A single DNA-binding protein from Pseudomonas aeruginosa homologous to proteins NS1 and NS2 (HU proteins) of Escherichia coli and other bacteria

The primary structure of the DNA-binding protein II from Clostridium pasteurianum

The complete amino acid sequence of the Clostridium pasteurianum DNA-binding protein II (DNAb-II) has been determined. The molecule contains 91 amino acid residues and has an Mr of 10 133. Sequence data were obtained from manual Edman degradation, using the DABITC/PITC double-coupling of the tryptic, peptic, chymotryptic and Staphylococcus protease peptides. A comparison of the amino acid sequence of the C. pasteurianum DNAb-II with those of the DNAb-II from Escherichia coli, Bacillus stearothermophilus, Thermoplasma acidophilum and Pseudomonas aeruginosa shows that the C. pasteurianum protein is more homologous to that of B. stearothermophilus (60%) than to that of E. coli (45%). All DNAb-II proteins have identical sequences Gly-Phe-Gly-X-Phe at positions 46-50 and Arg-Asn-Pro-X-Thr at positions 61-65.

The essential HupB and HupN proteins of Pseudomonas putida provide redundant and nonspecific DNA-bending functions

A protein mixture containing two major components able to catalyze a beta-recombination reaction requiring nonspecific DNA bending was obtained by fractionation of a Pseudomonas putida extract. N-terminal sequence analysis and genomic data base searches identified the major component as an analogue of HupB of Pseudomonas aeruginosa and Escherichia coli, encoding one HU protein variant. The minor component of the fraction, termed HupN, was divergent enough from HupB to predict a separate DNA-bending competence. The determinants of the two proteins were cloned and hyperexpressed, and the gene products were purified. Their activities were examined in vitro in beta-recombination assays and in vivo by complementation of the Hbsu function of Bacillus subtilis. HupB and HupN were equally efficient in all tests, suggesting that they are independent and functionally redundant DNA bending proteins. This was reflected in the maintenance of in vivo activity of the final sigma54 Ps promoter of the toluene degradation plasmid, TOL, which requires facilitated DNA bending, in DeltahupB or DeltahupN strains. However, hupB/hupN double mutants were not viable. It is suggested that the requirement for protein-facilitated DNA bending is met in P. putida by two independent proteins that ensure an adequate supply of an essential cellular activity.

Cloning and sequence analyses of the genes coding for the integration host factor (IHF) and HU proteins of Pseudomonas aeruginosa

Histone-like proteins, such as HU and the integration host factor (IHF), are small, dimeric, DNA-bending proteins which play a role in maintaining constrained DNA structures and hence in regulating gene expression. Two different strategies were used to isolate the genes coding for Pseudomonas aeruginosa (Pa) HU and IHF, two proteins that we have previously isolated from a mucoid strain. By use of a PCR-based technique with oligodeoxyribonucleotides (oligos) designed from the N-terminal amino acid (aa) sequences of HU and the beta-subunit of IHF, and Southern blot analyses, hupB and himD, encoding HU and IHF beta, respectively, have been cloned. The himA gene of Pa, encoding the alpha-subunit of IHF, was isolated using himA of Escherichia coli (Ec) as a probe in Southern blot analyses. The deduced hupB product (90 aa, 9 kDa) is 79% identical to HU beta and 61% to HU alpha of Ec. The predicted products of himA (100 aa, 11.5 kDa) and of himD (94 aa, 10.6 kDa) share 77 and 70% identity with IHF alpha and IHF beta of Ec, respectively. The promoter region of himD contains an IHF consensus sequence, as is the case for Ec himD.

AlgR, a response regulator controlling mucoidy in Pseudomonas aeruginosa, binds to the FUS sites of the algD promoter located unusually far upstream from the mRNA start site

Strong transcriptional activation of algD, a key event in the overproduction of alginate and establishment of mucoidy in Pseudomonas aeruginosa, depends on the functional algR gene. The predicted gene product of algR shows homologies to response regulators from bacterial signal transduction systems. The algR gene was overexpressed in Escherichia coli, its product (AlgR) was purified by utilizing its apparent affinity for heparin, and its sequence was verified by partial amino acid sequence analysis. AlgR was found to interact directly with the algD promoter. Deletion mapping analysis, in conjunction with mobility shift DNA-binding assays, indicated the presence of three regions within the algD promoter capable of specifically binding AlgR. A relatively weak interaction was observed with the algD promoter fragment containing the region immediately upstream of the algD mRNA start site (-144 to +11). However, when fragments spanning regions located very far upstream from the algD mRNA initiation site (-533 and -332) were used, strong specific binding was observed. These regions were separated by a DNA segment not binding AlgR and spanning positions -332 to -144. DNase I footprinting analysis further established the presence of discrete AlgR binding sites overlapping with FUS, the far-upstream sites required for full induction of algD transcription and its environmental modulation. There were two distinct binding sites: RB1, spanning nucleotides -479 to -457, and RB2, spanning nucleotides -400 to -380. Both of these sequences shared a highly conserved core region, ACCGTTCGTC. These results established a direct interaction of AlgR with the algD promoter and revealed an arrangement of binding sites highly unusual for response regulators of the AlgR type.

