Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes

The DNA sequence of 96.5 kilobases of the Escherichia coli K-12 genome has been determined, spanning the region between rrnA at 87.2 minutes and katG at 89.2 minutes on the genetic map. The sequence includes 84 open reading frames, of which 46 code for unidentified proteins. Six previously mapped but unsequenced genes have been identified in this span: mob, fdhD, rhaD, rhaA, rhaB, and kdgT. In addition, five new genes have been assigned: the heat shock genes hsIU and hsIV, and the genes fdoG, fdoH, and fdoI, which encode the three subunits of formate dehydrogenase-O. The arrangement of the genes relative to possible promoters and terminators suggests 57 potential transcription units. Other features include the precise location of the bacteriophage P2 attachment site attP2II, and eleven REP elements, including one containing 9 REP sequences--one of the largest such elements known. This segment brings the total length of contiguous finished sequence to 325 kilobases.

Genome sequencing on both strands: the Janus strategy

The design of large scale DNA sequencing projects such as genome analysis demands a new approach to sequencing strategy, since neither a purely random nor a purely directed method is satisfactory. We have developed a strategy that combines these two methods in a way that preserves the advantages of both while avoiding their particular limitations. Computer simulations showed that a specific balance of random and directed sequencing was required for the most efficient strategy, termed the Janus strategy, which has been used in the Escherichia coli genome sequencing project. This approach depended on obtaining sequence easily from either strand of a cloned insert, and was facilitated by inversion of the insert in the engineered M13 vector Janus, by site-specific recombination. The inversion was accomplished simply by growth on the appropriate host strain, when the DNA strand incorporated into the new single stranded phage was complementary to that in the original phage, and was sequenced by the same simple protocol as the first strand.

DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication

The DNA sequence of a 136-kb segment (81.5 to 84.5 min) from the Escherichia coli origin of replication region has been determined and analyzed. Of the 122 protein coding regions that were found, we could assign no gene name or function to half of them, even in this well-studied part of the genome. The newly sequenced region also includes five RNA genes. The arrangement of open reading frames and potential promoters suggests 63 transcription units. The sequence was also analyzed for bend sites and two types of repeated sequence elements. Together with our sequence of the 84.5 to 86.5 min region, this new determination forms a 227-kb contiguous region centered on oriC. A global analysis of this region reveals a remarkable symmetry: most genes are transcribed divergently from the replication origin, and Chi octanucleotide (5'GCTGGTGG3') recombinational hot spots are also strikingly oriented with respect to the directions of replication and translation.

Global regulation of gene expression in Escherichia coli

Global transcription responses of Escherichia coli to various stimuli or genetic defects were studied by measuring mRNA levels in about 400 segments of the genome. Measuring mRNA levels was done by analyzing hybridization to DNA dot blots made with overlapping lambda clones spanning the genome of E. coli K-12. Conditions examined included isopropyl-beta-D-thiogalactopyranoside (IPTG) induction, heat shock, osmotic shock, starvation for various nutrients, entrance of cells into the stationary phase of growth, anaerobic growth in a tube, growth in the gnotobiotic mouse gut, and effects of pleiotropic mutations rpoH, himA, topA, and crp. Most mapped genes known to be regulated by a particular situation were successfully detected. In addition, many chromosomal regions containing no previously known regulated genes were discovered that responded to various stimuli. This new method for studying globally regulated genetic systems in E. coli combines detection, cloning, and physical mapping of a battery of coregulated genes in one step.

Metal-binding chimeric antibodies expressed in Escherichia coli

Metallothionein, a well-characterized biological chelator of metals, has been genetically fused to the binding domain of an antibody and expressed in the periplasm of Escherichia coli. Specific delivery of 109Cd to immobilized hapten or to haptenated cells was demonstrated directly in periplasmic extracts. This approach is potentially useful for targeted radiotherapy and diagnostic imaging. We find six to seven atoms of metal per active antigen-combining site. Absence of the Fc portion of the immunoglobulin along with low immunogenicity of metallothionein-metal complexes should reduce immunologic reactions.

