Isolation and characterization of nucleoid proteins from Escherichia coli

Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines

The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.

RNAP Promoter Search and Transcription Kinetics in Live E. coli Cells

Bacterial transcription has been studied extensively in vitro, which has provided detailed molecular mechanisms of transcription. The in vivo cellular environment, however, may impose different rules on transcription than the homogeneous and well-controlled in vitro environment. How an RNA polymerase (RNAP) molecule searches rapidly through vast nonspecific chromosomal DNA in the three-dimensional nucleoid space and identifies a specific promoter sequence remains elusive. Transcription kinetics in vivo could also be impacted by specific cellular environments including nucleoid organization and nutrient availability. In this work, we investigated the promoter search dynamics and transcription kinetics of RNAP in live E. coli cells. Using single-molecule tracking (SMT) and fluorescence recovery after photobleaching (FRAP) across different genetic, drug inhibition, and growth conditions, we observed that RNAP's promoter search is facilitated by nonspecific DNA interactions and is largely independent of nucleoid organization, growth condition, transcription activity, or promoter class. RNAP's transcription kinetics, however, are sensitive to these conditions and mainly modulated at the levels of actively engaged RNAP and the promoter escape rate. Our work establishes a foundation for further mechanistic studies of bacterial transcription in live cells.

Nuclease dead Cas9 is a programmable roadblock for DNA replication

Limited experimental tools are available to study the consequences of collisions between DNA-bound molecular machines. Here, we repurpose a catalytically inactivated Cas9 (dCas9) construct as a generic, novel, targetable protein-DNA roadblock for studying mechanisms underlying enzymatic activities on DNA substrates in vitro. We illustrate the broad utility of this tool by demonstrating replication fork arrest by the specifically bound dCas9-guideRNA complex to arrest viral, bacterial and eukaryotic replication forks in vitro.

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as protein/ DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly compacted than that in the exponential phase. In addition to factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) here we have identified, three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Qβ (Hfq) and suppressor of td(-) phenotype A (StpA). Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, StpA and Hfq, while Dps occupies more than half of the stationary phase nucleoid. It has been known for a while that Dps is the main nucleoid-associated protein at stationary phase. From these results and the prevailing information, we propose a model for growth phase dependent changes in the structure and protein composition of nucleoid in E. coli.

Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme

Coliphage T4 endonuclease II (EndoII), encoded by gene denA, is a small (16 kDa, 136 aa) enzyme belonging to the GIY-YIG family of endonucleases, which lacks a C-terminal domain corresponding to that providing most of the binding energy in the structurally characterized GIY-YIG endonucleases, I-TevI and UvrC. In vivo, it is involved in degradation of host DNA, permitting scavenging of host-derived nucleotides for phage DNA synthesis. EndoII primarily catalyzes single-stranded nicking of DNA; 5- to 10-fold less frequently double-stranded breaks are produced. The Glu118Ala mutant of EndoII was crystallized in space group P2(1) with four monomers in the asymmetric unit. The fold of the EndoII monomer is similar to that of the catalytic domains of UvrC and I-TevI. In contrast to these enzymes, EndoII forms a striking X-shaped tetrameric structure composed as a dimer of dimers, with a protruding hairpin domain not present in UvrC or I-TevI providing most of the dimerization and tetramerization interfaces. A bound phosphate ion in one of the four active sites of EndoII likely mimics the scissile phosphate in a true substrate complex. In silico docking experiments showed that a protruding loop containing a nuclease-associated modular domain 3 element is likely to be involved in substrate binding, as well as residues forming a separate nucleic acid binding surface adjacent to the active site. The positioning of these sites within the EndoII primary dimer suggests that the substrate would bind to a primary EndoII dimer diagonally over the active sites, requiring significant distortion of the enzyme or the substrate DNA, or both, for simultaneous nicking of both DNA strands. The scarcity of potential nucleic acid binding residues between the active sites indicates that EndoII may bind its substrate inefficiently across the two sites in the dimer, offering a plausible explanation for the catalytic preponderance of single-strand nicks. Mutations analyzed in earlier functional studies are discussed in their structural context.

