Nucleotide sequence of bacteriophage lambda DNA

Molecular cloning of cDNA for murine interleukin-3

The cDNA sequence for murine interleukin-3, one of the colony stimulating factors that regulate haematopoiesis, codes for a polypeptide of 166 amino acids including a putative signal peptide. The predicted amino acid sequence indicates that formation of mature interleukin-3 involves proteolytic removal of not only the signal peptide but additional amino-terminal amino acids.

Direct calculation of the sizes of DNA fragments separated by gel electrophoresis using programmes written for a pocket calculator

In order to facilitate the direct computation of the sizes of DNA fragments separated by gel electrophoresis, we have written and evaluated programmes for the Hewlett-Packard 41C programmable calculator. The sizes estimated for DNA fragments of known length using some of these programmes were found to be more accurate than the estimates obtained by conventional graphical procedures. These programmes should be adaptable to other programmable calculators.

Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes

Protein genes can be found either by searching the DNA sequence for signals such as ribosome binding sites or by looking for the effects that coding for a protein has on the coding sequence. This paper describes how these coding effects can be measured and used to detect protein coding regions.

Accessibility of DNA-epoxycellulose to sequence-specific DNA-binding proteins

Phage lambda DNA was covalently coupled to epoxy-activated cellulose to form a stable DNA-cellulose matrix for affinity chromatography of sequence-specific DNA-binding proteins. The accessibility of three specific six-base sequences, GGATCC (BamHI), GAATTC (EcoRI) and AAGCTT (HindIII) was studied quantitatively and qualitatively by restriction analysis followed by labelling of their recessed ends. All sites are randomly accessible. The site accessibility is variable, BamHI greater than HindIII greater than EcoRI, and within the range 20-100% depending on base composition and internal structure of the sequence. DNA-epoxycellulose, because of its high efficiency of coupling, capacity, stability and accessibility, can be of great help in the isolation and characterization of sequence-specific DNA-binding proteins.

Genetics of bacteriophage phi 80--a review

The genetic maps of bacteriophage lambda and lambdoid phage phi 80 are compared. The gene organization of phi 80 is very similar to that of lambda, as shown by isolation and characterization of many am, ts and c (clear) mutants of the phage. In general, the essential genes located in the same position on the genetic map of the phages lambda and phi 80 fulfill the same functions. These include the gene clusters coding for the head and tail proteins, genes for DNA synthesis, and the genes controlling lysogeny and late gene expression. The specific regulatory features of phi 80 in relation to the N function of lambda are discussed, but they require further clarification. The two phages differ in immunity specificity, host range, conversion property and temperature sensitivity.

Mutational analysis of a regulatory region in bacteriophage lambda that has overlapping signals for the initiation of transcription and translation

The positively regulated PRE promoter of phage lambda structurally overlaps with the ribosome-binding and NH2-terminal coding region of the regulatory protein (cII) that activates PRE transcription. We have isolated and characterized 27 different point mutations that occur within the 36-base-pair overlapping region. A comparison of genetic crossover data with nucleotide separations as determined by DNA sequence analysis reveals that recombination frequencies are greatly depressed at very short distances. Moreover, recombination frequency is critically dependent upon the precise nucleotide sequence of the crossover region for distances of five nucleotides or less. The mutations define precise positions and sequences that are important to (i) PRE promoter function, (ii) translation of the cII gene, and (iii) cII gene function. Mutational changes that affect the function of one element in this region concomitantly define phenotypically silent alterations in the other two elements. Mutations deficient in promoter function (P-RE or cy) are clustered in two regions that lie approximately equal to 10 and approximately equal to 35 nucleotides before the initial base of PRE mRNA, analogous to mutations in other promoters. P-RE mutations in the -10 region alter bases that are conserved in prokaryotic promoters, but P-RE mutations in the -35 region do not affect bases that are normally conserved in other promoters. Several mutations deficient in cII gene activity affect the initiation of cII protein synthesis, including an A leads to G change four bases outside the cII coding region, and AUG leads to GUG, AUG leads to ACG, and AUG leads to AUA mutations in the initiation codon. In the region of overlap between the PRE promoter and the NH2-terminal region of the cII gene, most amino acid substitutions in the cII protein do not result in a loss of cII function, indicating that this region of the gene does not contain essential information for cII function. We suggest that the overlap itself is an evolutionarily conserved structure and that it somehow coordinates the bidirectional transcriptional and translational events that occur in this region.

