Abstract
Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30–40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.
Highlights
Gram-negative bacteria (e.g., Escherichia coli) encode factor for inversion stimulation (Fis), integration host factor protein (IHF), host factor for phage Qbeta RNA replication (Hfq), histone-like nucleoid structuring protein (H-NS) and its paralog suppressor of T4 Td mutant phenotype A (StpA), and DNA-binding protein from starved cells (Dps) [10]. Among these NAPs, H-NS is highly conserved within E. coli and related strains, and forspaced inversion stimulation (Fis) is conserved among Enterobacteriaceae [11]
Micrococcal nuclease assay, mass spectrometry, atomic force microscopy (AFM), and Hi-C, which are useful for identifying responsible for higher-order genome folding as well as medium-scale chromosome folds such as proteins for higher-order folding as and wellbacteria as medium-scale chromosome folds
On substrate lysis exhibits 30 and 80 nm nucleoid fiber from E. coli cell (b) [15], 30–40 nm globular structures from T. acidophilum cells (c), and ~10 nm fibrous structure from P. calidifontis cells (d) [31]. (e) Reconstituted chromatin structure formed on DNA with eukaryotic histone octamer; a 30 nm fiber is formed with further addition of linker histone H1 [32]. (f) Reconstituted archaeal chromosome structures formed with T
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Gram-negative bacteria (e.g., Escherichia coli) encode factor for inversion stimulation (Fis), integration host factor protein (IHF), host factor for phage Qbeta RNA replication (Hfq), histone-like nucleoid structuring protein (H-NS) and its paralog suppressor of T4 Td mutant phenotype A (StpA), and DNA-binding protein from starved cells (Dps) [10]. Among these NAPs, H-NS is highly conserved within E. coli and related strains, and Fis is conserved among Enterobacteriaceae [11]. We try to illustrate the principle of chromosome organization in the three domains
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