Novel histone H2A-like protein of escherichia coli

Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase

The genomic DNA of Escherichia coli occurs in compact bodies known as nucleoids. Organization and structure of nucleoids are poorly understood. Compact, characteristically shaped, nucleoids isolated by the polylysine-spermidine procedure were visualized by DNA fluorescence microscopy. Treatment with urea or trypsin converted compact nucleoids to partially expanded forms. The transition in urea solutions was accompanied by release of most DNA-associated proteins; the transition point between compact and partially expanded forms was not changed by the loss of the proteins nor was it changed in nucleoids isolated from cells after exposure to chloramphenicol or from cells in which Dps, Fis, or H-NS and StpA had been deleted. Partially expanded forms became dispersed upon RNase exposure, indicating a role of RNA in maintaining the partial expansion. Partially expanded forms that had been stripped of most DNA-associated proteins were recompacted by polyethylene glycol 8,000, a macromolecular crowding agent, in a cooperative transition. DNA-associated proteins are suggested to have relatively little effect on the phase-like behavior of the cellular nucleoid. Changes in the urea transition indicate that a previously described procedure for compaction of polylysine-spermidine nucleoids may have an artifactual basis, and raise questions about reports of repetitive local structures involving the DNA of lysed cells.

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.

Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli

The mukB gene codes for a 177 kDa protein, which might be a candidate for a force-generating enzyme in chromosome positioning in Escherichia coli. The mukB106 mutant produces normal-sized, anucleate cells and shows a temperature-sensitive colony formation. To identify proteins interacting with the MukB protein, we isolated three multicopy suppressors (msmA, msmB, and msmC) to the temperature-sensitive colony formation of the mukB106 mutation. The msmA gene, which could not suppress the production of anucleate cells, was found to be identical to the dksA gene. The msmB and msmC genes suppressed the production of anucleate cells as well as the temperature-sensitive colony formation. However, none of them could suppress both phenotypes in a mukB null mutation. DNA sequencing revealed that the msmB gene was identical to the cspC gene and that the msmC gene had not been described before. A homology search revealed that the amino acid sequences of both MsmB and MsmC possessed high similarity to proteins containing the cold-shock domain, such as CspA of E. coli and the Y-box binding proteins of eukaryotes; this suggests that MsmB and MsmC might be DNA-binding proteins that recognize the CCAAT sequence. Hence, the msmB and msmC genes were renamed cspC and cspE, respectively. Possible mechanisms for suppression of the mukB106 mutation are discussed.

Introduction of proteins into living bacterial cells: distribution of labeled HU protein in Escherichia coli

Growing bacterial cells forming division septa have sites near the septa that are sensitive to EDTA shock. Cells treated with EDTA incorporate proteins and other molecules from the surrounding medium, probably via vesiclelike lesions at the septa that are induced by EDTA. The amount of protein taken up is proportional to the protein concentration in the permeabilization medium. Incorporated molecules equilibrate throughout the cytoplasm, and those with affinity for DNA bind to the nucleoid. Conditions that promote the viability of permeabilized cells and help to avoid otherwise irreversible effects of EDTA are defined. Procedures for selecting cells that have incorporated protein and for studying the distribution of the protein and its effects in growing-dividing cells are described. The procedure may have several applications to molecular and cellular biology; however, we describe here the localization in living cells of the histonelike protein HU. Fluorescence microscopy of cells containing different amounts of fluorescein-labeled HU (varied from approximately 10(3) to 10(5) molecules per cell) showed that the HU concentrates in the nucleoid and is uniformly distributed throughout this structure. Control experiments demonstrated that unlabeled interior parts of the nucleoid can be resolved when labeled proteins that do not bind DNA or enter the nucleoid are introduced into living cells. It was concluded that in vivo added HU binds primarily DNA and that there are no intrinsic restrictions on major regions of the nucleoid to which the added HU protein may bind.

