Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?

Abstract

Sir, Gene expression is regulated by different mechanisms in different organisms. The bacterial core RNA polymerase (α2ββ′) discriminates between subsets of promoters by binding different σ factors. Eukaryotes have evolved a more complicated system making use of three RNA polymerases to direct synthesis from different promoter families. Archaea possess a simplified version of RNA polymerase II transcription machinery with a single multisubunit RNA polymerase and a subset, TBP and TFIIB, of general transcription factors (Reeve et al., 1997, Cell89: 999–1002). However, multiple transcription factor homologues have been identified in several archaea including Halobacterium NRC-1 (Ng et al., 1998, Genome Res8: 1131–1141), Haloferax volcanii (Thompson et al., 1999, Mol Microbiol33: 1081–1092) and Pyrococcus horikoshii OT3 (Kawarabayasi et al., 1998, DNA Res5: 147–155). With the impending completion of the Halobacterium NRC-1 genome project, this extreme halophile is turning out to be a champion of multiple transcription factors, with six tbp and seven tfb genes (http://zdna.micro.umass.edu/haloweb). Genome sequencing of Halobacterium NRC-1 suggests the presence of multiple TATA-binding proteins, four (TBPa, TBPb, TBPc and TBPd) coded by pNRC100, a 191 kbp minichromosome, and two (TBPe and TBPf) coded elsewhere in the genome (Fig. 1). Archaeal TBPs, like their eukaryotic counterparts, possess repeated domains that combine to form a saddle-like structure with two stirrups (DeDecker et al., 1996, J Mol Biol264: 1072–1084). This domain similarity is much higher in archaeal TBPs (≈ 42%) compared with eukaryotic TBPs (≈ 25% similarity) (Soppa, 1999, Mol Microbiol31: 1295–1305). In Halobacterium NRC-1, except for TBPa, which has a single C-terminal domain, the remaining five have C- to N-terminal domain similarities ranging from 39% to 61%. TBPa may function by dimerization. Sequence alignment for the six predicted Halobacterium TBPs. Amino acids conserved in five or all of the six sequences are shaded. Of the seven TFBs identified in Halobacterium NRC-1, all possess the N-terminal zinc-finger domain, six have the imperfect cyclin repeat and all are capable of adopting the HTH motif structure at their C-termini. The glycine (G) and lysine (K)/arginine (R) residues within the cyclin repeats, required for interaction with the TBP–DNA complex (Buratowski and Zhou, 1993, Proc Natl Acad Sci USA90: 5633–5637) were conserved in the seven proteins with the exception of TFBe, which lacked a positively charged residue at position 301 (Fig. 2). Phylogenetic analyses suggest that the TFBs and the TBPs evolved from single common ancestors. Sequence alignments for the seven predicted Halobacterium TFBs. Likely Zn-finger domains [(CXXC)X{15–17}(CXXC)] are boxed, amino acids conserved in five or all of the seven sequences are shaded (the amino acids involved in interaction with TBP are shaded in black) and the helix–turn–helix DNA binding motifs are underlined. Given this diversity of transcription factors in Halobacterium NRC-1 it is possible that the six TBPs and seven TFBs interact in up to 42 different combinations driving transcription from a correspondingly large set of promoters (Thompson et al., 1999, Mol Microbiol33: 1081–1092). The formation of alternative TBP–TFB–RNAP complexes, with the possibility of interactions with different accessory factors, may help to explain the diversity of halophilic promoters (Baliga and DasSarma, 1999, J Bacteriol181: 2513–2518; Soppa, 1999, Mol Microbiol31: 1295–1305) and the lack of a requirement for the BRE sequences (Littlefield et al., 1999, Proc Natl Acad Sci USA96: 13668–13673; Tsai and Sigler, 2000, EMBO J19: 25–36) in the expression of the Halobacterium NRC-1 bop gene (Baliga and DasSarma, 2000, Mol Microbiol 36: 000–000). This potential regulatory strategy is conceptually similar to the use of multiple sigma factors by bacterial RNA polymerase and represents an extension of the eukaryotic RNA polymerase II transcription system. Finally, the presence of TBP-like (Dantonel et al., 1999, Trends Biochem Sci24: 335–339) and TBP-related (Maldonado, 1999, J Biol Chem274: 12963–12966) proteins in some metazoan and mammalian cells, respectively, suggests that alternative TBP–TFB–RNAP complexes may be present in eukaryotic systems as well (Buratowski, 1997, Cell91: 13–15).