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Chapter 4 : DNA-Binding Proteins and Chromatin
Category: Microbial Genetics and Molecular Biology; Environmental Microbiology
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Procaryotic genomic DNA and associated proteins together form an irregularly shaped structure, designated as the nucleoid. In contrast to the range of different chromatin proteins identified in bacteria, almost all eucaryal genomes are compacted into nucleosomes, chromatin, and chromosomes by essentially the same four proteins, histones H2A, H2B, H3, and H4. This chapter describes several different families of archaeal chromatin proteins with unrelated structures, but with the common properties of abundance, small size, positive charge, and ability to bind to DNA with little or no sequence specificity. Alba does bind to both DNA and RNA in Sulfolobus species, but chromatin immunoprecipitation experiments argue convincingly that Alba is bound to genomic DNA and functions as a chromatin protein in S. solfataricus. Sul10a is the generic name of an abundant ~11 kDa DNA-binding protein investigated from S. acidocaldarius (Sac10a) and S. solfataricus (Sso10a). An NMR solution structure has been established for methanogen chromosomal protein 1 (MC1) from Methanosarcina sp. CHTI55. It is apparent that many different chromatin proteins have evolved, all of which must bind and compact DNA into complexes that are readily disassembled, or that are inherently compatible with DNA replication and transcription machineries. Gene expression requires transcription activators, for example, histone acetylases that help disassemble chromatin and so allow transcription factor access to the DNA. With the accumulation of genome sequences, it is now apparent that most archaea have the capacity to synthesize several different chromatin proteins.
Phylogenetic tree based on rDNA sequence alignments of selected organisms. Branch lengths do not reflect evolutionary distances, but the branching orders are correctly represented. The numbers of histones (H), Sul7d (S), Alba (A), MC1 (M), 7kMk and HU-family members encoded in the genomes of representative archaea are denoted in parentheses. The H. salinarium NRC-1 histone has two HFs in one polypeptide (*). M. kandleri has two members of the HMfB family of archaeal histones with one HF (^), and also HMk, an archaeal histone with two HFs.
(See the separate color insert for the color version of this illustration.) Sequences and structures of representative archaeal chromatin proteins. Primary sequences of HMfB from M. fervidus (A), Sul7d (Sac7d) from S. acidocaldarius (B), Alba (Sso10b1) from S. solfataricus (C), and MC1 from Methanosarcina sp. CHTI55 (D) are shown below the corresponding protein structure. The figure was constructed using structures available from the Protein Data Bank ( 11 ). Regions with α-helical and β-strand structures are colored identically in the sequence and in the corresponding structure.