl-phosphate. A comparison of the amino acid sequences of CP A1 polypeptide with the glutamine amidotransferase domains of anthranilate and p-amino-benzoate synthetases from various sources has revealed the presence in each of these sequences of three highly conserved regions of 8, 11 and 6 amino acids respectively. The 11-residue oligopeptide contains a cysteine which is considered as the active-site residue involved in the binding of glutamine. The distances (number of amino acid residues) which separate these homology regions are accurately conserved in these various enzymes. These observations provide support for the hypothesis that these synthetases have arisen by the combination of a common ancestral glutamine amidotransferase subunit with distinct ammonia-dependent synthetases. Little homology was detected with the amide transfer domain of glutamine phosphoribosyldiphosphate amidotransferase which may be the result of a convergent evolutionary process. The flanking regions of gene CP A1 have been sequenced, 803 base pairs being determined on the 5' side and 382 on the 3' side. Several features of the 5'-upstream region of CP A1 potentially related to the control of its expression have been noticed including the presence of two copies of the consensus sequence d(T-G-A-C-T-C) previously identified in several genes subject to the general control of amino acid biosynthesis.

Unique sequences are interspersed among tandemly repeated elements in the murine gamma 1 switch segment

Early in its differentiative pathway, a given B lymphocyte expresses immunoglobulin of the mu heavy chain class (IgM). Subsequent differentiative processes may involve rearrangement within the immunoglobulin heavy chain chromosomal locus to enable cells of the same lineage to synthesize immunoglobulins of other heavy chain classes (e. g. IgG, IgE or IgA), but with specificity for the same antigen as the original IgM molecule. Switch recombination, the molecular event which facilitates this chromosomal rearrangement, has been shown to occur between segments of DNA consisting of tandemly repeated unit sequences. These DNA segments have been functionally defined as switch regions. We have cloned the gamma 1 switch region from the BALB/c germline, and have demonstrated that significantly divergent sequence elements are interspersed among the tandemly repeated units characteristic of this switch region. We show that these unique elements exist in at least three copies within the switch segment, and discuss the implications of this novel and previously unreported primary structure.

Structural features and restricted expression of a human alpha-tubulin gene

The nucleotide sequence of a human alpha-tubulin gene (b alpha 1) is described. This gene is extensively homologous to a rat alpha-tubulin gene in its coding regions, 3'-untranslated region and, indeed, in segments of its largest intron. However, with the exception of three short conserved blocks of homology, the 5' flanking regions of the rat and human genes are unrelated. Hence, these genes each encoding an identical protein are transcribed under the influence of divergent promoters. Blot analyses using RNA from a variety of transformed cells derived from different tissues indicate that expression of the human alpha-tubulin gene is restricted to cells of neurological origin. Among neurological cell types b alpha 1 expression is further restricted to adherent cells that are morphologically differentiated. The data presented suggest that the b alpha 1 gene encodes a prominent neuronal and glial alpha-tubulin and that b alpha 1 expression is a function of the differentiated state of these cells.

Characterization of two class I major histocompatibility rat cDNA clones, one of which contains a premature termination codon

A cDNA clone that shares considerable homology with mRNA for class-I major-histocompatibility (MHC) antigens has been isolated from a cDNA library constructed from an insulin-secreting tumor of the NEDH rat (RIN). Although there is very strong homology between the third extracellular domain of this gene, and other class-I antigen genes, a stop codon was noticed at the junction between the external and transmembrane regions of its protein. Thus, this gene codes for a truncated class-I antigen that lacks both transmembrane and cytoplasmic domains but has hydrophilic amino acids towards its C-terminus and therefore resembles a soluble protein. This gene was found to be transcribed at significant levels in the rat testis and an insulin-secreting tumor, but transcription was negligible in liver and kidney. The partial nucleotide sequence of this gene in a Wistar rat genomic clone indicates that the cDNA clone is represented in the rat genome complete with premature termination codon, thus eliminating the possibility of artifactual origins for the clone.

In situ hybridization--visualization and quantitation of genetic expression in mammalian brain

In situ hybridization techniques have been developed that quantitate the relative levels of specific mRNAs in individual cell types of a heterogeneous tissue, the mammalian brain. Here, we discuss those special procedures and precautions necessary for hybridizing radiolabeled probes to developing and adult brain mRNAs. The probes discussed include double-stranded recombinant DNA, as well as single-stranded DNA, RNA, and polyuridylate. We detail the procedure for determining the relative numbers of hybrids formed and computing the ratio of specific mRNAs to total polyadenylated mRNA and discuss the importance of this ratio for comparison of relative levels of specific mRNAs within and among cell types in an individual brain or between brains.

Characterization of yeast strains with conditionally expressed variants of ribosomal protein genes tcm1 and cyh2

We placed a regulatory sequence derived from the GAL10 locus of Saccharomyces cerevisiae at various distances from the start sites of transcription of two yeast ribosomal protein genes, tcm1 and cyh2. The hybrid ribosomal protein genes were transcribed at wild-type levels in the presence of galactose. In the absence of galactose, the hybrid genes were transcribed either at a reduced level or essentially not at all. Yeast cells which transcribe the ribosomal protein genes at a reduced rate continued to grow, suggesting that enhanced translation of the ribosomal protein mRNA may permit an adequate rate of synthesis of the corresponding protein. Consistent with this suggestion is the finding that preexisting mRNA decayed at a reduced rate when transcription was halted abruptly by removal of galactose. Yeast cells unable to transcribe tcm1 or cyh2 without galactose did not grow. These conditional lethal strains demonstrate that the ribosomal proteins encoded by tcm1 and cyh2 are essential; furthermore, these strains are potentially useful for isolating mutations in the tcm1 and cyh2 proteins affecting their transport, assembly, or function.

Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors

Three kinds of improvements have been introduced into the M13-based cloning systems. (1) New Escherichia coli host strains have been constructed for the E. coli bacteriophage M13 and the high-copy-number pUC-plasmid cloning vectors. Mutations introduced into these strains improve cloning of unmodified DNA and of repetitive sequences. A new suppressorless strain facilitates the cloning of selected recombinants. (2) The complete nucleotide sequences of the M13mp and pUC vectors have been compiled from a number of sources, including the sequencing of selected segments. The M13mp18 sequence is revised to include the G-to-T substitution in its gene II at position 6 125 bp (in M13) or 6967 bp in M13mp18. (3) M13 clones suitable for sequencing have been obtained by a new method of generating unidirectional progressive deletions from the polycloning site using exonucleases HI and VII.

Expression of two Xenopus laevis ribosomal protein genes in injected frog oocytes. A specific splicing block interferes with the L1 RNA maturation

The expression of two Xenopus laevis ribosomal protein genes (L1 and L14) has been analysed by microinjection of the cloned genomic sequences into frog oocyte nuclei. While the injection of the L14 gene causes the accumulation of the corresponding protein in large excess with respect to that synthesized endogenously, the L1 gene does not. Analysis of the RNA shows that both genes are actively transcribed. The seven-intron-containing L14 transcript is completely processed to a mature form, while two out of nine intron sequences persist in the L1 transcript. This precursor RNA is confined to the nucleus; its accumulation is due to a specific block of splicing operating at the level of two defined introns and not to saturation of the processing apparatus of the oocyte. The different behaviour of the two genes may reflect different mechanisms of regulation which, in the case of the L1 gene, could operate at the level of splicing.

Human Cu/Zn superoxide dismutase gene: molecular characterization of its two mRNA species

Two cytoplasmic superoxide dismutase (SOD-1) mRNAs of about 0.7 and 0.9 kilobases (Kb.) were previously found in a variety of human cells. The two SOD-1 mRNAs are transcribed from the same gene and the major 0.7 Kb. species is approximately four times more abundant than the minor 0.9 Kb. mRNA. These two mRNAs differ in the length of their 3'-untranslated region and both have multiple 5'-ends. The longer transcript contains 222 additional nucleotides beyond the 3'-polyadenylated terminus of the short mRNA. S1 nuclease mapping and sequence analysis showed that these extra 222 nucleotides are specified by sequences contiguous to those shared by the two SOD-1 mRNAs. The 5'-termini of the two SOD-1 mRNAs were identified and mapped by both primer extension and S1 mapping. The majority of SOD-1 mRNA molecules (90-95%) have a 5'-start site located 23 base pairs (b.p.) downstream of the hexanucleotide -TATAAA-. The rest of the SOD-1 mRNA molecules have 5'-termini 30, 50 and 65 b.p. upstream from the major start region.

Nucleotide sequence of bacteriophage T4 gene 23 and the amino acid sequence of its product

We have determined the nucleotide sequence of gene 23 of bacteriophage T4 by the methods of Maxam and Gilbert and of Sanger. The identities of approximately 80% of the amino acid residues of the major capsid protein which is encoded by gene 23 were determined additionally by Edman degradation of the intact protein and its peptides. Fifteen gene 23 amber mutation sites have been located within the sequence, and the 3' transcription termination site for genes 21, 22 and 23 has been identified.

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.

The complete sequence of a full length cDNA for human liver glyceraldehyde-3-phosphate dehydrogenase: evidence for multiple mRNA species

A recombinant M13 clone (O42) containing a 65 b.p. cDNA fragment from human fetal liver mRNA coding for glyceraldehyde-3-phosphate dehydrogenase has been identified and it has been used to isolate from a full-length human adult liver cDNA library a recombinant clone, pG1, which has been subcloned in M13 phage and completely sequenced with the chain terminator method. Besides the coding region of 1008 b.p., the cDNA sequence includes 60 nucleotides at the 5'-end and 204 nucleotides at the 3'-end up to the polyA tail. Hybridization of pG1 to human liver total RNA shows only one band about the size of pG1 cDNA. A much stronger hybridization signal was observed using RNA derived from human hepatocarcinoma and kidney carcinoma cell lines. Sequence homology between clone 042 and the homologous region of clone pG1 is 86%. On the other hand, homology among the translated sequences and the known human muscle protein sequence ranges between 77 and 90%; these data demonstrate the existence of more than one gene coding for G3PD. Southern blot of human DNA, digested with several restriction enzymes, also indicate that several homologous sequences are present in the human genome.

Analysis of persistent virus infections by in situ hybridization to whole-mouse sections

Nucleic acid hybridization techniques have contributed significantly to the understanding of gene organization, regulation and expression. In the context of persistent or latent viral infections, hybridization with specific labelled probes represents the most sensitive assay presently available for detection of viral genomes. During the course of persistence, viral genomes may exist in multiple and yet quite segregated areas in an infected host, but examination of all tissues remains difficult and time-consuming. At present, the application of hybridization assays to in vivo infections requires either chemical extraction of nucleic acid coupled with dot-blot and gel transfer techniques or in situ hybridization to cryostat tissue sections. In both cases, selected tissues must be removed by dissection before analysis. We describe here a procedure which allows efficient and reproducible screening of all tissue in an infected host. Our technique allows detection of viral genetic material in whole-body sections of infected mice, and provides the first evidence in vivo for accumulation of viral genetic material with a parallel decrease in infectious virus during persistent virus infection. This technique should be widely applicable to studies of developmental regulation of gene expression, for monitoring locations of gene expression in transgenic mice and for analysis of molecular mechanisms in pathogenesis.

Isolation and nucleotide sequence of a full-length cDNA coding for aldolase B from human liver

Two recombinant clones, pA2 and pA3, containing cDNA sequences for human aldolase B have been isolated from a full length human liver cDNA library. The larger one, pA3, has been subcloned in M13 phage and completely sequenced with the chain terminator method. The sequence covers 1,600 nucleotides including the whole coding region (1,050 nucleotides), 67 nucleotides from the 5' non-coding region and the whole 3' non-coding region, 440 nucleotides long, down to the poly-A tail. Comparison with rabbit aldolase A and with a partial sequence of rat aldolase B, shows a homology of about 76% for aldolase A and of about 94% for aldolase B, which indicates that the sequenced cDNA codes for the liver isoenzyme. This is the first complete sequence reported for human aldolase B. The pA3 clone strongly hybridizes to 18S mRNA from human adult liver as expected from the size of the isolated cDNA.

The major promoter element of rRNA transcription in yeast lies 2 kb upstream

Conventional genetic analysis of the transcription of rDNA in yeast is precluded because the genes are highly reiterated. As an alternative strategy to determine which sequences modulate transcription of pre-rRNA, a series of artificial rRNA genes containing a fragment of DNA from E. coli bacteriophage T7 were introduced into the yeast Saccharomyces cerevisiae. Correct transcription of the artificial genes was observed. Three regions of ribosomal spacer are found to affect transcription of rRNA. Sequences within 210 bp of the 5' terminus of 35S rRNA support low levels of transcription, but at multiple initiation points. Sequences from -210 to -2230 direct correct initiation and increase somewhat the efficiency of transcription. Most striking is that sequences from -2230 to -2420 stimulate transcription 15-fold. The function of this major promoter element is absolutely orientation-dependent but relatively independent of position. Its activity is blocked when an rRNA transcription termination sequence is placed between it and the site of initiation.

Developmental regulation of gene expression in wheat embryos. Molecular cloning of a DNA sequence encoding the early-methionine-labelled (Em) polypeptide

The early-methionine-labelled (Em) polypeptide is the most abundant single polypeptide found in the cytosolic fraction (30 000 X g supernatant) of dry wheat embryos. Synthesis of this polypeptide is readily detectable during the earliest stages (0-3 h) of wheat embryo germination, by labelling with [35S]methionine. Thereafter, synthesis of the Em polypeptide declines rapidly. A DNA sequence encoding a portion of this polypeptide has been isolated by the molecular cloning of DNA complementary to the messenger RNA from dry wheat embryos. The identity of this cloned sequence has been confirmed by hybrid-selected translation of the Em messenger, the product being analysed by one- and two-dimensional polyacrylamide gel electrophoresis, and by analysis of its partial proteolytic digestion products. Gel blot hybridisation of RNA isolated from embryos at successive stages of germination with this cloned DNA sequence confirms that the decline in the synthesis of the Em polypeptide, detected by labelling in vivo, is a consequence of the degradation of its corresponding messenger RNA.

In vivo splicing products of the rabbit beta-globin pre-mRNA

Analysis of the rabbit beta-globin transcripts present in the steady-state RNA population of fetal liver reveals that there is no strict order in the removal of the two introns from the pre-mRNA, though IVS1 seems to be preferentially eliminated first. The population of RNA molecules contains, among other splicing products, two forms of full-length IVS2 (and presumably of IVS1), released from exon sequences. One of these forms is linear, while the other has a lariat structure (circle with tail), which results from looping of the intron sequence to itself and formation of a covalent bond between the 5' end and an internal IVS2 position at a distance of 31 bases from the 3' splice site. This branching point maps at the penultimate position of the heptamer TGCTAAC. Branched Y-forms of IVS2, presumably resulting from nicking of the lariat loop (in vivo or during purification) are also detected. Comparison of in vivo RNA with in vitro splicing products reveals corresponding lariat forms. However, the in vivo linear intron species are absent from the in vitro products, which, in contrast, contain more than one intron conformer.

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.

Two steroid 21-hydroxylase genes are located in the murine S region

A common inherited disorder of steroidogenesis in man, 21-hydroxylase (21-OH) deficiency, is linked to the HLA major histocompatibility complex (MHC), and is associated in particular with certain allotypes of the HLA-linked complement proteins. Recently, this disorder was demonstrated to result from a defective structural gene for the 21-OH enzyme, also termed cytochrome P-450C21. The human (HLA) and murine (H-2) MHCs are homologous in overall organization and in the structures of their component genes. To determine whether 21-OH genes are located in the H-2 complex, we have now used a bovine adrenal complementary DNA clone encoding part of 21-OH to examine a cluster of overlapping cosmid clones derived from the S region of the BALB/c mouse. We found that there are two 21-OH genes in this region, located immediately 3' to the C4 and Slp genes.

Respiratory nitrate reductase of Escherichia coli. Sequence identification of the large subunit gene

The nucleotide sequence is presented of part of the transcription initiation end of the nar operon of Escherichia coli K12, which encodes the respiratory nitrate reductase complex. The first coding sequence transcribed is the narG gene, encoding the large catalytic molybdoprotein of the complex. This sequence was assigned unambiguously by automated N-terminal amino acid sequencing of the purified large subunit. The deduced partial amino acid sequence of this polypeptide is hydrophilic and rich in basic residues. Membrane insertion does not involve N-terminal proteolytic processing of this subunit.

Nucleic acid sequence and chromosome assignment of a wheat storage protein gene

A cloned gliadin gene was isolated from a wheat genomic library, and 2.4 kb of its primary sequence determined. The gene, alpha-1Y, was found by Southern analysis to be located on chromosome 6A, and its derived amino acid sequence identifies it as a member of the A-gliadin subgroup of alpha-gliadins located on the short arm of that chromosome. alpha-1Y is apparently functional, and contains consensus TATA and CAAT boxes, and polyadenylation signals. This gliadin gene has no introns, and its noncoding flanking regions contain several short repeats and inverted sequences. The gene is contained in a 6.2 kb EcoRI genomic fragment whose apparent copy number varies in different wheat cultivars.

Molecular cloning and characterization of the glucoamylase gene of Aspergillus awamori

The filamentous ascomycete Aspergillus awamori secretes large amounts of glucoamylase upon growth in medium containing starch, glucose, or a variety of hexose sugars and sugar polymers. We examined the mechanism of this carbon source-dependent regulation of glucoamylase accumulation and found a several hundredfold increase in glucoamylase mRNA in cells grown on an inducing substrate, starch, relative to cells grown on a noninducing substrate, xylose. We postulate that induction of glucoamylase synthesis is regulated transcriptionally. Comparing total mRNA from cells grown on starch and xylose, we were able to identify an inducible 2.3-kilobase mRNA-encoding glucoamylase. The glucoamylase mRNA was purified and used to identify a molecularly cloned 3.4-kilobase EcoRI fragment containing the A. awamori glucoamylase gene. Comparison of the nucleotide sequence of the 3.4-kilobase EcoRI fragment with that of the glucoamylase I mRNA (as determined from molecularly cloned cDNA) revealed the existence of four intervening sequences within the glucoamylase gene. The 5' end of the glucoamylase mRNA was mapped to several locations within a region -52 to -73 nucleotides from the translational start. Sequence and structural features of the glucoamylase gene of the filamentous ascomycete A. awamori were examined and compared with those reported in genes of other eucaryotes.

Expression and regulation of the plasmid-encoded hemolysin determinant of Escherichia coli

As a first approach towards studying the regulation of hemolysin synthesis in Escherichia coli, we have fused lacZ into the four hly genes (hlyC, hlyA, hlyBa and hlyBb) using the Mud-1 (Mu::lacZ, Y, Apr) phage. The sites of insertion of Mud-1 within the various hly genes of the Hly plasmid pHly152 were determined by the hemolytic phenotype of the Hly- mutants (Hly-ex/Hly-in or Hly-ex/Hly+in) and by complementation of these Hly- mutants with recombinant plasmids carrying cloned hly genes. It was found that hlyC, hlyA and hlyBa are transcribed from a relatively weak promoter (hlypL) located in front of hlyC. The activity of beta-galactosidase is considerably lower when Mud-1 is integrated in hlyBa than when it is inserted in hlyC, suggesting a considerable decline in hly gene expression from hlyC to hlyBa. The DNA sequence upstream of the coding region of hlyC was found to promote galK gene expression when a fragment covering this region was inserted into the promoter-probe vector pKO-11. A putative promoter sequence, which could correspond to hlypL, was identified in this sequence. The hlyBb gene appears to be transcribed from a different promoter and the direction of transcription seems to be opposite to that of the hlyC, A, Ba operon. The strength of this promoter (hlypR), based on the level of beta-galactosidase activity of Mud-1 insertion mutants in hlyBb, is considerably higher than that of hlypL.(ABSTRACT TRUNCATED AT 250 WORDS)

Tandem promoters determine regulation of the Klebsiella pneumoniae glutamine synthetase (glnA) gene

Transcription of the structural gene for glutamine synthetase (glnA) in Klebsiella pneumoniae is controlled by the nitrogen regulatory genes ntrA, ntrB and ntrC. The nucleotide sequence of the regulatory region upstream of the glnA gene is reported here. High resolution S1 mapping of in vivo transcripts indicates that the regulatory region contains tandem promoters separated by 100 nucleotides. Measurements of beta-galactosidase activities determined in vivo from glnA-lac fusions suggest that the upstream promoter (for RNA2) is negatively regulated by the ntrBC gene products whereas transcription from the downstream promoter (for RNA1) is positively activated by the ntrA gene product in the presence of either the ntrBC or the nifA genes. The nucleotide sequence of the upstream promoter resembles the consensus sequence for E. coli promoters, whereas the downstream promoter shows homology with the nitrogen fixation (nif) promoters of K. pneumoniae.

Molecular cloning and characterisation of cDNAs complementary to mRNAs from wounded potato (Solanum tuberosum) tuber tissue

Five cDNA clones complementary to mRNAs representing different abundances and responses to wounding have been isolated from a library of Sau 3A fragments in the bacteriophage M13 mp8. These were characterised by hybrid-release translation and hybridisation to RNA blots. The levels of RNA complementary to two of the clones show a marked increase during the 24h after wounding, one shows a small increase and two show no appreciable changes except that caused by a general increase in the total amount of polyadenylated RNA per microgram of total RNA which increases 2.5-fold during the same period. The would-induced RNAs are not induced in diluted suspension-culture cells, but RNA complementary to each clone is present in varying levels in stems, leaves and roots of intact potato plants.

High-sensitivity S1 mapping with single-stranded [32P]DNA probes synthesized from bacteriophage M13mp templates

A method is described by which high-specific-activity single-stranded (ss) [alpha-32P]DNA of a defined size complementary to sequences cloned into bacteriophage M13 is synthesized. The ss DNA template is annealed with a universal sequencing primer, the primer extended with DNA polymerase I Klenow fragment and the DNA duplex cut at a unique site 5' to the multiple cloning sites in the M13 phage. The reaction products are denatured and the ss alpha-32P probe fragment complementary to the cloned sequence is separated from the template by electrophoresis. The utility of such probes for S1 mapping is shown by mapping the 3' ends of transcripts from a mutant Drosophila heat-shock gene. The method described here is up to 300 times more sensitive than conventional S1 mapping techniques.