A procaryotic regulatory factor with a histone H1-like carboxy-terminal domain: clonal variation of repeats within algP, a gene involved in regulation of mucoidy in Pseudomonas aeruginosa

A novel procaryotic transcriptional regulatory element, AlgP, with a histone H1-like carboxy-terminal domain was identified in Pseudomonas aeruginosa. AlgP is required for transcription of the key biosynthetic gene algD, which is necessary for production of the exopolysaccharide alginate causing mucoidy in P. aeruginosa. Mucoidy is a critical virulence determinant of P. aeruginosa invariably associated with the respiratory infections causing high mortality in cystic fibrosis. Here we show that AlgP and histones H1 both have repeated units of the Lys-Pro-Ala-Ala motif (KPAA) and its variations within their long (over 100 amino acids) carboxy-terminal domains. This region of histone H1 tails has been shown to bind to the linker DNA in eucaryotic chromatin fibers. A synthetic 50-mer peptide consisting of repeats from the AlgP carboxy-terminal domain was found to bind DNA in a mobility shift DNA-binding assay. AlgP is encoded by a gene that contains multiple direct repeats organized as tandem, head-to-tail, 12-base-pair (bp) units overlapping with six highly conserved 75-bp units. The repetitive structure of the algP gene appears to participate in the processes underlying the metastable character of mucoidy in P. aeruginosa. Relatively large DNA rearrangements spanning the region with tandem direct repeats encoding the carboxy-terminal histone H1-like structure of AlgP were detected in several strains upon conversion from the mucoid to the nonmucoid phenotype. The frequency of the detectable algP rearrangements associated with the transition into the nonmucoid state varied from strain to strain and ranged from 0 to 50%. The nonmucoid derivatives with the clearly rearranged chromosomal copy of algP were complemented to mucoidy with plasmids containing algP from P. aeruginosa PAO. When a random collection of mucoid strains, isolated from different cystic fibrosis patients, was analyzed by using polymerase chain reaction, an additional level of strain-dependent sequence variation in algP was observed. Variations in the number of the 12-bp repeats were found; however, they did not appear to influence the mucoid status of the strains examined. Thus, the repeated region of algP appears to be a hot spot for DNA rearrangements and strain-dependent variability.

Identification and sequence of the drpA gene from Escherichia coli

The drpA gene of Escherichia coli encodes a factor that is involved in global RNA synthesis. We establish that the drpA gene has been successfully cloned and describe the fine-structure map of three drpA-(Ts) mutations as well as the complete nucleotide sequence of the drpA gene. We identified a major sigma-70 promoter for the drpA gene on the bases of (i) its similarity to the consensus sequence and (ii) S1 protection and primer extension mapping data. In addition, the nucleotide sequence revealed a pair of dnaA boxes and a factor-independent terminator at the 5' end and 3' end of the gene, respectively. The deduced amino acid sequence of the DrpA protein showed a nucleotide-binding pocket found in some ATPases.

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.

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.

Developmental-form-specific DNA-binding proteins in Chlamydia spp

We identified DNA-binding proteins specific to the elementary body (EB) developmental form of Chlamydia spp. Chlamydial proteins from whole lysates were separated by polyacrylamide gel electrophoresis, transferred to nitrocellulose, and probed with nick-translated chlamydial DNA. By this method, C. trachomatis serovar L2 EBs had three unique protein bands of 58,000, 25,700, and 17,000 molecular weight not seen in the reticulate bodies. The 17,000-molecular-weight protein and the 25,700-molecular-weight protein were identified in an acid-soluble protein fraction and were resistant to high-salt elution, similar to other procaryotic nucleoproteins. The 17,000-molecular-weight protein was also detected in preparations with isolated chromosomes from EBs. Preliminary characterization indicated that the protein-DNA interaction was principally charge related.

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.

Terminase host factor: a histone-like E. coli protein which can bind to the cos region of bacteriophage lambda DNA

Terminase Host Factor (THF), an E. coli protein capable of fulfilling the host factor requirement for in vitro bacteriophage lambda terminase activity, displays properties characteristic of the prokaryotic type II DNA-binding or "histone-like" proteins. It is a 22 K basic, heat- and acid-stable protein which binds non-specifically to various DNAs. Conditions can be established, however, where THF binds preferentially to the cohesive end site (cos) of lambda DNA forming several distinct complexes as visualized by band retardation in polyacrylamide gels. DNase I footprinting reveals that THF can protect several regions of the top strand on the right side (+) of cos but does not bind as well to the left side (-). The binding regions are separated either by unprotected or by DNase I- hypersensitive bases. Under the conditions used in these experiments, DNA which does not contain cos lambda sequences does not show this pattern of protection. Several repeated motifs in the cos lambda nucleotide sequence may represent a consensus sequence for THF interaction. THF may be similar to other "histone-like" proteins which display both non-specific and selective DNA-binding capacities.

