Flanking Fragments Research Articles

Versatile PCR-mediated insertion or deletion mutagenesis

based procedure that can be used to generate precisely located mutants with any length of insertion or deletion. The strategy for insertion mutagenesis employs an established overlap extension PCR protocol, but involves three templates including an insert fragment of any length. The protocol for insertion requires four chimeric primers that are derived partly from the sequence to be inserted and partly from the template, in addition to two outermost flanking primers. Three PCR products are first prepared separately, including one insert fragment and two adjacent fragments using appropriate primer pairs. The insert fragment thus generated contains terminal complementarities at both ends to two adjacent fragments. In the second step, an overlap extension PCR is carried out, using the outermost primer

Recognition of translation initiation sites of eukaryotic genes based on an EM algorithm.

With the rapid increase of DNA databases of human and other eukaryotic model organisms, a large great number of genes need to be distinguished from the DNA databases. Exact recognition of translation initiation sites (TISs) of eukaryotic genes is very important to understand the translation initiation process, predict the detailed structure of eukaryotic genes, and annotate uncharacterized sequences. The problem has not been solved satisfactorily, especially for recognizing TISs of the eukaryotic genes with shorter first exons. It is an important task for extracting new features and finding new powerful algorithms for recognizing TISs of eukaryotic genes. In this paper, the important characteristics of shorter flanking fragments around TISs are extracted and an expectation-maximization (EM) algorithm based on incomplete data is used to recognize TISs of eukaryotic genes. The accuracy is up to 87.8% over a six-fold cross-validation test. The result shows that the identification variables are effectively extracted and the EM algorithm is a powerful tool to predict the TISs of eukaryotic genes. The algorithm also can be applied to other classification or clustering tasks in bioinformatics.

Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays.

We describe a method to screen pools of DNA from multiple transposon lines for insertions in many genes simultaneously. We use thermal asymmetric interlaced-PCR, a hemispecific PCR amplification protocol that combines nested, insertion-specific primers with degenerate primers, to amplify DNA flanking the transposons. In reconstruction experiments with previously characterized Arabidopsis lines carrying insertions of the maize Dissociation (Ds) transposon, we show that fluorescently labeled, transposon-flanking fragments overlapping ORFs hybridize to cognate expressed sequence tags (ESTs) on a DNA microarray. We further show that insertions can be detected in DNA pools from as many as 100 plants representing different transposon lines and that all of the tested, transposon-disrupted genes whose flanking fragments can be amplified individually also can be detected when amplified from the pool. The ability of a transposon-flanking fragment to hybridize declines rapidly with decreasing homology to the spotted DNA fragment, so that only ESTs with >90% homology to the transposon-disrupted gene exhibit significant cross-hybridization. Because thermal asymmetric interlaced-PCR fragments tend to be short, use of the present method favors recovery of insertions in and near genes. We apply the technique to screening pools of new Ds lines using cDNA microarrays containing ESTs for approximately 1,000 stress-induced and -repressed Arabidopsis genes.

Rapid amplification and cloning of Tn5 flanking fragments by inverse PCR.

A simple approach is described to efficiently amplify DNA sequences flanking transposon Tn5 insertions. The method involves: (i) digestion with a restriction enzyme that cuts within Tn5; (ii) self-ligation under conditions favouring the production of monomeric circles; (iii) four parallel PCR reactions using primers designed to amplify left or right flanking sequences, and to distinguish target amplicons from non-specific products. This reveals the number of Tn5 insertions and the size of flanking genomic restriction fragments, without Southern blot analysis. The amplified product contains restriction sites that facilitate cohesive-end cloning. This rapid method is demonstrated using Tn5 and Tn5-Mob tagged DNA sequences involved in albicidin biosynthesis in Xanthomonas albilineans. It is generally applicable for efficient recovery of DNA sequences flanking transposon Tn5 derivatives in insertional mutagenesis studies.

Characterization of the 5'-flanking region of the human RNA-specific adenosine deaminase ADAR1 gene and identification of an interferon-inducible ADAR1 promoter.

