Skip to main content

Proteins from the Prokaryotic Nucleoid. Structural and Functional Characterization of the Escherichia coli DNA-Binding Proteins NS (HU) and H-NS

  • Conference paper
Bacterial Chromatin

Abstract

In spite of the commonplace notion that prokaryotes do not contain histones and that their DNA is not organized in chromatin, evidence is accumulating that bacterial DNA is indeed organized in nucleosomelike structures by histonelike proteins. Since the problem of the physical packaging and confinement of the genetic material can be regarded as a fundamental problem in all biological systems and in light of the underlying architectural unity of all living cells, it appears unlikely that completely different strategies have evolved to meet the same basic need. If the general strategies are the same, or at least, very similar, then it is possible that the differences existing between the pro- and eukaryotic systems may merely reflect differences in the tactics that each system must have perfected in order to harmonize its DNA-packaging mechanism with its specific physiological requirements.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Bakayev W (1981) Structure of the chromosomal deoxyribonucleoproteins XL Organization of deoxyribonucleoprotein complex in the bacterial cell. Mol Biol (Engl transi) 15:1045–1056

    Google Scholar 

  • Berthold V, Gelder K (1976) Interaction of DNA with DNA-binding proteins. The characterization of protein HD from Escherichia coli and its nucleic acid complexes. Eur J Biochem 71:443–449

    Article  PubMed  CAS  Google Scholar 

  • Craig NL, Nash HA (1984) E. coli integration host factor binds to specific sites in DNA. Cell 39: 707–716

    Article  PubMed  CAS  Google Scholar 

  • Cukier-Kahn R, Jacquet M, Gros F (1972) Two heat resistant, low molecular weight proteins from Escherichia coli that stimulate DNA-directed RNA synthesis. Proc Natl Acad Sci USA 69: 3643–3647

    Article  PubMed  CAS  Google Scholar 

  • Dijk J, White SW, Wilson KS, Appelt K (1983) On the DNA binding protein II from Bacillus stearothemophilus. J Biol Chem 258:4003–4006

    PubMed  CAS  Google Scholar 

  • Dixon NE, Kornberg A (1984) Protein HU in the enzymatic replication of the chromosomal origin of Escherichia coli. Proc Natl Acad Sci USA 81:424–428

    Article  PubMed  CAS  Google Scholar 

  • Ehbrecht HJ, Pingoud A, Urbanke C, Maass G, Gualerzi C (1985) Linear diffusion of restriction endonucleases on DNA. J Biol Chem 260:6160–6166

    PubMed  CAS  Google Scholar 

  • Flamm EL, Weisberg RA (1985) Primary structure of the hip gene of Escherichia coli and of its product, the β subunit of integration host factor. J Mol Biol 183:117–128

    Article  PubMed  CAS  Google Scholar 

  • Geider K, Hoffmann-Berling H (1981) Proteins controlling the helical structure of DNA. Annu Rev Biochem 50:233–260

    Article  PubMed  CAS  Google Scholar 

  • Geyl D, Böck A, Isono K (1981) An improved method for two-dimensional gel electrophoresis: analysis of mutationally altered ribosomal proteins of Escherichia coli. Mol Gen Genet 181: 309–312

    Article  PubMed  CAS  Google Scholar 

  • Glikin GC, Ruberti I, Worcel A (1984) Chromatin assembly in Xenopus oocytes: in vitro studies. Cell 37:33–41

    Article  PubMed  CAS  Google Scholar 

  • Greene JR, Brennan SM, Andrew DJ, Thompson CC, Richards SH, Heinrikson RL, Geiduschek EP (1984) Sequence of the bacteriophage SP01 gene coding for transcription factor 1, a viral homologue of the bacterial type II DNA-binding proteins. Proc Natl Acad Sci USA 81:7031–7035

    Article  PubMed  CAS  Google Scholar 

  • Griffith JD (1976) Visualization of prokaryotic DNA in a regularly condensed chromatin-like fiber. Proc Natl Acad Sci USa 73:563–567

    Article  PubMed  CAS  Google Scholar 

  • Gualerzi C, Pon CL (1979) Radioactive chemical labeling of ribosomal proteins and translational factors in vitro. Methods Enzymol 59:782–795

