Bailey K A, Pereira S L, Widom J, Reeve J N
Department of Microbiology, The Ohio State University, Columbus, OH 43210-1292, USA.
J Mol Biol. 2000 Oct 13;303(1):25-34. doi: 10.1006/jmbi.2000.4128.
Archaeal histones and the eucaryal (eucaryotic) nucleosome core histones have almost identical histone folds. Here, we show that DNA molecules selectively incorporated by rHMfB (recombinant archaeal histone B from Methanothermus fervidus) into archaeal nucleosomes from a mixture of approximately 10(14) random sequence molecules contain sequence motifs shown previously to direct eucaryal nucleosome positioning. The dinucleotides GC, AA (=TT) and TA are repeated at approximately 10 bp intervals, with the GC harmonic displaced approximately 5 bp from the AA and TA harmonics [(GCN(3)AA or TA)(n)]. AT and CG were not strongly selected, indicating that TA not equalAT and GC not equalCG in terms of facilitating archaeal nucleosome assembly. The selected molecules have affinities for rHMfB ranging from approximately 9 to 18-fold higher than the level of affinity of the starting population, and direct the positioned assembly of archaeal nucleosomes. Fourier-transform analyses have revealed that AA dinucleotides are much enriched at approximately 10. 1 bp intervals, the helical repeat of DNA wrapped around a nucleosome, in the genomes of Eucarya and the histone-containing Euryarchaeota, but not in the genomes of Bacteria and Crenarchaeota, procaryotes that do not have histones. Facilitating histone packaging of genomic DNA has apparently therefore imposed constraints on genome sequence evolution, and since archaeal histones have no structure in addition to the histone fold, these constraints must result predominantly from histone fold-DNA contacts. Based on the three-domain universal phylogeny, histones and histone-dependent genome sequence evolution most likely evolved after the bacterial-archaeal divergence but before the archaeal-eucaryal divergence, and were subsequently lost in the Crenarchaeota. However, with lateral gene transfer, the first histone fold could alternatively have evolved after the archaeal-eucaryal divergence, early in either the euryarchaeal or eucaryal lineages.
古菌组蛋白与真核生物核小体核心组蛋白具有几乎相同的组蛋白折叠结构。在此，我们表明，重组嗜热甲烷栖热菌组蛋白B（rHMfB）从大约10¹⁴个随机序列分子的混合物中选择性掺入古菌核小体的DNA分子含有先前已证明可指导真核生物核小体定位的序列基序。二核苷酸GC、AA（=TT）和TA以大约10 bp的间隔重复，其中GC谐波相对于AA和TA谐波偏移约5 bp [（GCN₃AA或TA）ₙ]。AT和CG未被强烈选择，这表明在促进古菌核小体组装方面TA≠AT且GC≠CG。所选分子对rHMfB的亲和力比起始群体的亲和力水平高约9至18倍，并指导古菌核小体的定位组装。傅里叶变换分析表明，在真核生物和含组蛋白的广古菌门的基因组中，AA二核苷酸在围绕核小体缠绕的DNA的螺旋重复序列（约10.1 bp间隔）处大量富集，但在细菌和泉古菌门（不含组蛋白的原核生物）的基因组中则不然。因此，促进基因组DNA的组蛋白包装显然对基因组序列进化施加了限制，并且由于古菌组蛋白除了组蛋白折叠结构外没有其他结构，这些限制必定主要源于组蛋白折叠结构与DNA的相互作用。基于三域通用系统发育，组蛋白和依赖组蛋白的基因组序列进化最有可能在细菌 - 古菌分化之后但在古菌 - 真核生物分化之前就已进化，随后在泉古菌门中丢失。然而，通过横向基因转移，第一个组蛋白折叠结构也可能在古菌 - 真核生物分化之后，在广古菌门或真核生物谱系的早期进化而来。