The double-stranded RNA-specific adenosine deaminase (ADAR1) is inducible by interferon (IFN) and is implicated in the editing of viral RNAs during lytic and persistent infection. We have now isolated and characterized human genomic clones that contain the promoter region required for transcription of the ADAR1 gene. Rapid amplification of cDNA 5'-ends (5'-RACE) identified additional upstream exon 1 sequence that was localized on P1-phage and lambda-phage genomic clones by Southern gel-blot analysis and sequence analysis. A Northern gel-blot analysis using a probe corresponding to the 5'-RACE exon 1 sequence and adjacent exon 2 sequence detected a major RNA transcript of approximately 6.7kb that was IFN-inducible in human amnion U cells. Transient transfection assays, using chloramphenicol acetyltransferase (CAT) as the reporter in constructs possessing various 5'-flanking fragments of the ADAR1 gene, led to the identification of a functional TATA-less promoter that directed IFN-inducible transcription of CAT. Sequence determination and deletion analysis of the promoter region revealed a consensus copy of the IFN-Stimulated Response Element (ISRE) involved in IFN inducibility that was flanked by a Kinase Conserved Sequence (KCS)-like element previously found to be unique to the human and mouse PKR gene promoters. A 63-bp minimal promoter fragment possessing the KCS-like and ISRE elements was sufficient to drive IFN-inducible transcription.

Rapid and efficient cloning of proviral flanking fragments by kanamycin resistance gene complementation.

We have developed a technique for the rapid cloning of unknown flanking regions of transgenic DNA. We complemented a truncated kanamycin resistance gene of a bacterial plasmid with a neomycin resistance gene fragment from a gene transfer vector. Optimized transformation conditions allowed us to directly select for kanamycin-resistant bacteria. We cloned numerous proviral flanking fragments from growth factor-independent cell mutants that were obtained after infection with a replication incompetent retroviral vector and identified integrations into the cyclin D2 and several unknown genomic sequences. We anticipate that our method could be adapted to various vector systems that are used to tag and identify genes and to map genomes.

Mechanism of interferon action: identification of essential positions within the novel 15-base-pair KCS element required for transcriptional activation of the RNA-dependent protein kinase pkr gene.

RNA-dependent protein kinase PKR is an important regulator of gene expression in interferon (IFN)-treated and virus-infected cells. The 50-kb gene encoding human PKR kinase (pkr) is inducible by IFN. Transfection analyses, using chloramphenicol acetyltransferase (CAT) as the reporter in constructs possessing various 5'-flanking fragments of the human pkr gene, led to the identification of a functional TATA-less promoter that directed IFN-inducible transcription. Sequence determination and mutational analysis of the pkr promoter region revealed, in addition to a functional copy of the IFN-stimulated response element (ISRE) responsible for inducibility by type I IFN, a novel 15-bp element required for optimal promoter activity mediated by the ISRE. This element (5' GGGAAGGCGGAGTCC 3'), designated KCS for kinase-conserved sequence, is exactly conserved between the human and mouse pkr promoters in sequence and position relative to the ISRE. We have now carried out an extensive mutational analysis of the 15-bp KCS element. Site-directed mutagenesis was performed, whereby every base pair position within the KCS element was replaced by each of the other three alternatives. Forty-five substitution mutants were analyzed for promoter activity by transient transfection analysis of untreated and IFN-treated human cells. The results establish 5' NNRRRGG(C,A,T)GGRGYYN 3', where R stands for purine and Y stands for pyrimidine, as the consensus sequence for the KCS element, both for basal and for IFN-inducible promoter activity. KCS-binding proteins were detected by electrophoretic mobility shift analysis (EMSA). Competition EMSA established that constitutively expressed nuclear proteins bound the KCS element selectively; KCS protein binding activity correlated with promoter activity in the transient transfection reporter assay.

Cloning and physical mapping of the EcoRI fragments of the giant linear plasmid SCP1.

A cosmid library was constructed for the 350-kb giant linear plasmid SCP1 and aligned on a successive linear map. Only a 0.8-kb gap has remained uncloned in the terminal inverted repeats close to both ends. Partial digestion of the aligned cosmids with EcoRI and hybridization with the flanking fragments of the vector enabled physical mapping of all of the EcoRI fragments. On this map, the methylenomycin biosynthetic gene cluster, the insertion sequence IS466, and the sapCDE genes coding for spore-associated proteins were localized.