Recombinant antibody-metallothionein: design and evaluation for radioimmunoimaging

We have produced a chimeric antibody (Ab) in which metallothionein, a well-characterized biological chelator of metals, was genetically fused to the F(ab') domain of the S107 Ab heavy chain. Coexpression with the Ab light chain that conveys specificity for the synthetic antigen phosphocholine was achieved in plasmacytoma cells. Metal- and antigen-binding domains of the Ab-metallothionein hybrid function with normal avidity and specificity. Ab-metallothionein can be efficiently loaded with 99mTc and used to specifically bind phosphocholine-haptenated cells in vitro or to localize plasma-cell ascites tumors in mice. The approach offers potential advantages for producing radiolabeled Ab for targeted radiotherapy and diagnostic imaging.

Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes

The DNA sequence of 91.4 kilobases of the Escherichia coli K-12 genome, spanning the region between rrnC at 84.5 minutes and rrnA at 86.5 minutes on the genetic map (85 to 87 percent on the physical map), is described. Analysis of this sequence identified 82 potential coding regions (open reading frames) covering 84 percent of the sequenced interval. The arrangement of these open reading frames, together with the consensus promoter sequences and terminator-like sequences found by computer searches, made it possible to assign them to proposed transcriptional units. More than half the open reading frames correlated with known genes or functions suggested by similarity to other sequences. Those remaining encode still unidentified proteins. The sequenced region also contains several RNA genes and two types of repeated sequence elements were found. Intergenic regions include three "gray holes," 0.6 to 0.8 kilobases, with no recognizable functions.

Rapid detection of antigen binding by antibody fragments expressed in the periplasm of Escherichia coli

Bacterial expression systems can greatly facilitate protein engineering of antibodies. We have developed a system for high-level expression of antibodies, antibody fragments, or hybrid antibodies with novel effector functions in the periplasm of Escherichia coli. From 5 ml of cells, a simple extraction yields sufficient material for SDS-gel electrophoresis, detection and characterization of hapten binding. To demonstrate our system, heavy-chain variable regions and lambda 1 light chains of a mouse anti-NP antibody were synthesized as hybrid proteins with a bacterial signal peptide (Omp F). Each chain is secreted into the periplasm where processing (cleavage of the signal peptide), folding and heterodimer association take place. Periplasmic proteins are released by cold osmotic shock, and hapten-binding activity is easily detected without further manipulation. The ease of genetic engineering in this system will facilitate the production of immunoglobulin derivatives designed for specific applications, and expression of these molecules in a native state will allow the rapid screening of combinatorial libraries and the results of mutagenesis.

Immunoglobulin D switching can occur through homologous recombination in human B cells

Prototypical class switching in mouse and human immunoglobulin heavy chains occurs through recombination of tandem blocks of short repeats located 5' to each heavy chain constant region (CH) except C delta. Deletion of C mu in immunoglobulin D (IgD)-secreting murine plasmacytomas occurs illegitimately. We demonstrate here that in human IgD-secreting myeloma cells freshly isolated from patient bone marrow and in normal peripheral blood B lymphocytes, an IgD switch can occur through homologous recombination of a direct repeat consisting of a 442-bp sequence 1.5 kbp 3' of the JH complex and a 443-bp sequence that is duplicated almost perfectly (96% similarity) 1.7 kbp 5' of the C delta gene (442/443-base-pair [bp] repeat). This homologous recombination mechanism is not exclusive for IgD switching, since C mu deletion endpoints in two established IgD-secreting myeloma cell lines fall outside the 442/443-bp repeat. The 442/443-bp mediated recombination shows cell type specificity, and we propose that it represents a unique mode for increased levels of IgD secretion in humans.

