Application of recombinant DNA technology to questions of developmental biology: a review

Detection of Histidine-Tagged Protein in Escherichia coli by Single-Cell Inductively Coupled Plasma-Mass Spectrometry

We have developed a rapid and precise quantification method for a histidine (His)-tagged recombinant protein produced in Escherichia coli (E. coli) by single-cell inductively coupled plasma-mass spectrometry (SC-ICP-MS). Plasmid vector containing enhanced green fluorescent protein (EGFP) or red fluorescent protein (mCherry) gene fused with His-tag was transformed into E. coli. The transformed E. coli was exposed to nickel (Ni) chloride or cobalt (Co) chloride for labeling His-tag with the Ni or Co ion. Then, E. coli was analyzed by SC-ICP-MS to determine the amount of EGFP or mCherry protein on the basis of the signal of Ni or Co bound to His-tag. By comparing Ni and Co contents in E. coli expressing His-tagged mCherry with those in nontagged mCherry, the specific binding of Co to His-tag was more clearly detected than that of Ni. The Co contents were increased until 6 h after the protein induction, and this observation was coincident with the increases in fluorescence intensity of EGFP or mCherry measured by a flow cytometer. However, the Co contents were decreased for EGFP and kept at a constant level for mCherry from 6 to 24 h despite the continuous increase in the fluorescence intensity through incubation. The fluorescent proteins were mainly recovered in the insoluble fraction 24 h after the induction. This can be explained by the fact that the overexpressed fluorescent proteins with His-tag are transferred into inclusion bodies, which hampers the binding of the fluorescent proteins to the Co ion. SC-ICP-MS can be a useful technique to precisely quantify soluble recombinant proteins in E. coli without the extraction and purification process.

Tinkering with genes and embryos: the multiple invention of transgenic mice c. 1980

Genetically modified or 'transgenic' mice are a routine experimental tool in biomedical research, commonly produced by injecting DNA into one-cell embryos. These animals were independently invented in 1980 by multiple university groups in the United States and Europe that combined expertise in mouse developmental biology and recombinant DNA techniques, or 'genetic engineering'. In this article, I examine this multiple invention and argue that research strategies, experimental practices, and funding arrangements that led to transgenic mice are best described as tinkering. These creative and speculative endeavors, combined with partial knowledge of what was happening in competing laboratories, created a fruitful atmosphere for research which led to the multiple invention. The tinkering was, however, underpinned by infrastructures that were crucial to success, some long established, such as mouse supply or embryological tools, and some emerging, such as the informal exchange of isolated genes.

Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system

Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the 'genetic toolbox' that can be used alone or in combination with other SSRs in heterologous hosts.

N-myc proto-oncogene expression during organogenesis in the developing mouse as revealed by in situ hybridization

The N-myc proto-oncogene is expressed during embryogenesis, suggesting that it plays a role in normal development. Since the myc-family oncogenes have been implicated in the control of cell growth, the embryonic expression may reflect rapid proliferation known to occur in development. Alternatively, N-myc expression may be involved in specific differentiation stages. In many embryonic tissues, early and late differentiation events occur in different locations. By in situ hybridization of tissue sections, we now demonstrate a restricted expression of N-myc mRNA to a few tissues and to areas where the first differentiation stages occur. N-myc expression was most strongly expressed in the developing kidney, hair follicles, and in various parts of the central nervous system. In these tissues, expression was restricted to a few cell lineages. In all lineages, expression was confined to early differentiation stages, and, at onset of overt differentiation, the level of expression decreased dramatically. Several rapidly proliferating tissues showed very little, if any, N-myc expression. In the brain, post-mitotic but not yet differentiated cells expressed high levels of N-myc mRNA. Therefore, N-myc expression is not a simple marker for proliferation in the embryo. Rather, N-myc expression seems to be a feature of early differentiation stages of some cell lineages in kidney, brain, and hair follicles, regardless of the proliferative status of the cell. The results raise the possibility that N-myc may participate in the control of these early differentiation events.