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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Purification of the FLP site-specific recombinase by affinity chromatography and re-examination of basic properties of the system

The FLP protein, a site-specific recombinase encoded by the 2 micron plasmid of yeast, has been purified to near homogeneity from extracts of E. coli cells in which the protein has been expressed. The purification is a three column procedure, the final step employing affinity chromatography. The affinity ligand consists of a DNA polymer with multiple FLP protein binding sites arranged in tandem repeats. This protocol yields 2 mg of FLP protein which is 85% pure. The purified protein is highly active, stable for several months at -70 degrees C and free of detectable nucleases. The molecular weight and N-terminal sequence are identical to that predicted for the FLP protein by the DNA sequence of the gene. Purified FLP protein primarily, but not exclusively, promotes intramolecular recombination. Intermolecular recombination becomes the dominant reaction when E. coli extracts containing no FLP protein are added to the reaction mixture. These extracts are not specifically required for recombination, but demonstrate that some properties previously attributed to FLP protein can be assigned to contaminating proteins present in E. coli.

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.

Nucleotide sequence of a type II DNA topoisomerase gene. Bacteriophage T4 gene 39

T4 DNA topoisomerase is a type II enzyme and is thought to be required for normal T4 DNA replication T4 gene 39 codes for the largest of the three subunits of T4 DNA topoisomerase. I have determined the nucleotide sequence of a region of 2568 nucleotides of T4 DNA which includes gene 39. The location of the gene was established by the identification of the first fifteen amino acids in the large open reading frame in the DNA sequence as those found at the amino-terminus of the purified 39-protein. The coding region of gene 39 has 1560 bases, and it is followed by two in-frame stop codons. The gene is preceded by a typical Shine-Dalgarno sequence as well as possible promoter sequences for E. coli RNA polymerase. T4 39-protein consists of 520 amino acids, and it has a calculated molecular weight of 58,478. By comparing the amino acid sequences, T4 39-protein is found to share homology with the gyrB subunit of DNA gyrase. This suggests that these topoisomerase subunits may be equivalent functionally. Some of the characteristics of the 39-protein and its structural features predicted from the DNA sequence data are discussed.

The FI gene product of bacterial virus Lambda is related to the E. coli chromosomal protein NS2 and is involved in intracellular DNA organization

A likely function of the Lambda FI gene product (gpFI) is condensation of developmental forms of the bacteriophage DNA in the host cell. Several characteristics of gpFI support this hypothesis: it is similar in its structure and properties to E. coli NS proteins whose involvement in the bacterial DNA condensation has been established and it comigrates with DNA during fractionation of host cell lysate through a sucrose gradient.

Histones and their modifications

Histones constitute the protein core around which DNA is coiled to form the basic structural unit of the chromosome known as the nucleosome. Because of the large amount of new histone needed during chromosome replication, the synthesis of histone and DNA is regulated in a complex manner. During RNA transcription and DNA replication, the basic nucleosomal structure as well as interactions between nucleosomes must be greatly altered to allow access to the appropriate enzymes and factors. The presence of extensive and varied post-translational modifications to the otherwise highly conserved histone primary sequences provides obvious opportunities for such structural alterations, but despite concentrated and sustained effort, causal connections between histone modifications and nucleosomal functions are not yet elucidated.

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.

Membrane particles from Escherichia coli and Bacillus subtilis, containing penicillin-binding proteins and enriched for chromosomal-origin DNA

Rapid-sedimenting DNA-membrane complexes were obtained from both Bacillus subtilis and Escherichia coli by a method involving gentle lysis followed by restriction enzyme digestion and sucrose gradient fractionation. These complexes were substantially enriched in chromosomal origin DNA, and in B. subtilis, the complexes were enriched in penicillin-binding proteins relative to that of the total membrane. Such complexes may represent procaryotic membrane domains which are topographically and functionally distinct.

Nucleotide sequence binding specificity of the LexA repressor of Escherichia coli K-12

The specificity of LexA protein binding was investigated by quantifying the repressibility of several mutant recA and lexA operator-promoter regions fused to the Escherichia coli galactokinase (galK) gene. The results of this analysis indicate that two sets of four nucleotides, one set at each end of the operator (terminal-nucleotide contacts), are most critical for repressor binding. In addition, our results suggest that the repressor-operator interaction is symmetric in nature, in that mutations at symmetrically equivalent positions in the recA operator have comparable effects on repressibility. The symmetry of this interaction justified reevaluation of the consensus sequence by half-site comparison, which yielded the half-site consensus (5')CTGTATAT. Although the first four positions of this sequence were most important, the last four were well conserved among binding sites and appeared to modulate repressor affinity. The role of the terminal-nucleotide contacts and the mechanism by which the internal sequences affected repressor binding are discussed.

