Sequence arrangement and biological activity of cloned feline leukemia virus proviruses from a virus-productive human cell line

We examined 14 different feline leukemia virus proviruses from the productively infected human cell line RD(FeLV)-2 after cloning in the modified lambda vector Charon 4A. Each isolate was characterized by restriction digestion and Southern blot analysis. The DNA of each isolate was tested for competence to express virus after uptake by sensitive animal cells (transfection). All but one isolate contained an apparently complete provirus, but only four were infectious. Seven isolates (four noninfectious, three infectious) were studied by heteroduplexing followed by electron microscopy or by S1 nuclease treatment and gel electrophoresis. No regions of nonhomology between proviruses were detected by either criterion, and in no case did we observe homology between flanking sequences. Random shearing or removal of flanking sequences by S1 nuclease had no effect on the status of infectivity of the clones. Thus, we were unable to find molecular differences between infectious and noninfectious proviruses. Our data are consistent with either of the following hypotheses: (i) that there is a short host sequence which is essential as a promoter for virus expression; or (ii) that lack of infectivity is due to small mutations within the proviral genome.

Terminally redundant sequences in cellular intracisternal A-particle genes

The sequences coding for intracisternal A-particle RNA form a family of related but not identical genetic elements which are present in 650 to 1,000 copies within the mouse genome. We showed that different intracisternal A-particle genes had a terminally redundant sequence of about 400 base pairs, one-half of which arose from the 3' end of the intracisternal A-particle RNA. A second portion of the redundant region did not contain 3-related sequences and was probably derived from the 5' end of intracisternal A-particle RNA. Thus, there were endogenous intracisternal A-particle genes in the cellular DNA-3'-5'--3'-5'-cellular DNA configuration identified for type B and C retroviruses. This indicated that the initial integration of intracisternal A-particle genes into the Mus musculus genome occurred by the same mechanism as the integration of other retroviruses. Two types of heterogeneity were identified among the 5' sequences of the two genes.

Characterization of Alu family repetitive sequences which flank human beta-type globin genes

Heteroduplex mapping has determined the size, location, and orientation of three Alu family sequences from the human beta-type globin gene cluster. Two of these sequences have the same orientation. One (231 bp long) is 2 kb to the 5' side of the B gamma-globin gene and the other (222 bp) is l kb 5' to the pseudo-beta-l-globin gene. The third (300 bp), 3-4 kb 3' to the pseudo-beta-l-globin gene, has the opposite orientation. Their orientations relative to five previously characterized Alu sequences from this cluster have been established. One of these, 2.5 kb 5' to the epsilon-globin gene, was shown by Southern blot hybridization to be similar but not identical to other family members, whereas the region separating it from a neighbouring inverted repeat is not widely distributed in the human genome.

The actin genes of Drosophila: protein coding regions are highly conserved but intron positions are not

The entire set of six closely related Drosophila actin genes was isolated using recombinant DNA methodology, and the structures of the respective coding regions were characterized by gene mapping techniques and by nucleotide sequencing of selected portions. Structural comparisons of these genes have resulted in several unexpected findings. Most striking is the nonconservation of the positions of intervening sequences within the protein-encoding regions of these genes. One of the Drosophila actin genes, DmA4, is split within a glycine codon at position 13; none of the remaining five genes is interrupted in the analogous position. Another gene, DmA6, is split within a glycine codon at position 307; at least two of the Drosophila actin genes are not split in the analogous position. Additionally, none of the Drosophila actin genes is split within codon four, where the yeast actin gene is interrupted. The six Drosophila actin genes encode several different proteins, but the amino acid sequence of each is similar to that of vertebrate cytoplasmic actins. None of the genes encodes a protein comparable in primary sequence to vertebrate skeletal muscle actin. Surprisingly, in each of these derived actin amino acid sequences in the initiator methionine is directly followed by a cysteine residue, which in turn precedes the string of three acidic amino acids characteristic of the amino termini of mature vertebrate cytoplasmic actins. We discuss these findings in the context of actin gene evolution and function.