    Article  PubMed  CAS  Google Scholar 

  • Haselkorn R, Rouviere-Yaniv J (1976) Cynaobacterial DNA-binding protein related to Escherichia coli HU. Proc Natl Acad Sci USA 73:1917–1920

    Article  PubMed  CAS  Google Scholar 

  • Holck A, Kleppe K (1985) Affinity of protein HU for different nucleic acids. FEBS Lett 185: 121–124

    Article  PubMed  CAS  Google Scholar 

  • Hübscher U, Lutz H, Kornberg A (1980) Novel histone H2A-like protein of Escherichia coli. Proc Natl Acad Sci USA 77:5097–5101

    Article  PubMed  Google Scholar 

  • Isenberg I (1979) Histones. Annu Rev Biochem 48:159–191

    Article  CAS  Google Scholar 

  • Kavenoff R, Bowen BC (1976) Electron microscopy of membrane-free folded chromosomes from Escherichia coli. Chromosoma (Berl) 59:89–101

    Article  CAS  Google Scholar 

  • Kimura M, Wilson KS (1983) On the DNA binding protein II from Bacillus stearothermophilus II. The amino acid sequence and its relation to those of homologous proteins from other prokaryotes. J Biol Chem 258:4007–4011

    PubMed  CAS  Google Scholar 

  • Kishi F, Ebina Y, Miki T, Nakazawa T, Nakazawa A (1982) Purification and characterization of a protein from Escherichia coli which forms complexes with superhelical and single stranded-DNAs. J Biochem (Tokyo) 92:1059–1068

    CAS  Google Scholar 

  • Kleppe K. Lossius I, Aasland R, Sjastad K, Holk A, Haarr L (1984) The structure of the bacterial nucleoid. In: Hübscher U, Spadari S (eds) Proteins involved in DNA replication. Plenum, New York, pp 457–466

    Google Scholar 

  • Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132

    Article  PubMed  CAS  Google Scholar 

  • Laine B, Kmiecik D, Sautiere P, Biserte G, Cohen-Solal M (1980) Complete amino-acid sequences of DNA-binding proteins HU-1 and HU-2 from Escherichia coli. Eur J Biochem 103:447–461

    Article  PubMed  CAS  Google Scholar 

  • Laine B, Sautiere P, Spassky A, Rimsky S (1984) A DNA-binding protein from E. coli. Isolation, characterization and its relationship with proteins H1 and B1. Biochem Biophys Res Commun 119:1147–1153

    Article  PubMed  CAS  Google Scholar 

  • Lammi M, Paci M, Gualerzi CO (1984a) Proteins from the prokaryotic nucleoid. The interaction between protein NS and DNA involves the oligomeric form of the protein and at least one Arg residue. FEBS Lett 170:99–104

    Article  CAS  Google Scholar 

  • Lammi M, Paci M, Pon CL, Losso MA, Miano A, Pawlik RT, Gianfranceschi GL, Gualerzi CO (1984b) Proteins from the prokaryotic nucleoid. Biochemical and 1H NMR studies on three bacterial histone-like proteins. In: Hübscher U, Spadari S (eds) Proteins involved in DNA replication. Plenum, New York, pp 467–477

    Google Scholar 

  • Lathe R, Buc H, Lecocq JP, Bautz EK (1980) Prokaryotic histone-like protein interacting with RNA Polymerase. Proc Natl Acad Sci USA 77:3548–3552

    Article  PubMed  CAS  Google Scholar 

  • Losso MA, Miano A, Gianfranceschi GL, Gualerzi CO (1982) Proteins from the prokaryotic nucleoid II. Inhibition of DNA transcription by NS1 and NS2 (HU proteins). Biochem Int 5: 423–427

    CAS  Google Scholar 

  • Losso MA, Pawlik RT, Canonaco MA, Gualerzi CO (1986) Proteins from the prokaryotic nucleoid. A protein-protein crosslinking study on the quaternary structure of Escherichia coli DNA-binding proteins NS (HU). Eur J Biochem 155:27–32