Field inversion gel electrophoresis applied to the rapid, multi-enzyme restriction mapping of phage lambda clones

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Definition of T-cell specific DNA-binding factors that interact with a 3'-silencer in the CD4+ T-cell gene Rpt-1

Analysis of the region 3' to the CD4+ T-cell gene Rpt-1 (encoding regulatory protein T-lymphocyte 1) led to the definition of a silencer element that inhibits heterologous gene expression in certain CD4+ T-cell lines but not in B-cell or non-lymphoid cell lines. Functional silencer activity in vivo was associated with the presence of a specific silencer-DNA-protein complex in electrophoretic mobility shift assays with T-cell extracts. Formation of this complex was selectively inhibited by the region in HIV-1 containing a silencer element. We discuss the possibility that DNA-binding factors may coregulate HIV-1 and Rpt-1 gene expression through a common transcriptional silencer element.

DNA looping induced by bacteriophage lambda O protein: implications for formation of higher order structures at the lambda origin of replication

A plasmid has been constructed, pOri2, which contains two lambda replication origin sequences separated by 1068 bp; both lambda sequences having the same orientation. When lambda initiation protein O is reacted with linearized pOri2 and examined by electron microscopy it is found to contain a looped area in which two parts of the plasmid are bound together by the O protein complex. Length measurements show that the O protein binds at the expected positions of the lambda origin sequences and that the looped area represents the DNA segment between the two O protein binding domains. Similar looping occurs in reactions with supercoiled pOri2 or if an amino-terminal fragment of O protein is used. When looped molecules are reacted with psoralen, crosslinked by irradiation with uv light, and then denatured, it is found that the looped area is more thermostable than the rest of the molecule. This indicates that the DNA within the looped segment is torsionally constrained while that outside the loop is free to rotate and suggests that simultaneous binding of O to two origins fixes the linkage number of the intervening DNA. The double origin binding ability of O may be diagnostic of the details of the reaction of O with a single origin sequence. A model is presented that rests on the assumption that O can produce microscopic looping between O protein binding sites within a single ori sequence.

The human immunoglobulin C mu-C delta locus: complete nucleotide sequence and structural analysis

The entire nucleotide sequence (approximately 20 kbp) spanning the human immunoglobulin IgM (mu) and IgD (delta) heavy chain constant region genes has been determined from DNA of mu-delta producing chronic lymphocytic leukemic B cells. As in the murine IgM + IgD double-producing B cells, no rearrangement has occurred in the C mu-C delta region in the leukemic cells. The C mu locus is highly conserved between mouse and human with the exception of the nucleotide sequence between the C mu 4 and mu M1 exons, which has diverged dramatically. The intergenic sequence between human C mu and C delta is three times larger than the analogous region in the mouse and contains notable features absent from the mouse, including a 443 bp segment that is 96% identical to a 442 bp sequence that occurs just 3' to the heavy chain enhancer, a 366 bp sequence that is directly repeated with 76% homology, and 12 tandem copies of a 35 bp sequence. The human C delta gene contains two additional exons relative to mouse C delta, but shares with the mouse the unique distal location of both secreted and membrane coding segments. Several polymorphisms in the human population have been identified in the intergenic region and in C delta but not in C mu.

The human immunoglobulin C mu-C delta locus: regulation of mu and delta RNA expression during B cell development

Whether the immunoglobulin (Ig) heavy chain genes C mu and C delta are expressed singly or in combination, their transcripts undergo differentiation-specific alterations in membrane (M) versus secreted (S) forms as well as in abundance. To better understand this regulation, we have cloned cDNAs for human delta m and delta s to establish the 3' end of the C mu-C delta transcription unit. Steady state mRNA levels and transcription rates were then analyzed in normal and transformed human B cells representing different maturation and activation states. The ratio of micron/microsecond RNA and of delta m/delta s RNA correlated with developmental stage, with a higher ratio at earlier stages. Steady state ratios of total mu/delta RNA paralleled ratios of C mu/C delta nascent transcription, suggesting no major posttranscriptional control for differential expression. However, at all developmental stages, transcription termination occurred downstream of the micron exons, suggesting a strong posttranscriptional regulatory component for production of secreted versus membrane forms of mu RNA. The relative abundance of mature delta S RNA was considerably higher in the human than in the mouse, correlating with the increased levels of circulating IgD in the former species. Stimulation of human splenocytes with mitogens did not increase delta RNA; in fact, splenocytes activated with pokeweed mitogen were nearly devoid of delta RNA, and Staphylococcus aureus Cowan I caused only a minor change.