Recognition of messenger RNA during translational initiation in Escherichia coli

The structural aspects of recognition by E. coli ribosomes of translational initiation regions on homologous messenger RNAs have been reviewed. Also discussed is the location of initiation region on mRNA, its confines, typical nucleotide sequences responsible for initiation signal, and the influence of RNA macrostructure on protein synthesis initiation. Most of the published DNA nucleotide sequences surrounding the start of various E. coli genes and those of its phages have been collected.

Structural and sequence-dependent aspects of drug intercalation into nucleic acids

Information gained from X-ray crystallographic studies on drug-nucleic acid complexes is described, with emphasis on the intercalation process. Relevant data from NMR experiments are examined in order to highlight similarities and differences between solution and solid-state structures. Theoretical analyses of intercalation complexes are also discussed and evaluated, with respect to the structural methods, with special reference being made to nucleic acid conformation and positions of drug molecules in the binding sites.

Proteinase sensitivity of bacteriophage lambda tail proteins gpJ and pH in complexes with the lambda receptor

Previous studies have shown that bacteriophage lambda initially binds to liposomes bearing its receptor protein by the tip of the tail fiber (type 1 complex). It then associates more directly so that the hollow tail tube is in direct contact with the membrane (type 2 complex). DNA can be injected across the lipid bilayer into the liposome from type 2 complexes. We show here that gpJ, the tail fiber protein, becomes more sensitive to proteolytic degradation in type 2 complexes, indicating that the tail fiber does not pass into the liposome and that the tail fiber may undergo a conformational change in type 2 complexes. Another bacteriophage protein, pH, is sensitive to proteolytic degradation in free bacteriophage, type 1 complexes, or type 2 complexes formed with free receptor, but is resistant to proteinases in type 2 complexes formed with liposomes. This finding suggests that pH associates with the membrane. We suggest that this association is part of the mechanism by which a transmembrane hole for DNA entry is formed.

Structure and inherent properties of the bacteriophage lambda head shell. IV. Small-head mutants

Missense mutants of bacteriophage lambda that produce small proheads were found among prophage mutants defective in the major head protein gpE. Measurements of the sedimentation coefficient and molecular weight of the small proheads showed that they have the T = 4 structure composed of 240 molecules of gpE instead of the wild-type T = 7 structure composed of 420 molecules of gpE. When the phage mutants were grown in groE mutants of Escherichia coli, they produced small unprocessed proheads, which contained a smaller number (about 60) of the core protein (gpNu3) molecules than normal unprocessed proheads, which contain about 180 molecules of gpNu3. This shows that the major head protein determines the size of not only the shell but also the core of unprocessed proheads. These mutants by themselves produce very few mature small-headed phage particles, partly because the lambda DNA molecule, whose cos sites are separated at a distance of 48,500 bases, is too long to be packaged into the small proheads. However, the small proheads can package shorter DNA in vivo and in vitro at somewhat reduced efficiency, if the length or a multiple of the length between the cos sites of the DNA is 13,000 to 19,000 bases.

Cholera toxin genes: nucleotide sequence, deletion analysis and vaccine development

Nucleotide sequence and deletion analysis have been used to identify the regulatory and coding sequences comprising the cholera toxin operon (ctx). Incorporation of defined in vitro-generated ctx deletion mutations into Vibrio cholerae by in vivo genetic recombination produced strains which have practical value in cholera vaccine development.

Location of the Rz gene in bacteriophage lambda

We report the nucleotide sequence of the Tn903 insertion in phage lambda dk23 identifying the Rz gene. The insertion is located after bp 46008 in the lambda nucleotide sequence. This is 43 bp after the start of the Rz gene, which is 459 bp long. Complementation experiments verify that the lysis defect in the lambda Rz::Tn903 mutant lies on a restriction fragment spanning the lysis region.