Genomic organization of major sperm protein genes and pseudogenes in the nematode Caenorhabditis elegans

The major sperm proteins (MSPs) are a family of closely related, small, basic proteins comprising 15% of the protein in Caenorhabditis elegans sperm. They are encoded by a multigene family of more than 50 genes, including many pseudogenes. MSP gene transcription occurs only in late primary spermatocytes. In order to study the genomic organization of transcribed MSP genes, probes specific for the 3' untranslated regions of sequenced cDNA clones were used to isolate transcribed genes from genomic libraries. These and other clones of MSP genes were located in overlapping cosmid clones by DNA fingerprinting. These cosmids were aligned with the genetic map by overlap with known genes or in-situ hybridization to chromosomes. Of 40 MSP genes identified, 37, including all those known to be transcribed, are organized into six clusters composed of 3 to 13 genes each. Within each cluster, MSP genes are not in tandem but are separated by at least several thousand bases of DNA. Pseudogenes are interspersed among functional genes. Genes with similar 3' untranslated sequences are in the same cluster. The six MSP clusters are confined to only three chromosomal loci; one on the left arm of chromosome II and two near the middle of chromosome IV. Additional sperm-specific genes are located in one cluster of MSP genes on chromosome IV. The multiplicity of MSP genes appears to be a mechanism for enhancing MSP synthesis in spermatocytes, and the loose clustering of genes could be a result of the mechanism of gene duplication or could play a role in regulation.

Length polymorphism in rDNA indicates somatic alterations in the genome of Triturus vulgaris

We have analyzed the EcoRI restriction pattern of ribosomal genes (rDNA) isolated from several organs of single individuals of the newt Triturus vulgaris by Southern blotting and hybridization with corresponding Xenopus probes (r11 and r12). Using length polymorphism of rDNA spacers as a molecular marker, it became evident that in individual newts the pattern of ribosomal genes is not always constant but varies between different tissues of the same animal suggesting the occurrence of genome alterations during ontogenesis.

Differentiation and transformation of neural plate cells

The developmental potential of presumptive neural plate cells of prestreak chick embryos (stage 1) and neural plate cells from definitive streak chick embryos (stage 4) has been examined in cell culture using specific markers that identify the major cell types in the vertebrate central nervous system. The prestreak presumptive neural plate (PSPNP) cells, stage 1, assume an epithelial appearance in vitro and synthesize cellular fibronectin, but do not express markers for the neuronal, astrocytic, melanocytic, or oligodendrocytic lineages. Conversely, definitive-streak neural plate (DSNP) cells contain precursors which express cell-type-specific markers for terminally differentiated neurons, astrocytes, and melanocytes, and synthesize an extracellular matrix of cellular fibronectin. Differentiation of DSNP cells in vitro can be prevented by infection with a temperature-sensitive mutant of Rous sarcoma virus (RSV), tsNY68. Differentiation of DSNP cell transformants can be resumed by a temperature shift to the nonpermissive temperature. The morphological and biochemical changes associated with tsNY68 transformation are accompanied by alterations in pp60src kinase activity in the transformed cells.

Progress in visualization of eukaryotic gene transcription

Methods for visualization of the ultrastructure of transcriptionally active eukaryotic genes have been developed using chromatin from giant nuclei of amphibian oocytes (Miller and Beatty 1969). Rapidly isolated chromatin is subjected to low salt treatment in order to dissociate most chromatin associated proteins. As a result, gene-chromatin with associated RNA polymerase particles and RNA transcripts can be directly analysed in electron microscope chromatin spread preparations. More recently, progress has been made in utilising living amphibian oocyte nuclei as a transcription system for cloned eukaryotic genes. In this article, an account of such experiments is given, with emphasis on results and problems of chromatin and transcription organization of microinjected cloned genes. The described transcription assay system possesses important potential for investigation of gene mutations and in particular for the elucidation of molecular aspects of experimental oncology and molecular human genetics.

Developmental switches in reiterated genes may reduce the rate of age changes in DNA

The possible role of the redundancy of genetic information in the regulation of the ageing rate has been discussed in several works. However, it was shown recently that the gene reiteration in most cases is represented by families of similar, but not identical genes. Their expression usually related to the different stages of development and when "early" embryonic or fetal genes are active, the "late" or adult genes are repressed. It is known that the DNA repair needs double stranded structure of DNA which is usual for inactive genes. Genes which are being transcribed and active are repressed by unwound, relaxed DNA which is less protected by the DNA repair enzymes. Aging of genetic information in somatic cells can be, therefore, considered as stage specific and alterations of "early" embryonic and fetal genes do not constitute the genetic load which influences the ageing rate of differentiated cells.