    Article  PubMed  CAS  Google Scholar 

  • Luchnik AN, Bakayev W, Zbarsky IB, Georgiev GP (1982) Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin. EMBO J 1:1353–1358

    PubMed  CAS  Google Scholar 

  • McGhee JD, Felsenfeld G (1980) Nucleosome structure. Annu Rev Biochem 49:1115–1156

    Article  PubMed  CAS  Google Scholar 

  • Mende L, Timm B, Subramanian AR (1978) Primary structures of two homologous ribosome-associated DNA-binding proteins of Escherichia coli. FEBS Lett 96:395–398

    Article  PubMed  CAS  Google Scholar 

  • Menzel R, Geliert M (1983) Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell 34:105–113

    Article  PubMed  CAS  Google Scholar 

  • Mets LJ, Bogorad L (1974) Two-dimensional Polyacrylamide gel electrophoresis: an improved method for ribosomal proteins. Anal Biochem 57:200–210

    Article  PubMed  CAS  Google Scholar 

  • Miano A. Losso MA, Gianfranceschi GL, Gualerzi CO (1982) Proteins from the prokaryotic nucleoid I. Effect of NS1 and NS2 (HU) proteins on the thermal stability of DNA. Biochem Int 5:415–422

    CAS  Google Scholar 

  • Mizuuchi K (1983) In vitro transposition of bacteriophage Mu: A biochemical approach to a novel replication reaction. Cell 35:785–794

    Article  PubMed  CAS  Google Scholar 

  • Paci M, Pon CL, Losso MA, Gualerzi C (1984) High resolution 1H NMR spectroscopic study of Escherichia coli DNA-binding proteins NS1 and NS2. Eur J Biochem 138:193–200

    Article  PubMed  CAS  Google Scholar 

  • Pawlik RT, Littlechild J, Pon C, Gualerzi C (1981) Purification and properties of Escherichia coli initiation factors. Biochem Int 2:421–428

    CAS  Google Scholar 

  • Pettijohn DE (1982) Structure and properties of the bacterial nucleoid. Cell 30:667–669

    Article  PubMed  CAS  Google Scholar 

  • Pettijohn D, Pfenninger O (1980) Supercoils in prokaryotic DNA restrained in vivo. Proc Natl Acad Sci USA 77:1331–1335

    Article  PubMed  CAS  Google Scholar 

  • Pingoud A, Urbanke C, Alves J, Ehbrecht HJ, Zabeau M, Gualerzi C (1984) Effect of polyamines and basic proteins on cleavage of DNA by restriction endonucleases. Biochemistry 23:5697–5703

    Article  PubMed  CAS  Google Scholar 

  • Read CM, Baldwin JP, Crane-Robinson C (1985) Structure of subnucleosomal particles. Tetrameric (H3/H4)2 146 base pair DNA and hexameric (H3/H4)2 (H2A/H2B), 146 base pair DNA complexes. Biochemistry 24:4435–4450

    Article  PubMed  CAS  Google Scholar 

  • Rouviere-Yaniv J (1977) Localization of the HU protein in the E. coli nucleoid. Cold Spring Harbor Symp Quant Biol 42:439–447

    Google Scholar 

  • Rouviere-Yaniv J, Gros F (1975) Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli. Proc Natl Acad Sci USA 72: 3428–3432

    Article  PubMed  CAS  Google Scholar 

  • Rouviere-Yaniv J, Kjeldgaard NO (1979) Native Escherichia coli HU protein is a heterotypic dimer. FEBS Lett 106:297–300

    Article  PubMed  CAS  Google Scholar 

  • Rouviere-Yaniv J, Yaniv M, Germond J-E (1979) E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA. Cell 17:265–274

    Article  PubMed  CAS  Google Scholar 

  • Ryoji M, Worcel A (1984) Chromatin assembly in Xenopus oocytes: in vivo studies. Cell 37:21–32

    Article  PubMed  CAS  Google Scholar 

  • Ryoji M, Worcel A (1985) Structure of the two distinct types of minichromosomes that are assembled on DNA injected in Xenopus oocytes. Cell 40:923–932

    Article  PubMed  CAS  Google Scholar 

  • Schäfer R, Zillig W (1973) κ (kappa), a novel factor for the arrest of transcription in vitro by DNA-dependent RNA Polymerase from Escherichia coli at specific sites of natural templates. Eur J Biochem 33:201–206