DNA dynamic flexibility and protein recognition: differential stimulation by bacterial histone-like protein HU

The abundant E. coli "histone-like" protein HU is shown to be a differential effector of DNA recognition by three diverse control proteins. DNA recognition by lac repressor and catabolite activator protein is greatly stimulated, while specific aroH DNA recognition by trp repressor is inhibited. BaCl2, an agent previously shown to promote DNA bending, mimics the HU effect to give the same qualitative differential stimulation spectrum. The HU activation involves cooperativity, further suggesting that the various DNA bends and distortions induced during assembly of higher order HU:DNA structures are important for the HU stimulation. Thus, E. coli chromosomal DNA regulation is likely strongly influenced by HU protein that may promote a variety of alternative DNA structures that either facilitate or inhibit specific recognition by diverse control proteins.

Isolation, characterization and microsequence analysis of a small basic methylated DNA-binding protein from the Archaebacterium, Sulfolobus solfataricus

DNA-binding proteins have been extracted from the thermoacidophilic archaebacterium Sulfolobus solfataricus strain P1, grown at 86 degrees C and pH 4.5. These proteins, which may have a histone-like function, were isolated and purified under standard, non-denaturing conditions, and can be grouped into three molecular mass classes of 7, 8 and 10 kDa. We have purified to homogenity the main 7 kDa protein and determined its DNA-binding affinity by filter binding assays and electron microscopy. The Stokes radius of gyration indicates that the protein occurs as a monomer. The complete amino-acid sequence of this protein contains 14 lysine residues out of 63 amino acids and the calculated Mr is 7149. Five of the lysine residues are partially monomethylated to varying extents and the methylated residues are located exclusively in the N-terminal (positions 4 and 6) and the C-terminal (positions 60, 62 and 63) regions only. The protein is strongly homologous to the 7 kDa proteins of Sulfolobus acidocaldarius with the highest homology to protein 7d. Accordingly, the name of this protein from S. solfataricus was assigned as DNA-binding protein Sso7d.

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.

Histonelike proteins of bacteria

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Primary structure of the hip gene of Escherichia coli and of its product, the beta subunit of integration host factor

We describe the isolation and sequencing of the hip gene of Escherichia coli and show that it encodes the beta subunit of integration host factor (IHF beta). In order to locate the coding region, we constructed a set of deletion mutants by exonucleolytic digestion of a fragment containing hip, determined which mutants were hip+ and which hip- by complementation, and then sequenced the ends of the critical deletions. The 5' end of the coding region was located precisely by comparing the deduced amino acid sequence to the actual N-terminal amino acid sequence of IHF. Our assignment of the coding region was further substantiated by the nucleotide sequences of a hip point mutant and of internal replacement mutations. We found a probable promoter for hip located about 85 base-pairs upstream from the initial AUG codon and about 75 base-pairs downstream from the 3' end of the neighboring gene, rpsA, and we constructed an IHF beta overproducer by fusing the coding sequences to the lambda pL promoter. A survey of known protein sequences revealed a close relationship between IHF beta and the type II prokaryotic DNA binding proteins (the "histone-like" proteins). This relationship is shared to a considerable extent by the other subunit of IHF, IHF alpha. A hip missense mutation that replaces a completely conserved glycine with aspartate has a null phenotype, suggesting that the conserved regions are functionally important.

Characterization and primary structures of DNA-binding HU-type proteins from Rhizobiaceae

The DNA-binding HU-type proteins from several species of Rhizobiaceae including Rhizobium meliloti, two strains of Rhizobium leguminosarum with highly different phenotypic characters and Agrobacterium tumefaciens, were characterized and their amino acid sequences were determined. HU-type proteins isolated from R. leguminosarum L18 and A. tumefaciens are identical and show slight differences with the R. meliloti HU-type protein. On the other hand the R. leguminosarum L53 HU-type protein is quite different from the proteins cited above; several amino acid substitutions encountered in this protein result in significant changes in the folding of the polypeptide chain. The biochemical characteristics of these proteins are in good agreement with the respective position of these bacteria in the phylogeny determined by numerical taxonomy.