Escherichia coli HU protein has a role in the repair of abasic sites in DNA

HU is one of the most abundant DNA binding proteins in Escherichia coli. We find that it binds strongly to DNA containing an abasic (AP) site or tetrahydrofuran (THF) (apparent K(d) approximately 50 nM). It also possesses an AP lyase activity that cleaves at a deoxyribose but not at a THF residue. The binding and cleavage of an AP site was observed only with the HUalphabeta heterodimer. Site-specific mutations at K3 and R61 residues led to a change in substrate binding and cleavage. Both K3A(alpha)K3A(beta) and R61A(alpha)R61A(beta) mutant HU showed significant reduction in binding to DNA containing AP site; however, only R61A(alpha)R61A(beta) mutant protein exhibited significant loss in AP lyase activity. Both K3A(alpha)K3A(beta) and R61K(alpha)R61K(beta) showed slight reduction in AP lyase activities. The function of HU protein as an AP lyase was confirmed by the ability of hupA or hupB mutations to further reduce the viability of an E. coli dut(Ts) xth mutant, which generates lethal AP sites at 37 degrees C; the hupA and hupB derivatives, respectively, had a 6-fold and a 150-fold lower survival at 37 degrees C than did the parental strain. These data suggest, therefore, that HU protein plays a significant role in the repair of AP sites in E. coli.

Heat shock-induced excessive relaxation of DNA in Escherichia coli mutants lacking the histone-like protein HU

Plasmid DNA in exponentially growing Escherichia coli immediately relaxes after heat shock but the relaxed DNA re-supercoils rapidly, the despite continued presence of the heat shock conditions. We have now obtained genetic evidence indicating that the histone-like protein HU of E. coli is required for this re-supercoiling of DNA. Plasmid DNA in a hupA-hupB double gene-disruption mutant relaxed excessively after heat shock, while the relaxation of DNA in a himA-himD double gene-disruption mutant and in an hns insertion mutant was transient, thereby indicating that HU protein, but not IHF or H-NS proteins, is required for the re-supercoiling of DNA. Exposure of the hupA-hupB double mutant to a temperature of 50 degrees C led to both excessive relaxation of DNA and to a decrease in viable cell number but temperatures lower than 46 degrees C did not lead to these events. Based on these results, we propose that HU protein maintains the negative supercoiling of DNA during thermal stress and contributes to cellular thermotolerance in E. coli.

Isolation and characterization of spermidine nucleoids from Escherichia coli

Nucleoids isolated from Escherichia coli at low salt concentrations in the presence of spermidine (Kornberg et al., Proc. Natl. Acad. Sci. USA, 71, 3189-3193 (1974)) retain large amounts of protein and RNA and are, thus, potentially useful in structural and other studies. However, these preparations have neither been visualized nor extensively characterized with regard to their protein and other components. We have investigated this type of nucleoid preparation and here supply both light and electron microscope appearances and a description of the DNA-associated proteins. Light microscopy is used to follow the stages of nucleoid release and to demonstrate characteristically rounded nucleoids after chloramphenicol treatment of the cells from which the nucleoids were isolated. The nucleoids are "envelope-associated" particles. Electron microscopy shows an irregular central core that is partially covered with small, membranous vesicles. A significant fraction of the nucleoids have a characteristic doublet/dumbbell-shaped appearance by light microscopy. The nucleoids contain large amounts of protein and RNA in addition to DNA. The DNA and RNA are rendered acid-soluble by very low levels of nucleases, indicating an open structure. A small group of proteins, including H-NS, FIS, HU, and RNA polymerase, is released from the particles upon enzymatic digestion of the DNA.

Nucleoid proteins

This article examines the published evidence in support of the classification of organisms into three groups (Bacteria, Archae, and Eukarya) instead of two groups (prokaryotes and eukaryotes) and summarizes the comparative biochemistry of each of the known histone-like, nucleoid DNA-binding proteins. The molecular structures and amino acid sequences of Archae are more similar to those of Eukarya than of Bacteria, with a few exceptions. Cytochemical methodology employed for localizing these proteins in archaeal and bacterial cells has also been reviewed. It is becoming increasingly apparent that these proteins participate both in the organization of DNA and in the control of gene expression. Evidence obtained from biochemical properties, structural and functional differences, and the ultrastructural location of these proteins, as well as from gene mutations clearly justifies the division of prokaryotes into bacterial and archaeal groups. Indeed, chromosomes, whether they be nuclear, prokaryotic, or organellar, are invariably complexed with abundant, small, basic proteins that bind to DNA with low sequence specificity. These proteins include the histones, histone-like proteins, and nonhistone high mobility group (HMG) proteins.