Avian reticuloendotheliosis virus: characterization of genome structure by heteroduplex mapping

The genome structure of defective, oncogenic avian reticuloendotheliosis virus (REV) was studied by heteroduplex mapping between the full-length complementary DNA of the helper virus REV-T1 and the 30S REV RNA. The REV genome (5.5 kilobases) had a deletion of 3.69 kilobases in the gag-pol region, confirming the genetic defectiveness of REV. In addition, REV lacked the sequences corresponding to the env gene but contained, instead, a contiguous stretch (1.6 to 1.9 kilobases) of the specific sequences presumably related to viral oncogenicity. Unlike those of other avian acute leukemia viruses, the transformation-specific sequences of REV were not contiguous with the gag-pol deletion. Thus, REV has a genome structure similar to that of a defective mink cell focus-inducing virus or a defective murine sarcoma virus. An additional class of heteroduplex molecules containing the gag-pol deletion and two other smaller deletion loops was observed. These molecules probably represented recombinants between the oncogenic REV and its helper virus.

Homology between Escherichia coli plasmids ColE1 and p15A

The location and extent of the homology between plasmids ColE1 and p15A were determined by analysis of heteroduplexes formed between them as well as with a related plasmid, pBR322, and by hybridization of radioactive deoxyribonucleic acids to restriction fragments of p15A and ColE1. The homology between the plasmids contained the entire region of ColE1 required for its replication as well as an additional 400 base pairs downstream from the origin of replication. This region on p15A, which was 980 +/- 43 base pairs, started at 0.1 of the molecular length from one end formed by cleavage with the restriction endonuclease BglI and extended to 0.54 of the molecular length from the same end. Restriction cleavage maps for the enzymes BglI, HpaI, HaeII, HaeIII, and HincII are also presented.

The molecular cloning of a dispersed set of developmentally regulated genes which encode the major larval serum protein of D. melanogaster

We have isolated chromosomal segments of D. melanogaster DNA that encode the alpha, beta and gamma polypeptides of the major larval serum protein (LSP1) from libraries of recombinant phage. The recombinant DNAs hybridize in situ to polytene chromosome regions 11A, 21D of 61A, consistent with the known cytogenetic positions of the alpha, beta and gamma genes, respectively. The three genes each encode a 2.85 kb polyadenylated RNA molecule. We have positioned these coding sequences, by both Southern hybridization analysis and R loop mapping. Heteroduplex analysis reveals comparatively close homology between the alpha and beta genes, less homology between the beta and gamma genes and least homology between the alpha and gamma genes.

Structure of a naturally occurring plasmid with genes for enterotoxin production and drug resistance

A physical map of the 117-kilobase conjugative plasmid pCG86 was constructed using electron microscope heteroduplex analysis. This plasmid carries the genes elt, for heat-labile enterotoxin, and estA, for heat-stable enterotoxin, as well as the genes for resistance to tetracycline, streptomycin, sulfonamides, and mercury. These genes were mapped using deletions and Tn5 insertions as physical markers. Analysis of a heteroduplex between pCG86 and a previously described enterotoxin plasmid (EntP307) showed a 48-kilobase region of complete homology which included the genes elt and estA. An 8.8-kilobase BamHI fragment of EntP307 carrying elt, cloned by others, was also shown to be completely homologous with pCG86. The position of elt on the fragment was verified, and it was shown to carry estA as well. A 44-kilobase region of pCG86 showed partial homology with the region of EntP307 previously shown to contain conjugal transfer genes. The gene for tetracycline resistance is carried on a stem-loop structure with the dimensions of Tn10, and the genes for the other drug resistance markers are carried on a 14.6-kilobase segment that forms an insertion loop in heteroduplexes with EntP307. These studies suggest that pCG86 arose either by recombination between an enterotoxin plasmid of incompatibility group FI, like EntP307, and a multiple resistance factor of incompatibility group FII, or by transposition into EntP307 of two transposons.

DNA electron microscopy

In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).

Cloning of human immunoglobulin mu gene and comparison with mouse mu gene

We have cloned a 12 kb DNA segment containing human mu gene and its flanking sequence from human fetal liver DNA library using mouse mu gene as a probe. Partial nucleotide sequence determination shows that the cloned DNA contains the sequence encoding human mu chain. This is the first constant region gene of the human heavy chain that is cloned. We have compared human and mouse mu genes by heteroduplex analysis and Southern blot hybridization. The results clearly show that not only the sequence encoding the CH4 domain but also the 5'-flanking (S mu) sequence is conserved between human and mouse mu genes, suggesting that the nucleotide sequence in the S mu region has an important biological function, presumably a recognition signal for the class switch recombinant as proposed previously.