Q-mediated late gene transcription of bacteriophage lambda: RNA start point and RNase III processing sites in vivo

The location of the RNA start point of in vivo Q-activated late gene RNA of bacteriophage lambda has been determined to be identical to the start point of in vitro 6 S RNA. The 6 S RNA is made early in infection and is efficiently antiterminated by Q. Two RNase III cut sites are located within Q-dependent RNA sequences, 209 and 270 bp from the beginning of the late transcript, and lie on the stem of an inverted repeat which has features in common with previously described RNase III processing sites. This is the third example of RNase III cut sites immediately downstream of transcription termination points in lambda, the others being antiterminated N gene mRNA and int gene mRNA.

Initiation protein induced helix destabilization at the lambda origin: a prepriming step in DNA replication

The interaction of the lambda phage initiator protein, O, with the lambda origin sequence, ori, has been investigated. Binding of O, or its amino-terminal fragment, causes a major structural change within a 60 bp AT-rich region just to the right of the O-binding site. ATP or other molecular energy sources are not required. The modification, as assayed by nuclease sensitivity, is reduced when certain ori mutant sequences, which bind O but fail to replicate, are substituted for the wild-type sequence. The modification of DNA structure caused by the interaction of O is absolutely dependent on the presence of superhelical tension at the lambda origin sequence, and has several properties consistent with a strand separation reaction. We propose that this modification is a fundamental prepriming event that is the first stage in initiation of bidirectional replication in lambda after O binding.

A new human immunoglobulin VH family preferentially rearranged in immature B-cell tumours

The prevalent forms of adult and childhood B-cell neoplasia are chronic lymphocytic (CLL) and acute lymphocytic (ALL) leukaemia, and are typified by a nearly monoclonal accumulation of cells expressing a single heavy (H) and light (L) chain variable (V) region. V gene selection could be random, or quite biased if the disease or the developmental status of the transformed cell somehow influenced DNA rearrangement. We have cloned and sequenced three germ-line VH gene segments that constitute a new human VH family (subgroup V) linked within 160 kilobase pairs of the DH-JH complex. One VH(V) member is rearranged in about 30% of patients with CLL and ALL, but not in IgM-expressing B-cell lines from peripheral blood. In some tumours, we detect a truncated (VH(V) RNA devoid of constant regions that originates from unrearranged VH(V) genes. In other tumours and in resting splenocytes, we detect large amounts of normally sized VH(V)-associated mRNA, although stimulation by mitogen of splenic B cells results in loss of VH(V)-hybridizing RNA. These features suggest that biased rearrangement of subgroup V may be under developmental selection.

Direct evidence for DNA bending at the lambda replication origin

Replication initiation in bacteriophage lambda appears to require wrapping of origin DNA on an approximately 50 angstrom radius in or around the complex with the initiator protein O. Since short lengths of DNA are not that flexible, it may be that runs of coherently spaced deoxyadenylate residues constitute bend sites in the ori sequence that facilitate the process. Earlier data showed that ori DNA has electrophoretic anomalies characteristic of bend sites and that these are augmented by initiator protein binding. Here origin bending is examined by direct measurement of the ability of polymerized ori sequences to form small circles. The smallest circles observed (84 residues) are compatible with the required radius of curvature. Bend sites within the O protein binding sites, bend sites in the spacers between them, plus the inherent flexibility of non-bent DNA in the origin may all contribute to origin bending. The data also show that a bend site is required for O protein binding to DNA.