Macromolecular crowding effects on the interaction of DNA with Escherichia coli DNA-binding proteins: a model for bacterial nucleoid stabilization

DNA-binding protein fractions from exponential and stationary phase cell extracts of E. coli were isolated by affinity chromatography on native DNA-cellulose. The ability of these fractions to convert DNA into a readily-sedimented form was compared in the absence or presence of added polymers. In the absence of polymers, large amounts of the proteins were required. In the presence of polyethylene glycol or polyvinylpyrrolidone, much smaller amounts of the DNA-binding proteins were required, indicating a macromolecular crowding effect from these polymers. The enhanced binding under crowded conditions appears to resolve a paradox between the cellular abundance of the DNA-binding proteins and the amounts required in earlier in vitro studies. The 'histone-like' protein HU from the DNA-binding protein fraction was preferentially incorporated into the pelleted DNA in the presence of polymers. Purified HU at roughly similar amounts caused a similar conversion of DNA to a readily-sedimentable ('condensed') form. Crowding-enhancement of DNA condensation by promoting the binding of proteins to the DNA provides a model for the stabilization of systems such as the bacterial nucleoid or kinetoplast DNA.

HU and functional analogs in eukaryotes promote Hin invertasome assembly

The prokaryotic protein HU functions as an accessory factor in many different biochemical reactions. We have characterized the role of HU in assembling the invertasome, an intermediate nucleoprotein complex involved in Hin-mediated site-specific recombination. Formation of this complex requires the looping of intervening DNA segments between sites bound by the Hin recombinase and the Fis protein. HU stimulates this process on substrates containing intervening segments of length < 100 bp. Characterization of the activity of HU in Hin-mediated recombination in vitro and in vivo yields evidence that its role in this reaction is primarily to facilitate the looping of the intervening DNA segment. By using this reaction as an assay, we identify proteins from mammals, yeast, trypanosomes, and wheat which can fulfill the same function in vitro. Using ligase-mediated circularization of short DNA fragments we also show that HU, the high mobility group (HMG) 1 and 2 proteins from mammals, and a protein from yeast can bend DNA extremely efficiently. These results support the view that this ubiquitous class of proteins enhance the assembly of nucleoprotein complexes under conditions of limited DNA flexibility.

Plastid DNA synthesis and nucleic acid-binding proteins in developing barley chloroplasts

Activation of plastid DNA synthesis occurred early in barley leaf chloroplast development. High rates of DNA synthesis were observed in the leaf basal meristem of dark-grown plants where plastid transcription activity was low. DNA synthesis activity decreased in later stages of chloroplast development. Plastid nuclei acid-binding proteins were detected after lithium dodecylsulfate (LDS)-polyacrylamide gel separation and renaturation. One set of nucleic acid-binding proteins was associated with plastid nucleoids. A second set of nucleic acid-binding proteins co-sedimented with ribosomes and most probably corresponds to ribosomal proteins. Changes in the composition of the nucleic acid-binding proteins were characterized as a function of chloroplast development in dark-grown and illuminated barley plants.

The potential of cryofixation and freeze substitution: observations and theoretical considerations

The theoretical and experimental evidence in favour of cryofixation and freeze-substitution are critically reviewed. The solubility of macromolecules in water is due to the hydration shells. Their behaviour at different temperatures and the consequences of their removal during the processing for embedding are explained. Gelation prior to the transfer into solvents prevents macromolecules aggregating. During substitution at low temperatures, DNA is gelled, justifying the use of the term cryofixation. It is proposed that the preservation of hydration shells at the lowest temperature, and their transformation into minute gaps after a rise of temperature, facilitates the exhibition of epitopes.