Lambda Charon vectors (Ch32, 33, 34 and 35) adapted for DNA cloning in recombination-deficient hosts

New phage lambda-based cloning vectors, Charons 32, 33, 34 and 35, have been constructed. These vectors allow cloning of large (19-21 kb) DNA fragments in up to six cloning sites. DNA cloned in these vectors can be propagated on recA- Escherichia coli hosts.

DNA sequences necessary for packaging of bacteriophage lambda DNA

The extent of DNA flanking the "cohered cohesive end" site of bacteriophage lambda DNA, which is required for packaging, was determined by using defined DNA fragments and a cosmid in vivo packaging assay. From the right end of lambda DNA a 20- to 36-base-pair stretch extending from the center of the cohered cohesive ends is shown to be required, whereas the packaging efficiency of cosmids extending to 70 base pairs into the left lambda arm is reduced to 10% (compared to a fragment extending until about 80 base pairs). A 60-base-pair stretch of the left arm leaves an efficiency of only 1%. The segment thus delineated, by the nature of the assay, is both necessary and sufficient for the binding of packaging proteins to the DNA, the packaging of DNA itself, the DNA cleavage, and successful injection of the DNA into a bacterial host. By contrast, in vitro packaging of restriction fragments of mature lambda DNA directly demonstrated the selectivity of the packaging proteins for the fragment originating from the left end of the DNA. The results of the two complementary experiments are discussed in terms of the various steps before, during, and after packaging for which different sequences flanking and including the cohered cohesive ends might be required.

An improved positive selection plasmid vector constructed by oligonucleotide mediated mutagenesis

An Escherichia coli plasmid vector, pUN121, has been constructed which allows for positive selection of transformants harboring DNA inserts. The positive selection of transformants harboring DNA inserts. The vector is based on plasmid pTR262 (Roberts et al. Gene, 12, (1980), 123-127) in which the tetracycline resistance gene is under transcriptional control of the repressor protein coded by the phage lambda cI gene. This plasmid has been rearranged, using in vitro recombinant techniques including oligonucleotide mediated mutagenesis to yield a smaller plasmid (4.4 kb) with unique cloning sites for EcoRI, XmaI and SmaI in addition to the unique HindIII and BclI sites. The plasmid has a functional ampicillin resistance gene and the new restriction sites (EcoRI, XmaI and SmaI) when used for cloning, give rise to tetracycline resistant transformants.

Lambda replacement vectors carrying polylinker sequences

To simplify the construction and screening of genomic libraries, we have made a new family of lambda replacement vectors (EMBL1, EMBL2, EMBL3, EMBL4) and derivatives containing amber mutations (EMBL3 Sam, EMBL3 AamBam, EMBL3 AamSam). These vectors have a large capacity and polylinker sequences flanking the middle fragment. The polylinkers allow a choice of cloning enzymes and, especially useful in the case of cloning of Sau3A partial digests, the excision of the entire insert by flanking SalI (EMBL3) or EcoRI (EMBL4) sites. Phages with inserts can be selected either biochemically (particularly EMBL3) or genetically by their Spi- phenotype. Amber derivatives of the EMBL3 vector allow the application of genetic screening procedures based on selection for the products of homologous recombination events, and for the selective cloning of DNA sequences linked to supF genes.

Construction and characterization of plasmid vectors for cloning in Staphylococcus aureus and Staphylococcus carnosus

Several plasmid vectors for cloning in Staphylococcus aureus and S. carnosus have been constructed and characterized. The chimeric plasmids are composed of parts of the following parental plasmids: The chloramphenicol-resistance plasmid, pC194, the tetracycline-resistance plasmid, pMK148, and the erythromycin-resistance plasmid, pE12. All the chimeric plasmids confer two selectable antibiotic-resistance markers on host cells. Insertional inactivation of the various antibiotic-resistance markers occurred at the BclI site of pE12, and the Sau96- or AvaII-site of pMK148; only a slight inactivation of the chloramphenicol-resistance marker occurred at the HaeIII-site of pC194. The chimeric plasmids pCT20 and pCE10 are both stable in S. aureus and S. carnosus. In addition, the hybrid plasmids of pCT20 and pCE10, containing lambda-DNA fragments in various restriction sites between 0.4 and 1.2 kb, are stably maintained. The inserted lambda-DNA fragments appear unchanged.

