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Sequence analysis and phenotypic characterization of groEL mutations that block lambda and T4 bacteriophage growth.

The groES and groEL genes of Escherichia coli have been shown previously to belong to a single operon under heat shock regulation. Both proteins have been universally conserved in nature, as judged by the presence of similar proteins throughout evolution. The GroEL protein has been shown to bind promiscuously to many unfolded proteins, thus preventing their aggregation. ATP hydrolysis by GroEL results in the release of the bound polypeptides, a process that often requires the action of GroES. In an effort to understand GroEL and GroES structure and function, we have determined the nucleotide changes of nine mutant alleles of groEL. All of these mutant alleles were isolated because they block bacteriophage lambda growth. Our sequencing results demonstrate that (i) many of these alleles are identical, in spite of the fact that they were independently isolated, and (ii) most of the different alleles are clustered in the same region of the gene. One of the mutant alleles was shown to possess two nucleotide alterations in the groEL coding phase, one of which is located in a putative ATP-binding domain. The two nucleotide changes were separated by genetic engineering, and each individual change was shown to exert an effect on bacteriophage growth. But, using genetic analyses, we demonstrate that the restriction on bacterial growth at elevated temperatures is conferred only by the mutation within the putative ATP-binding domain. We have cloned the mutant alleles on multicopy plasmids and overexpressed their products. By testing for the ability of bacteriophage either to propagate or to form colonies at 43 degrees C, we have been able to divide the mutant proteins into those with no activity and those with residual activity under the various conditions tested.

Bacterial Proteins↗

Bacteriophage lambda-based expression vectors.

Bacteriophage lambda has been in use as a cloning vector for over 25 years, and has been used extensively as an expression vector. The efficiency of packaging and infection, and the simplicity of plaque screening are advantages of lambda as a cloning vector. A number of ingenious modifications help overcome the disadvantages associated with its mode of growth and its size. Some lambda vectors have been designed to be readily converted into plasmids or phagemids, and there are a variety of promoters and fusions that can be used to drive expression of foreign genes. Screening lambda libraries with antibodies or ligands is a powerful way of identifying novel genes.

Bacteriophage lambda↗

Lambda bacteriophage-mediated transduction of ColE1 deoxyribonucleic acid having a lambda bacteriophage-cohesive end site: selection of packageable-length deoxyribonucleic acid.

An in vitro recombinant ColE1-cos lambda deoxyribonucleic acid (DNA) molecule, pKY96, has 70% of the length of lambda phage DNA. The process of lambda phage-mediated transduction of pKY96 generated a small amount of transducing phage particles containing ColE1-cos lambda DNA molecules of 80 or 101% of the length of lambda phage DNA, in addition to those containing original pKY96 DNA molecules. The newly isolated larger plasmid DNAs were transduced 100 times more efficiently than pKY96 DNA. Their structures were compared with that of a prototype pKY96 DNA, and the mechanism of the formation of these molecules is discussed.

Bacteriophage lambda↗

The topological mechanism of phage lambda integrase.

Bacteriophage lambda integrase (Int) is a versatile site-specific recombinase. In concert with other proteins, it mediates phage integration into and excision out of the bacterial chromosome. Int recombines intramolecular sites in inverse or direct orientation or sites on separate DNA molecules. This wide spectrum of Int-mediated reactions has, however, hindered our understanding of the topology of Int recombination. By systematically analyzing the topology of Int reaction products and using a mathematical method called tangles, we deduce a unified model for Int recombination. We find that, even in the absence of (-) supercoiling, all Int reactions are chiral, producing one of two possible enantiomers of each product. We propose that this chirality reflects a right-handed DNA crossing within or between recombination sites in the synaptic complex that favors formation of right-handed Holliday junction intermediates. We demonstrate that the change in linking number associated with excisive inversion with relaxed DNA is equally +2 and -2, reflecting two different substrates with different topology but the same chirality. Additionally, we deduce that integrative Int recombination differs from excisive recombination only by additional plectonemic (-) DNA crossings in the synaptic complex: two with supercoiled substrates and one with relaxed substrates. The generality of our results is indicated by our finding that two other members of the integrase superfamily of recombinases, Flp of yeast and Cre of phage P1, show the same intrinsic chirality as lambda Int.