Cloned embryonic DNA sequences flanking the mouse immunoglobulin C gamma 3 and C gamma 1 genes

To investigate the DNA surrounding genes for immunoglobulin heavy chain constant (CH) regions, we have isolated two clones bearing a C gamma 3 gene and two bearing a C gamma 1 gene from a library of mouse embryo DNA fragments. The C gamma 3 clones span 8.6 kilobase pairs (kb) on the 5' side of the gene and 6.7 kb on its 3' side, while the C gamma 1 clones together span 13 kb of 5' flanking sequence and 2.5 kb of 3' flanking sequence. Restriction mapping of the C gamma 3 gene indicates that intervening sequences divide the gene into segments of domain size, as in other CH genes. Hybridization of clone fragments to restriction digests of mouse DNA indicates that both the C gamma 1 and C gamma 3 genes probably occur as single copies in the genome. Moreover, the entire cloned sequences on the 5' side of both genes appear to be unique in the genome, indicating that no large common sequences flank CH genes. Restriction data suggest that the C gamma 3 gene is 37-40 kb 5' to the C gamma 1 gene.

A family of long reiterated DNA sequences, one copy of which is next to the human beta globin gene

An unusually long repeated DNA sequence was identified in cloned DNA, three kb 3' to the human beta-globin gene. Other members of this repeated sequence family were isolated from a human genomic DNA library and characterized by Southern blotting techniques, electron microscopy, and solution hybridization. The copy located next to the beta-globin gene was found to be 6.4 +/- 0.2 kb long and continuous over that length. This repeated sequence family comprises about 1% of the human genome and contains 3000-4800 copies of moderate sequence divergence which are interspersed with other less-highly repeated DNA. The 6.4 kb repeated unit does not appear to be composed of any smaller tandemly repeated subunits, nor is it expressed at a high level in bone marrow cell RNA.

General occurrence and transcription of intervening sequences in mouse genes expressed via polyadenylated mRNA

cDNA of modal size approximately 1600 nucleotides, transcribed from mouse brain polyadenylated mRNA, was annealed with excess of high molecular weight (approximately kb) genomic DNA. The S1 nuclease method was then applied to determine possible sequence discontinuity between the cDNA and genomic DNA. A substantial reduction in the average size of the annealed cDNA was observed following S1 nuclease treatment. Large single copy genomic DNA, annealed with excess high molecular weight DNA, and cDNA, hybridized with its template mRNA, were resistant to cleavage by S1 nuclease. We interpret these results to indicate a high frequency of discontinuous coding sequences in the genomic DNA that annealed with the cDNA. The same result was obtained using fractionated cDNA, enriched in transcripts of relatively infrequent or abundant mRNA species. The result obtained with the infrequent sequence class cDNA indicates that tens of thousands of split genes exist in the mouse genome. Extensive cleavage of the cDNA by S1 nuclease was also observed after hybridization with greater than 30S nuclear RNA, indicating that intervening sequences are generally transcribed.

Molecular cloning of the pyruvate dehydrogenase complex genes of Escherichia coli

The three components of the pyruvate dehydrogenase complex of Escherichia coli are encoded by three linked genes, ace E (pyruvate dehydrogenase, E1), aceF (dihydrolipoamide acetyltransferase, E2) and lpd (lipoamide dehydrogenase, E3, situated close to the nadC (quinolinate phosphoribosyltransferase) and aroP (general aromatic amino acid permease) genes with the gene order: nadC-aroP-aceE-aceF-lpd. Several types of transducing phages, lambda nadC and lambda lpd, carrying the nadC and lpd genes were isolated from populations of artificially constructed transducing phages containing R.HindIII or R.EcoRI fragments of bacterial DNA, by selecting for their ability to complement the metabolic lesions of the corresponding mutants. The cloned fragments were extended to include a functional ace operon by in vivo methods involving prophage insertion into the nadC-lpd region and aberrant excision to yield lambda nadC-lpd and lambda lpd-ace phages. These contained overlapping segments of bacterial DNA capable of expressing the aceE, aceF and lpd genes. A physical map of a 20 kilobase pairs (kb) segment of bacterial DNA encoding the entire nadC-lpd region, bounded by R.HindIII and R.EcoRI targets and possessing several internal restriction targets, R.HindIII (3) and R.EcoRI (2), was constructed. Using a combination of nutritional and enzymological studies with dilysogens and genetic analysis with ace mutants the approximate positions of the genes specifying the pyruvate dehydrogenase complex were traced to a 9.5 kb segment of the restriction map. The cloned lpd gene was expressed in the complete absence of a functional ace operon and when the major lambda promoters were repressed. This confirms that the lpd gene can be independently transcribed from its own promoter.