Quantitation with monoclonal antibodies of Escherichia coli H protein suggests histone function

The abundance of the histonelike H protein of Escherichia coli (U. Hübscher, H. Lutz, and A. Kornberg, Proc. Natl. Acad. Sci. U.S.A. 77:5097-5101, 1980) was determined by using monoclonal antibodies against H protein, immunoblotting, and homogeneous H protein as a standard. H protein was found to be present at approximately 120,000 monomeric molecules per fast-growing E. coli cell. This amount of H protein corresponds to a ratio of one H protein molecule to approximately 200 base pairs of the bacterial chromosome. Together with previous results, these findings suggest that H protein has histonelike function similar to that of histone protein H2A, its counterpart in the eucaryotic cell.

Characterization of a mitochondrial protein binding to single-stranded DNA

A DNA-binding protein from Xenopus laevis oocyte mitochondria which has been found associated with the D-loop also shows a strong preference for single-stranded DNA. The binding to polynucleotides is dependent on the base composition, but no sequence specificity was found. This protein, called mtSSB, binds tightly and cooperatively to single-stranded DNA. By its amino-acid composition and its binding properties it appears to be similar to the single-stranded DNA-binding proteins found in prokaryotes.

Herpes simplex virus cloned DNA fragments induce coumermycin A1 resistance in Escherichia coli

We have taken a new approach to identify and fine map previously undescribed herpes simplex virus (HSV) functions. In experiments described in this report the antibiotic coumermycin A1 was used to select two HSV type 1 BamHI fragments cloned in pBR322 that confer partial resistance to drug-susceptible Escherichia coli. The genes encoding these HSV functions have been designated cour-1 and cour-2 and have been fine mapped to the HSV sequences. HSV-cour1 is located at the left end of BamHI-F near HSV type 1 genomic map coordinate 0.645. cour-2 maps to BamHI-M', which is a 159-base-pair internal component of the alpha ICP4-coding sequence located in the reiterated sequences of the S component. In pBR322 both inserts apparently rely on the tet promoter for expression. Additionally, cour-2 functions when present as a BamHI insert in pUC7. The analysis of cour-2 "maxi" cell proteins reveals the presence of proteins produced by the fusion of HSV-1 BamHI-M' sequences and the sequences of the vector genes, i.e., the major tet product for pBR322 and the modified beta-galactosidase for pUC7. These data suggest that the development of bacterial assays for fusion products of eucaryotic DNA open reading frames in plasmid vectors may be a useful technique for initiating gene function studies.

Isolation and characterization of nucleoid proteins from Escherichia coli

Of the molecular species of proteins associated with the nucleoids of Escherichia coli cells, those with relatively high affinity to bind to DNA were isolated and characterized. Seven classes of nucleoid proteins with molecular weights of 9,000, 17,000 (two molecular species), 22,000, 24,000, 27,000 and 28,000 were isolated at more than 90% purity or were partially purified. On the basis of its amino acid composition and other chemical properties, the 9,000 dalton protein was identified as HLP II (or HU protein or BH2) (Pettijohn 1982; Rouvière-Yaniv and Gros 1975; Varshavsky et al. 1978). The 17 K protein consisted of two molecular species and one of these, 17 K (a) protein, seemed to be identical with HLPI (or protein 1 or BH1) reported previously (Pettijohn 1982; Varshavsky et al. 1977; Varshavsky et al. 1978). The 26 K protein was identical to the 22 K protein (Kishi et al. 1982). The 27 K protein showed immunological cross-reactivity with the antibody for histone H2A and was thus identified as the H protein reported previously (Hübscher et al. 1980). Two basic proteins, 9 K and 17 K(a), showed relatively high binding affinities to DNA, while the 28 K protein showed moderate binding affinity. The biological significance of these nucleoid proteins, which constitute a family of proteins participating in formation of the nucleoid structure, is discussed.

H1a, an E. coli DNA-binding protein which accumulates in stationary phase, strongly compacts DNA in vitro

We characterize a component of the E. coli bacterial nucleoid H1a, which accumulates in stationary phase. This protein, identical with the major component of a plasmid-protein complex previously isolated in our laboratory, has a pI close to 7.5. Acrylamide gel electrophoresis and sedimentation in sucrose gradient have shown that the protein H1a induces significant compaction into DNA. This compaction is equivalent to that observed in nucleosome core although it introduces only a slight change in linking number. In addition, the structural change induced in the lactose L8UV5 promoter by H1a results in the decrease in the kinetic of formation of the open complex with RNA polymerase.