Differential sensitization to deoxyribonuclease I of Xenopus vitellogenin and albumin genes during primary and secondary induction of vitellogenesis by oestradiol

The sensitivity to DNAase (deoxyribonuclease) I (which preferentially digests transcribed sequences) of vitellogenin and albumin genes in liver and erythrocytes of male Xenopus after primary and secondary induction of vitellogenesis by oestrogen was measured by hybridization to cDNA (complementary DNA) of the residual DNA after enzymic digestion of isolated nuclei. Vitellogenin sequences were rendered selectively more sensitive to limited DNAase-I digestion (15-20% of DNA rendered acid-soluble) during primary hormonal activation (5 days) of vitellogenin genes in liver, but not erythrocyte, nuclei. Hormone withdrawal (25 days after first injection) did not result in reversion to a pre-activation gene configuration, nor did secondary hormonal stimulation (5 days after second and 25 days after first injection) augment the sensitivity of the genes to digestion by the nuclease. Similar hormone treatment did not affect the sensitivity of the constitutively expressed albumin genes in liver nuclei, nor their insensitivity in erythrocyte nuclei. Under the same conditions, globin genes remained indigestible in liver nuclei. It is concluded that primary induction of vitellogenesis in male Xenopus liver is accompanied by relatively long-lasting (3-4 weeks) change in the configuration of vitellogenin genes in hepatic nuclei which is not reversed or further modified during short-term oestrogen withdrawal or upon secondary stimulation.

Evolutionary conservation of vitellogenin genes

Homologous and heterologous hybridizations in solution were performed between sheared genomic DNA and DNA complementary to vitellogenin mRNA of Xenopus, chicken, and migratory locust. The kinetics of hybridization and the thermal stability of the hybrids formed suggested a high degree of conservation of coding sequences of insect, amphibian, and avian vitellogenin genes. These cDNA probes hybridized to calf thymus DNA to a slight, but significant, extent, and not at all to Micrococcus lysodektikus DNA. DNA complementary to Xenopus albumin mRNA did not cross-hybridize significantly with locust or chicken DNA. Further evidence for the evolutionary conservation of vitellogenin genes was obtained from Southern blot analysis of restriction endonuclease-digested genomic DNA from a variety of vertebrate and invertebrate oviparous animals (Xenopus, chicken, migratory and desert locusts, yellow meal worm, carab moth, and Mediterranean fruitfly). When probed with cloned vitellogenin cDNAs from Xenopus and migratory locust, the DNA of these organisms showed varying degrees of homology of parts of the vitellogenin coding sequences. Southern blot analysis also showed that a part of the sequence specified in the cloned Xenopus vitellogenin cDNA was represented as repetitive DNA in the locust genome. However, cloned locust vitellogenin cDNA hybridized to discrete fragments of the restricted vertebrate DNA. These studies demonstrate a remarkably high degree of conservation of insect, amphibian, and avian vitellogenin genes.

Isolation and fine structure organisation of an avian vitellogenin gene coding for the major estrogen-inducible mRNA

Two phage lambda recombinant DNA clones covering the entire sequence of an avian vitellogenin gene, plus flanking regions, have been isolated from an erythrocyte DNA gene library and characterized by R-loop and restriction mapping. The total length of this avian vitellogenin gene is 23 kb. The cloned sequences flanking the gene at the 5' and 3' end are 7 and 3 kb, respectively. The total length of exons in the two clones is 6.7 kb (vitellogenin mRNA is 6.6 kb). The gene is interrupted by at least 25 introns with a mean intron length of 940 bp. Some 6--10 additional very small introns may also be present but they were not observed reproducibly. The mean exon length is 250 bp. Restriction endonuclease digests of total liver genomic DNA and lambda recombinant DNA were also analyzed by electrophoresis. Southern blotting and hybridization with cloned vitellogenin cDNA. The results show an identity of organisation of this vitellogenin in the DNA from the two sources, thus ruling out a possible cloning artifact. In contrast to Xenopus vitellogenin we have found no evidence to suggest that avian vitellogenin is encoded by a small family of related genes.