Bacteriophage P1↗

Formation of transmembrane channels in liposomes during injection of lambda DNA.

Bacteriophage lambda binds to unilamellar liposomes bearing its receptor protein, LamB, and the lambda DNA can be injected into the internal aqueous space. During this process, transmembrane channels are formed in the liposomes which permit the entry and escape of small molecules, but not proteins. The channels are stable and persist after DNA injection.

Adenosine Triphosphate↗

Suppression of transcription termination by phage lambda.

The bacteriophage lambda N gene product positively controls development by preventing termination of transcription at terminator sites critical to the sequential expression of phage genes. Many host transcription factors, including RNA polymerase, are involved in N gene action. Recent findings have shown that ribosomal proteins are also involved. The current understanding of how the N protein affects transcription termination is reviewed, and a possible model and current problems are discussed.

Bacterial Proteins↗

Genetic selection for mutations that impair the co-operative binding of lambda repressor.

Bacteriophage lambda repressor binds co-operatively to adjacent pairs of DNA target sites. A novel combination of positive genetic selections, involving two different operon fusions derived from P22 challenge phages, was used to isolate mutant lambda repressors that have lost the ability to bind co-operatively to tandem sites yet retain the ability to bind a strong, single site. These cb (co-operative binding) mutations result in 10 different amino acid changes, which define eight residues in the carboxyl-terminus of repressor. Because challenge phage derivatives may be applied to study essentially any specific protein-DNA interaction, analogous combinations of genetic selections may be used to explore the ways that a variety of proteins interact to assemble regulatory complexes.

Amino Acid Sequence↗

Roles for lambda Orf and Escherichia coli RecO, RecR and RecF in lambda recombination.

Bacteriophage lambda lacking its Red recombination functions requires either its own gene product, Orf, or the product of Escherichia coli's recO, recR and recF genes (RecORF) for efficient recombination in recBC sbcB sbcC mutant cells (the RecF pathway). Phage crosses under conditions of a partial block to DNA replication have revealed the following: (1) In the presence of Orf, RecF pathway recombination is similar to lambda Red recombination; (2) Orf is necessary for focusing recombination toward the right end of the chromosome as lambda is conventionally drawn; (3) RecORF-mediated RecF pathway recombination is not focused toward the right end of the chromosome, which may indicate that RecORF travels along the DNA; (4) both Orf- and RecORF-mediated RecF pathway recombination are stimulated by DNA replication; and (5) low level recombination in the simultaneous absence of Orf and RecORF may occur by a break-copy mechanism that is not initiated by a double strand break. Models for the roles of Orf and RecO, RecR and RecF in recombination are presented.

Bacterial Proteins↗

Dynamics and DNA substrate recognition by the catalytic domain of lambda integrase.

Bacteriophage lambda integrase (lambda-Int) is the prototypical member of a large family of enzymes that catalyze site-specific DNA recombination via the formation of a Holliday junction intermediate. DNA strand cleavage by lambda-Int is mediated by nucleophilic attack on the scissile phosphate by a conserved tyrosine residue, forming an intermediate with the enzyme covalently attached to the 3'-end of the cleaved strand via a phosphotyrosine linkage. The crystal structure of the catalytic domain of lambda-Int (C170) obtained in the absence of DNA revealed the tyrosine nucleophile at the protein's C terminus to be located on a beta-hairpin far from the other conserved catalytic residues and adjacent to a disordered loop. This observation suggested that a conformational change in the C terminus of the protein was required to generate the active site in cis, or alternatively, that the active site could be completed in trans by donation of the tyrosine nucleophile from a neighboring molecule in the recombining synapse. We used NMR spectroscopy together with limited proteolysis to examine the dynamics of the lambda-Int catalytic domain in the presence and absence of DNA half-site substrates with the goal of characterizing the expected conformational change. Although the C terminus is indeed flexible in the absence of DNA, we find that conformational changes in the tyrosine-containing beta-hairpin are not coupled to DNA binding. To gain structural insights into C170/DNA complexes, we took advantage of mechanistic conservation with Cre and Flp recombinases to model C170 in half-site and tetrameric Holliday junction complexes. Although the models do not reveal the nature of the conformational change required for cis cleavage, they are consistent with much of the available experimental data and provide new insights into the how trans complementation could be accommodated.