Charons 36 to 40: multi enzyme, high capacity, recombination deficient replacement vectors with polylinkers and polystuffers

New phage lambda based cloning vectors, Charons 36-40, have been constructed which allow cloning of large (up to 24 kb) DNA fragments with up to sixteen cloning enzymes. Several of these could not be used previously with lambda vectors. Clones produced with these vectors can be propagated under recombination deficient conditions. A novel polystuffer method has been developed that permits vector arms to be purified by simple precipitation and which allows reliable identification of clones that have reincorporated any part of the stuffer. Three of the vectors are available with amber mutations in essential genes.

Personal access to sequence databases on personal computers

A comprehensive package of software has been developed to access nucleic acid and protein sequence databases on stand-alone IBM personal computers. The software combines keyword search on the annotation fields of the data with pattern matching algorithms on the biological sequences. Sequences containing complex sites like promoters or kink sites can be identified as well as sequences that are similar to a query sequence. Protein sequences with particular patterns of amino acids such as hydrophobic regions can be identified as well. Considering the relatively inexpensive hard disks now available, personal computers have become a cost-effective alternative to mainframe processing for sequence databases.

Binding and bending of the lambda replication origin by the phage O protein

We have characterized the binding of lambda phage replication initiation protein O to the phage origin of replication. The minimal DNA segment required for O binding is the single iteron, a 19-bp sequence of hyphenated dyad symmetry that is repeated with variations four times in the origin. The isolated amino terminus of O protein is also sufficient to bind DNA. Electrophoretic studies show that the amino terminus of O protein induces bending of a single iteron. The DNA-protein interaction was characterized by ethylation interference, dimethyl sulfate protection and neocarzinostatin footprinting. Points of DNA-protein contact are largely concentrated in two areas symmetrically disposed with respect to the dyad symmetry of the iteron. This suggests the protein interacts as a dimer with half sites in the DNA. However, a few non-symmetrical contacts are found, indicating that O protein may distort the helix. This may correlate with the bending effects demonstrated electrophoretically. Cylindrical DNA projections were used to model O protein binding to the lambda origin and compare it with the lambda repressor-operator interaction. Whereas bound repressor nearly encircles the DNA in the major groove, O protein leaves the major groove on the opposite side exposed.

Sequence-induced DNA curvature at the bacteriophage lambda origin of replication

DNA replication in bacteriophage lambda begins at a unique origin between residues 39,000 and 39,200 of the lambda genome. This segment of DNA serves a dual function since it also lies within the coding sequence of the lambda replication initiator protein O which binds origin DNA. The lambda origin sequence contains four 19-base-pair (bp) segments (iterons) which have dyad symmetry, followed by a 40-bp A + T-rich zone of highly asymmetrical base composition. It was noted earlier that lambda origin DNA exhibits an anomalous electrophoretic mobility on gels; that is, the length of DNA as determined by DNA sequencing is approximately 20% less than is predicted from electrophoretic mobility. Recent studies of kinetoplast minicircle DNA (K-DNA) from the protozoan Leishmania tarentolae have led to the proposal that sequence-induced DNA curvature could account for such electrophoretic anomalies by alteration of the shape of the DNA molecule. We now present evidence that the lambda origin contains a static curve.

Human immunoglobulin D: genomic sequence of the delta heavy chain

The DNA coding for the human immunoglobulin D(IgD) heavy chain (delta, delta) has been sequenced including the membrane and secreted termini. Human delta, like that of the mouse, has a separate exon for the carboxyl terminus of the secreted form. This feature of human and mouse IgD distinguishes it from all other immunoglobulins regardless of species or class. The human gene is different from that of the mouse; it has three, rather than two, constant region domains; and its lengthy hinge is encoded by two exons rather than one. Except for the third constant region, the human and mouse genes are only distantly related.