Vitellogenesis and the vitellogenin gene family

Vitellogenin is synthesized under estrogen control in the liver, extensively modified, transported to the ovary, and there processed to the yolk proteins lipovitellin and phosvitin. In the frog Xenopus laevis there are at least four distinct but related vitellogenin genes. The two genes A1 and A2 have a 95 percent sequence homology in their messenger RNA coding regions, and contain 33 introns that interrupt the coding region (exons) at homologous positions. Sequences and lengths of analogous introns differ, and many introns contain repetitive DNA elements. The introns in these two genes that have apparently arisen by duplication have diverged extensively by events that include deletions, insertions, and probably duplications. Rapid evolutionary change involving rearrangements and the presence of repeated DNA suggests that the bulk of the sequences within introns may not have any specific function.

Gene expression in eukaryotes

Gene expression in eukaryotes is influenced by a wide variety of mechanisms including the loss, amplification, and rearrangement of genes. Genes are differentially transcribed, and the RNA transcripts are variably utilized. Multigene families regulate the amount, the diversity, and the timing of gene expression. The present level of understanding of gene expression in eukaryotes is attributable mainly to biochemical methods rather than to traditional genetics. The new techniques that permit analysis and modification of purified genes of known function will identify both the control regions in eukaryotic genes as well as the molecules within cell that influence gene expression.

Expression of simian virus 40-rat preproinsulin recombinants in monkey kidney cells: use of preproinsulin RNA processing signals

The complete rat preproinsulin gene I was cloned into a simian virus 30 (SV 40) vector. Most of the late region of the viral vector, including the SV40 intervening sequences (introns) and all of the major splice junctions, was deleted and replaced by the entire rat insulin gene. The recombinant molecules and a temperature-sensitive helper virus (tsA28) were inoculated into monkey kidney cultures. The formation of stable transcripts of the insulin insert was as efficient as the production of late SV40 mRNA. Analysis of these transcripts indicated that the rat preproinsulin gene nucleotide signals involved in RNA splicing and poly(A) addition were used. Examination of the 5' ends of the mRNAs showed several classes, one of which was the same size as the authentic rat insulinoma mRNA. This suggests that a portion of the transcripts may be initiated or processed faithfully, or both, at their 5' ends within rat insulin sequences. Significant quantities of a protein identified as rat proinsulin were synthesized. Detection of most of the proinsulin in the tissue culture medium suggests that this protein was secreted.

Intervening sequences in a Dictyostelium gene that encodes a low abundance class mRNA

Using S1 nuclease protection experiments and DNA sequencing, we have identified two intervening sequences (introns) within a Dictyostelium gene that codes for a low abundance class mRNA. The two introns are located within the protein coding region of this gene. Both are small (approximately 100 bp) and extremely (approximately 95%) A + T rich. The splice junction sequences are similar to the splice sites in other eukaryotes. Finally, we have shown that these introns are transcribed as part of a higher molecular weight nuclear precursor.

The protein-coding sequence of the bovine ACTH-beta-LPH precursor gene is split near the signal peptide region

The pituitary hormones corticotropin (ACTH) and beta-lipotropin (beta-LPH) are formed from a large common precursor. Recently, we have elucidated the whole primary structure of the bovine ACTH-beta-LPH precursor (designated alternatively as preproopiocortin) by determining the nucleotide sequence of cloned DNA complementary to the mRNA coding for the precursor protein. The amino acid sequence assigned has disclosed a characteristic repetitive structure of the ACTH-beta-LPH precursor. The repetitive units of the precursor protein each contain a melanotropin (MSH) sequence (alpha-, beta- or gamma-MSH) as well as other peptide components such as beta-endorphin and corticotropin-like intermediate lobe peptide (CLIP). The repetitive units as well as their peptide components are each bounded by paired basic amino acid residues, which apparently represent the sites of proteolytic processing. Several studies have confirmed the translational initiation site and protein structure assigned (see also ref. 11 and refs therein). In view of the recent knowledge about the organization of eukaryotic genes (see refs 12, 13 for reviews), it would be of particular interest to investigate the relationship between the repetitive structure of the ACTH-beta-LPH precursor containing different functional components and the arrangement of the protein-coding sequence in its gene. We have now isolated and characterized bovine genomic DNA fragments encoding this precursor protein and have demonstrated that the protein sequence is encoded by two non-consecutive DNA segments. An intron (intervening sequence) of approximately 2.2 kilobase pairs separates the smaller exon (mRNA-coding sequence), which contains the gene sequence encoding the signal peptide, from the larger exon, which contains the gene sequence for most of the protein structure, including the known biologically active component peptides.