Infectious poxvirus vectors have capacity for at least 25 000 base pairs of foreign DNA

To test the capacity of poxviruses for added foreign DNA, a recombinant was constructed that contains 24 700 bp of bacteriophage lambda DNA inserted within the vaccinia virus thymidine kinase (TK) gene. The recombinant is stable, infectious and replicates in tissue culture at the same rate and to the same titer as standard vaccinia virus. This size flexibility of the poxvirus genome and the lack of stringent packaging requirements are useful features for an infectious eukaryotic cloning vector.

Primary structure and genetic organization of phage T4 DNA ligase

The primary structure of phage T4 DNA ligase has been determined by DNA sequencing of a cloned restriction fragment containing its gene, and partial amino acid sequence analysis of the protein. The molecule has a Mr of 55,230, and contains 487 amino acids. The DNA sequence may also encode all of one and parts of two other, hitherto unidentified, T4 proteins. The four genes are closely packed, with overlaps between terminator and initiator codons of adjacent genes. Potential terminator and promoter sites for transcription are located within the coding sequence of one of the genes.

Comparison of the physical properties and assembly pathways of the related bacteriophages T7, T3 and phi II

To understand constraints on the evolution of bacteriophage assembly, the structures, electrophoretic mobilities (mu) and assembly pathways of the related double-stranded DNA bacteriophages T7, T3 and phi II, have been compared. The characteristics of the following T7, T3 and phi II capsids in these assembly pathways have also been compared: (1) a DNA-free procapsid (capsid I) that packages DNA during assembly; (b) a DNA packaging-associated conversion product of capsid I (capsid II). The molecular weights of the T3 and phi II genomes were 25.2 X 10(6) and 25.9 (+/- 0.2) X 10(6) (26.44 X 10(6) for T7, as previously determined), as determined by agarose gel electrophoresis of intact genomes. The radii of T7, T3 and phi II bacteriophages were indistinguishable by sieving during agarose gel electrophoresis (+/- 4%) and measurement of the bacteriophage hydration (+/- 2%) (30.1 nm for T7, as previously determined). Assuming a T = 7 icosahedral lattice for the arrangement of the major capsid subunits (p10A) of T7, T3 and phi II best explains these data and data previously obtained for T7. At pH 7.4 and an ionic strength of 1.2, the solid-support-free mu values (mu 0 values) of T7, T3 and phi II bacteriophages, obtained by extrapolation of mu during agarose gel electrophoresis to an agarose concentration of 0 and correction for electro-osmosis, were -0.71, -0.91 and -1.17(X 10(-4) cm2V-1 s-1. The mu 0 values of T7, T3 and phi II capsids I were -1.51, -1.58 and -2.07(X 10(-4] cm2V-1 s-1. For the capsids II, these mu 0 values were -0.82, -1.07 and -1.37(X 10(-4] cm2V-1 s-1. The tails of all three bacteriophages were positively charged and the capsid envelopes (heads) were negatively charged. In all cases the procapsid had a negative mu 0 value larger in magnitude than the negative mu 0 value for bacteriophage or capsid II. A trypsin-sensitive region in capsid I-associated, but not capsid II-associated, T3 p10A was observed (previously observed for T7). The largest fragment of trypsinized capsid I-associated p10A had the same molecular weight in T7 and T3, although the T3 p10A is 18% more massive than the T7 p10A. It is suggested that the trypsin-resistant region of capsid I-associated p10A determines the radius of the bacteriophage capsid.

