Histone-like protein

D. G. Searcy, T. Montenay-Garestier, D. J. Laston, and C. Helene, Tyrosine environment and phosphate binding in the archaebacterial histone-like protein HTa, Biochim. Biophys. Acta 953, 321-333 (1988). 

In recent years, several papers appeared in the literature concerning NMR and X-ray studies of thermostable ribonucleases. Among archaebacteria, several histone-like proteins from Sulfolobus strains have been identified and grouped into molecular mass classes. From the 7 kDa class, Sac7e from S. acidocaldarius and Sso7d from S. solfataricus, possessing DNA binding activity in combination with non-specific RNase activity, were identified. ... 

Megraw, T.L. and Chae, C.B. (1993) Functional complementarity between the HMGl-like yeast mitochondrial histone HM and the bacterial histone-like protein HU. J. Biol. Chem. 268, 12758-12763. 

The DNA in a bacterium is a supercoiled double-stranded circular molecule that is packaged in the nucleoid region of the cell. The DNA is negatively supercoiled, complexed to several histone-like proteins (mainly proteins HU, HSP-1 and H-NS) and organized into about 50 domains bound to a protein scaffold. 

The DNA of a bacterial cell, such as Escherichia coli, is a circular double-stranded molecule often referred to as the bacterial chromosome. In E. coli this DNA molecule contains 4.6 million base pairs. The circular DNA is packaged into a region of the cell called the nucleoid (see Topic Al) where it is organized into 50 or so loops or domains that are bound to a central protein scaffold, attached to the cell membrane. Fig. la illustrates this organization, although only six loops are shown for clarity. Within this structure, the DNA is actually not a circular double-stranded DNA molecule such as that shown in Fig. lb but is negatively supercoiled, that is, it is twisted upon itself (Fig. lc) and is also complexed with several DNA-binding proteins, the most common of which are proteins HU, HLP-1 and H-NS. These are histone-like proteins (see below for a description of histones). 

R. N. Reusch, O. Shabalin, A. Crumbaugh, R. Wagner, O. Schroder and R. Wurm (2002). Post-translational modification of E. coli histone-like protein H-NS and bovine histones by short-chain poly-(R)-3-hydroxybutyrate (cPHB). FEBS Lett., 527, 319-322. 

Unlike the initiation of Okazaki fragments during elongation, initiation at oriC requires RNA polymerase (in contrast to primase it is sensitive to rifampicin, see Chap. 17), and DnaA, DnaB, DnaC, and the histone-like protein HU. The role of RNA polymerase is thought to be in bringing about transcriptional activation of oriC. This presumably facilitates the multiple molecular steps leading to successful initiation. 

Thermostabilization of double-stranded DNA is provided by base pairing (1) and base stacking (see Reference 27 and references therein) complemented by positive supercoiling by reverse gyrase [in hyperthermophiles (8, 9, 28)] and by stabilization via interactions with histone-like proteins (29, 30). The relative contribution of base paring and base stacking into the thermostability of double-stranded DNA has been a subject of extensive studies for more than four decades (1, 27, 31). We will consider here this question, based on the results of recent experimental and computational works (31, 32). 

Stein DB, Searcy DG. Physiologically important stabilization of DNA by a prokaryotic histone-like protein. Science 1978 202 219-221. 

Additional regulatory mechanisms can involve various host proteins (i.e., not encoded by the transposon) that are involved in transposome assembly and/or activity. For example, the Escherichia coli histone-like proteins IHF and HU are required for bacteriophage Mu. IHF and HNS, although not required, stimulate TnlO (IS70) transposition. A more systematic smdy has revealed several additional host factors that affect transposition of various TE in E. coli either positively or negatively (15). Finally, in the case of the eukaryotic transposon. Sleeping Beauty, the HMG protein is required for integration. 

Fig. 2. Alignments of histones and histone-like proteins from archaebacteria, eubacteria and eukaryotes. Conserved amino acids in all sequences are in bold (R=K and I=L=V). Adapted from refs. [23,41]. The numbers of asterisks correspond to the number of amino acids identical with the...

Although the data on the archaebacterial DNA world are far from exhaustive, it is nevertheless already possible to draw tentative phylogenetic considerations. In their transcription and translation machineries, archaebacteria exhibit several eukaryotic-like features, compared to those in eubacteria, such as an RNA polymerase and elongation factors of the eukaryotic type (see ref. [151], and other chapters of this volume). Several features of the DNA world have been frequently considered to be eukaryotic the presence of histone-like proteins, first HTa[152], more recently HMf[23], the sensitivity of halobacteria to drugs otherwise specific of the eukaryotic DNA topoisomerasell [103], and the existence of an aphidicolin-sensitive DNA polymerase [124]. However, it appears that HTa is a close relative of eubacterial HU proteins (see Fig. 2), that Haloferax Type II DNA topoisomerase is very similar to eubacterial DNA gyrases (see Fig. 9) and that aphidicolin also inhibits an eubacterial DNA polymerase. HMf is clearly homologous to eukaryotic histones, but HMf nucleosomes are drastically different from eukaryotic ones furthermore, one cannot exclude the existence of HMf-related proteins in eubacteria. 

Kothekar, V., Raha, K. Prasad, H. K. (1998). Molecular dynamics simulation of interaction of histone-like protein of mycobacterium tuberculosis (Hlpmt) and histone of clostridium pasteurianum (DBHclopa) with 35 based paired GC rich U-bend DNA. J Biomol Struct Dyn 16(2), 223-35. 

One of the most extensively studied kDNA netwoiks is that of the spedes Orithidiajmciculata. The kDNA network (approximately 10 by 15 pm in dimensions ) is condensed in the mitochondrial matrix into a disk-like structure of about 1 by 0.35 pm. Several histone-like proteins are involved in the structural oiganization of the condensed network. The kinetoplast... 

Pomati F, Neilan BA (2004) PCR-based positive hybridization to detect genranic diversity associated with bacterial secondary metabolism. Nucleic Acids Res 32 e7 Taroncher-Oldenburg G, Anderson DM (2000) Identification and characterization of three differentially expressed genes, encoding S-adenosylhomocysteine hydrolase, methionine aminopeptidase, and a histone-like protein, in the toxic dinollagellate Alexandrium fundyense. Appl Environ Microbiol 66 2105-2112... 

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