A theory of modular evolution for bacteriophages

The modular theory of virus evolution has clear experimental support among the temperate bacteriophages of the enteric bacteria. However, there is also similar genetic and DNA heteroduplex evidence for such evolution among other families of bacteriophages: the virulent bacteriophages of the enterics comprise several families: the T-even group, the T3-T7 group (which has many members among different species of bacteria, including bacteria as widely divergent as E. coli and Caulobacter crescentus. It nicely explains the diffusion of very similar homologous bacteriophages into hosts whose own DNAs have diverged very greatly from each other in nucleotide sequence. It also accounts for the rigorous maintenance of regulatory schemes while units of function (including regions coding for proteins) diverge more rapidly. It should also be noted that the considerations that make modular evolution seem advantageous for bacteriophages apply equally well to viruses of higher organisms. Furthermore, the kinds of heteroduplex similarity observed among animal viruses are reminiscent of what is found for bacteriophages. Viruses found in widely divergent hosts show much greater similarity than would be expected; quite possibly animal viruses also evolve as a population of interchangeable modules.

Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments

The human immune system offers special advantages for study of the development and evolution of the immune response. A variety of human cell lines are available that are arrested at various stages of development, and human genes provide a convenient evolutionary point of comparison with the already well characterized genes of the mouse. In this paper, we describe the procedure we have used to clone the human kappa chain genes in both germline and rearranged configurations. We have taken advantage of distantly related probes derived from the mouse and nonstringent conditions of hybridization to find the human genes among phage lambda recombinants formed with partially purified genomic restriction fragments of human DNA. In addition to establishing a physical map of the human kappa C and J regions, we have determined the entire sequence of a germline human constant region gene (the Inv3 allele) and two of its J segments, as well as the V/J recombination site of an active human kappa chain gene. For purposes of comparison, we also determined the sequence of the chromosomal mouse constant region gene and its flanking sequences. Although mouse and human sequences have changed extensively during the 70 million years since the two species diverged. significant blocks of homology have been conserved selectively. Some of these have obvious significance in terms of DNA and RNA splicing reactions. By forming heteroduplex structures between mouse and human genes we were able to identify four human J regions that are much more stringently conserved throughout their coding sequences than are the C region genes. In addition, the middle j structure (J3) of the mouse (which is thought to be inactive) appears to be missing from the human genome.

Related single copy sequences in the human genome

Human single copy DNA renatured under relatively non-stringent conditions (50 degrees C, 0.36 M Na+) forms two components with different thermal stabilities: a high temperature component melting at a temperature (81 degrees C, 0.18 M Na+) expected for well-paired duplex and a low temperature component melting at 55 degrees C (0.18 M Na+). The production of the high and low temperature components has been examined as a function of C0t (product of concentration and time in units of mol/s per l) value and renaturation temperature. The duplex formed has been characterized by its resistance to S1 endonuclease and its length has been determined by gel electrophoresis. As a result of these experiments and related controls we conclude that the low temperature component is not an artifact of DNA fragment length, nonspecific base pairing or hydroxyapatite chromatography conditions. We attribute the low thermal stability of this component to the renaturation of distantly related single copy sequences to form a highly mismatched duplex DNAs with an average length of about 100 base pairs.

A phase diagram of the binding of mismatched duplex DNAs to hydroxyapatite

The hydroxyapatite binding properties of imperfectly base-paired DNA have been investigated and summarized in a phase diagram. This diagram defines the conditions at which thermal elution results in both denaturation and desorption of mismatched duplex DNA from hydroxyapatite.