Secondary structures for splice junctions in eukaryotic and viral messenger RNA precursors

Thermodynamically stable secondary structures have been found for adjacent splice junctions of 17 introns from 10 eukaryotic and viral mRNA precursors. Complementary regions in these structures position the exons to be ligated in a favourable orientation for splicing. The possible role of these structures in a general splicing mechanism in described.

Comparative analysis of the structural organization of two closely related vitellogenin genes in X. laevis

The structural organization of the two closely related vitellogenin genes A1 and A2 has been determined and compared by electron microscopy. In both genes the mRNA-coding sequence of 6 kb is interrupted 33 times, leading to a total gene length of 21 kb for gene A1 and 16 kb for gene A2. Thus both genes have a mean exon length of 0.175 kb, while the mean intron length is 0.45 kb in gene A1 and 0.31 kb in gene A2. Because the introns interrupt the structural sequence at homologous positions in genes A1 and A2, we suggest that these two genes are the products of a duplication of an ancestral gene which has an intron-exon arrangement similar to that of the extant genes. Since the duplication event, the sequence and length of the analogous introns have changed rapidly, whereas homologous exons have diverged to an extent of only 5% of their sequences. The results suggest different mechanisms of evolution for exons and introns. While the exons evolved primarily by point mutations, such mutations, as well as deletion, insertion and duplication events, were important in the evolution of the introns.

Chicken lens crystallin DNA sequences show at least two delta-crystallin genes

Restriction analysis of chicken DNA using probes derived from a cloned cDNA and analysis of cloned genomic DNA fragments containing delta-crystallin gene sequences have indicated the presence of at least two non-allelic genes for delta-crystallin, the first and principal crystallin synthesised in the embryonic chicken lens. Electron microscopic analyses of three cloned genomic fragments revealed that the delta-crystallin mRNA gene sequences are interrupted at least 14 times in one of the delta-crystallin genes.

Purification and characterization of winter flounder antifreeze peptide messenger ribonucleic acid

The serum of winter flounder contains a group of small antifreeze peptides which lower the freezing point of their body fluids during the winter months. The poly(A)-containing mRNA coding for these peptides has been isolated from livers of the winter specimens. When the isolated antifreeze mRNA was analyzed by a denaturing polyacrylamide gel electrophoresis, at least two distinct bands approximately 450 nucleotides in length are visible. In a wheat germ cell-free protein synthetic system these mRNAs direct the synthesis of small peptides which can be precipitated by antisera against purified winter flounder antifreeze peptides. Full-length cDNA was synthesized from the isolated antifreeze mRNA by avian myeloblastosis reverse transcriptase. From the RNA excess hybridization kinetic analysis, there are probably three different mRNAs coding for the antifreeze peptides. Using the radioactive cDNA probe, it was estimated that 1% of the total RNA in liver of a January specimen is antifreeze mRNA. RNA from a summar specimen showed no significant hybridization even at high concentrations of RNA. These results indicate that the control of antifreeze peptide biosynthesis relies at least in part on the synthesis or degradation of translatable mRNA.

Sequence of the human insulin gene

The human insulin gene contains two intervening sequences, one is within the region transcribed into the 5'-untranslated segment of the mRNA and the other interrupts the C-peptide encoding region. A comparison of the human with the rat insulin genes indicates potential regulatory regions in the DNA segment preceding the gene and suggests that the ancestral form of the insulin gene had two intervening sequences.