Histones in protistan evolution

The potential of comparative studies on histones for use in protistan evolution is discussed, using algal histones as specific examples. A basic premise for the importance of histones in protistan evolution is the observation that these proteins are completely absent in prokaryotes (and cytoplasmic organelles), but with few exceptions, the same five major histone types are found in all higher plants and animals. Since the histone content of the algae and other protists is not constant, some of these organisms may represent transition forms between the prokaryotic and eukaryotic modes of packaging the genetic material. Comparative studies of protistan histones may thus be of help in determining evolutionary relationships. However, several problems are encounter with protistan histones, including difficulties in isolating nuclei, proteolytic degradation, anomalous gel migration of histones, and difficulties in histone identification. Because of the above problems, and the observed variability in protistan histones, it is suggested that several criteria be employed for histone identification in protists.

The amino acid sequence of a small DNA binding protein from the archaebacterium Sulfolobus solfataricus

The thermoacidophilic archaebacterium Sulfolobus solfataricus possesses several DNA binding proteins which may have a histone-like function. Two particularly dominant species have molecular masses of 7 and 10 kDa, respectively. We have purified one of the small proteins which occurs in relatively large amount and have determined its amino acid sequence. The protein is characterized by a high lysine content; in the N-terminal region the lysine residues occur in an alternating order: X-K-X-K-X-K-X-K. The amino acid sequence does not indicate any obvious homology to those DNA binding proteins whose sequences have been determined.

3-A resolution structure of a protein with histone-like properties in prokaryotes

The 3-A structure of DNA-binding protein II, which exhibits histone-like properties in bacteria, has been determined. The molecule is dimeric and appears to bind to the phosphate backbone of DNA through two symmetry-related arms. A mechanism by which the protein induces DNA supercoiling is proposed.

Comparative study of the DNA-binding HU-type proteins from slow growing and fast growing strains of Rhizobiaceae

The DNA-binding HU-type proteins have been isolated from two very different strains of Rhizobiaceae : Agrobacterium tumefaciens and Rhizobium japonicum. These proteins have been called HAt and HRj respectively. Their electrophoretic mobility on polyacrylamide gel, amino acid composition and crossed immunoreactivity have been compared to that of the homologous protein isolated from Rhizobium meliloti: the protein HRm . The proteins HAt and HRm show close similarities whereas the protein HRj differs markedly from the two others. The physico-chemical characteristics of the HU-type proteins from these Rhizobiaceae are in good agreement with the respective position of these bacteria in the taxonomy.

Interaction of the HB protein of Bacillus globigii with nucleic acids. Analysis of the binding to DNA and polynucleotides

Fluorescence of the phenylalanine residues of the HB protein of Baccillus globigii was found to be quenched upon binding to nucleic acids. Using this phenomenon, the binding properties were investigated on the basis of an approach published recently. The stoichiometric numbers were about 10 basepairs per bound protein molecule for double-stranded DNA and about 10 bases for single-stranded polynucleotides, independent of salt concentration. Cooperativity parameters were in the range of 50-250. Binding constants were about 5 X 10(6) M-1 (at 0.1 M NaCl) and decreased with increasing salt concentration. From the salt dependence it is inferred that about one Na+ ion is displaced upon binding of a protein molecule to DNA. Therefore the binding site should contain one positively charged amino acid residue. The protein was found to bind with comparable strength to double-stranded and single-stranded DNA as well as to poly(rA). Hence it is concluded that the HB protein does not belong to the category of 'melting proteins'.

Proteins from the prokaryotic nucleoid. High-resolution 1H NMR spectroscopic study of Escherichia coli DNA-binding proteins NS1 and NS2

The 1H-NMR spectra of the two Escherichia coli basic, low-Mr (approximately equal to 9000) DNA-binding proteins NS1 and NS2 and of their native complex NS were studied at 400 MHz and a number of resonances and resonance peaks were assigned. As in the case of some eukaryotic histones, the presence of a large number of high-field perturbed Phe resonances, several shielded and deshielded methyl resonances and backbone NH protons quite inaccessible to the solvent clearly indicate the existence of extensive tertiary and, even more so, quaternary structures involving hydrophobic interactions. These structures are lost upon heating, but readily reform upon cooling. Spectral differences between NS1, NS2 and NS and the greater thermal stability of NS indicate that molecules of the heterologous subunits (NS1 and NS2) aggregate (dimerize) preferentially in comparison to the self-aggregation of the homologous subunits. Unlike those of the eukaryotic histones, the tertiary and quaternary structures of NS are insensitive to extensive variations of the ionic strength.

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.