Chapter 6 : Transcription: Mechanism and Regulation

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The biochemical machinery involved in the processes of DNA replication, transcription, and translation shows a striking similarity and phylogenetic relationship to the equivalent machinery in eucarya. In particular, RNA polymerase (RNAP) and the basal transcriptional machinery of archaea share many properties with the eucaryal RNA polymerase II (RNAP II) transcription apparatus. Regulators of archaeal transcription repress initiation by preventing TFB/TBP access to the TATA-box region or RNAP recruitment to the transcription start site. The DNA-binding site of LrpA overlaps the RNAP-binding site, and DNA-bound LrpA inhibits transcription by blocking RNA polymerase recruitment. NrpR controls the transcription of the operon by binding cooperatively to two tandem operator sequences, OR and OR, located downstream of the transcription start site. The stronger and promoter proximal NrpR-binding site (OR) can mediate repression of nif transcription during growth on ammonia. Heat shock-induced upregulation of some TFB genes from haloarchaea and of TFB2 from have been reported. In cell-free transcription reactions, the addition of the substrate (maltodextrins) of this transporter system causes TrmB to dissociate from the promoter and relieves inhibition of RNA synthesis. The lack of genetic systems in many archaea hampers analysis of transcriptional regulation in vivo. The striking similarity of the archaeal and eucaryal genetic machinery is described in this chapter.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 1

Initiation of transcription in archaea. The first step of promoter recognition is binding of TBP to the archaeal TATA box. This complex is stabilized by the association of TFB. Bound TFB interacts with the purinerich BRE sequence 5ʹ of the TATA box. This complex recruits the RNA polymerase that binds to the DNA region downstream of the TATA box and covers the transcription start site and the DNA downstream region to position +18.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 2

Domain structure of TFB. The major structural features of TFB and their interactions with other components of the transcriptional machinery.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 3

Subunit structure of RNAPs from the three domains of life. The largest subunit in the and in the is split into two subunits, A1 and A2, in the In methanogens, subunit B is also split into two polypeptides, Bʹ and Bʹ. Different parts of bacterial subunit are encoded by the genes for the archaeal subunits D and L. Subunits E1, F, H, N, and P are only shared between the and The pattern shown is based on separation of subunits by polyacrylamide gel electrophoresis under denaturing conditions. The numbers in the subunits of the eucaryal RNAP A (I), B (II), and C (III) indicate the molecular mass.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 4

(.) Structural similarity of RNAP (A) and yeast RNAPII (B). Comparison of interactions of an archaeal RNAP inferred from Far-Western analysis with interactions of yeast RNAPII observed in the crystal structure of the enzyme. The width of the lines connecting subunits is a measure of the intensity of the interaction. Modified from ( ) with additional data from ( ).

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 5

Mechanism of transcription by an archaeal RNAP. (A) TFE facilitates binding of the TFB zinc ribbon domain to the core domain of RNAP. (B) After open complex formation, the B finger of TFB stabilizes the template strand in the active center of RNAP. TFE provides additional stability to this complex by closing the clamp of RNAP. (C) After synthesis of a transcript longer than 10 nucleotides, RNAP reaches the elongation committed state. RNAP moves synchronously with RNA synthesis from this point.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 6

The two major transitions in archaeal transcription initiation. (A) In the preinitiation complex and during synthesis of the first five nucleotides, RNAP is in close contact with transcription factors and the transcription bubble extends from position — 7 to +5. (B) After synthesis of 6/7 nucleotides, the upstream edge of RNAP loses contact with transcription factors but the downstream edge is unchanged. (C) At position +10/+11, promoter clearance occurs and RNAP moves continuously to enable RNA synthesis.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 7

Interaction of a heat shock regulator (Phr) with heat shock promoters. Phr binds specifically to a conserved palindromic sequence of archaeal heat shock promoters overlapping the transcription start site. When bound to the DNA, Phr blocks RNAP recruitment. The factors modulating the DNA-binding properties of Phr are unknown.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 8

The archaeal regulator TrmB responds to different ligands when bound at different promoters. In the absence of any ligands, TrmB binds to its operator sequences at the maltose and maltodextrin promoter. At the promoter, TrmB binding is influenced by maltose as inducer, but not by maltodextrins. At the promoter maltose has no effect on TrmB binding but maltodextrins lower its affinity for the operator. The TrmB-binding sites differ substantially at both promoters, and the TrmB-binding site overlaps the transcription start site at the promoter, and the BRE/TATA box sequence at the promoter. The smaller triangle represents maltose, and the larger triangle, maltodextrins. The TATA box is indicated; the DNA-binding sequence of TrmB is represented by a shaded box and shown on both promoters, and the binding sequence is shown below TrmB. The transcription start site is indicated by +1. The binding site of TrmB contains a palindrome at the promoter and is represented by two horizontal arrows. Only one half of it is conserved in the promoter.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 9

The ROMA approach. Fragmented genomic DNA is transcribed in a cell-free transcription system in the presence and absence of a regulator. Each DNA fragment harbors on average one promoter. Some promoters are unaffected (no regulation) by a given regulator, some are upregulated (by activators), and some are downregulated (by repressors). The in vitro RNA is converted to labeled cDNA and hybridized with a whole-genome microarray. By comparison of the hybridization patterns of RNAs synthesized in the presence and absence of a regulator the genes modulated by the regulatory protein can be identified.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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