Comparison of three methods for measuring locations of long range base pairing in single-stranded DNA by electron microscopy

A comparison was made of three procedures used for measuring the locations of long range base pairing in single-stranded DNA. All three procedures gave equivalent results for the location of a transposon, Tn903, and for a loop created by pairing between the nut and operator segments on an EcoRI restriction fragment of lambda DNA. DNA molecules prepared by a T4 gene 32 protein procedure had the best contrast. The highest frequency of measurable loops resulted from a procedure which utilized ammonium acetate/formamide spreading conditions. This procedure also appeared to be the simplest and most satisfactory procedure. Only one procedure revealed the fact that the nutR and oR regions are separated by several hundred bases, but this procedure, which involves crosslinking with trioxsalen, gave generally unsatisfactory DNA morphology. None of the procedures revealed the existence of a short "bulge" loop of single-stranded DNA located between nutL and oL and a longer "bulge" loop located between nutR and oR.

The complete nucleotide sequence of the gene coding for diphtheria toxin in the corynephage omega (tox+) genome

A segment of corynephage omega (tox+) DNA, containing the gene for diphtheria toxin (tox) was fragmented with restriction enzymes and the fragments cloned into M13 vectors for nucleotide sequence determination. A long open reading frame was shown to encode the tox gene by comparing the predicted amino acid sequence with that of peptides derived from the mature toxin molecule. Analysis of the nucleotide sequence shows RNA polymerase and ribosome binding signals preceding a GTG codon in the open reading frame: if this is the correct starting signal for translation, then a 25 amino acid signal peptide can be predicted for the toxin molecule.

Nucleotide sequence of the trpD and trpC genes of Salmonella typhimurium

We have completed the nucleotide sequence determination of trpD and trpC, the second and third genes of the trp operon of Salmonella typhimurium. These genes encode two bifunctional proteins thought to have arisen by gene fusions: the trpD polypeptide contains the glutamine amido transferase and the phosphoribosyl anthranilate transferase activities, and the trpC protein possesses the N-(5'-phosphoribosyl)-anthranilic acid isomerase and the indole-3-glycerol phosphate synthetase activities. The trpD gene consists of 1593 nucleotides encoding 531 amino acids, and possesses an internal promoter (p2) located within a region from about 1400 to 1441 of the nucleotide sequence. The trpC gene contains 1356 nucleotides encoding 452 amino acids. In this paper we compare the trpD and trpC genes of S. typhimurium to those of Escherichia coli with respect to codon usage, nucleotide and amino acid conservation, p2 promoter characteristics and intercistronic regions. The sequence of the two genes we present here completes the sequence determination of the trp operon of S. typhimurium and should prove useful in comparisons with the E. coli trp operon and in future studies of operon structure in S. typhimurium.

Lambda phage DNA sequences affecting the packaging process

Our previous work identified a minimal region of bacteriophage lambda DNA that is necessary for packaging into phage particles. It consists of 40 bp of the right arm and 45 bp of the left arm [Miwa and Matsubara, Gene 20 (1982)267-279]. A part of this region, 22 bp of the right arm and 38 bp of the left arm, is sufficient for cutting at cos lambda (the minimal sequence for cos lambda cutting). An 84-bp region to its right contains a binding site for lambda terminase, a complex of Nu1 and A gene products. This second region, which we called the enhancing region for packaging, stimulates cutting at cos lambda as well as packaging. This region is not active if it is physically separated from the minimal packaging region. The enhancing region has 15-bp inverted repeats. These sequences are conserved in the corresponding region of bacteriophage phi 80, which has the same packaging specificity as lambda.

The nucleotide sequence of the HhaII restriction and modification genes from Haemophilus haemolyticus

We have determined the nucleotide sequence of a cloned 1710-bp segment of Haemophilus haemolyticus DNA which contains the HhaII restriction (r) and modification (m) genes. The m gene is 513 bp in length and the rgene is 681 bp in length. Both are in the same reading frame, being separated by a 21-bp region. A ribosome-binding site is identified in front of each gene, but no Haemophilus promoter is apparent on the cloned fragment. Transcription originates from a plasmid promotor and proceeds in the direction m to r.