    Article  PubMed  Google Scholar 

  • Sinden RR, Carlson JO, Pettijohn DE (1980) Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell 21:773–783

    Article  PubMed  CAS  Google Scholar 

  • Sinden RR, Pettijohn DE (1981) Chromosomes in living Escherichia coli are segregated into domains of supercoiling. Proc Natl Acad Sci USA 78:224–228

    Article  PubMed  CAS  Google Scholar 

  • Sloof P, Maagdelijn A, Boswinkel E (1983) Folding of prokaryotic DNA. Isolation and characterization of nucleoids from Bacillus licheniformis. J Mol Biol 163:277–297

    Article  PubMed  CAS  Google Scholar 

  • Spassky A, Buc HC (1977) Physico-chemical properties of a DNA binding protein: Escherichia coli factor H1. Eur J Biochem 81:79–90

    Article  PubMed  CAS  Google Scholar 

  • Spassky A, Rimsky S, Garreau H, Buc H (1984) H1a, an E. coli DNA binding protein which accumulates in stationary phase, strongly compacts DNA in vitro. Nucleic Acids Res 12:5321–5340

    Article  PubMed  CAS  Google Scholar 

  • Steinhäuser KG, Woolley P, Epe B, Dijk J (1982) Structure of ribosomal protein L6 from Escherichia coli. A fluorescence study. Eur J Biochem 127:587–595

    Article  PubMed  Google Scholar 

  • Suryanarayana T, Subramanian AR (1978) Specific association of two homologous DNA-binding proteins to the native 30S ribosomal subunits of Escherichia coli. Biochim Biophys Acta 520: 342–357

    PubMed  CAS  Google Scholar 

  • Swank RT, Munkres KD (1971) Molecular weight analysis of Oligopeptides by electrophoresis in Polyacrylamide gel with sodium dodecyl sulfate. Anal Biochem 39:462–477

    Article  PubMed  CAS  Google Scholar 

  • Tanaka I, Appelt K, Dijk J, White SW, Wilson KS (1984) 3-A resolution structure of a protein with histone-like properties in prokaryotes. Nature 310:376–381

    Article  PubMed  CAS  Google Scholar 

  • Ullmann A, Geider K (1977) Interaction of DNA with DNA binding proteins III. Infectivity of protein-complexed phage fd DNA in Escherichia coli spheroplasts. Biochim Biophys Acta 474: 639–645

    Google Scholar 

  • Varshavsky AJ, Bakayev VV, Nedospasov SA, Georgiev GP (1977a) On the structure of eukaryotic, prokaryotic and viral chromatin. Cold Spring Harbor Symp Quant Biol 42:457–473

    Google Scholar 

  • Varshavsky AJ, Nedospasov SA, Bakayev W, Bakayeva TG, Georgiev GP (1977b) Histone-like proteins in the purified Escherichia coli deoxyribonucleoprotein. Nucleic Acids Res 4:2725–2745

    Article  PubMed  CAS  Google Scholar 

  • Worcel A, Burgi E (1972) On the structure of the folded chromosome of Escherichia coli. J Mol Biol 71:127–147

    Article  PubMed  CAS  Google Scholar 

  • Zachau HG, Igo-Kemenes T (1981) Face to phase with nucleosomes. Cell 24:597–598

    Article  PubMed  CAS  Google Scholar 

  • Zentgraf H, Berthold V, Geider K (1977) Interaction of DNA with DNA binding proteins II. Displacement of Escherichia coli DNA unwinding protein and the condensed structure of DNA complexed with protein HD. Biochim Biophys Acta 474:629–638

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1986 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Gualerzi, C.O. et al. (1986). Proteins from the Prokaryotic Nucleoid. Structural and Functional Characterization of the Escherichia coli DNA-Binding Proteins NS (HU) and H-NS. In: Gualerzi, C.O., Pon, C.L. (eds) Bacterial Chromatin. Proceedings in Life Sciences. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-71266-1_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-71266-1_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-71268-5

  • Online ISBN: 978-3-642-71266-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics