PROSITE documentation PDOC00044
Bacterial histone-like DNA-binding proteins signature


Bacteria synthesize a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [1,2]. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilizing it from denaturation under extreme environmental conditions. The sequence of a number of different types of these proteins is known:

  • The HU proteins, which, in Escherichia coli, are a dimer of closely related α and β chains and, in other bacteria, can be dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae [3].
  • The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [4] in enterobacteria.
  • The bacteriophage sp01 transcription factor 1 (TF1) which selectively binds to and inhibits the transcription of hydroxymethyluracil-containing DNA, such as sp01 DNA, by RNA polymerase in vitro.
  • The African Swine fever virus protein A104R (or LMW5-AR) [5].

As a signature pattern for this family of proteins, we use a twenty residue sequence which includes three perfectly conserved positions. According to the tertiary structure of one of these proteins [6], this pattern spans exactly the first half of the flexible DNA-binding arm.

Last update:

December 2004 / Pattern and text revised.


Technical section

PROSITE method (with tools and information) covered by this documentation:

HISTONE_LIKE, PS00045; Bacterial histone-like DNA-binding proteins signature  (PATTERN)


1AuthorsDrlica K. Rouviere-Yaniv J.
TitleHistonelike proteins of bacteria.
SourceMicrobiol. Rev. 51:301-319(1987).
PubMed ID3118156

2AuthorsPettijohn D.E.
TitleHistone-like proteins and bacterial chromosome structure.
SourceJ. Biol. Chem. 263:12793-12796(1988).
PubMed ID3047111

3AuthorsWang S.L. Liu X.-Q.
TitleThe plastid genome of Cryptomonas phi encodes an hsp70-like protein, a histone-like protein, and an acyl carrier protein.
SourceProc. Natl. Acad. Sci. U.S.A. 88:10783-10787(1991).
PubMed ID1961745

4AuthorsFriedman D.I.
TitleIntegration host factor: a protein for all reasons.
SourceCell 55:545-554(1988).
PubMed ID2972385

5AuthorsNeilan J.G. Lu Z. Kutish G.F. Sussman M.D. Roberts P.C. Yozawa T. Rock D.L.
TitleAn African swine fever virus gene with similarity to bacterial DNA binding proteins, bacterial integration host factors, and the Bacillus phage SPO1 transcription factor, TF1.
SourceNucleic Acids Res. 21:1496-1496(1993).
PubMed ID8464748

6AuthorsTanaka I. Appelt K. Dijk J. White S.W. Wilson K.S.
Title3-A resolution structure of a protein with histone-like properties in prokaryotes.
SourceNature 310:376-381(1984).
PubMed ID6540370

PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)