A control system which causes alternating turn-off/turn-on of transcription on insertion element IS1

Presence of insertion element IS1 within an operon leads to absence of expression of genes distal to its integration site. This strong polar effect is observed irrespective of the orientation of IS1. Here I report on a mutant of E. coli K12 which allows turn-on of genes located distally to IS1. This turn-on is due to activation of transcription starting within IS1. The activation of transcription is under the control of a regulatory locus (sis1) which acts in trans. The regulatory locus itself changes its state, which leads to an alternating turn-off/turn-on of genes located distal to IS1: The rate of turn-off was observed with a frequency of about 0.3% (per cell and per generation), that of turn-on with a frequency of about 0.015% (per cell and per generation).

Structure of the bacteriophage lambda cohesive end site: location of the sites of terminase binding (cosB) and nicking (cosN)

The extents of the sites for nicking (cosN) and binding (cosB) of bacteriophage lambda DNA by terminase have been determined by studying cos cleavage and terminase binding in vitro. The cosN site is located in the segment from -22 to +24 bp (numbered from the center of the cohesive end sequence in the circular lambda genome). The cosB site is located in the segment from +51 to +120 (the +120 boundary determined by Miwa and Matsubara, 1983). Additional sequences are necessary for packaging into infectious phage particles, including regions to the left (Rz gene side) of cosN, and between cosN and cosB. Small deletions (7 and 11 bp) between cosN and cosB abolish packaging in vivo without affecting cos binding and cleavage in vitro, whereas a large deletion (26 bp) abolishes packaging in vivo and cleavage in vitro.

Efficient expression of influenza virus NS1 nonstructural proteins in Escherichia coli

RNA segment 8 of the influenza A virus genome codes for two nonstructural proteins, NS1 and NS2, for which the functions are unknown. Cloned cDNA copies of this gene from three different influenza A virus strains were inserted into an Escherichia coli plasmid expression vector, pAS1, carrying the strong regulatable lambda phage promoter, PL. After induction, the NS1 proteins were overproduced to levels of 20-25% of total cellular protein. This was surprising in that the codon composition for these eukaryotic genes is similar to that for weakly expressed proteins in E. coli. Thus, under the appropriate conditions, it appears that high level expression of genes containing a relatively large proportion of minor codons can be obtained. The NS1 protein produced in bacteria from a cloned cDNA copy of the A/PR/8/34 virus NS gene was purified to apparent homogeneity and used to generate a high-titer monospecific rabbit antiserum. Immunoprecipitation studies showed this antibody to be crossreactive against the NS1 proteins produced by several different influenza A virus strains. Immunofluorescence experiments in Madin-Darby canine kidney cells showed the NS1 proteins to be located in the nucleoplasm early in infection for all strains examined. With some of the strains, NS1-specific immunofluorescence was observed predominantly in the nucleoli later in infection. This technology can be used to obtain other viral proteins in pure form for structural, functional, and immunological studies.

Unexpected relationships between bacteriophage lambda hypothetical proteins and bacteriophage T4 tail-fiber proteins

Hypothetical lambda protein ORF314 shows significant homology with the carboxyl end of phage T4 tail-fiber protein gp37. Homology can also be demonstrated between hypothetical lambda protein ORF194 and a fragment of bacteriophage T4 protein gp38. This sequence homology is also reflected in the genomic sequences of these two phages.

Three sequence-specific endonucleases from Escherichia coli RFL47

The characterization of the new restriction enzyme Eco47III recognizing a hexanucleotide palindromic sequence 5'AGC decreases GCT and cleaving, as indicated by the arrow, is reported. It was isolated from Escherichia coli strain RFL47. Another two specific endonuclease Eco47I (isoschizomer of AvaII) and Eco47II (isoschizomer of AsuI) were also found in this strain. There are two Eco47III recognition sites on lambda DNA at 20997 and 37060 basepairs. The central Eco47III fragment can be replaced by a cloned fragment in lambda vector mutant in tR2 gene; i.e., lambda gt.