Effect of mutation, electric membrane potential, and metabolic inhibitors on the accessibility of nucleic acids to ethidium bromide in Escherichia coli cells

The uptake of ethidium bromide by Escherichia coli K 12 cells has been studied by using 14C-labeled ethidium and spectrofluorometry on three E. coli strains: the first one (AB1157) has an ethidium-resistant phenotype; the second one derives from the first one after a single mutation (at 10 min on the E. coli genetic map) and has an ethidium-sensitive (Ebs) phenotype; the third one is the acrA strain which appeared to have the same phenotype as the Ebs strain. When the cells are in exponential growth, no ethidium enters wild-type cells, and a very limited amount of ethidium enters Ebs and acrA cells. Massive quantities of ethidium enter AB1157, Ebs, and acrA cells treated by uncouplers and respiring Ebs cells treated by the membrane ATPase-inhibitor dicyclohexylcarbodiimide. A small amount of ethidium enters cells treated in M9 succinate medium by metabolic inhibitors such as KCN or cells starved with oxygen in the same M9 medium. The amount of ethidium and ethidium dimer retained at equilibrium by either type of cell, and by cells infected by T5 phage, as well as the kinetics of influx and efflux, has been measured under a variety of situations (membrane energized or not, and/or membrane ATPase inhibited or not). Furthermore, it was shown that ethidium binds to both RNA and DNA when it enters CCCP-treated wild-type E. coli cells, whereas it binds mainly to DNA when it enters Ebs and acrA cells in exponential growth. As it will be discussed, it is difficult to account for the EthBr uptake by invoking only membrane functions and active transport. Therefore, it is proposed that the variations of the nucleic acid accessibility in E. coli cells might play a role in the control of this uptake. Accordingly, in ethidium-sensitive cells, the mutation would have caused a significant part of the chromosomal DNA (10-20%) to become accessible to ethidium. Hansen [Hansen M. T. (1982) Mutat. Res. 106, 209-216], after a study of the photobinding of psoralen to nucleic acids in the acrA mutant, also suggested that DNA environment was modified in acrA cells.

Regulation of polyamine biosynthesis in Escherichia coli by basic proteins

In Escherichia coli, the biosynthetic ornithine and arginine decarboxylases (EC 4.1.1.17 and 4.1.1.19, respectively) are responsible for the biosynthesis of polyamines from ornithine and arginine, respectively. When E. coli cells are grown in the presence of increasing amounts of polyamines, a progressive increase in the amount of antizyme 1 and antizyme 2 occurs. The amino acid compositions of antizymes 1 and 2 show them to be basic proteins; antizyme 1 has an amino acid composition similar to that of the E. coli histone-like protein HU and of the eukaryotic histone H2B; antizyme 2 is characterized by an unusually high arginine content. We find these proteins to be specific inhibitors of both the biosynthetic ornithine decarboxylase and the biosynthetic arginine decarboxylase. They do not inhibit the corresponding biodegradative ornithine and arginine decarboxylases, nor do they inhibit lysine decarboxylase or S-adenosylmethionine decarboxylase. These properties of the antizymes favor their function in the regulation of polyamine biosynthesis in E. coli. The ability of the purified antizymes to inhibit the ornithine and arginine decarboxylases is stabilized in acidic buffers and is lost upon prolonged exposure to solutions at neutral or basic pH.

DNA-binding proteins of Haemophilus influenzae: purification and characterization of a major intracellular binding protein

A heat- and acid-stable protein which bound both native and denatured DNA but not RNA was extensively purified from extracts of Haemophilus influenzae Rd strain com-58-A. The active species had an apparent subunit molecular weight of 15,000. The interaction of the protein with denatured DNA appeared to be cooperative, as judged by the sigmoid shapes of binding curves. This cooperativity increased with increasing ionic strength and was more pronounced with sodium ions than with potassium ions. Gel filtration suggested that the native protein formed aggregates in solution. The presence of the binding protein protected single-stranded DNA from the action of S1 endonuclease; approximately 30 nucleotide residues were protected per subunit equivalent of protein. The number of subunit equivalents per cell of this protein has been estimated at 10,000. The protein, which we designate DNA-binding protein II, is most probably a major histone-line protein of H. influenzae.

Primary structure of the DNA-binding protein HRm from Rhizobium meliloti

The amino acid sequence of protein HRm, a DNA-binding HU-type protein of 90 residues (Mr 9303), isolated from Rhizobium meliloti, has been established from automated sequence analysis of the protein and from structural data provided by peptides derived from cleavage of the protein at arginine and aspartic acid residues. The comparison of the primary structure of protein HRm with that of other HU-type proteins shows that two short sequences, of 7 and 6 residues respectively, located in the median part of the molecule, appear highly conserved and may be important in the function of the protein.

Host cell metabolic energy is not required for injection of bacteriophage T5 DNA

The addition of various metabolic inhibitors (uncouplers, cyanide, arsenate, ionophores) separately or together (for example, arsenate and an uncoupler) or even harsher methods of energy depletion did not prevent bacteriophage T5 from injecting its first-step-transfer DNA (a DNA segment 3 micron long) into the cytoplasm of host cells. The same indifference to metabolic energy was observed if first-step-transfer DNA was decapsidated and uncoiled before injection, thus precluding any energetic help from the phage capsid or from some tension stored in DNA tightly packed in the head. Penetration of the second-step-transfer DNA across the cytoplasmic membrane was studied by determining injection of superinfecting T5 A2- amber phages into Sup- bacteria containing proteins A1 and A2 previously encoded by the first-step-transfer DNA of a primary wild-type phage. The addition of various metabolic inhibitors after synthesis of proteins A1 and A2 but before superinfection did not prevent this penetration of second-step-transfer DNA. Thus, we conclude that traversal of the cytoplasmic membrane by the entire T5 DNA (a molecule 34 micron long) must occur by diffusion through protein channels.

Visualization of a Spinach Plastid Transcriptionally Active DNA-Protein Complex in a Highly Condensed Structure

A transcriptionally active DNA-protein complex isolated from spinach Spinacia oleracea plastids is visualized by electron microscopy in different conditions. This structure, after glutaraldehyde fixation, is highly condensed. DNA is supertwisted with proteins bound to it producing a beaded substructure. When glutaraldehyde fixation is omitted this structure is less condensed and DNA fibrils come out from a proteinous central body. The DNA-protein complex can be separated into two populations by CsCl centrifugation: one with a buoyant density of 1.570 grams per cubic centimeter and the other of 1.610 grams per cubic centimeter. By visualization of these two populations, it is concluded that proteins are either firmly bound to DNA in the central body, or more loosely bound to the DNA fibrils. These latter proteins could play a role in enzymic functions and/or in the supercoiling of DNA.The DNA from the DNA-protein complex possesses all fragments that belong to pure circular chloroplast DNA hydrolyzed by two restriction enzymes: Bam HI and Eco RI. Some molecules observed in a supercondensed form with a beaded substructure probably contain entire chloroplast DNA molecules.A hydrolysis test with microccocal nuclease gives no indication of the presence of ;nucleosome-like' structures. Thirty-six polypeptides with molecular weights ranging from 12,000 to 180,000 are present in the complex, and seven of them are highly soluble in 0.4 n H(2)SO(4); their molecular weights range from 14,000 to 46,000 as shown by two-dimensional gel electrophoresis.No linolenic acid can be detected in the preparation, indicating the absence of chloroplast membranes.

[Structural arrangement of chromatin (author's transl)]

Recent observations and hypotheses on the structure of chromatin are reviewed. Elementary "subunit" for higher structural orders is the nucleosome, consisting of a histone octamer and doublehelical DNA wrapped around it. During the last years details of the nucleosomal structure could be deduced down to a resolution of 2 nm. In the chromatin fiber, built up by (mono-)nucleosomes, the superhelical DNA has a tertiary structure, from which structures of still higher order (quaternary structure of DNA) can be formed. The correlation of these structures to the terms euchromatin and heterochromatin are discussed. Finally, some functional aspects, especially transcription and replication, are discussed in view of the new knowledge of chromatin structure.

Recognition of base sequences by regulatory proteins in procaryotes and eucaryotes

A model is described whereby (i) regulatory proteins recognize one face of the DNA double helix on non-adjacent DNA regions brought close together in space through folding around nucleosomes, (ii) regulatory sequences may occur inside gene structures, and (iii) the recognition of regulatory sequences might be modulated by short (4-6 base-pairs) insertions or deletions in introns or upstream from the transcription start site. This model might apply not only to eucaryotes but also to procaryotic organisms whose DNA is organized through interactions with histone-like proteins. Consequences of the model regarding the binding of regulatory proteins in procaryotes are suggested.