The making of strand-specific M13 probes

Cleaving DNA at any predetermined site with adapter-primers and class-IIS restriction enzymes

A four-component system has been designed that makes it possible to prepare a double-stranded (ds) DNA fragment; one fragment end is predesigned (by the use of a class-IIS restriction enzyme and adapter-primer), and the other end corresponds to any normal restriction cut. The system is composed of the phage M13mp7 single-stranded (ss) target DNA; the Fok I restriction enzyme; an oligodeoxynucleotide adapter-primer, which permits one to introduce Fok I cuts at any specified site in the target DNA; and DNA polymerase, which converts the ss target into a ds form ready for cloning. In this system, the oligodeoxynucleotide adapter-primer serves several purposes. The 5' hairpin ds domain of the adapter-primer contains the Fok I recognition site. Its 3' ss domain selects a complementary site on the target ss DNA, hybridizes with it to form the ds cleavage site, and serves as a primer to convert the ss M13mp7 target to ds DNA.

Nucleotide sequence and genetic analysis of the nifB-nifQ region from Azotobacter vinelandii

A 3.8-kilobase-pair EcoRI fragment which corrects the mutations carried by the NifB- Azotobacter vinelandii strains CA30 and UW45 was cloned, and its nucleotide sequence was determined. Four complete open reading frames (ORFs) and two partial ORFs were found. The translation product of the first partial ORF is the carboxy-terminal end of a protein homologous to the nifA gene product from Klebsiella pneumoniae. A 285-base-pair sequence containing a potential nif promoter and nif regulatory sites separates this nifA gene from the first complete ORF which encodes a protein homologous to nifB gene products from K. pneumoniae and Rhizobium species. The Tn5 insertion in strain CA30 and the nif-45 mutation of strain UW45 are located within this nifB gene. The ORF downstream from nifB predicts an amino acid sequence with a cysteine residue pattern that is characteristic of ferredoxins. No similarities were found between the translation product of the third complete ORF and those of nif genes from other organisms. At the carboxy-terminal end of the predicted translation product of the fourth complete ORF, 30 of 60 amino acid residues were identical with the sequence of the nifQ gene product from K. pneumoniae. The partial ORF located at the end of the fragment encodes the N-terminal part of a potential protein with an unknown function. Northern (RNA) blot analysis indicated that transcripts from the region containing the four complete ORFs were NH4+ repressible and that the transcription products were identical in cells derepressed under conditions of Mo sufficiency or Mo deficiency or in the presence of vanadium. In contrast to the NifB- strain CA30, which is Nif- under all conditions, mutants that carry mutations affecting the C-terminal end of nifB or genes located immediately downstream from nifB, grew under all N2-fixing conditions. However, in the presence of Mo, most of the strains required 1,000 times the amount of molybdate that is sufficient for maximal growth of the wild-type strain CA under N2-fixing conditions. Growth data from strain CA37, which carries a Kanr insertion in nifQ, indicate that nifQ in A. vinelandii is not required for N2 fixation in the presence of V2O5 or under Mo-deficient conditions. Growth studies and acetylene reduction assays performed on two nifEN deletion strains showed that nifE and nifN are required for N2 fixation under Mo sufficiency, as previously observed (K. E. Brigle, M. C. Weiss, W. E. Newton, and D. R. Dean, J. Bacteriol. 169:1547-1553, 1987), but not under conditions of Mo deficiency or in the presence of 50 nM V2O5.

Detection of toxigenic Escherichia coli using biotin-labelled DNA probes following enzymatic amplification of the heat labile toxin gene

Several types of DNA probes labelled with biotin were compared for their sensitivity to detect the heat labile toxin (LT) gene in toxigenic Escherichia coli. In addition, a procedure was developed for enzymatically amplifying LT gene sequences in toxigenic E. coli. Probes were labelled with biotinylated nucleotides by either nick translation; 3' tailing; primer extension of probe DNA cloned into bacteriophage M13; sandwich hybridization; or oligolabelling of isolated DNA fragments. A single stranded probe consisting of a DNA fragment from the LT gene cloned into the bacteriophage M13mp18 and detected by hybridization to oligolabelled biotinylated M13mp18 RF DNA in a sandwich hybridization was able to detect as little as 10 pg of toxin gene DNA. Cloned LT gene DNA was serially diluted and amplified enzymatically using synthetic oligonucleotide primers. Amplified DNA was detected using biotin-labelled M13-based probes. As little as 1 fg of LT DNA could be amplified to detectable levels by this method. Experiments with LT+ bacteria resulted in the detection of as few as 1000 bacteria. The combination of enzymatic amplification coupled with M13-based DNA probes provides a highly sensitive tool for detecting pathogenic microorganisms.

The beta-tubulin gene family of Arabidopsis thaliana: preferential accumulation of the beta 1 transcript in roots

The genome of Arabidopsis thaliana (L.) Heynh. was shown to contain a beta-tubulin gene family consisting of at least seven distinct genes and/or pseudogenes. Genomic clones of five different beta-tubulin genes and/or pseudogenes have been isolated and partially characterized. The complete nucleotide sequence of one A. thaliana beta-tubulin gene, designated beta 1, has been determined. A comparison of the predicted amino acid sequence of the A. thaliana beta 1-tubulin with the predicted sequences of beta-tubulins of animals and protists indicated that this plant beta-tubulin shows a high degree of homology with other beta-tubulins. However, the beta 1-tubulin contains a novel single amino acid insertion at position 41. The A. thaliana beta 1-tubulin gene is transcribed, as shown by RNA blot hybridization and S1 nuclease analyses. A 3'-noncoding gene-specific probe was used to examine the expression of the beta 1-tubulin gene in leaves, roots, and flowers by blot hybridization analyses of total RNA isolated from these tissues. The results showed that the transcript of the beta 1 gene accumulates predominantly in roots, with low levels of transcript in flowers, and barely detectable levels of transcript in leaves. A second genomic clone was shown to contain two essentially identical beta-tubulin coding sequences in direct tandem orientation and separated by 1 kb.

The structure of the gene for cecropin B, an antibacterial immune protein from Hyalophora cecropia

Pupae of the moth Hyalophora cecropia respond to an injection of live bacteria by the production of a potent antibacterial activity. The broad-spectrum property of this activity is due chiefly to two small proteins, cecropins A and B. Sequences of the proteins showed them to be homologous and to contain 37 and 35 amino acid residues respectively. The subsequent isolation of two cDNA clones for cecropin B showed that this protein is made as a prepro molecule composed of 62 amino acid residues. We have now prepared a genomic bank and studied four genomic clones for cecropin B. The coding regions were found in two neighbouring BglII fragments, one 0.79 kb and another varying in size from 3.1 kb to 4.9 kb for different clones. One transcriptional unit for preprocecropin B was sequenced and found to be 1035 bp long with a single intron, 514 bp in size. A conserved, insect specific cap site, ATCATTC, was identified by S1 mapping and primer extension experiments. Indications were found for the presence of multigene families and multicopy genes.

Fine mapping of an Alzheimer disease-associated gene encoding beta-amyloid protein

We have sublocalized an Alzheimer Disease-associated gene, which encodes for cerebrovascular beta-amyloid protein, to the region from the centromere through the proximal half of band 21q21 using both somatic cell and in situ mapping techniques. In addition we found repeatedly significant but weaker hybridization of the beta-amyloid protein probe to the short arm of chromosome 20. 794 cells were analyzed from whole blood, lymphoblastoid and skin cultures. The latter two types of cultures had parts of the 21st chromosome translocated to other chromosomes facilitating sublocalization.

Sensitive non-radioactive dot-blot hybridization using DNA probes labelled with chelate group substituted psoralen and quantitative detection by europium ion fluorescence

A new labelling method for cloned DNA probes used in hybridization assays is described. The DNA insert of recombinant plasmid DNA was made partially single-stranded for the labelling reaction by a restriction enzyme digest, followed by a controlled exonuclease III incubation. A thiol-containing psoralen derivative was covalently bound through irradiation with UV-light to the remaining double-stranded region of the plasmid DNA. The psoralen-SH groups were labelled with a large number of metal chelators (diethylentriamine pentaacetic acid, DTPA) using poly-L-lysine as a macromolecular carrier. The main advantage of the labelling procedure is that a high degree of labelling is achieved without modification of the single-stranded DNA hybridizing sequences. The specific hybrids were labelled after filter hybridization with europium ions through the chelating groups of DTPA. The europium ions were quantitatively detected by time-resolved fluorometry. The sensitivity of the assay for target DNA detection was in the low picogram range, comparable to radioactively labelled DNA probes.

The effects of hydrocortisone on c-fos, c-myc and c-ras oncogene expression in IMR-90 fibroblasts

The effects of hydrocortisone on oncogene expression in human IMR-90 fibroblasts was analyzed by Northern blotting of total RNA. In synchronized fibroblasts stimulated with serum alone, there were two time periods of increased c-fos expression during the G1 phase of the cell cycle. There was no significant difference between cells treated with serum plus hydrocortisone, and cells treated with serum alone with respect to c-fos expression. Quiescent cells showed no change in c-fos expression during the G1 phase of the cell cycle. Three peaks of c-fos expression occur when cells are treated with hydrocortisone alone, but hydrocortisone in the absence of serum is insufficient to initiate DNA synthesis. Hydrocortisone has no effect on c-myc or c-Ha-ras expression in the presence or absence of serum in synchronized fibroblasts. Therefore, the control of mRNA production of the nuclear oncogenes c-fos and c-myc, and the cytoplasmic oncogene c-ras are independent and hydrocortisone may enhance DNA synthesis by increasing c-fos expression.

Comparison of the structure and cell cycle expression of mRNAs encoded by two histone H3-H4 loci in Saccharomyces cerevisiae

The haploid genome of Saccharomyces cerevisiae contains two nonallelic sets of histone H3 and H4 gene pairs, termed the copy I and copy II loci. The structures of the mRNA transcripts from each of these four genes were examined by nuclease protection and primer extension mapping. For each gene, several species of mRNAs were identified that differed in the lengths of their 5' and 3' untranslated regions. The cell cycle accumulation pattern of the H3 and H4 mRNAs was determined in cells from early-exponential-growth cultures fractionated by centrifugal elutriation. The RNA transcripts from all four genes were regulated with the cell division cycle, and transcripts from the nonallelic gene copies showed tight temporal coordination. Cell cycle regulation did not depend on selection of a particular histone mRNA transcript since the ratio of the multiple species from each gene remained the same across the division cycle. Quantitative measurements showed significant differences in the amounts of mRNA expressed from the two nonallelic gene sets. The mRNAs from the copy II H3 and H4 genes were five to seven times more abundant than the mRNAs from the copy I genes. There was no dosage compensation in the steady-state levels of mRNA when either set of genes was deleted. In particular, there was no increase in the amount of copy I H3 or H4 transcripts in cells in which the high-abundance copy II genes were deleted.

Molecular study of the retrovirus-like transposable element 412, a 20-OH ecdysone responsive repetitive sequence in Drosophila cultured cells

Used at a physiological concentration, the steroid hormone 20-hydroxyecdysone (20-OHE) induces, in Kc cultured Drosophila melanogaster cells, important and specific changes. Modifications occur at morphological and enzymatical levels. Variations in specific protein synthesis are observed. At the molecular level, 20-OHE particularly induces a decrease in expression of the mobile dispersed genetic element 412. This repeated element which belongs to the "copia-like" family is more widely represented in Kc cells (80 fold) compared to fly cells (25 fold). 412 transcripts are heterogeneous in size, essentially polyadenylated and restricted to the nucleus. A minimal concentration of 10(-8) M and a time treatment of 16 hours are necessary to obtain a strong decrease in 412 expression. The decrease is at least an effect on these sequences at the transcriptional level. Structural similarities between the 412 element and the proviral forms of vertebrate retroviruses are strengthened by the characterization of extrachromosomal circular DNA forms revealed by the 412 probe. Quantifying experiments have shown that the steady state level of such forms is not affected by the steroid treatment.

Newly synthesized small nuclear RNAs appear transiently in the cytoplasm

Newly synthesized small nuclear RNA (snRNA) species U1 and U2 are easily identified in cytoplasmic fractions prepared by standard aqueous cell fractionation. However, because the mature stable snRNA species leak from isolated nuclei during cell fractionation, the possibility exists that these newly synthesized species also leak from the nucleus. To overcome the problems of nuclear leakage, mouse L929 cells were fractionated by cell enucleation. Enucleation extrudes the nuclei from cytochalasin-treated cells and produces cytoplasts that, by several criteria, are a bona fide cytoplasmic fraction uncontaminated by nuclear material. All six of the major snRNAs are present in the cytoplasts (c-snRNAs) shortly after synthesis. The species are identified by immunoprecipitation with specific antisera against the ribonucleoproteins and by Northern blotting and hybrid selection using cloned probes. This confirms and extends similar studies that used non-aqueous cell fractionation and manual dissection to overcome nuclear leakage. Kinetic studies demonstrate that the c-snRNAs return to the interphase nucleus after approximately 20 minutes in the cytoplasm. The U2 precursor U2' is processed to mature-sized U2 in the cytoplast fractions before returning to the nucleus. The c-snRNAs occur in ribonucleoprotein particles with similar antigenicity to the mature nuclear particles within six minutes of transcription. This suggests that in mammalian cells, important steps in the assembly of these ribonucleoproteins occur in the cytoplasm.

A promoter of the rat insulin-like growth factor II gene consists of minimal control elements

We have characterized the cis-control signals in one of the two promoters of the developmentally regulated rat insulin-like growth factor II gene (rIGF-II) by a combination of in-vivo transient expression, in-vitro transcription, footprinting, gel band-shifting and methylation-interference experiments, using a series of deletion mutant templates. Our results indicate that this simple (minimal) promoter (P2) consists of no more than 128 base-pairs, which include an ATA box and four proximal upstream GC boxes binding the general transcription factor Sp1. Three of the latter sites deviate from the known Sp1 consensus recognition sequence. The two types of cis-acting regulatory signals (GC/ATA motif) of the P2 promoter are inter-dependent and sufficient for transcription. A model for the operation of this type of minimal promoter is discussed. S1 nuclease-hypersensitive sites, localized by in-vitro mapping to the region of the P2 Sp1-binding sites, are also present in vivo and correlate with the transcriptional state of chromatin in the rIGF-II locus. We show that recognition sites for Sp1 binding are a subset of sequences that exhibit hypersensitivity to S1.

Antigenic variation of a cysteine-rich protein in Giardia lamblia

The WB isolate of Giardia lamblia expresses a cysteine-rich 170-kD surface antigen (CRP170) that undergoes antigenic variation. An (6E7), cytotoxic for isolates expressing CRP170, was used in another study to select antigenic variants from clones of the WB isolate of Giardia. CRP170 was replaced by surface-labeled bands ranging in size from approximately 50 to 170 kD. In this study, mAb 6E7 was used to isolate a 1-kb portion of the CRP170 gene (M2-1) from a lambda gt 11 expression library. The M2-1 clone hybridized to a 5.4-kb transcript from isolates expressing CRP170 but did not hybridize to RNA from antigenic variants. Evidence was found for frequent rearrangements at the CRP170 gene locus. DNA sequencing of the M2-1 clone revealed the presence of long tandem repeats. The putative amino acid sequence of M2-1 reveals a 12% cysteine content, and CRP170 is readily labeled in vivo with cysteine.

Expression of the insulin-like growth factor II gene in the choroid plexus and the leptomeninges of the adult rat central nervous system

The rat insulin-like growth factor II gene, encoding a fetal somatomedin, expresses a multitranscript family in embryonic/fetal tissues and in the adult brain and spinal cord. By performing in situ hybridization on tissue sections of adult brain and spinal cord, we have found that these transcripts are not expressed in neural or glial cells but are expressed in the epithelium of the choroid plexus of each cerebral ventricle and in the leptomeninges. We propose that the choroidal epithelial cells synthesize and secrete insulin-like growth factor II into the cerebrospinal fluid.

Nucleotide sequence and determination of the extremities of the 26S ribosomal RNA gene in wheat mitochondria: evidence for sequence rearrangements in the ribosomal genes of higher plants

The nucleotide sequence of the wheat mitochondrial 26S ribosomal RNA gene and flanking regions was determined and compared with mitochondrial 26S rRNA genes from maize and Oenothera. All three genes exhibit a high degree of homology except within two variable regions. When the plant mitochondrial 26S rRNA genes are compared with Escherichia coli 23S rRNA and chloroplast 23S and 4.5S rRNA genes, a third variable region is apparent close to the 3' end of the gene. The 5' and 3' ends of the wheat mitochondrial gene were determined by S1 nuclease mapping. Computer analysis of the wheat mitochondrial gene revealed several small sequences present either in the 5' region of the 26S rRNA gene or in the 18S rRNA gene.

Construction of a Stable α-Galactosidase-Producing Baker's Yeast Strain

Molasses is widely used as a substrate for commercial yeast production. The complete hydrolysis of raffinose, which is present in beet molasses, by Saccharomyces strains requires the secretion of α-galactosidase, in addition to the secretion of invertase. Raffinose is not completely utilized by commercially available yeast strains used for baking, which are Mel − . In this study we integrated the yeast MEL1 gene, which codes for α-galactosidase, into a commercial mel 0 baker's yeast strain. The Mel + phenotype of the new strain was stable. The MEL1 gene was expressed when the new Mel + baker's yeast was grown in molasses medium under conditions similar to those used for baker's yeast production at commercial factories. The α-galactosidase produced by this novel baker's yeast strain hydrolyzed all the melibiose that normally accumulates in the growth medium. As a consequence, additional carbohydrate was available to the yeasts for growth. The new strain also produced considerably more α-galactosidase than did a wild-type Mel + strain and may prove useful for commercial production of α-galactosidase.

Filamentous phages as cloning vectors

The virtue of Ff vectors goes beyond the fact that they deliver a single strand in a convenient package for sequencing and oligonucleotide-directed mutagenesis. Of all vectors in common use they are the easiest to propagate and process. Their genomes can be easily manipulated, and the knowledge acquired over a quarter century of basic research makes their behavior reasonably predictable. For this reason I have emphasized the general properties of Ff phage in this review and dealt at some length with applications that are still not fully developed, I hope this review will inspire readers to continue the tradition of imaginative exploitation of this unique class of viruses.

The mitochondrial S13 ribosomal protein gene is silent in wheat embryos and seedlings

The sequence of a wheat mitochondrial reading frame encoding a protein homologous to the E. coli S13 small subunit ribosomal protein has been determined. The gene is located immediately downstream of a 1.4 kb recombinationally-active repeat element that contains the ATPase subunit 6 gene. The coding regions of the two genes are separated by only 153 bp, the shortest distance yet observed between protein-coding genes in plant mitochondria. However, their transcript profiles differ markedly. The ATPase 6 gene displays a single, prominent mRNA of approximately 1.4 kb, whereas the S13 gene shows no stable transcript as judged by Northern blot analysis of wheat mitochondrial RNA isolated from different developmental stages. A short segment of the 26S rRNA gene is located downstream of the S13 gene and its presence illustrates the frequent DNA duplication/rearrangements found in wheat mitochondria.

Transcriptional control of yeast ribosomal protein synthesis during carbon-source upshift

Shifting a yeast culture from an ethanol-based medium to a glucose-based medium causes a coordinate increase of the cellular levels of ribosomal protein mRNAs by about a factor 4 within 30 min. Making use of hybrid genes encompassing different portions of the 5'-flanking region of the L25-gene, we could show that the increase in mRNAs is a transcriptional event, mediated through DNA sequences upstream of the ribosomal protein (rp) genes. Further analysis revealed that sequence elements are involved that many rp-genes have in common and that previously were identified as transcription activation sites (RPG-boxes or UASrpg). Using appropriate deletion mutants of the fusion genes we could demonstrate that a single RPG-box is sufficient for the transcriptional upshift. In addition, both copy genes encoding rp28 which differ considerably in their extent of transcriptional activity, show the upshift effect in a proportional manner. Definite proof for the role of the UASrpg in nutritional regulation was obtained by examining the effect of a synthetic RPG-box on transcription.

Primary structure of human placental anticoagulant protein

The primary structure of human placental anticoagulant protein was determined by a combination of amino acid and nucleotide sequencing techniques. The carboxymethylated protein was digested with cyanogen bromide, and the resulting peptides were separated by gel filtration and high-performance liquid chromatography. A total of 239 out of 319 amino acid residues were identified from 7 cyanogen bromide fragments. A full-length cDNA clone encoding placental anticoagulant protein was isolated from a human placenta cDNA library. This clone was 1.6 kilobases long and contained a translation initiation site coding for methionine, 957 nucleotides encoding for the mature protein, a stop codon, a poly(A) recognition site, and a poly(A) tail. Analysis of the tryptic-blocked peptide that originated from the NH2-terminus of the protein showed that the terminal methionine was removed and the adjacent alanine residue was acetylated by posttranslational events. Placental anticoagulant protein is composed of 319 amino acids with acetylalanine as the NH2-terminus and has a high degree of sequence identity with lipocortins I and II. It contains four internal repeats, each including a sequence corresponding to a putative Ca2+-dependent phospholipid binding site. Placental anticoagulant protein is a member of the lipocortin/calpactin family.

Nucleotide sequence and molecular characterization of a maize mitochondrial plasmid-like DNA

The mitochondrial genome of Black Mexican Sweet maize consists of the principal genome, a 2.3 kb minilinear DNA, a 1,913 bp (1.9 kb) and a 1,445 bp (1.4 kb) minicircular DNA. The three extrachromosomal DNAs exhibit characteristics of autonomous replication in cell suspension culture. The complete sequence of the 1.4 kb minicircle was determined. It has 61 bp of near perfect sequence homology to the 1.9 kb minicircle. Both minicircular DNAs are transcriptionally active; the longest open reading frame of the 1.4 kb minicircle was 231 bp. A putative origin of replication was identified as a high A + T sequence. These minicircles were present in some but not all of 20 maize lines surveyed. None of the lines examined carried the 1.4 kb minicircle without the 1.9 kb minicircle. Nuclear DNA of one line of the seven examined carried homology to both DNAs.

Phenotypic expression and genetic heterogeneity of lincosamide inactivation in Staphylococcus spp

We examined the resistance phenotype and the genetic basis of lincosamide modification in 25 clinical isolates of Staphylococcus spp. inactivating lincomycin and clindamycin. The strains were resistant to high levels of lincomycin but remained susceptible to clindamycin. However, MBCs and inoculum effects showed that the activity of clindamycin was impaired. The distribution in these strains of nucleotide sequences related to linA and linA', the genes encoding lincosamide nucleotidylation in Staphylococcus haemolyticus BM4610 and S. aureus BM4611, respectively, was studied by dot blot hybridization. The genes responsible for lincosamide inactivation in Staphylococcus spp. were found to constitute a family of related sequences which are not species specific.

Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences

A partial nucleotide sequence that included 1,693 base pairs of the M12 (emm12) gene of group A streptococci (strain CS24) and adjacent upstream DNA was determined. Type 12 M protein-specific mRNA of strain CS24 is transcribed from two promoters (P1 and P3) separated by 30 bases. The transcription start sites of the emm12 gene were located more than 400 bases downstream of a deletion that causes decreased M-protein gene transcription in strain CS64. Deletion analysis of M protein-expressing plasmids indicated that an upstream region greater than 1 kilobase is required for M-protein gene expression. The M-protein gene transcriptional unit appears to be monocistronic. Analysis of the emm12 DNA sequence revealed three major repeat regions. Two copies of each repeat, A and B, existed within the variable 5' end of the gene; repeat C demarcated the 5' end of the constant region shared by emm12 and emm6.

Identification of the lesion in the stimulatory GTP-binding protein of the uncoupled S49 lymphoma

The stimulatory GTP-binding protein (Gs) of the uncoupled mutant of S49 lymphoma cells is deficient in its ability to transduce hormonal signals from ligand-bound beta-adrenergic receptors to the catalytic component of adenylate cyclase. In order to define the genetic defect in the Gs of uncoupled S49 cells, a complementary DNA clone encoding the alpha-subunit of Gs was analyzed and the deduced primary structure of the defective subunit compared to that of the wild-type subunit. A single nucleotide transversion was found that coded for a proline rather than an arginine at residue 389. The results indicate a domain of the alpha-subunit of Gs that specifically interacts with hormone receptors.

Organization and sequence of the hsd genes of Escherichia coli K-12

The nucleotide sequence of the hsdR and M genes, together with that for hsdS comprises an 8400 base segment spanning the entire hsd region of Escherichia coli K-12. The three hsd genes are transcribed in the same direction, but from two promoters. hsdR and hsdM are separated by 492 base-pairs, whereas the termination codon of hsdM overlaps the initiation codon of hsdS. pres precedes hsdR, and our data indicate a transcription termination signal in the interval between hsdR and pmod, as expected if transcription of hsdM and S is dependent on pmod. Transcription from pres is not influenced by the products of the hsdM and S genes, and the mechanism whereby restriction is prevented when the hsd region is transferred to a modification-deficient cell remains to be elucidated. A segment of the predicted amino acid sequence of the M polypeptide shares homology with a variety of adenine methylases and may identify part of the active site for methylation of specific adenine residues. The R polypeptide shows homology with a variety of ATPases, and pronounced regions of alpha-helical structure are predicted, one of which is amphipathic.

Evidence for group A-related M protein genes in human but not animal-associated group G streptococcal pathogens

Group G streptococci have on their surface antiphagocytic M protein-like antigens. To determine if these organisms have genes similar to the M protein genes of Streptococcus pyogenes (group A), DNA from independent group G isolates of human and animal origin were tested for homology to probes representing sequences encoding the carboxy-terminus and leader peptide of the type 12 M protein (M12) of group A streptococci. All eight human-associated group G strains tested had DNA homologous to the carboxy-terminal probe. Six of these strains also had DNA that hybridized with the leader peptide probe. Using probes representing the group A M12 gene (emm12) and adjacent 5' sequences, we found that one of these strains, known to produce an M12 antigen, had a nearly complete duplication of the group A emm12 gene, differing only in 0.26 kb of sequence at the 5' end. The other human-associated strains did not hybridize with emm12-specific sequences. None of the group G strains had homology to 5' proximal sequences thought to be associated with group A emm12 regulation, but all the human-associated strains had DNA homology to a 1.5 kb DNA segment which mapped 2.5 kb upstream of the emm12 gene in group A streptococci. None of the twelve animal-associated strains tested hybridized with any of the probes used in this study. These results suggest that human but not animal-associated group G isolates have group A-related M protein genes. We propose that expression of these genes are critical for infection of the human host and that group A and G shared upstream sequences could encode additional virulence factors.

Characterization of a class of small auxin-inducible soybean polyadenylated RNAs

Four new auxin-responsive RNAs from soybean (Glycine max (L.) Merr., var. Wayne) are described. The RNAs were identified by hybridization to three cDNA probes obtained from a library enriched for sequences which increase in abundance within 60 min after 2,4-D (2,4-dichlorophenoxyacetic acid) treatment. These RNAs appear to define a new class of small (i.e. approximately 550 nucleotides) RNAs that respond extremely rapidly to application of exogenous auxin. In excised elongating hypocotyl sections, an increase in the abundance of these RNAs can be detected 2 to 5 min after treatment with 50 μM 2,4-D. This response is half maximal after 10 min and reaches steady state in 60 min. RNA blot analysis shows that these RNAs are expressed differentially in various parts of the seedling. The degree of inducibility by auxin is also organ-specific, with the elongating hypocotyl being the most responsive of the organs tested. The RNAs display identical response specificities with one exception. Accumulation of one RNA, designated 10A, is completely abolished by simultaneous addition of cycloheximide and 2,4-D. This RNA also displays a different 2,4-D dose response than other RNAs examined. These results suggest that more than one mechanism is involved in rapid modulation of gene expression by auxin.

Euglena gracilis chloroplast DNA: the untranslated leader of tufA-ORF206 gene contains an intron

Structural features of a dicistronic 1.95 kb mRNA coding for the chloroplast specific elongation factor Tu and ORF206 are described. The unspliced pre-mRNA is composed of 2562 nucleotides and undergoes four splicing events which remove a total of 606 nucleotides. The first intron splits the untranslated leader, two introns dissect the tufA coding region and the forth intron is within ORF206, which codes for a putative protein that is to 34% homologous with the putative protein of chloroplast ORF184 of tobacco. Introns neither belong to group I nor II, and 5' and 3' intron boundaries do not follow consensus sequences. Potential ribosome binding sites are located 58 and 32 positions upstream of the tufA and ORF206 start codon, respectively.

Homology of pCS1 Plasmid Sequences with Chromosomal DNA in Clavibacter michiganense subsp. sepedonicum : Evidence for the Presence of a Repeated Sequence and Plasmid Integration

Restriction fragments of pCS1, a 50.6-kilobase (kb) plasmid present in many strains of Clavibacter michiganense subsp. sepedonicum (“ Corynebacterium sepedonicum ”), have been cloned in an M13mp11 phage vector. Radiolabeled forms of these cloned fragments have been used as Southern hybridization probes for the presence of plasmid sequences in chromosomal DNA of this organism. These studies have shown that all tested strains lacking the covalently closed circular form of pCS1 contain the plasmid in integrated form. In each case the site of integration exists on a single plasmid restriction fragment with a size of 5.1 kb. Southern hybridizations with these probes have also revealed the existence of a major repeated sequence in C. michiganense subsp. sepedonicum. Hybridizations of chromosomal DNA with deletion subclones of a 2.9-kb plasmid fragment containing the repeated sequence indicate that the size of the repeated sequence is approximately 1.3 kb. One of the copies of the repeated sequence is on the plasmid fragment containing the site of integration.

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Effects of modulation of RNase H production on the recovery of DNA synthesis following UV-irradiation in Escherichia coli

The requirements for the recovery of DNA synthesis in UV-irradiated Escherichia coli were analysed in strains having varied levels of RNase H and RecA protein. We have previously shown (Khidhir et al. 1985) that the recovery of DNA synthesis in E. coli following UV treatment is an inducible SOS function requiring protein synthesis. We proposed that this reflected the need for the synthesis of specific induced replisome reactivation factor(s) for recovery. In this study we now show that recovery of DNA synthesis can in fact take place in the absence of protein synthesis in a mutant lacking RNase H and having high (constitutive) levels of RecA protein. We also show that expression of rnh is inhibited during the SOS response in recA+ but not in a recA- strain. The results are discussed in relation to the mechanism of recovery of DNA synthesis following UV irradiation in E. coli.

Expression of M type 12 protein by a group A streptococcus exhibits phaselike variation: evidence for coregulation of colony opacity determinants and M protein

Three major categories of colony opacity were observed for natural variants of the M type 12 (M12) group A streptococcus strain CS24. Colony opacity variants that switched between two alternative categories at significantly high frequencies were identified and are referred to as switching between more opaque (Op+) and less opaque (Op-) phenotypes. Twenty lineages of such variants were derived for analysis and were assessed for resistance to phagocytosis, acid-extractable M12 antigen, and M12 mRNA, criteria which define the M protein-positive phenotype (M+). Transition from the M+ to the M protein-negative phenotype (M-) correlated with a change from Op+ to Op-. Reversion to the Op+ phenotype was accompanied by reversion to the M+ state in all variants except one and occurred at a higher frequency than the forward M+ to M- switch. These data demonstrate the existence of M12 protein phaselike switching in the group A streptococcus strain CS24. The discovery of an Op+ M- revertant confirmed that colony opacity and M protein can be expressed independently and are distinct gene products. We suggest that coregulation of colony opacity and M protein expression accounts for their association among descendents of strain CS24. Southern blot hybridization analyses of digested genomic DNA from 27 M- variants and 15 M+ revertants were performed with DNA probes containing M12 protein and adjacent upstream sequences. DNA deletions were identified only in two stable M- variants, approximately 1.3 and 1.4 kilobases upstream from the M12 gene, respectively, whereas all unstable M- variants lacked detectable rearrangements. This suggests that deletions within or adjacent to the structural gene are unlikely to be responsible for the reversible switch in M protein expression. However, the association with the stable M- phenotype and the location of these deletions, as well as two other deletions, approximately 0.5 kilobase upstream from the M12 promoter in two previously described variants of strain CS24 suggests that a second gene product is required for full expression of M12 protein synthesis in this strain.

Structure of the gene for human beta 2-adrenergic receptor: expression and promoter characterization

The genomic gene coding for the human beta 2-adrenergic receptor (beta 2AR) from A431 epidermoid cells has been isolated. Transfection of the gene into eukaryotic cells restores a fully active receptor/GTP-binding protein/adenylate cyclase complex with beta 2AR properties. Southern blot analyses with beta 2AR-specific probes show that a single beta 2AR gene is common to various human tissues and that its flanking sequences are highly conserved among humans and between man and rabbit, mouse, and hamster. Functional significance of these regions is supported by the presence of a promoter region (including mRNA cap sites, two "TATA boxes," a "CAAT box," and three G + C-rich regions that resemble binding sites for transcription factor Sp1) 200-300 base pairs 5' to the translation initiation codon. In the 3' flanking region, sequences homologous to glucocorticoid-response elements might be responsible for the increased expression of the beta 2AR gene observed after treatment of the transfected cells with hydrocortisone. In addition, 5' to the promoter region, an open reading frame encodes a 251-residue polypeptide that displays striking homologies with protein kinases and other nucleotide-binding proteins.

Replication control genes of plasmid pE194

pE194, a 3.7-kilobase plasmid, confers resistance to macrolide, lincosamide, and streptogramin B antibiotics. The previously identified cop and repF genes of pE194 have been further localized by molecular cloning and mutational analysis together with DNA sequencing. The CfoIB fragment of pE194 is capable of autonomous replication and contains both genes. Most of this region has been resequenced, and two errors reported in a previous study have been corrected. The corrected sequence indicates that the replication region contains a single large open reading frame, which we propose encodes the repF product. Northern blot (RNA blot) analysis of this region detected six transcripts, all transcribed in the same direction as one another and opposite to repF. A 350-base transcript is synthesized from the region containing cop. No in vivo transcript for the repF gene was detected, but a protein was observed in an in vitro transcription-translation system which appears to be its product. An ochre mutation was inserted in the putative repF open reading frame, and a nonsense fragment was detected in the in vitro system. When carried passively on a pUB110 replicon, this mutant product appears capable of inhibiting pE194 replicons in trans. The pE194 origin of replication has been localized to within 200 bases.

Amounts of mitochondrial DNA and abundance of some mitochondrial gene transcripts in early mouse embryos

The contents of mitochondrial DNA (mtDNA) and the steady-state amounts of 12 and 16 S mitochondrial rRNAs and the mRNAs for cytochrome c oxidase subunits I and II (COI and COII) were determined in dot hybridization experiments with cloned mtDNA fragments as probes during development from the one-cell to the blastocyst stage. The mtDNA content remained constant during this period at about 2.13 pg or 119,000 mtDNA molecules per embryo, suggesting an absence of mtDNA replication. The amounts of mitochondrial rRNA and the mRNAs for COI and COII varied markedly depending on developmental stage. They remained low between the end of oocyte growth and the late two-cell stage but increased 25-50X during cleavage from two-cell to early blastocyst. In the early blastocyst, the number of mitochondrial mRNA molecules was estimated at 7.9 X 10(6) or about 23% of the total embryo poly(A)+ RNA. These results suggest that the mitochondrial genome is largely inactive in the egg and two-cell embryo but that a high rate of mitochondrial transcription is initiated during cleavage. The activation of the mitochondrial genome coincides with a pronounced structural and functional differentiation of the mitochondria.

Processing of precursor RNAs from mitochondria of Neurospora crassa

Neurospora mitochondrial DNA is transcribed into long molecules containing the information of several genes. Processing leads to formation of functionally active RNAs. It has been shown previously that when tRNA sequences are present in these transcripts excision of mRNAs occurs at the acceptor stem of these tRNA sequences. We have investigated the processing of precursor RNAs transcribed from a region of the mitochondrial genome devoid of tRNA genes. This region comprises the genes encoding subunit 6 of the mitochondrial ATPase, subunit 2 of cytochrome aa3 and a mitochondrial ATPase proteolipid-like gene. We have proved that a common precursor of the putative mRNAs of these genes exists and we have determined the positions of the 5' and 3' ends of processing intermediates and of the mature mRNAs. We will discuss possible processing routes and secondary structures that substitute for tRNA sequences as processing sites.

Molecular cloning and genetic analysis of the suppressor-of-white-apricot locus from Drosophila melanogaster

We report genetic and molecular analysis of the suppressor-of-white-apricot [su(wa)] locus, one of several retrotransposon insertion allele-specific suppressor loci in Drosophila melanogaster. First, we isolated and characterized eight new mutations allelic to the original su(wa)1 mutation. These studies demonstrated that su(wa) mutations allelic to su(wa)1 affected a conventional D. melanogaster complementation group. Second, we cloned the chromosomal region containing the su(wa) complementation group by P element transposon tagging. The ca. 14-kilobase region surrounding the su(wa) complementation group contained five distinct transcription units, each with a different developmentally programmed pattern of expression. Third, we used a modified procedure for P-mediated gene transfer to identify the transcription unit corresponding to su(wa) by gene transfer. Fourth, we found that the presumptive su(wa) transcription unit produced a family of transcripts (ranging from ca. 3.5 to ca. 5.2 kilobases) in all developmental stages, tissue fractions, and cell lines we examined, suggesting that the gene is universally expressed.

Molecular cloning of an endogenous cat retroviral element (ECE 1)--a recombinant between RD-114 and FeLV-related sequences. Brief report

A lambda L 47.1 clone library was constructed from BamHI digests of cellular cat DNA and was screened with cDNA probes specific for the 3'-terminus of the replication competent RD-114 virus. The first analysis of one clone (lambda-ECE 1) shows that it consists at least of a 3'-LTR and a 5' adjacent env gene. The LTR nucleotide sequences of the RD-114 cDNA clones and ECE 1 are identical within the R region and unrelated to FeLV. Otherwise, the region upstream from the 3'-LTR of ECE 1 shows homology to the transmembrane protein encoding gene of FeLV, but not to RD-114. These results imply that ECE 1 is a recombinant between an RD-114-like 3'-LTR and a FeLV-related env portion.

Differential protooncogene expression characterizes histopathologically indistinguishable tumors of the peripheral nervous system

We have found highly predictable patterns of protooncogene expression in cell lines and tumor tissue of neuroblastoma (NB), a tumor of the peripheral nervous system (PNS). These patterns make it possible to recognize two different genetically definable subgroups among histopathologically indistinguishable tumors. Additionally, we have identified a difference in neurotransmitter biosynthetic enzyme activity in these two subgroups of NB. The patterns of protooncogene expression and neurotransmitter biosynthetic enzymes suggests that these tumors arise in different cells of the PNS.

Gene expression in archaebacteria: Physical mapping of constitutive and UV-inducible transcripts from the Sulfolobus virus-like particle SSV1

The transcription of the genome of the UV-inducible Sulfolobus virus-like particle SSV1 was studied. Eight different transcripts could be distinguished by Northern analysis that were present in uninduced cells and the coordinately increased in amount after UV induction of SSV1. Using single-stranded DNA probes from different parts of the genome, the approximate map positions of these RNAs and the directions of transcription were determined. In two cases, terminator read-through resulted in the formation of more than one RNA species from a single 5' end and therefore the eight different RNAs corresponded to only five different transcriptional starts. Two RNAs sharing a common 5' end encode SSV1 structural proteins. The 5' end of these transcripts was determined by S1 nuclease analysis. About 20 nucleotides upstream of the transcriptional start of these RNAs, there is an AT-rich region resembling putative promoter sequences which have been found at a similar distance 5' to the genes encoding stable RNAs in Thermoproteus. In addition to the eight constitutive transcripts, a UV-inducible RNA of 0.3 kb was mapped on the SSV1 genome. In contrast to all other RNAs, it was not detectable in uninduced cells and it is expressed shortly before the amplification and packaging of the SSV1 genome commences.

The transcription unit of the Drosophila engrailed locus: an unusually small portion of a 70,000 bp gene

Transcripts from the engrailed gene of Drosophila melanogaster have been characterized by Northern, S1 nuclease sensitivity, and primer extension analyses. The engrailed gene encodes three poly(A)+ transcripts (3.6 kb, 2.7 kb, and 1.4 kb) that derive from a 3.9-kb portion of the genome. No other transcribed regions were found up to 16 kb downstream and 48 kb upstream of the engrailed transcription unit, the portion of the genome to which engrailed mutations have been mapped. The structures of the engrailed transcripts are unaffected by lethal engrailed mutations that break the locus at points in the transcriptionally silent regions. Transcripts expressed by 145 kb of DNA that surround the engrailed locus were also identified by Northern analysis. In contrast to the large portion of the engrailed gene that is transcriptionally inactive, most of the surrounding regions are 10-fold more densely populated with transcripts. We presume that the unusually large silent region at the periphery of the engrailed transcription unit signify the presence of special mechanisms that regulate its expression.

In situ hybridization

In situ hybridization is the hybridization-mediated detection of specific nucleic acid sequences within structurally intact cells or tissues. As such it uniquely provides localization of nucleic acid superimposed on observable cellular and subcellular structural detail, allowing analysis unobtainable by other hybridization techniques. The technique is highly sensitive, particularly when the target nucleic acid is contained within a small percentage of a sample of cells. Innovations have increased the versatility of in situ hybridization which is now capable of specific detection of DNA, or RNA of sense or anti-sense polarity, application to samples prepared with a variety of fixation and embedding procedures, and analysis at the macroscopic, light microscopic, or electron microscopic level. These characteristics have made in situ hybridization a powerful and important means of analysis in a diversity of scientific fields.

Cloning of the ADPglucose pyrophosphorylase (glgC) and glycogen synthase (glgA) structural genes from Salmonella typhimurium LT2

The structural genes of ADPglucose pyrophosphorylase (glgC) and glycogen synthase (glgA) from Salmonella typhimurium LT2 were cloned on a 5.8-kilobase-pair insert in the SalI site of pBR322. A single strand specific radioactive probe containing the N terminus of the Escherichia coli K-12 glgC gene in M13mp8 was used to hybridize against a S. typhimurium genomic library in lambda 1059. DNA from a plaque showing a positive hybridization signal was isolated, subcloned into pBR322, and transformed into E. coli K-12 RR1 and E. coli G6MD3 (a mutant with a deletion of the glg genes). Transformants were stained with iodine for the presence of glycogen. E. coli K-12 RR1 transformants stained dark brown, whereas G6MD3 transformants stained greenish yellow, and they both were shown to contain a 5.8-kilobase-pair insert in the SalI site of pBR322, designated pPL301. Enzyme assays of E. coli K-12 G6MD3 harboring pPL301 restored ADPglucose pyrophosphorylase and glycogen synthase activities. The specific activities of ADPglucose pyrophosphorylase and glycogen synthase in E. coli K-12 RR1(pPL301) were increased 6- to 7-fold and 13- to 15-fold, respectively. Immunological and kinetic studies showed that the expressed ADPglucose pyrophosphorylase activity in transformed E. coli K-12 G6MD3 cells was very similar to that of the wild-type enzyme.

Genetic control of capsid length in bacteriophage T4: DNA sequence analysis of petite and petite/giant mutants

The T4 gene 23 product (gp23) encodes the major structural protein of the mature capsid. Mutations in this gene have been described which disrupt the normal length-determining mechanism (A.H. Doermann, F.A. Eiserling, and L. Boehner, J. Virol. 12:374-385, 1973). Mutants which produce high levels of petite and giant phage (ptg) are restricted to three tight clusters in gene 23 (A.H. Doermann, A. Pao, and P. Jackson, J. Virol. 61:2823-2827, 1987). Twenty-six of these ptg mutations were cloned, and their DNA sequence alterations were determined. Each member of this set of ptg mutants arose from a single mutation, and the set defined 10 different sites at which ptg mutations can occur in gene 23. Two petite (pt) mutations in gene 23 (pt21-34 and ptE920g), which produce high frequencies of petite particles but no giants, were also sequenced. Both pt21-34 and ptE920g were shown to include multiple mutations. The phenotypes attributed to both pt and ptg mutations are discussed relative to the mechanism of capsid morphogenesis. A site-directed mutation (SD-1E) was created at the ptgNg191 site, and its phenotypic consequences were examined. Plaque morphology revertants arising from a gene 23 mutant derivative of pt21-34 and from SD-1E were isolated. A preliminary mapping of the mutation(s) responsible for their revertant phenotypes suggested that both intra- and extragenic suppressors of the petite phenotype can be isolated by this method.