Promoters and autogenous control of the Escherichia coli hupA and hupB genes

Three start sites and a single start site for transcription of the hupB and hupA genes, respectively, have been identified in Escherichia coli. Preceding the RNA start sites are DNA sequences that conform to canonical promoter consensus sequences. The two most upstream promoters of the hupB gene function in vivo at comparable efficiency, while the third is not expressed significantly. Both hupB and hupA genes possess a DNA sequence with a rho-independent transcriptional terminator in their respective regions downstream from the coding regions. The hup genes are both transcribed in vivo into monocistronic mRNA molecules. Upon introduction of an HU-overproducing plasmid carrying either the hupB or the hupA gene into the wild-type and hup single deletion mutants, the intracellular levels of mRNA from the chromosomal hup genes are reduced. The HU-1 and HU-2 proteins both repress both hup genes, repression of the hupB gene being less efficient. The HU protein selectively represses mRNA synthesis starting at the hup promoters in the hupB promoter-CmR and hupA promoter-KmR fusion genes, but does not have a negative regulatory effect on mRNA synthesis from the true CmR and KmR promoters. These findings suggest that the signals for the actions of HU proteins are located in the DNA regions upstream from the sites near the 5' extremities of the coding regions of the hupB and hupA genes.

Characterization of HU-like protein from Bifidobacterium longum

A HU-like protein (HBl) of Bifidobacterium longum was purified and characterized. HBl is heat-stable and acid-resistant, and has a molecular weight of about 9.1 kDa as estimated by its mobility on electrophoresis. HBl is intermediate in basicity (pI 9.8) between the HU-1 and HU-2 proteins of Escherichia coli, and is dissociated from a calf thymus DNA-cellulose column at 300-400 mM NaCl. Its amino acid composition shows many similarities with that of E coli HU. The NH2-terminal amino acid sequence of HBl also shows significant similarities to the consensus sequence deduced from the sequences of eleven HU-like proteins from prokaryotic sources. Chemical crosslinking analysis indicated that the HBl protein predominantly forms a homotypic dimer.

Maintenance of plasmids in HU and IHF mutants of Escherichia coli

Complementation and sequencing analyses revealed that the hopD mutants, which could not support stable maintenance of mini-F plasmids (Niki et al. 1988), had mutations in the hupB gene, and that the hopD410 mutation was an ochre mutation at the 5th Gln position of HU-1. Maintenance and stability of various plasmids, mini-P1 plasmids, mini-F plasmids, and oriC plasmids, were studied in the hupA and hupB mutants (HU mutants), and himA and hip mutants (IHF mutants). Mini-P1 plasmids and mini-F plasmids could not be introduced into the delta hupA-delta hupB double deletion mutant. Replication of mini-F plasmids was partially inhibited in the hupB mutants, including the delta hupB and hopD(hupB) mutants, whereas replication of oriC plasmids was not significantly affected even in the delta hupA-delta hupB double deletion mutant. The mini-P1 plasmid was slightly unstable in the himA-hip mutant, whereas the mini-F plasmid was stable.

DNA replication in Escherichia coli mutants that lack protein HU

DNA replication in Escherichia coli cells lacking protein HU was studied. HU has been suggested to be involved in the initiation of replication from in vitro studies. The isolated HU mutants, however, are viable under normal growth conditions (M. Wada, Y. Kano, T. Ogawa, T. Okazaki, and F. Imamoto, J. Mol. Biol. 204:581-591, 1988). Chromosomal replication in the mutants appeared to be normal with respect to bidirectional replication from oriC and to its dependence on dnaA and some other dna gene products. No significant defect was observed in DNA synthesis in vitro with a crude enzyme fraction prepared from the mutant cells. These results, along with the earlier in vitro studies, suggest that other histonelike protein(s) may substitute for HU in the initiation of replication in the mutant cells. Minichromosomes were more unstable in the mutants. In the absence of either the mioC promoter, from which transcription enters oriC, or the DnaA box (DnaA protein-binding site) just upstream of the mioC promoter, the minichromosomes were especially unstable in the HU mutant and were integrated into the chromosomal oriC region under conditions selective for the plasmid-harboring cells.

Transcription mapping of the Escherichia coli chromosome by electron microscopy

The distinctive double Christmas tree morphology of rRNA operons as visualized by electron microscopy makes them easy to recognize in chromatin spreads from Escherichia coli. On the basis of the pattern of nascent transcripts on nearby transcription units and the relative distances of the operons from one another and the replication origin, we are now able to specifically identify five of the seven rRNA operons in E. coli. The use of rRNA operons as markers of both position and distance has resulted in the morphological mapping of a significant portion of the E. coli chromosome; over 600 kilobase pairs in the 84- to 90-min and 72-min regions can now be recognized. Since individual rRNA operons could be identified, direct comparisons could be made of their transcriptional activities. As judged by the densities of RNA polymerases along the operons, rrnA, rrnB, rrnC, rrnD, and rrnE were all transcribed at similar levels, with one RNA polymerase every 85 base pairs. The ability to recognize individual operons and specific regions of the chromosome allows direct comparisons of various genetic parameters.

