Archaeal transcription factors and their role in transcription initiation

Abstract

Archaeal RNA polymerases show a weak ability in vitro to bind to promoter DNA and/or to initiate transcription with low activity independent of upstream regulatory DNA sequences. Active transcription in vitro and in vivo, however, depends strictly on a TATA box resembling the TATA box of eucaryal polII promoters. This TATA box is recognized by a polypeptide related to eucaryal TATA-binding protein (TBP) that was formerly designated aTFB. Template competition studies showed that this archaeal TATA-binding protein (aTBP) is stably sequestered at the promoter by interaction with the second archaeal transcription factor, aTFA, which is related to eucaryal transcription factor IIB (TFIIB). The association of archaeal TFIIB (aTFIIB) with the aTBP-promoter complex leads to template commitment, indicating that aTFIIB recruits archaeal RNA polymerase to the preinitiation complex. These analyses suggest the following order for assembly of transcription factors on the archaeal promoter: aTBP, aTFIIB, RNA polymerase, and provide evidence for a common molecular mechanism of transcription initiation by eucaryal RNA polymerase II and archaeal RNA polymerases. The sequence of the genes encoding aTBP and aTFIIB (TFB) showed all the characteristics conserved in their eucaryal counterparts. The degree of sequence similarity between archaeal and eucaryal transcription factors is between 27 to 35% for TFIIB and between 36 to 41% for TBP. The findings discussed here indicate that TBP and TFIIB perform analogous functions in Archaea and Eucarya and show that four essential components of archaeal and eucaryal transcriptional machineries. RNA polymerase, TATA box, TBP and TFIIB are homologous.

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

“…The evolutionary basis for the fundamental differences that distinguish eubacteria and archaebacteria, but which more or less uniformly unite the respective groups, could be sought in the age of biochemical discovery during the persistence of proto-eubacterial and protoarchaebacterial lineages living within the confines of their energy-laden mineral incubator. Such differences would include their use of many fundamentally different cofactors such as pterin derivatives versus tetrahydrofolate, coenzyme B, methanofuran, coenzyme F420, coenzyme M and cobamids in many archaebacteria (see DiMarco et al 1990;Thauer 1998;White 2001), their use of different pathways for the same metabolic intermediates such as IPP (Lange et al 2000) or their differences in purine biosynthesis (White 1997), their use (archaebacteria) or disuse (eubacteria) of small nucleolar RNAs for the modification of ribosomes (Omer et al 2000), the differences between their DNA maintenance and repair machineries (Tye 2000), the differences between their transcriptional regulatory apparatus (Thomm 1996;Bell et al 2001) and RNA polymerases (Langer et al 1995;Bell & Jackson 1998), their quinones (Schü tz et al 2000;Berry 2002), or, and what is probably the most important point for this paper, the differences between their membrane lipid biosynthetic pathways and cell-wall constituents (Kandler 1982). Many other such differences could be listed.…”

The RPB7 Orthologue E′ Is Required for Transcriptional Activity of a Reconstituted Archaeal Core Enzyme at Low Temperatures and Stimulates Open Complex Formation

“…Despite their morphological similarity to Bacteria, Archaea have a transcriptional machinery that is more akin to the eukaryotic machinery (1)(2)(3).…”

Primary Structure of Selected Archaeal Mesophilic and Extremely Thermophilic Outer Surface Layer Proteins

“…The promotor sequence (TATA-box, boxA; DNA-dependent RNA-polymerase binding region) and the BRE-box (transcription factor B recognition element) correspond largely to the proposed consensus sequences of methanogenic archaea (THOMM, 1996). In contrast to Methanococcus jannaschii, several tandem promotors have been described for the S-layer gene of Methanococcus voltae (KANSY et al 1994).…”

“…Based on data from the literature (THOMM, 1996) we propose signal sequences for transcription and translation of the S-layer genes of methanococci (AKÇA et al, 2002; Table 7). The promotor sequence (TATA-box, boxA; DNA-dependent RNA-polymerase binding region) and the BRE-box (transcription factor B recognition element) correspond largely to the proposed consensus sequences of methanogenic archaea (THOMM, 1996).…”