Structural analysis of the murine IgG3 constant region gene

We have determined the complete sequence of the gamma 3 heavy chain constant (C gamma 3) region gene of the BALB/c mouse including the 5'-flanking region up to the switch site and the 3'-flanking region past the end of the membrane exons. The C gamma 3 coding region, typical of other IgGs, is divided into six exons corresponding to the protein domains (C gamma (3)1, hinge, C gamma (3)2, and C gamma (3)3) and to the membrane carboxyl terminus (M1 and M2). The predicted amino acid sequence of the gamma 3 chain has three potential N-linked carbohydrate addition sites (including one in the membrane spacer segment), as compared with a single occurrence in the other mouse IgGs. Between the switch recombination region and the body of the C gamma 3 gene, there is a remarkable homology with a sequence between C mu and C delta which provides a rationale for an alternative, T cell-independent class-switch mechanism. We have used a computer to analyze the secondary structure of the gamma 3 mRNA precursor for the membrane form. We predict that this RNA precursor (approximately 12 000 bp) folds into four leaf-like domains which correspond to the variable region, the large IVS, the body of the constant region, and the membrane exons. This organization may have a role to play in the function of the mRNA precursor.

Illegitimate recombination generates a class switch from C mu to C delta in an IgD-secreting plasmacytoma

We present here the sequence characterization of a C mu----C delta immunoglobulin (Ig) heavy chain class switch. In the murine IgD-secreting plasmacytoma TEPC 1017, deletion of most of the mu switch recombination region (S mu) and the entire C mu gene occurred in the absence of switch region sequences 5' to C delta. This unique rearrangement resulted from an illegitimate recombination of sequences with only patchy homology to each other. The infrequent and variable nature of illegitimate recombination may explain the low frequency of IgD-secreting plasma cells in normal mouse tissues.

The molecular biology of immunoglobulin D

Immunoglobulin D (IgD) is co-expressed with immunoglobulin M (IgM) on the membranes of most B cells, yet its biological function has remained a mystery. Recent detailed information on the structure and transcription of the unusual IgD heavy chain (delta) gene in mouse suggests a complex genetic control. A model is presented for the developmental regulation of IgM and IgD and roles suggested for the membrane and secreted forms of IgD in the immune network.

A computer package for DNA sequence analysis

We have developed a comprehensive software-hardware package for a CP/M based or other microcomputer which can perform four major functions in a molecular biology laboratory: (1) the acquisition and analysis of DNA sequence data, (2) word processing in the preparation of scientific manuscripts and figures, (3) general lab computation and data reduction, and (4) as a data terminal for communication of data over the phone line.

An efficient method for scoring base pair interactions

A simple method is described for speeding up the computation of base pairing interractions. It is especially effective on microcomputers.

Unusual sequences in the murine immunoglobulin mu-delta heavy-chain region

The delta heavy (H) chain of mouse immunoglobulin D (IgD) is unusual both in its structure and in its differential expression relative to immunoglobulin M (IgM; reviewed in ref. 1). The region of DNA between IgM and IgD H-chain constant-region genes is probably implicated in this control. So far only fragments of the area have been sequenced. Now, however, we present the complete sequence as well as the sequence of the introns of the C delta gene. We have found several interesting features (Fig. 1), including an open reading frame (ORF) between Cmu and C delta which encodes 146 amino acids that might represent a previously unsuspected domain-like protein; three blocks of simple repetitive sequences; a 162-base pair (bp) unique-sequence inverted repeat; and a domain-like pseudogene in the large intron of C delta. We have not found, however, any sequence 5' of C delta resembling the switch (S) recombination sequences associated with class switching in other heavy chains. Moreover, we have determined the 3' deletion end point of an IgD-producing myeloma and find no sequences reminiscent of switch sites nearby.

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.