Insertion element IS102 resides in plasmid pSC101

In vivo recombination was found to occur between plasmid pHS1, a temperature-sensitive replication mutant of pSC101 carrying tetracycline resistance, and plasmid ColE1 after selection for tetracycline resistance at the restrictive temperature, 42 degrees C. Extensive analysis of the physical structures of three of these recombinant plasmids, using restriction endonucleases and the electron microscope heteroduplex method, revealed that the plasmid pHS1 was integrated into different sites on ColE1. The recombinant plasmids contained a duplication of a unique 1-kilobase (kb) sequence of pHS1 in a direct orientation at the junctions between the two parental plasmid sequences. This was confirmed by comparing the nucleotide sequence of the recombinants and their parental plasmids. Nucleotide sequence analysis further revealed that nine nucleotides at the site of recombination of ColE1 were duplicated at the junction of each of the 1-kb sequences. The formation of recombinants was independent of RecA function. Based on our previous finding that a plasmid containing a deoxyribonucleic acid insertion (IS) element can recombine with a second plasmid to generate a duplication of the IS element, we conclude that the 1-kb sequence is an insertion sequence, which we named IS102. For convenience, we have also denoted the IS102 sequence as eta theta to assign the orientation of the sequence. Eighteen nucleotides at one end (eta end) were found to be repeated in an inverted orientation at the other end (theta end) of IS102. The nucleotide sequence of the eta end of the sequence was found to be identical to the sequence at the ends of the transposon Tn903, which is responsible for transposition of the kanamycin resistance gene.

Sequence organization of cloned intracisternal A particle genes

Seven recombinant DNA clones containing mouse intracisternal A particle genes were isolated and analyzed by restriction enzyme digestion, Southern blot analysis and heteroduplex mapping. The sequence organization of the individual genes was found to differ, with one end of the gene region being most variable, while a central segment of 1.8 kb was missing from two of the clones. A third region, common to all the clones and containing the 3' end of the gene, is present in about 1800 copies per haploid genome, but the central portion is found in only 650 copies. The same reiteration frequency is found in both myeloma tumor and mouse liver DNA. The most abundant intracisternal A particle RNA in two different myeloma lines was found to be 3.5 kb, and RNA/DNA hybrids show that the RNA is homologous to all but a small internal segment of one of the clones.

Defined oligomeric SV40 DNA: a sensitive probe of general recombination in somatic cells

We have constructed well defined oligomeric molecules of simian virus 40 (SV40) DNA as probes for investigating mechanisms by which cultured somatic cells recombine DNA. Restriction enzyme fragments from different temperature-sensitive mutants were joined in a head-to-tail orientation to create partial dimers 1.84 genome lengths in size. These molecules are too large to fit into a viral capsid. Therefore an assay that depends on production of progeny virus after infection with oligomeric DNA is a selective measure of precise conversion of oligomers to monomers. By constructing oligomers from appropriate combinations of temperature-sensitive DNAs, we have been able to study the conversion process in several defined regions of the SV40 genome. Our results indicate that conversion of oligomers to monomers occurs uniformly throughout the genome and is not dependent on normal viral DNA replication. These data indicate that conversion occurs primarily by general, homology-dependent recombination. At least one secondary mechanism that generates a low level of wild-type progeny was also detected. Studies with heteroduplex molecules indicate that repair of mismatched bases may be the secondary mechanism.

Nucleotide sequences of heat shock activated genes in Drosophila melanogaster. I. Sequences in the regions of the 5' and 3' ends of the hsp 70 gene in the hybrid plasmid 56H8

We present the sequences at the 5' and 3' ends of one hsp 70 gene variant which is derived from the chromosomal locus 87A7. The 5' end of the hsp 70 mRNA has also been determined. 550 bp upstream from the 5' end of the hsp 70 mRNA, there is a very A+T rich region shown by heteroduplex analysis to be also present at the same position in other hsp 70 genes9. The 5' end of the hsp 70 mRNA was found 26 bp after a characteristic "Hogness box". The first ATG codon was found 250 bp downstream from the 5' end of the hsp 70 mRNA. We also determined the termination codon at the 3' end of the hsp 70 gene. Comparisons with other genes are discussed.

[Physical mapping of Streptomyces coelicolor A3(2) actinophage DNA. II. Transposon-like structure in DNA molecules of phiC43 phage DNA, localization of region responsible for establishment of the lysogenic state]

Structural properties of DNA molecules of phages phi C43, phi C43del and mutant phage phi C311yg33 were studied. Actinophages phi C43del and phi C311yg33 have been isolated and shown to have a phenotype characteristic of phages defective in integration, i. e. turbid plaques and inability to establish the lysogenic state. By means of heteroduplexing, deletions were mapped in the genomes of these phages. DNA molecules of phi C43del and phi C11yg33 are devoid of the common fragment, which suggests that the mutant phenotypic character is associated with structural alterations in DNA molecules. The presence of transposon-like structure in phi C43 DNA molecules has been inferred from the analysis of phi C43/phi C43del heteroduplexes and phi C43 homoduplexes. Also, a deletion in phi C43 genome has been detected covering the same region where deletions in phi C43del and phi C11yg33 DNAs were located.

