Archaeal chromatin and transcription

Abstract

SummaryArchaea contain a variety of sequence-independent DNA binding proteins consistent with the evolution of several different, sometimes overlapping and exchangeable solutions to the problem of genome compaction. Some of these proteins undergo residuespecific post-translational lysine acetylation or methylation, hinting at analogues of the histone modifications that regulate eukaryotic chromatin structure and transcription. Archaeal transcription initiation most closely resembles the eukaryotic RNA polymerase II (RNAPII) system, but Archaea do not appear to have homologues of the multisubunit complexes that remodel eukaryotic chromatin and activate RNAPII initiation. In contrast, they have sequence-specific regulators that repress and perhaps activate archaeal transcription by mechanisms superficially similar to the bacterial paradigm of regulating promoter binding by RNAP. Repressors compete with archaeal TATAbox binding protein (TBP) and TFB for the TATA-box and TFB-recognition elements (BRE) of the archaeal promoter, or with archaeal RNAP for the site of transcription initiation. Transcript-specific regulation by repressors binding to sites of transcript initiation is consistent with such sites having very little sequence conservation. However, most Archaea have only one TBP and/or TFB that presumably must therefore bind to similar TATA-box and BRE sequences upstream of most genes. Repressors that function by competing with TBP and/or TFB binding must therefore also make additional contacts with transcript-specific regulatory sites adjacent or remote from the TATA-box/ BRE region. The fate of the archaeal TBP and TFB following transcription initiation remains to be determined. Based on functional homology with their eukaryotic RNAPII-system counterparts, archaeal TBP and possibly also TFB should remain bound to the TATA-box/BRE region after transcription initiation. However, this seems unlikely as it might limit repressor competition at this site to only the first round of transcription initiation.

Targeted analysis and discovery of posttranslational modifications in proteins from methanogenic archaea by top-down MS

“…5A Inset). From none of the growth stages of this organism (34) were any of the histone proteins detected to harbor PTMs, consistent with a complete lack of histone-modifying enzymes in the M. jannaschii genome (13) and of histone tails (known to be PTM rich in Eukarya) (42). This finding is in stark contrast to eukaryotic histones such as those from histone H4 isolated from S. cerevisiae.…”

“…A detailed study of the PTM dynamics present on yeast histones is beyond the scope of this study. For M. jannaschii, with no histone-modifying enzymes, no ''histone code'' (43) involving modifications appears operative, making regulation by differential histone expression or changes in dimerization partner more likely (42). However, M. acetivorans has predicted histone-modifying enzymes, such as a histone acetyl transferase (Q8TSH0) and a histone deacetylase (HDAC, Q8TLY4) detectable by homology searching.…”

TRF2: TRansForming the view of general transcription factors

“…The TATA box is conserved from archaebacteria to humans. 10 Although the TATA box is wellknown and extensively studied, it is only present in 10%-15% of mammalian core promoters, and in about 20% of Drosophila genes. 7,[11][12][13][14][15] The BRE motifs function together with the TATA box.…”

Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double‐stranded DNA complex

“…5,6 Crenarchaeota, another main kingdom of Archaea, lacks histones. 4 A number of DNA-binding proteins, such as Sul7d, CC1, and so forth, have been identified as chromatin proteins in some crenarchaeal species. However, most of them are not conserved in Crenarchaeota.…”