Asymmetric effects of deletions and substitutions on high negative interference in coliphage lambda

Experiments have been performed to help clarify the role of nonhomologies in phage lambda recombination. Three-factor crosses were carried out, and the frequencies of single and double recombinants in the two adjoining intervals were compared when the central marker was either a double point mutation (v1v3) or deletion (rex-cI deletion) or nonhomologous substitution (imm434). In all cases the lefthand marker was a bio substitution (Fec- phenotype, which does not permit plating on recA-), and the righthand marker was an amber mutation in gene O. Experiments were performed in all four possible arrangements of the central and rightward markers, while selecting for the Fec+ phenotype on the recA- host. As anticipated, high negative interference (HNI) was observed with point mutations, but when the central marker was a substitution nonhomology, HNI was reduced about tenfold. Surprisingly, when the central marker was a simple deletion, a dramatic asymmetry in results was observed, with HNI being exhibited only when the central deletion marker was acquired by the double recombinant. These results indicate that under normal conditions (red+, gam+, rec+) and with noninhibited DNA replication, recombination in coliphage lambda entails a highly asymmetric step that could be at the level of strand transfer or mismatch repair.

Cloning and characterization of the Escherichia coli chromosomal region surrounding the dnaG Gene, with a correlated physical and genetic map of dnaG generated via transposon Tn5 mutagenesis

A 24 kilobase pair region of the E. coli chromosome surrounding the dnaG gene has been cloned and characterized. A lambda phage library was constructed by ligating a Sau3A( decreases GATC) partial DNA digest of the entire E. coli chromosome into the lambda BamHI(G decreases GATCC) cloning vector charon 28. Partial digestion was performed to generate overlapping chromosomal fragments and to allow one to walk along the chromosome. This library was probed with a nick-translated plasmid (pRRBl) containing the rpoD gene, which maps adjacent to dnaG at 66 min. Four bacteriophages: lambda 3, lambda 4, lambda 5, lambda 6 that hybridized to the probe were isolated from the 2,500 plaques screened. One phage recombinant lambda 4, was shown to contain the dnaG gene. Three recombinant plasmids containing dnaG: pGL444, pGL445, pBS105, were constructed via subcloning of lambda 4 using different restriction of fragments. Plasmids pGL444 and pBS10 5 were subjected to transposon Tn5 mutagenesis and 88 Tn5 inserts into the cloned region were isolated. The location of the Tn5 inserts were mapped by restriction enzyme analysis of the plasmids and the insertion mutations were checked for ability to complement of dnaGts chromosomal marker at nonpermissive 40 degrees C. In this manner a correlated physical and genetic map of dnaG was determined. A large number of Tn5 inserts map to a specific 900 b.p. region which we propose may be involved in the regulation of dnaG gene expression.

Formal description of a DNA oriented computer language

A computer language termed DNA has been devised to aid in the description of DNA sequence manipulations. This was an outgrowth of a DNA sequence editor which has been implemented for a microcomputer. A formal description of the language in the BNF formalism is presented.

Mouse IgA heavy chain gene sequence: implications for evolution of immunoglobulin hinge axons

The complete nucleotide sequence of the gene and mRNA coding for the constant (C) region of the secreted form of the BALB/c mouse IgA immunoglobulin alpha heavy (H) chain has been determined. As in other immunoglobulins, the three C region domains of the alpha protein, C alpha 1, C alpha 2, and C alpha 3 are coded in separate exons. However, the hinge region of C alpha is not coded on a separate exon as it is in other hinge-containing immunoglobulins. Instead, the alpha hinge is coded as a 5' extension of the C alpha 2 exon, and we suggest that it may have evolved by duplication leading to incorporation of an acceptor RNA splice site into the coding portion of the C alpha 2 exon. Extensions of this concept could provide an explanation for duplications in the human alpha 1 chain.