Proteus mirabilis phages 5006M, 5006M HFT k and 5006M HFT ak: physical comparison of genome characteristics

The genomes of proteus mirabilis phages 5006M, kanamycin resistance transducing variant 5006M HFT k and kanamycin-ampicillin resistance transducing variant 5006M HFT ak have been compared. Homo- and heteroduplex and partial denaturation mapping analyses were performed. The results confirm a sequential headful packaging mechanism, facilitate mapping of the ampicillin resistance marker, demonstrate a hairpin loop structure in both variants, reveal a common insertion site for 8 X 10(6) mol. wt. non-phage DNA in both variants and implicate a role for the non-inducible cryptic host strain prophage 5006M in the generatin cycle of the variant phages.

[Physical mapping of Streptomyces coelicolor A3(2) actinophage DNA. I. Location of the c-region of actinophage phiC31]

Mutants of temperate actinophage phi C31 Streptomyces coelicolor A3(2) having an increased resistance to chelating agents (sodium EDTA and sodium citrate) were isolated. Most of these mutants were not able to lysogenize sensitive cultures (c-mutants). DNA molecules of four c-mutants resistant to chelating agents were shown to be deleted by electron microscopy of DNA heteroduplexes. The four deletions were located in the central region of phi C31 DNA molecule. The deleted segment of 1000 base pairs common for molecules of all c-mutants is located in a region 47,2--49,9% and indicates the position of c-region on the physical map of phi C31 actinophage. The size of the region containing delections of all analyzed c-mutants is 1700 base pairs. The c-region on the heteroduplex map was oriented in relation to the known genetic map of phi C31.

Extensive diversity among Drosophila species with respect to nucleotide sequences within the adenine + thymine-rich region of mitochondrial DNA molecules

Mitochondrial DNA (mtDNA) molecules from species of the genus Drosophila contain a region exceptionally rich in adenine + thymine (A+T). Using agarose gel electrophoresis and electron microscopy, we determined that in the mtDNA molecules of D. melanogaster, D. simulans, D. mauritiana, D. yakuba, D. takahashii, and D. virilis, the A+T-rich regions, which are 5.1, 4.8, 4.6, 1.1, 2.2, and 1.0 kilobase pairs in size, respectively, are at homologous locations relative to various common EcoRI and HindIII cleavage sites. Under conditions highly permissive for base pairing (35% formamide), heteroduplexes were constructed between EcoRI fragments and whole circular molecules of mtDNAs of the above mentioned six species in a variety of combinations. Complete pairing of molecules outside the A+T-rich region was found in all heteroduplexes examined. However, in contrast, A+T-rich regions of the different species failed to pair in all but those combinations of mtDNAs involving the three most closely related species. In heteroduplexes between D. melanogaster and D. simulans, and between D. melanogaster and D. mauritiana mtDNAs, up to 35% of the A+T-rich regions appeared double-stranded. These data indicate that much more extensive divergence of sequences has occurred in A+T-rich regions than in other regions of Drosophila mtDNA molecules.

Ribosomal ribonucleic acid similarities in the classification of Rhodococcus and related taxa

Duplexes were prepared between 14C-labelled rRNA from both Rhodococcus equi C7 and Rhodococcus rhodochrous N54 and DNA from 16 actinomycetes representing the genera Rhodococcus, Mycobacterium, Nocardia, Saccharopolyspora and Streptomyces. The relationships between the organisms were determined by plotting the temperature at which 50% of the duplex was denatured (Tm(e)) against the percentage of rRNA binding (microgram 14C-labelled rRNA duplexed per 100 micrograms filter-bound DNA). All of the strains formed stable duplexes but each organism occupied a definite area on the rRNA similarity map. All of the organisms share a close phylogenetic relationship but representatives of the genera Rhodococcus, Mycobacterium, Nocardia and Streptomyces fell into four recognizable clusters on the similarity map. These data support and extend current trends in the classification of Rhodococcus and allied taxa. The guanine plus cytosine content of the DNA from the test strains was within the range 69.3 to 76.9 mol %.