Myb and Ets Proteins Are Candidate Regulators of c-kit Expression in Human Hematopoietic Cells

Kit is a tyrosine kinase receptor that plays an important role in human hematopoietic cell growth. The promoter elements that modulate the gene's expression have not been extensively studied. Because of c-kit's acknowledged importance in hematopoiesis, we sought to address this issue in more detail. To perform these studies we analyzed a human c-kit 5′ flanking fragment ∼1 kilobase in length. Deletion constructs showed a region ∼139 nucleotides upstream from the translation initiation site that was critical for promoter activity. A region containing a potential silencing element was also identified. Sequence analysis indicated several potential Myb- and Ets-binding sites. The functional significance of these sites was explored by showing that both wild-type Myb and Ets-2 protein, but not a DNA binding-deficient Myb mutant protein, bound to distinct 5′ flanking fragments that included these sites. Furthermore, binding of recombinant Myb and Ets-2 protein to these fragments could be competed with an excess of double stranded oligodeoxynucleotides containing canonical, but not mutated,Myb- or Ets-binding sites. We also showed that the 5′ flanking region of c-kit exhibited promoter activity in nonhematopoietic cells only when the cells were transfected with c-myb or ets-2 expression vectors. Moreover,Myb and Ets-2 coexpression in such cells augmented transactivation of c-kit promoter constructs in comparison to that observed in cells transfected with either construct alone. Promoter constructs lacking various Myb and Ets sites deleted were much less effective in this same system. Finally,Myb and Ets-2 mRNA expression was detected in CD34+, Kitlow as well as CD34+, Kitbright cells. In aggregate, these data further define the human c-kit promoter's functional anatomy and suggest that Myb and Etsproteins play an important, perhaps cooperative, role in regulating expression of this critical hematopoietic cell receptor.

Myb and Ets Proteins Are Candidate Regulators of c-kit Expression in Human Hematopoietic Cells

AbstractKit is a tyrosine kinase receptor that plays an important role in human hematopoietic cell growth. The promoter elements that modulate the gene's expression have not been extensively studied. Because of c-kit's acknowledged importance in hematopoiesis, we sought to address this issue in more detail. To perform these studies we analyzed a human c-kit 5′ flanking fragment ∼1 kilobase in length. Deletion constructs showed a region ∼139 nucleotides upstream from the translation initiation site that was critical for promoter activity. A region containing a potential silencing element was also identified. Sequence analysis indicated several potential Myb- and Ets-binding sites. The functional significance of these sites was explored by showing that both wild-type Myb and Ets-2 protein, but not a DNA binding-deficient Myb mutant protein, bound to distinct 5′ flanking fragments that included these sites. Furthermore, binding of recombinant Myb and Ets-2 protein to these fragments could be competed with an excess of double stranded oligodeoxynucleotides containing canonical, but not mutated,Myb- or Ets-binding sites. We also showed that the 5′ flanking region of c-kit exhibited promoter activity in nonhematopoietic cells only when the cells were transfected with c-myb or ets-2 expression vectors. Moreover,Myb and Ets-2 coexpression in such cells augmented transactivation of c-kit promoter constructs in comparison to that observed in cells transfected with either construct alone. Promoter constructs lacking various Myb and Ets sites deleted were much less effective in this same system. Finally,Myb and Ets-2 mRNA expression was detected in CD34+, Kitlow as well as CD34+, Kitbright cells. In aggregate, these data further define the human c-kit promoter's functional anatomy and suggest that Myb and Etsproteins play an important, perhaps cooperative, role in regulating expression of this critical hematopoietic cell receptor.

Isolation of the Interferon-Inducible RNA-Dependent Protein KinasePkrPromoter and Identification of a Novel DNA Element within the 5′-Flanking Region of Human and MousePkrGenes

The RNA-dependent protein kinase (PKR) is inducible by interferon (IFN) and is implicated in the antiviral and antiproliferative actions of IFN. We have now isolated human genomic clones that contain the promoter region required for transcription of thePkrgene. Transient transfection analyses, using chloramphenicol acetyltransferase (CAT) as the reporter in constructs possessing various 5′-flanking fragments of thePkrgene, led to the identification of a functional TATA-less promoter that directed IFN-inducible transcription of CAT. Sequence determination and deletion analysis of the promoter region revealed an element (5′GGAAAACGAAACT3′) involved in IFN inducibility that corresponds to the consensus sequence of the IFN-stimulated response element (ISRE). Comparison of the promoter sequence of the humanPkrgene to that of the mouse homolog identified a novel element (5′GGGAAGGCGGAGTCC3′) immediately upstream of the ISRE element which so far is unique to the human and mousePkrgene promoters. We have designated this new motif as KCS, for kinase conserved sequence. Deletion and substitution mutants of thePkrpromoter region showed that the ISRE element was required for transcriptional induction by type I IFN, whereas the KCS motif increased promoter activity mediated by the ISRE. Additional potential regulatory cis-elements were identified in the humanPkrpromoter that are commonly associated with growth control regulation and differentiation. Other than the ISRE and novel KCS elements, the overall organization of potential binding sites for transcription factors was not well conserved between the IFN-inducible promoters of the human and mousePkrgenes. The strict conservation of sequence, distance, and position of KCS, relative to ISRE, together with mutagenesis results, suggest an important functional role for the newly recognized KCS motif.