Isolation of two closely related vitellogenin genes, including their flanking regions, from a Xenopus laevis gene library

A gene library of Xenopus laevis was constructed from embryonic DNA partially digested with restriction endonucleases Hae III and Alu I and joined to the phage lambda Charon 4 cloning vector with EcoRI linkers. Nucleotide sequences from three of the four related vitellogenin genes have been isolated. Two of the genes (called A1 and A2) were isolated in their entirety together with long stretches of flanking sequences. These two closely related vitellogenin genes have lengths of about 21 and 16 kilobases, but both produce a vitellogenin mRNA of 6.3 kilobases.

Sequence of a ribosomal RNA gene intron from Tetrahymena

Recently, several genes coding for messenger RNA, transfer RNA and ribosomal RNA in eukaryotes have been found to be interrupted in their coding regions by DNA sequences which are not represented in the mature RNA transcripts (see ref. 1 for review). Many of these intervening sequences, or introns, are now known to be transcribed in the precursor RNA, from which they are subsequently processed out to form the mature RNA. As the intron-exon junctions must in some way be recognised for accurate splicing, the nucleotide sequences of these regions from a number of protein-coding and tRNA genes have been analysed. Sequence homologies were found at the splice points of the protein-coding gene introns from diverse organisms, but the tRNA intron boundaries were not similar to these. This has led to the speculation that different splicing activities are necessary for the processing of introns in mRNA and tRNA precursors. We report here the sequence of a ribosomal RNA gene intron from Tetrahymena in which intron-exon junctions differ from those analysed to date.

Induction of a basement membrane glycoprotein in embryonic kidney: possible role of laminin in morphogenesis

The glycoprotein laminin is found exclusively in the basement membranes of adult tissues, not in the mesenchymal stroma. We studied the appearance and distribution of laminin during the early formation of kidney tubules in mouse embryos and in an in vitro transfilter model system. In immunofluorescence using affinity-purified antibodies, the distribution of laminin showed a clear correlation, both spatially and temporally, to the early stages of tubule formation. In vivo, laminin was first detected in a punctate pattern in areas where the pretubular aggregates form; later, it became confined to the basement membranes of the tubules. In experiments in vitro, the nephrogenic mesenchyme was found to form tubules after 12-24 hr of transfilter contact with the inductor. The first laminin spots were found after 12 hr of culture, 24 hr before overt morphogenesis. As the mesenchymal cells began to aggregate and elongate (at 36 hr), laminin was detected in those cells destined to become epithelial, and at 48 hr it was not found in cells remaining in the stroma. In more mature tubules (at 72 hr), laminin was seen as a sharp band in the basement membranes. It is suggested that laminin is involved in the increased cell adhesiveness during the early aggregation of the nephrogenic mesenchyme.

Identification, organization and processing intermediates of the putative precursors of Xenopus vitellogenin messenger RNA

To understand the mechanism of estrogen-induced activation of the vitellogenin genes in the liver of Xenopus, it is essential to characterize the transcriptional products of these genes. In this paper we describe large nuclear RNAs containing vitellogenin mRNA sequences as revealed by hybridization of cloned vitellogenin cDNAs to nuclear RNA separated on agarose gels. Putative vitellogenin mRNA precursors, which are recovered as poly(A)-containing RNA, have been identified for the four known vitellogenin mRNAs. From electron microscopic analysis of R loops, prepared between enriched mRNA precursors and cDNA specific for the A1 vitellogenin mRNA, we conclude that the precursor molecules contain sequences complementary to vitellogenin mRNA which are interrupted by additional RNA segments probably representing transcribed introns. Within the 3.7 kb of the 3' end of the A1 vitellogenin mRNA we have discovered seven large and at least five small transcribed introns. Some of the R loops have been found to contain only a few transcribed introns, and we assume that they represent processing intermediates. Comparison of these putative intermediates suggests that the splicing order of different introns does not follow a single pathway.