The histone-like H protein of Escherichia coli is ribosomal protein S3

We report the purification of four proteins from Escherichia coli that stimulate or inhibit inter- and/or intramolecular recombination promoted by the yeast plasmid-encoded FLP protein. The proteins are identified as the ribosomal proteins S3 (27 kDa), L2 (26 kDa), S4 (24 kDa), and S5 (16 kDa), on the basis of N-terminal sequence analysis. The S3 protein is found to be identical to H protein, an E. coli histone-like protein that is related to histone H2A immunologically and by virtue of amino acid content. The H protein/S3 identity is based on co-migration on polyacrylamide gels, heat stability, amino acid analysis, and effects on FLP-promoted recombination. These results are relevant to current studies on the structure of the E. coli nucleoid. Since the H protein has previously been found associated with the E. coli nucleoid, the results indicate that either (a) some ribosomal proteins serve a dual function in E. coli, or, more likely, (b) ribosomal proteins can and are being mis-identified as nucleoid constituents.

Construction and characterization of the deletion mutant of hupA and hupB genes in Escherichia coli

Insertion and deletion mutations of the hupB and hupA genes, which encode the HU-1 and HU-2 proteins, respectively, of Escherichia coli, have been constructed in vitro and transferred to the hup loci on the bacterial chromosome. The mutations were constructed by inserting a gene encoding chloramphenicol resistance or kanamycin resistance into the coding region of the hupB or hupA gene, respectively. A complete deletion of the hupA gene was constructed by replacing the entire hupA coding region with the kanamycin resistance gene. Cells in which either the hupB or the hupA gene is defective grow normally, but cells in which both of the hup genes are defective exhibit phenotypes different from the wildtype strain. The hupA-hupB double mutants are cold-sensitive, although their growth rate is normal at 37 degrees C. Furthermore, the viability of the hupA-hupB double mutants is severely reduced when the cells are subjected to either cold shock or heat shock, indicating that the hup genes are essential for cell survival under some conditions of stress. The double mutants also exhibit filamentation when grown in the lower range of permissive growth temperature.

Intracellular location of the histonelike protein HU in Escherichia coli

Immunocytochemical labeling of thin sections of cryosubstituted, Lowicryl-embedded Escherichia coli cells with protein A-colloidal gold was used to study the structural organization of the bacterial nucleoid. We found that the histonelike protein HU was not associated with the bulk DNA in the nucleoid but was located in areas of the cell where metabolically active DNA is associated with ribosomes and where single-stranded DNA, RNA polymerase, and DNA topoisomerase I were also located. The resolution of the methods used did not allow us to decide whether HU was associated either with ribosomes or with transcriptionally active DNA, nor could we demonstrate interaction of HU with either.

Proteins from the prokaryotic nucleoid: primary and quaternary structure of the 15-kD Escherichia coli DNA binding protein H-NS

The primary sequence of H-NS (136 amino acid residues, Mr = 15,402), an abundant Escherichia coli DNA-binding protein, has been elucidated and its quaternary structure has been investigated by protein-protein cross-linking reactions. It was found that H-NS exists predominantly as a dimer, even at very low concentrations, but may form tetramers at higher concentrations and that the protein-protein interaction responsible for the dimerization is chiefly hydrophobic.

About the organisation of condensed and decondensed non-eukaryotic DNA and the concept of vegetative DNA (a critical review)