Determination of transcription initiation sites and promoter activity of the human 5-HT 2 A receptor gene

The regulation of 5-HT 2 A receptor (5-HT 2 A R) expression has been implicated in a variety of pathological processes. Previous data addressing the regulation of this receptor are extremely complicated and controversial. In order to understand the mechanisms of regulation of this receptor, we have identified the promoter region of the human 5-HT 2 A R gene. Anchored PCR has mapped a cluster of transcription initiation sites at nucleotides -1157, -1137, -1127 (numbered sequentially as sites 1, 2 and 3). An additional initiation site (site 4) was detected at -496, 631 bp downstream of site 3. Promoter activity was defined by transfection studies. Several 5′ flanking fragments linked to the human growth hormone reporter gene were transfected into two human cell lines, SHSY-5Y (neuroblastoma) and HeLa (cervic carcinoma) which express 5-HT 2 A R. A 0.74 kb HaeIII/PvuII fragment, which encompasses the initiation sites 1 to 3 and 5′ of the downstream initiation site 4, exhibited significant promoter activity in both cell lines. Inclusion of additional sequences upstream (the 1.6 kb PvuII/PvuII fragment) had little effect on the promoter activity, but the extension of the 0.74 kb fragment downstream to include a 0.45 kb PvuII/SmaI fragment drastically decreased the promoter activity. These results suggest that the promoter activity for human 5-HT 2 A R gene resides in the 0.74 kb HaeIII/PvuII fragment and the 0.45 kb PvuII/SmaI fragment may contain a silencer for the gene expression.

Transcription factor repression and activation of the human acetylcholinesterase gene.

Acetylcholinesterase in man is encoded by a single gene, ACHE, located on chromosome 7q22. In this study, the transcription start sites and major DNA promoter elements controlling the expression of this gene have been characterized by structural and functional studies. Immediately upstream of the first untranslated exon of the gene are GC-rich sequences containing consensus binding sites for several transcription factors, including Sp1, EGR-1 and AP2. In vitro transcription studies and RNase protection analyses of mRNA isolated from human NT2/D1 teratocarcinoma cells reveal that two closely spaced transcription cap sites are located at a consensus initiator (Inr) element similar to that found in the terminal transferase gene. Transient transfection of mutant genes shows that removal of three bases of this initiator sequence reduces promoter activity by 98% in NT2/D1 cells. In vitro transcription studies and transient transfection of a series of 5' deletion mutants of the ACHE promoter linked to a luciferase reporter show an Sp1 site at -71 to be essential for promoter activity. Purified Sp1 protein protects this site from DNase cleavage during in vitro footprinting experiments. A conserved AP2 consensus binding site, located between the GC box elements and the Inr, is protected by recombinant AP2 protein in DNase footprinting experiments, induces a mobility shift with AP2 protein and AP2-containing cell extracts, and fosters inhibition of transcription by AP2 as measured by transient transfection in mouse and human cell lines and in in vitro transcription reactions. These results indicate that AP2 functions as a repressor of human ACHE and mouse Ache transcription.

Ten allelic apolipoprotein[a] 5' flanking fragments exhibit comparable promoter activities in HepG2 cells.