Amino Acid Sequence↗

Shutoff of lambda gene expression by bacteriophage T4: role of the T4 alc gene.

Bacteriophage T4 normally contains 5-hydroxymethylcytosine instead of cytosine in its DNA. Multiple mutants of T4 which synthesize DNA with cytosine do not transcribe their late genes due to the action of the T4 alc gene (Snyder et al., Proc. Natl. Acad. Sci. U.S.A. 73:3098--3102, 1976), which is also responsible for unfolding the host nucleoid after T4 infection (Sirotkin et al., Nature [London] 265:28--32, 1977; Tigges et al., J. Virol. 24:775--785, 1977). It seems reasonable that T4 alc function plays a role in shutting off host transcription, and the observation that some of the RNA made after infection with a T4 alc mutant hybridizes to Escherichia coli DNA (Sirotkin et al., Nature [London] 265:28--32, 1977; Tigges et al., J. Virol. 24:775--785, 1977) supports this hypothesis. Although it is likely that the roles of the alc function in the blocking of some types of transcription and in the unfolding of the host nucleoid are related, it is not known how these effects are achieved or, in fact, whether all types of transcription are affected equally by the alc function. In an attempt to answer these questions, we studied the effect of T4 alc function on bacteriophage lambda transcription and on the structure of intracellular lambda DNA. We found that the alc function is responsible for the shutoff of lambda late transcription but probably not for the shutoff of lambda early transcription. We also found that alc does not block lambda transcription by directly removing the supercoils from circular lambda DNA via either a nicking or topoisomerase activity. Furthermore, we conclude that T4 infection also prevents the translation of non-T4 mRNA because late lambda mRNA's were made after superinfection by a T4 alcs mutant and were of normal length but were not translated into lambda late proteins.

5-Methylcytosine↗

Specialized lambda transducing bacteriophage which carries hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase.

A number of specialized lambda transducing bacteriophages which carry the Escherichia coli gene guaB were isolated from E. coli. One of these bacteriophages, lambda cI857 Sam7 d guaB-2, also carries hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase (EC 6.1.1.21). Histidyl-transfer ribonucleic acid synthetase activities in induced and uninduced lysogens carrying lambda d guaB-2 indicate that the phage carries the entire structural gene and that the gene is under the control of an E. coli promoter. These conclusions were confirmed by the in vivo production of a protein encoded by the phage which comigrates with authentic histidyl-transfer ribonucleic acid synthetase on two-dimensional polyacrylamide gels.

Amino Acyl-tRNA Synthetases↗

Affinity selection of cDNA libraries by lambda phage surface display.

Bacteriophage lambda surface display was used to isolate cDNA clones encoding autoantigens recognized by sera from patients with Sjögren's syndrome (SS). We made cDNA libraries from human HeLa and HepG2 cells, using the expression vector lambdafoo. By repeating affinity selection of the libraries with the sera immobilized in microtiter wells, we isolated three clones that encode previously unknown antigens as well as four clones previously known as SS autoantigens. The newly identified autoantigens include TRK-fused gene product (TFG), survival motor neuron gene product (SMN) and pM5, which has a similarity to the metal-binding domain of human fibroblast collagenase. Thus, the bacteriophage lambda surface display is powerful for isolating cDNA clones by affinity screening.

Antibody Affinity↗

Physical and genetic localization of ilv regulatory sites in lambda ilv bacteriophages.