Isolation of cloned DNA sequences containing ribosomal protein genes from Saccharomyces cerevisiae

Yeast mRNA enriched for ribosomal protein mRNA was obtained by isolating poly(A)+ small mRNA from small polysomes. A comparison of cell-free translation of this small mRNA and total mRNA, and electrophoresis of the products on two-dimensional gels which resolve most yeast ribosomal proteins, demonstrated that a 5-10 fold enrichment for ribosomal protein mRNA was obtained. One hundred different recombinant DNA molecules possibly containing ribosomal protein genes were selected by differential colony hybridization of this enriched mRNA and unfractionated mRNA to a bank of yeast pMB9 hybrid plasmids. After screening twenty-five of these candidates, five different clones were found which contain yeast ribosomal protein gene sequences. The yeast mRNAs complementary to these five plasmids code for 35S-methionine-labeled polypeptides which co-migrate on two-dimensional gels with yeast ribosomal proteins. Consistent with previous studies on ribosomal protein mRNAs, the amounts of mRNA complementary to three of these cloned genes are controlled by the RNA2 locus. Although two of the five clones contain more than one yeast gene, none contain more than one identifiable ribosomal protein gene. Thus there is no evidence for "tight" linkage of yeast ribosomal protein genes. Two of the cloned ribosomal protein genes are single-copy genes, whereas two other cloned sequences contain two different copies of the same ribosomal protein gene. The fifth plasmid contains sequences which are repeated in the yeast genome, but it is not known whether any or all of the ribosomal protein gene on this clone contains repetitive DNA.

Expression of ribosomal DNA insertions in Drosophila melanogaster

Approximately half of the ribosomal genes on the X chromosome of Drosophila melanogaster are interrupted by an insertion of type 1. Nuclear RNA from D. melanogaster embryos was transferred to DBM paper and hybridized with cloned type 1 insertion sequences. With a DNA fragment derived specifically from large insertions, transcripts were detected between 5 and 10 kb. These insertion transcripts represent less than one RNA molecule per nucleus, which is more than three orders of magnitude below the concentration of nascent rRNA chains, as determined by kinetics of hybridization. With a DNA fragment derived from the right end of large insertions which is also complementary to short insertions, more discrete RNA bands appeared with sizes between 1 and 8.5 kb, representing altogether about 13 RNA molecules per nucleus. Insertion transcripts large enough to be potential precursors to 28S rRNA represent less than one molecule per nucleus. It was shown by sandwich hybridization that at least some of the insertion transcripts are derived from rDNA. No significant difference was found between insertion transcripts in RNA extracted from ovaries, embryos, larvae, pupae or adult flies. Unless a mechanism other than splicing is involved, ribosomal genes with insertions cannot contribute significantly to the synthesis of 28S rRNA. A cytoplasmic RNA approximately 1 kb long, which is complementary to a short insertion and to ribosomal gene sequences flanking both sides of the insertion, was found. The abundance of this short unspliced RNA is about 50 molecules per embryo cell.

The structure and transcription of four linked rabbit beta-like globin genes

Rabbit chromosomal DNA contains a cluster of four linked beta-like globin genes arranged in the orientation 5'-beta 4-(8kb)-beta 3-(5 kb)-beta 2-(7-kb)-beta 1-3'. Determination of the nucleotide sequence of gene beta 1 confirms that this gene corresponds to the second type of two common co-dominant alleles encoding the adult beta-globin chain. With the exception of two nucleotide substitutions in the large intervening sequence (intron), the intron and flanking sequences are identical with the nucleotide sequence of the first type determined by Weissmann et al. (1979). A 14S polyadenylated transcript containing large intron sequences (possibly a mRNA precursor) is detected in the bone marrow cells of anemic rabbits. Gene beta 2 has limited sequence homology to adult and embryonic beta-globin probes and lacks a detectable mRNA transcript in the erythropoietic tissues examined. It contains at least one intervening sequence analogous to the large intron in gene beta 1. Genes beta 3 and beta 4 both contain an intron of 0.8 kb. Partial DNA sequence analysis indicates that the large intron in beta 4 is located between codons for amino acids lysine and leucine in an analogous position to that of the large intron in beta 1. In addition, a second smaller intron interrupts the 5' coding sequences of gene beta 4. Both genes beta 3 and beta 4 are transcribed in embryonic globin-producing cells. Their DNA sequence homology is limited, however, to a segment of approximately 0.2 kb located on the 5' side of the large intron.