Plasma levels of the atherogenic lipoprotein[a] represent a quantitative genetic trait that is primarily controlled by the polymorphic apolipoprotein[a] locus on chromosome 6q. The more than 1000-fold variation in lipoprotein[a] plasma levels is explained to a large extent by a remarkable size polymorphism of the apolipoprotein[a] gene which is translated into apolipoprotein[a] isoforms and by unidentified sequence variation in apo[a]. In a recent report, sequence variation in a 1.5 kb fragment from the 5' flanking region of the apolipoprotein[a] gene was associated with different promoter activities, which led to the suggestion that transcriptional control of the apolipoprotein[a] gene might contribute significantly to lipoprotein[a] plasma levels. We have used a reporter gene assay to compare the promoter activities of these 1.5 kb fragments which were cloned from ten well-characterized apolipoprotein[a] alleles. These ten allelic apolipoprotein[a] fragments revealed, despite the same sequence variation as previously reported, comparable and relatively weak promoter activities in HepG2 hepatocarcinoma cells. Promoter activity for the same fragment in non-liver cells and the identification of a liver cell-specific DNaseI hypersensitive site 3 kb upstream from the ATG start codon suggest that longer fragments must be used in order to analyze the transcriptional regulation of the apolipoprotein[a] gene.

Functional analysis of human alpha 1(I) procollagen gene promoter. Differential activity in collagen-producing and -nonproducing cells and response to transforming growth factor beta 1.

To gain a further understanding of the regulation of human type I collagen gene expression under physiologic and pathologic conditions, we characterized 5.3 kilobase pairs (kb) of the human alpha 1(I) procollagen gene promoter. A series of deletion constructs containing portions of the alpha 1(I) procollagen 5'-flanking region (with end points from -5.3 kb to -84 base pairs (bp)) ligated to the chloramphenicol acetyltransferase (CAT) reporter gene were transiently transfected into NIH/3T3 cells. Maximal CAT activity was observed with constructs having 5' end points from -804 to -174 bp. A further 5' deletion to -84 bp caused a marked reduction in CAT activity. Cells transfected with plasmids containing longer 5'-flanking fragments of the alpha 1(I) procollagen gene (-2.3 or -5.3 kb) showed reduced CAT activity compared with the -804 bp construct. The activity of the alpha 1(I) procollagen promoter was much lower in cells that do not normally express type I collagen (HeLa cells) compared with collagen-producing NIH/3T3 cells. The CAT activity of deletion constructs containing longer 5' regions than -84 bp was increased by approximately 2-fold in NIH/3T3 cells treated with transforming growth factor beta 1 (TGF beta 1). Electrophoretic mobility shift assays indicated that protein-DNA complex formation with a probe corresponding to the -170 to -80 bp fragment of the alpha 1(I) procollagen promoter was markedly enhanced in nuclear extracts prepared from TGF beta 1-treated fibroblasts as compared with untreated fibroblasts. The DNA binding activity stimulated by TGF beta 1 was specific for an Sp1-like sequence at positions -164 to -142 bp in the promoter. These results demonstrate that 1) there are both positive and negative cis-acting regulatory elements in the human alpha 1(I) procollagen promoter, 2) these regulatory regions function differently in collagen-producing and -nonproducing cells, 3) the alpha 1(I) procollagen promoter contains TGF beta 1-responsive sequences located between -174 and -84 bp from the transcription start site, and 4) TGF beta 1 caused marked stimulation of the DNA binding activity of a nuclear factor interacting with an Sp1-like binding site located within a region encompassing -164 to -142 bp of the alpha 1(I) procollagen promoter.

Library-independent cloning of genomic fragments adjacent to vector integration sites: Isolation of the EB4-PSV gene from a Dictyostelium gene disruption transformant

We have designed an efficient procedure to clone genomic DNA adjacent to the integration site of transformation vectors. Using this method on a Dictyostelium gene disruption transformant, we have cloned a 5kb fragment which has previously escaped isolation by conventional library screening. Our protocol eliminates recloning of the original vectors which are often integrated in multiple tandem copies (1) but specifically recovers vectors containing genomic fragments adjacent to the integration site. The protocol is useful to isolate flanking fragments in gene disruption transformants to characterize flanking regions which may influence the expression of transformed genes by position effects and to identify sites of insertional mutagenesis.

Rearrangement of a DNA sequence homologous to a cell-virus junction fragment in several Moloney murine leukemia virus-induced rat thymomas.

