Archaeal RNA polymerase subunits E and F are not required for transcription <i>in vitro</i>, but a <i>Thermococcus kodakarensis</i> mutant lacking subunit F is temperature‐sensitive

Hirata, Akira; Kanai, Tamotsu; Santangelo, Thomas J.; Tajiri, Momoko; Manabe, Kenji; Reeve, John N.; Imanaka, Tadayuki; Murakami, Katsuhiko

doi:10.1111/j.1365-2958.2008.06430.x

Cited by 43 publications

(49 citation statements)

References 43 publications

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“…A heterodimer of AC40 and AC19 resembles Rpb3-Rpb11 in Pol II, but AC40 contains an additional 'toe' domain where the archaeal subunit D contains a domain with an iron-sulphur cluster 13 ( Fig. 1c and Extended Data Fig.…”

Section: Pol I Structurementioning

confidence: 99%

RNA polymerase I structure and transcription regulation

Engel

Sainsbury

Cheung

et al. 2013

Nature

199

305

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Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I fromthe yeast Saccharomyces cerevisiae at 2.8A˚ resolution reveals all 14 subunits of the 590-kilodalton enzyme, and shows differences to Pol II. An ‘expander’ element occupies the DNA template site and stabilizes an expanded active centre cleft with an unwound bridge helix. A ‘connector’ element invades the cleft of an adjacent polymerase and stabilizes an inactive polymerase dimer. The connector and expander must detach during Pol I activation to enable transcription initiation and cleft contraction by convergent movement of the polymerase ‘core’ and ‘shelf’ modules. Conversion between an inactive expanded and an active contracted polymerase state may generally underlie transcription. Regulatory factors can modulate the core–shelf interface that includes a ‘composite’ active site for RNA chain initiation, elongation, proofreading and termination

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Section: Pol I Structurementioning

confidence: 99%

RNA polymerase I structure and transcription regulation

Engel

Sainsbury

Cheung

et al. 2013

Nature

199

305

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“…One interesting example involved the in vivo disruption and analysis of a gene encoding reverse gyrase on the T. kodakaraensis genome, which revealed that the gene product functions in adaptation to high temperature, because reverse gyrase is highly conserved only in hyperthermophiles (Atomi et al, 2004). These efficient genetic tools have already been used to investigate several biological systems, such as the glycolysis pathway (Yoshida et al, 2006;Matsumi et al, 2007), natural product biosynthesis (Yokooji et al, 2009;Borges et al, 2010), transcription factors (Kanai et al, 2007(Kanai et al, , 2010, and operon transcription and translation machinery Hirata et al, 2008). However, these useful and powerful techniques have not yet been applied to the analysis of DNA repair.…”

Section: Introductionmentioning

confidence: 99%

Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis

Fujikane

Ishino

et al. 2010

Genes Genet. Syst.

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Extensive biochemical and structural analyses have been performed on the putative DNA repair proteins of hyperthermophilic archaea, in contrast to the few genetic analyses of the genes encoding these proteins. Accordingly, little is known about the repair pathways used by archaeal cells at high temperature. Here, we attempted to disrupt the genes encoding the potential repair proteins in the genome of the hyperthermophilic archaeon Thermococcus kodakaraensis. We succeeded in isolating null mutants of the hjc, hef, hjm, xpb, and xpd genes, but not the radA, rad50, mre11, herA, nurA, and xpg/fen1 genes. Phenotypic analyses of the gene-disrupted strains showed that the xpb and xpd null mutants are only slightly sensitive to ultraviolet (UV) irradiation, methyl methanesulfonate (MMS) and mitomycin C (MMC), as compared with the wild-type strain. The hjm null mutant showed sensitivity specifically to mitomycin C. On the other hand, the null mutants of the hjc gene lacked increasing sensitivity to any type of DNA damage. The Hef protein is particularly important for maintaining genome homeostasis, by functioning in the repair of a wide variety of DNA damage in T. kodakaraensis cells. Deletion of the entire hef gene or of the segments encoding either its nuclease or helicase domain produced similar phenotypes. The high sensitivity of the Δhef mutants to MMC suggests that Hef performs a critical function in the repair process of DNA interstrand crosslinks. These damage-sensitivity profiles suggest that the archaeal DNA repair system has processes depending on repair-related proteins different from those of eukaryotic and bacterial DNA repair systems using homologous repair proteins analyzed here.

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“…Some differences in promoter sequence preferences and protein pairing have been noted in TBP-TFB isoform pairs (36)(37)(38)(39)(40)(41), but these minor differences are not on par with the clear but not always radical promoter sequence differences noted for alternative factors in bacterial transcription (39,42). TFE also appears essential, and it is currently unclear if this essentiality is due to necessary activities during transcription initiation or some other role in the transcription cycle (26,43,44).…”

Section: Basal Transcription Factorsmentioning

confidence: 99%

“…Several studies have shown that the presence of the RNAP stalk domain-unique to archaeoeukaryotic RNAPs and comprised of two subunits, RpoE and RpoF in archaea and Rpo4 and Rpo7 in eukaryotes-is essential for the full activity of TFE␣ (59,62,63). The predicted interaction between TFE␣ and the stalk domain was bolstered by copurification of TFE␣ with intact RNAP and the loss of TFE␣ from RNAP preparations wherein the stalk domain was missing (44). A recent structure-function study identified critical interactions between TFE␣ and RpoE of the stalk domain (26).…”

Section: Basal Transcription Factorsmentioning

confidence: 99%

Transcription Regulation in Archaea

2016

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The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription. RNA polymerase (RNAP) is a well-conserved, multisubunit essential enzyme that transcribes DNA to generate RNA in all cells. Although RNA synthesis is carried out by RNAP, the activities of RNAP during each phase of transcription are subject to basal and regulatory transcription factors. Substantial differences in transcription regulatory strategies exist in the three domains (Bacteria, Archaea, and Eukarya). Only a single transcription factor (NusG or Spt5) is universally conserved (1, 2), and the roles of many archaeon-encoded factors have not been evaluated using in vivo and in vitro techniques. Archaea are reliant on a transcription apparatus that is homologous to the eukaryotic transcription machinery; similarities include additional RNAP subunits that form a discrete subdomain of RNAP (3, 4) as well as basal transcription factors that direct transcription initiation and elongation (5-8).The shared homology of archaeal-eukaryotic transcription components aligns with the shared ancestry of Archaea and Eukarya, and this homology often is exclusive of Bacteria. Archaea are prokaryotic, but the transcription apparatus of Bacteria differs significantly from that of Archaea and Eukarya.The archaeal transcription apparatus is most commonly summarized as a simplified version of the eukaryotic machinery. In some respects this is true, as homologs of only a few eukaryotic transcription factors are encoded in archaeal genomes, and archaeal transcription in vitro can be supported by just a few transcription factors. However, much regulatory activity in eukaryotes is devoted to posttranslational modifications of chromatin, RNAP, and transcription factors, and this complexity seemingly does not transfer to the Archaea, where few posttranslational modifications or chromatin-imposed regulation events are currently known. The ostensible simplicity of archaeal transcription is under constant revision, as more detailed examinations of archaeon-encoded factors become possible through increasingly sophisticated in vivo and in vitro techniques. This review will highlight the current understanding of archaeal transcriptio...

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Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature‐sensitive

Cited by 43 publications

References 43 publications

RNA polymerase I structure and transcription regulation

RNA polymerase I structure and transcription regulation

Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis

Transcription Regulation in Archaea

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