Experiments are reviewed that allow one to assign naturally occurring DNA-containing plasmas to either of two classes by virtue of their sensitivity to aggregation upon dehydration in organic solvents. The interphase nuclei of higher cells are relatively insensitive, while the DNA plasmas represented by bacterial nucleoids, vegetative bacteriophage and the chromosomes of dinoflagellates are sensitive. In higher cells the bulk of DNA is organised with histones in the form of nucleosomes. In prokaryotes and in the pool of vegetative phage DNA the most abundant histone-like protein HU is not associated with the bulk DNA, but localised in the border region with ribosomes where transcription and translation occur. These experimental results strongly suggest that the two classes of DNA plasmas are distinguishable by a low (1:10) or high (1:1) protein-to-DNA ratio. The hypothesis is formulated that the vegetative DNA (replicating and transcribing), throughout the living world, is nucleosome-free; during evolution, nucleosomes would have been introduced as a simple and adequate means for compacting the resting DNA. Condensation of DNA does not occur with prokaryotic nucleoids, but does take place when DNA is withdrawn from the vegetative phage pool to become packaged into phage heads. Dinoflagellate chromosomes are rather condensed although structurally different from eukaryotic chromosomes (e.g., those from Euglena) and are much more aggregation-sensitive.

Histonelike proteins of bacteria

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Cloning and sequencing of the HU-2 gene of Escherichia coli

The Escherichia coli HU-2 gene was cloned using a DNA fragment from the HU-1 gene as a probe. The amino acid sequence of the HU-2 protein deduced from the nucleotide sequence is in good agreement with the published sequence. The nucleotide sequence has a possible promoter and a typical ribosomal binding site upstream of the translation initiation codon (AUG) and a possible rho-independent terminater site downstream of the termination codon (UAA) of the gene.

DNA-binding properties and primary structure of HB protein from Bacillus globigii

The binding of Bacillus globigii HB protein to synthetic deoxyoligonucleotides of different length and sequence has been studied by polyacrylamide gel electrophoresis. Without detectable sequence specificity the protein binds to single-stranded and double-stranded DNA. Under the conditions employed, binding of HB protein to deoxyoligonucleotides with six or less nucleotides per strand cannot be detected while eight or more nucleotide units per strand of single-stranded DNA or base pairs of double-stranded DNA are sufficient for binding. The complete amino acid sequence of HB protein has been determined by manual Edman degradation of tryptic peptides. Like most DNA-binding proteins of its class, HB protein does not contain cysteine, tyrosine or tryptophan residues. The primary structure of HB protein shows 84% homology with the sequence of the related DNA-binding protein II from Bacillus stearothermophilus.

Molecular cloning and nucleotide sequence of the mutT mutator of Escherichia coli that causes A:T to C:G transversion

The Escherichia coli mutator gene mutT, which causes A:T----C:G transversion, was cloned in pBR 322. mutT+ plasmids carry a 0.9 kb PvuII DNA fragment derived from the E. coli chromosome. Specific labelling of plasmid-encoded proteins by the maxicell method revealed that mutT codes for a polypeptide of about 15,000 daltons. The protein was overproduced when the mutT gene was placed under the control of the lac regulatory region on a multicopy runaway plasmid. The nucleotide sequence of the mutT gene was determined by the dideoxy method.

A bacterial protein requirement for the bacteriophage lambda terminase reaction

The bacteriophage lambda terminase enzyme cleaves the cohesive-end sites of lambda DNA to yield the protruding 5'-termini of the mature molecule. In vitro, this endonucleolytic event requires a protein factor which has been isolated and purified from extracts of uninfected E. coli. The terminase host factor (THF) is a heat stable basic protein of M.W. approximately 22,000. The integration host factor (IHF) protein of E. coli can efficiently substitute for THF in the terminase reaction; however, THF can be demonstrated to be physically present in, and isolated with full biological activity from extracts of cells defective or deficient in IHF.

Genetic characterization of the gene hupB encoding the HU-1 protein of Escherichia coli

The gene hupB encoding the HU-1(HU beta) protein of Escherichia coli was mapped between proC at min 9 and minA at min 10 on the K-12 genome by plasmid integration and chromosome transfer studies. Genetic studies using plasmid rescue techniques demonstrated that the lon gene is located very close to the 5' end of hupB and that the two genes are both transcribed clockwise on the E. coli map [Bachmann, Microbiol. Rev. 47 (1983) 180-230].

Molecular cloning and nucleotide sequence of the HU-1 gene of Escherichia coli

The Escherichia coli HU-1 was cloned by use of mixed synthetic oligonucleotides (17-mer) predicted from a portion of its amino acid sequence. The amino acid sequence of the HU-1 protein deduced from the nucleotide sequence is in good agreement with the published sequence. The nucleotide sequence has a possible promoter and a typical ribosomal binding site upstream from the translational initiation codon (GUG) of the HU-1 gene.