We have studied the integrated proviruses in Moloney murine leukemia virus-induced rat thymomas. By Southern blot analysis, we found several complete integrated proviruses in each tumor. In most tumors, we could not detect defective or recombinant proviruses. Several of these integrated proviruses (with their flanking cellular sequences) from a single tumor were cloned in Charon 4A. Their flanking cellular fragments were subcloned into pBR322 and used as a probe to screen other thymoma DNAs. With one clone (pMo-lC) used as a probe, we could detect novel fragments in 11 out of 20 thymoma DNAs analyzed. In three of these thymomas we could analyze in more detail, it appears that these novel fragments are generated by the insertion of a provirus. This specific integration of Moloney provirus in the host genome may represent an important genetic event leading to tumor formation.

Cloning of the am (glutamate dehydrogenase) gene of Neurospora crassa through the use of a synthetic DNA probe

In a previous study the alteration in the amino acid sequence of Neurospora crassa NADP-specific glutamate dehydrogenase (GDH) resulting from two mutually compensating frameshift mutations was used to deduce the first 17 nucleotides of the coding sequence of the am gene. In the work reported here, a synthetic 17-mer corresponding to the deduced sequence was shown to hybridize strongly to a 9-kb HindIII fragment from N. crassa wild-type DNA but not to any corresponding fragment from the DNA of a mutant strain known to be deleted for most or all of the gene. Wild-type HindIII fragments were fractionated for size and a fraction centering around 9 kb was cloned in vector λL47. Two clones carrying the strongly hybridizing fragment were identified. The hybridization to the 17-mer was localized within a 2.7-kb BamHI fragment and, within this, to a 700-bp BamHI- BglII subfragment. 5' end-labelled polyadenylated RNA isolated from wild-type mycelium hybridized to the 2.7-kb BamHI fragment and not appreciably to flanking fragments. The partial sequence analysis of the BamHI- BglII fragment has confirmed that the 17-mer probe matches the coding sequence at the 5' end of the gene and has also revealed an intervening sequence 67 bp in length, interrupting codon 15. Both the 9-kb HindIII fragment and the 2.7-kb BamHI fragment have been shown to be capable of transforming the deletion mutant to prototrophy and ability to produce GDH. Analysis of one transformant showed that the am gene was integrated, together with a part of the long arm of the lambda vector, at an unusual locus. This transformant, in which the am gene does not show its normal linkage to the linkage group 5 marker inl, was found to produce GDH to about 20% of the normal level.

Molecular cloning of the fnr gene of Escherichia coli K12.

Mutations in the fnr gene of Escherichia coli have pleiotrophic effects leading to deficiencies in the reduction of fumarate and nitrate, hydrogen production and the ability to grow anaerobically with fumarate or nitrate as terminal electron acceptors. Transducing phages (lambda fnr) carrying the wild-type fnr gene were isolated from populations of artificially-constructed recombinant lambda phages by their ability to complement the lesions of fnr mutants. The lambda fnr phages restored anaerobic growth with fumarate and nitrate as electron acceptors and as prophages, they promoted normal synthesis of fumarate reductase, nitrate reductase and hydrogenase in fnr mutants. Five independently-isolated lambda fnr phages each contained a R.HindIII fragment (11.5 kilobases) that possessed three internal R.EcoRI targets and had inserted with the same orientation relative to the phage. A physical map of the fnr region was constructed by restriction analysis and flanking fragments were identified by DNA : DNA hybridization.

Genetic and physical characterization of lambda transducing phages (lambda frdA) containing the fumarate reductase gene of Escherichia coli K12.

Two types of fumarate reductase transducing phages, lambda frdA, carrying the wild-type frdA gene but differing in the orientation of a R.HindIII fragment of bacterial DNA were isolated from populations of recombinant transducing phages by their ability to complement the lesions of frdA mutants of E. coli. In lysogens, the cloned frdA gene was controlled by its own promoter and was fully responsive to normal regulatory stimuli. The lambda frdA phages would not complement the defects of succinate dehydrogenase (sdh) mutants. Genetic studies showed that the R.HindIII fragment contains ampA, the cis-acting regulatory locus for the chromosomal beta-lactamase gene ampC. No evidence for the presence of other markers was detected but the bacterial segment could be extended to produce plaque-forming phage derivatives containing the amp operon and a gene concerned with bacteriophage morphogenesis, groE(mop). A physical map of the 4.9 kb R.HindIII fragment was constructed by restriction analysis and flanking fragments were identified by DNA:DNA hybridization analysis. The frdA region contained a single asymmetric R.EcoRI target 3.33 kb from one end and the orientation of the physical map with respect to the E.coli linkage map was established.