Expression of the phage lambda recombination genes exo and bet under lacPO control on a multi-copy plasmid

The bacteriophage lambda genes exo and bet, whose products (lambda exonuclease and beta protein, respectively; Red phenotype) mediate homologous recombination of lambda phages, have been cloned under lacPO lacIq control on multi-copy plasmids. Induction of recA3 cells harboring these plasmids with isopropylthiogalactoside (IPTG) resulted in lambda exonuclease levels (assayed in vitro) that were proportional to the time of induction (for at least 4 h); recombination of lambda Red- phages in vivo was similarly inducible. Only one out of 25 bet delta plasmids (constructed by a variety of in vitro techniques) expressed lambda exonuclease, a result consistent with the polarity of several known phage bet mutations. A general method for transferring phage exo and bet mutations to plasmids was devised and plasmids bearing polar (bet3) and nonpolar (bet113) mutations were constructed. Mutant derivatives of the plasmid showed the same complementation pattern as analogous phage red mutants. When lambda bet3 phages (Exo-Bet-) infected IPTG-induced recA3 bacteria containing exo+bet+ plasmids, recombination frequencies were not more than twice those typical for infection of plasmid-free recA3 cells with exo+bet+ phages, even in the case of IPTG induction sufficient to elevate the production of lambda exonuclease about 100-fold. Even when plasmid induction was delayed till as late as 50 min after infection, recombination was significant. Preliminary experiments suggest that these plasmids encode a polypeptide with Gam activity that corresponds to the 98-amino acid "shorter" open reading frame assigned to gam by Sanger et al. (J. Mol. Biol. 162 (1982) 729-773).

S gene product: identification and membrane localization of a lysis control protein

The product of the bacteriophage S gene has been previously shown to be required for an essential step in triggering host cell lysis. By using two different protein labeling systems, maxicells and UV-irradiated infected cells, we identified the S gene product as an 8,500-molecular-weight polypeptide associated with the cell envelope. The apparent molecular weight is significantly less than the 11,500 predicted from the S gene sequence. We were unable to confirm two previous identifications of S gene products, an acidic 15,000-molecular-weight polypeptide found by two-dimensional gel electrophoresis of infected cells and a 5,500-molecular-weight polypeptide in purified phage particles.

New approaches for computer analysis of nucleic acid sequences

A new high-speed computer algorithm is outlined that ascertains within and between nucleic acid and protein sequences all direct repeats, dyad symmetries, and other structural relationships. Large repeats, repeats of high frequency, dyad symmetries of specified stem length and loop distance, and their distributions are determined. Significance of homologies is assessed by a hierarchy of permutation procedures. Applications are made to papovaviruses, the human papillomavirus HPV, lambda phage, the human and mouse mitochondrial genomes, and the human and mouse immunoglobulin kappa-chain genes.

Bacteriophage lambda protein cII binds promoters on the opposite face of the DNA helix from RNA polymerase

The bacteriophage lambda transcriptional activator protein, cII, coordinately regulates transcription from two phage promoters that control lysogenic development. We demonstrate that cII is a DNA binding protein that selectively interacts with a repeat sequence in the -35 region of the promoter. Furthermore, cII is shown to bind mainly one face of the DNA helix and to make its contacts primarily in the major groove of the DNA. RNA polymerase sees this same region from the opposite side and sandwiches the DNA helix between itself and cII.

Isolation and characterisation of DraI, a type II restriction endonuclease recognising a sequence containing only A:T basepairs, and inhibition of its activity by uv irradiation of substrate DNA

A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus ATCC 27603 recognises the palindromic hexanucleotide sequence (formula; see text) and cleaves it, as indicated by the arrows, to produce blunt-ended fragments. The yield of enzyme is 100 to 1000 times that of the only other known type II restriction endonuclease that recognises a sequence composed solely of A:T basepairs, the isoschizomer AhaIII (1). Ultraviolet irradiation of the DNA substrate at relatively low doses inhibits the activity of DraI by "protecting" the recognition sequence and this may be exploited to give control of partial digestion of DNA by DraI.