Pleiotropic mutations within two yeast mitochondrial cytochrome genes block mRNA processing

The mRNAs from two yeast mitochondrial genes cob-box (cytochrome b) and oxi-3 (cytochrome oxidase 40,000 dalton subunit) are processed from large (7-10 kb) precursors. Certain mutations in each gene block the maturation of the RNAs from both genes at a variety of specific steps. The pleiotropic cytochrome b mutants seem to lack a functional trans-acting RNA required for the processing of both messengers. In contrast, the oxi-3 mutants may act by producing an activity that inhibits specific steps.

Lengths of transcribed rDNA repeating units in spermatocytes of Drosophila hydei: only genes without an intervening sequence are expressed

In Drosophila hydei a 5 kb long intervening sequence (ivs) which is limited to only one of the three nucleolus organizers occurs in the 28S coding region of the rDNA (Kunz and Glätzer, 1979). This raises the possibility to study transcription of repeated genes with long intervening sequences. Three genotypes of males were studied each having only one defined nucleolus organizer. Spermatocytes of single males were spread in a solution of low salt and examined by electron microscopy. The length distributions of the repeating units, matrix units, and the apparent spacer units did not reveal two classes with a 5 kb length difference. The data suggest that in D. hydei the 5 kb long intervening sequence is not transcribed and that, in fact, the entire gene which contains an intervening sequence remains silent in primary spermatocytes. There is evidence that genes with an intervening sequence are not intermingled with "normal" genes at random.

Expression of the mitochondrial genome in Xenopus laevis: a map of transcripts

The twelve most abundant transcripts in X. laevis mitochondria were characterized, and their coding regions were mapped on the mitochondrial DNA (mtDNA) by R loop mapping in the electron microscope and by RNA gel transfer hybridization. The transcripts map in nonoverlapping positions with one exception, and they account for about 80% of the coding capacity of mtDNA. Ten of the twelve RNA molecules contain poly(A): the two poly(A)-lacking transcripts are the rRNAs. Analysis withe single-strand-specific nucleases clearly demonstrated the absence of intervening sequences from the coding regions for seven RNAs. For two RNAs, uninterrupted coding sequences are strongly suggested and one RNA could not be analyzed. Eight transcripts of low abundance and high molecular weight were characterized, and their coding regions were mapped approximately. They overlap the coding regions of the abundant mitochondrial RNAs and could be precursors of these RNAs. Most of the RNA molecules characterized were shown to be transcribed from the heavy strand of mtDNA. No abundant discrete light-strand transcript was found.

The structure and evolution of the two nonallelic rat preproinsulin genes

In the rat, there are two nonallelic genes for preproinsulin. The insulin end products are very similar and are equally expressed. We have isolated clones carrying these genes and their flanking sequences, and characterized them by DNA sequencing and electron microscopic analysis. We have established the primary structure of the preproinsulin mRNAs and the signal peptides of these two proteins. One of the genes contains two introns: a 499 bp intron interrupting the region encoding the connecting peptide and a 119 bp intron interrupting the segment encoding the 5 noncoding region of the mRNA. The introns are transcribed and present in a preproinsulin mRNA precursor. The other gene possesses the smaller, but not the larger, of the two introns. Calculations based on the divergence of the two preproinsulin nucleotide and amino acid sequences indicate that these genes are the products of a recent duplication. Thus one of the genes gained or lost an intron since that time.

Enrichment and characterization of the DNA coding for vitellogenin in Xenopus laevis

Purified vitellogenin mRNA of Xenopus laevis was incubated with mechanically sheared DNA in high concentrations of formamide and the resulting R-loops (i.e. RNA . DNA hybrid fragments) separated from the bulk DNA by caesium chloride buoyant density centrifugation. Hybridization with 125I-labeled vitellogenin mRNA revealed a 15--30-fold enrichment of the DNA coding for vitellogenin. Restriction analysis of the R-loop-enriched DNA demonstrated that all known endonuclease HindIII fragments coding for vitellogenin of unfractionated Xenopus DNA were also present in the enriched material, including the specific fragments for the oligo(A)-containing segment of the RNA. Comparison of these restriction data with the structure found in cloned vitellogenin cDNA, indicates the presence of at least one intervening sequence in the genomic DNA coding for vitellogenin.