Location of the multivalent control site for the ilvEDA operon of Escherichia coli

A strain of Escherichia coli K-12 containing a deletion extending from early in the ilvE gene toward the ilvG gene was shown to exhibit a higher expression of the downstream genes, ilvD and ilvA, than did an ilv+ strain. The elevated expression was under apparently normal ilv-specific control, however. The deletion was transferred to the ilv region of lamba h80dilv and shown by restriction endonuclease and heteroduplex analysis to extend through the deoxyribonucleic acid (DNA) shown, in the preceding paper (C. S. Subrahmanyam, G. M. McCorkle, and H. E. Umbarget, J. Bacteriol 142:547--555, 1980), to contain the ilvO determinant. The deletion was also transferred to an ilv-lac fusion strain and shown to cause an increase in beta-galactosidase formation while allowing retention of ilv-specific control. Transducing phages excised from these fusion strains with and without the ilvO determinant were compared. The phage carrying the ilvO+ determinant contained ilv DNA extending only into but not through the ilvG gene. It did not exhibit an ilv-specific control of beta-galactosidase formation. The phage carrying the deletion of ilvO but containing ilv DNA extending beyond the ilvG gene exhibited ilv-specific control of beta-galactosidase formation. It was concluded that the multivalently controlled ilv-specific promoter affecting ilv operon expression lies upstream from ilvG and that the ilvO region in the wild-type K-12 strain is a region of polarity preventing ilvG expression and reducing ilvEDA expression.

The lactose transposon Tn951: characterization of transposition

Transposition of the lactose transposon Tn951 was found to still occur in the absence of its original host plasmid pGC1. Transposition was recA-independent. These results show that Tn951 is indeed a transposon. A computer program was developed to facilitate mapping of transposon integration sites in plasmids from restriction data.

Molecular cloning of Snyder-Theilen feline leukemia and sarcoma viruses: comparative studies of feline sarcoma virus with its natural helper virus and with Moloney murine sarcoma virus

Extrachromosomal DNA obtained from mink cells acutely infected with the Snyder-Theilen (ST) strain of feline sarcoma virus (feline leukemia virus) [FeSV(FeLV)] was fractionated electrophoretically, and samples enriched for FeLV and FeSV linear intermediates were digested with EcoRI and cloned in lambda phage. Hybrid phages were isolated containing either FeSV or FeLV DNA "inserts" and were characterized by restriction enzyme analysis, R-looping with purified 26 to 32S viral RNA, and heteroduplex formation. The recombinant phages (designated lambda FeSV and lambda FeLV) contain all of the genetic information represented in FeSV and FeLV RNA genomes but lack one extended terminally redundant sequence of 750 bases which appears once at each end of parental linear DNA intermediates. Restriction enzyme and heteroduplex analyses confirmed that sequences unique to FeSV (src sequences) are located at the center of the FeSV genome and are approximately 1.5 kilobase pairs in length. With respect to the 5'-3' orientation of genes in viral RNA, the order of genes in the FeSV genome is 5'-gag-src-env-c region-3'; only 0.9 kilobase pairs of gag and 0.6 kilobase pairs of env-derived FeLV sequences are represented in ST FeSV. Heteroduplex analyses between lambda FeSV or lambda FeLV DNA and Moloney murine sarcoma virus DNA (strain m1) were performed under conditions of reduced stringency to demonstrate limited regions of base pair homology. Two such regions were identified: the first occurs at the extreme 5' end of the leukemia and both sarcoma viral genomes, whereas the second corresponds to a 5' segment of leukemia virus "env" sequences conserved in both sarcoma viruses. The latter sequences are localized at the 3' end of FeSV src and at the 5' end of murine sarcoma virus src and could possibly correspond to regions of helper virus genomes that are required for retroviral transforming functions.

Transposition of Tn951 (Tnlac) and cointegrate formation are thermosensitive processes

The frequency of transposition of Tnlac to pGC200, an IncFII R plasmid, increased during the storage of the host strain. This result is explained by the fact that the transpositional event is temperature-dependent: it occurred readily when the host strain was grown at 30 degrees C but it was nearly undetectable when the host strain was grown and kept at 37 degrees C. Fusions between two different plasmids carrying Tnlac with pGC200 were also thermosensitive, suggesting a relation between cointegrate formation and transposition. Lactose did not influence the frequency of transposition of Tnlac.