Complete nucleotide sequence of the Escherichia coli gdhA gene

The DNA sequence of the gdhA gene of Escherichia coli K12, which encodes the 447 amino acid polypeptide subunit of NADP-specific glutamate dehydrogenase, is presented. The deduced protein sequence is strongly homologous to the corresponding enzyme of the eukaryotic fungus Neurospora crassa. The upstream DNA sequence includes several overlapping promoter consensus sequences. The downstream DNA sequence contains inverted repeats, predicted as forming long stable stem-loop structures in RNA, homologous to those found in several enterobacterial intergenic regions.

A processed gene defining a gene family encoding a human non-muscle tropomyosin

We have isolated and characterized a human genomic DNA sequence that defines a family of closely related sequences. At least one member of this family expresses a 2.5 X 10(3) base messenger RNA transcript encoding a 30,000 molecular weight tropomyosin in human fibroblasts. The coding sequence of this mRNA but not the non-coding sequence is also related to that of a 1.1 X 10(3) base mRNA encoding a 36,000 molecular weight non-muscle tropomyosin. This demonstrates the existence of at least two functional genes encoding human non-muscle tropomyosins.

Clustered repeat sequences in the genome of Epstein Barr virus

The genome of Epstein-Barr virus is composed of unique DNA interspersed with repetitive sequences. This organization suggests that Epstein-Barr virus provides a useful model for studying the function(s) of repetitive sequences in eukaryotic chromosomes. The primary structure of two of the repeat sequences, the 3072 bp large internal repeat, or BamHI-W repeat, and a smaller 125 bp, G, C-rich NotI repeat, are presented here. Their structures and possible functions are discussed.

Size fractionation of Trypanosoma brucei DNA: localization of the 177-bp repeat satellite DNA and a variant surface glycoprotein gene in a mini-chromosomal DNA fraction

We have size-fractionated intact DNA from Trypanosoma brucei into a major large DNA fraction (greater than 350S) and minor middle-sized (60-250S) and small (less than 60S) DNA fractions. Large DNA contains the rRNA genes, the basic copy genes for several variant surface glycoproteins (VSGs), including one which lies near a telomer, and the expression-linked copies of the two VSG genes. The middle-sized DNA contains at least one VSG gene, but the hybridization of this fraction with probes for the conserved repetitive sequences that mark the edges of the transposed segments of VSG genes, suggests that it may contain many VSG genes. The 177-bp repeat satellite DNA is also exclusively found in this fraction.

Vectors for high conditional expression of cloned genes

Several multicopy plasmids carrying the control region of bacteriophage lambda lysogeny, including the gene of a thermosensitive repressor CI857 have been constructed. The phages allow high expression of proteins under the transcription control of lambda promoter PR and translation control of Cro. The method has been assayed by measuring expression of either intact beta-galactosidase, truncated beta-galactosidase or beta-galactosidase fused to a mitochondrial gene product. It is shown that use of a strain with low endogeneous proteolytic activities strongly improves the conditional yield of foreign proteins, so that a high overproduction can be achieved (10-20 per cent of the total protein content of the cell).

EaeI: a restriction endonuclease from Enterobacter aerogenes

We describe the isolation and characterization of a type II restriction endonuclease from Enterobacter aerogenes. This recognises and cleaves the family of related sequences: 5'-Py-G-G-C-C-Pu-3' to generate DNA fragments with 5'-tetranucleotide extensions. EaeI may be useful in molecular cloning experiments, especially in conjunction with other enzymes which generate the same terminal extensions. Potential problems in the methods used to determine the cleavage specificity are discussed.

A partial restriction map of the proA-purE region of the Escherichia coli K12 chromosome

EcoRI restriction mapping data for fragments larger than 0.7 kb and contained in a 350-kb region of the Escherichia coli K-12 chromosome are presented. 75% of these fragments have been located relative to proA, B, argF, lac, proC, purE, and various insertion sequence elements normally present in this region. BglII and BamHI maps for the regions near argF and purE are also provided.