Sequence organization of the origins of DNA replication in lambdoid coliphages

We have determined the sequences of the ori region DNA of several phage lambda mutants and hybrids, which shed light on the mechanism of DNA replication in the lambdoid phages. These include the heterologous substitution hybrids lambda rep82:lambda and lambda rep80:lambda, a pseudorevertant of the ori-r93 mutant lambda r93hot5, and the insertion mutant lambda pk35. The ori regions of the three lambdoid phages, lambda, phi 80 and 82, all have repeated sequences, termed iterons, and A . T-rich zones. We note that a similar arrangement of DNA is also found in several other prokaryotic origins of replication. lambda and phi 80 have four iterons, and 82 has five. The origin of lambda r93hot5 is unusual in that contains only three iterons, yet the phage grows normally. Analysis of this mutant indicates that the spacing of iterons is crucial to ori function, whereas their number is not. This argues against the cloverleaf model for lambda ori structure (Hobom et al., 1979). In lambda pk35 the drug resistance element Tn903 is inserted into the "inceptor" (ice) site, proposed to be crucial for lambda replication initiation (Hobom et al., 1979); yet this phage grows normally.

Nucleotide sequence of the chi recombinational hot spot chi +D in bacteriophage lambda

Chi sites in bacteriophage lambda stimulate recombination promoted by the RecBC pathway of Escherichia coli. Mutations which create these sites occur at four widely separated loci in lambda. We report here the nucleotide sequence surrounding the site of one of these loci, chi D, located near the S gene. The mutations creating the active Chi site, designated chi +D, are transversions from CG to AT. This mutation, like the chi +B and chi +C mutations previously analyzed, leads to a nucleotide sequence common to all three active chi sites.

Mouse immunoglobulin D: construction and characterization of a cloned delta chain cDNA

TEPC 1017 is a BALB/c plasmacytoma that synthesizes IgD in large enough amounts to permit the isolation of mRNA for mouse delta chains. cDNA has been prepared from this mRNA, and an 880-base-pair fragment of it has been cloned by recombinant DNA techniques. The hybridization selection technique has been used to show that this cDNA clone specifically binds only mRNA that can be translated into immunoprecipitable delta chains. the sequence of a portion of this clone has been determined and, when translated, shows homology with the C delta 3 of a human myeloma protein. Using this cDNA clone as a probe, we have found that several different-sized delta RNAs are present in TEPC 1017 and in another IgD-secreting plasmacytoma, TEPC 1033.

Mapping of heavy chain genes for mouse immunoglobulins M and D

A single DNA fragment containing both mu and delta immunoglobulin heavy chain genes has been cloned from normal BALB/c mouse liver DNA with a new lambda phage vector Charon 28. The physical distance between the membrane terminal exon of mu and the first domain of delta is 2466 base pairs, with delta on the 3' side of mu. A single transcript could contain a variable region and both mu and delta constant regions. The dual expression of immunoglobulins M and D on spleen B cells may be due to alternate splicing of this transcript.

Mouse immunoglobulin D: messenger RNA and genomic DNA sequences

The molecular structure of a mouse immunoglobulin D from a plasmacytoma tumor and that of the normal mouse gene coding for immunoglobulin D are presented. The DNA sequence results indicate an unusual structure for the tumor delta chain in two respects: (i) Only two constant (C) region domains, termed C delta 1 and C delta 3 by homology considerations, are found; the two domains are separated by an unusual hinge region C delta H that lacks cysteine residues and thus cannot provide the covalent cross-links between heavy chains typically seen in immunoglobulins. The two domains and hinge are all coded on separate exons. (ii) At the carboxyl end of the delta chain there is a stretch of 26 amino acids that is coded from an exon located 2750 to 4600 base pairs downstream from the rest of the gene. Analogy with immunoglobulin M suggests that this distally coded segment C delta DC may have a membrane-binding function; however, it is only moderately hydrophobic. A fifth potential exon (C delta AC), located adjacent to the 3' (carboxyl) end of C delta 3, could code for a stretch of 49 amino acids. The tumor's expression of the delta gene may be aberrant, but the simplest interpretation would be that this tumor expresses one of the several biologically significant forms of the delta chain.