A set of nine lambda dilv phages were used to transduce bacterial recipients containing point mutations or deletions in the ilv genes located at 84 min on the Escherichia coli K-12 chromosome. This genetic analysis indicated that two phages carry the entire ilvGEDAC cluster; others carry the complete ilvC gene and, in addition, bacterial DNA that extends to a termination point between ilvA and ilvC, within ilvD, within ilvE, or within ilvG. DNA extracted from the lambda dilv phages was digested with EcoRI, HindIII, KpnI, PstI, SalI, and SmaI. The restriction maps revealed that these phages were generated after insertion at four distinct insertion sites downstream (clockwise) of ilvC. The physical relationships between the various phages were further examined by electron microscopic heteroduplex analysis. The physical maps of the phages thus generated were straightforward and in complete accord with the genetic data. No evidence for genetic rearrangements of ilv DNA in the phage was obtained, thus validating conclusions based on the use of these phages in previous and ongoing research projects. Bacterial cells with deletions of the ilv genes were made lysogenic with lambda dilv phage to examine the regulation of ilv genes present in the phage. The results confirm previous studies showing that one site for control by repression and derepression is upstream (counterclockwise) of ilvG. It was shown, in addition, that the activities of dihydroxy acid dehydrase and threonine deaminase were increased when the prototrophic lysogens were grown with 20 mM leucine. Since this increase was exhibited even when the ilvG-linked control region was not carried by the lambda dilv phage, additional control sites must be located within the ilvEDA region of the ilvGEDA transcription unit.

Amino Acids, Branched-Chain↗

The purification of 5-enolpyruvylshikimate 3-phosphate synthase from an overproducing strain of Escherichia coli.

The Escherichia coli aroA gene which codes for the enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSP synthase) has been cloned from the lambda-transducing bacteriophage lambda pserC. The gene has been located on a 4.7 kilobase pair PstI DNA fragment which has been inserted into the multiple copy plasmid pAT153. E. coli cells transformed with this recombinant plasmid overproduce EPSP synthase 100-fold. A simple method for the purification of homogeneous enzyme in milligram quantities has been devised. The resulting enzyme is indistinguishable from enzyme isolated from untransformed E. coli.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗

Isolation and heteroduplex mapping of a lambda transducing bacteriophage carrying the structural genes for carbamoylphosphate synthase: regulation of enzyme synthesis in Escherichia coli K-12 lysogens.

A N-lambda bacteriophage transducing the structural genes for Escherichia coli K-12 carbamoylphosphate synthase (glutamine) (CPSase; EC 2.7.2.9) has been isolated and analyzed both genetically and physically. The whole int-N region is substituted for a short chromosomal segment corresponding almost exactly to the car locus. The study of CPSase, ornithine carbamoyltransferase, and aspartate carbamoyltransferase regulation in carriers of lambdadcar confirms the previously reported participation of the argR gene product in the control of CPSase synthesis and points to the existence of a regulatory molecule involved in the control of both CPSase and aspartate carbamoyltransferase synthesis. The general usefulness of using N- lambda transducing bacteriophages for the recovery of large amounts of gene products is discussed.

Arginine↗

Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet.

Scanning force microscopy (SFM) was used to image intact, nearly fully elongated lambda bacteriophage DNA molecules, fixed onto freshly cleaved mica surfaces. Molecular elongation and fixation were accomplished using a newly characterized fixation technique, termed "fluid fixation." Here convective fluid flows generated within an evaporating droplet of DNA solution efficiently elongate DNA molecules for fixation onto suitably charged surfaces. SFM images of a very large bacteriophage genome, G, showed the presence of double-stranded bubbles. We speculate that these structures may contain putative replication forks. Overall, the experiments presented here demonstrate the viability of using fluid fixation for the preparation of DNA molecules for SFM imaging. The combination of largely automatable optically based techniques with the high-resolution SFM imaging presented here will likely produce a high-throughput system for detailed physical mapping of genomic DNA or clones.

Bacteriophage lambda↗