Archaeal RNA polymerase and transcription regulation

Abstract

To elucidate the mechanism of transcription by cellular RNA polymerases (RNAPs), high resolution X-ray crystal structures together with structure-guided biochemical, biophysical and genetics studies are essential. The recently-solved X-ray crystal structures of archaeal RNA polymerase (RNAP) allow a structural comparison of the transcription machinery among all three domains of life. The archaea were once thought of closely related to bacteria, but they are now considered to be more closely related to the eukaryote at the molecular level than bacteria. According to these structures, the archaeal transcription apparatus, which includes RNAP and general transcription factors, is similar to the eukaryotic transcription machinery. Yet, the transcription regulators, activators and repressors, encoded by archaeal genomes are closely related to bacterial factors. Therefore, archaeal transcription appears to possess an intriguing hybrid of eukaryotic-type transcription apparatus and bacterial-like regulatory mechanisms. Elucidating the transcription mechanism in archaea, which possesses a combination of bacterial and eukaryotic transcription mechanisms that are commonly regarded as separate and mutually exclusive, can provide data that will bring basic transcription mechanisms across all three domains of life.

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

“…S22). Interestingly, rpoB2 , which encodes for the RNA polymerase subunit B’’, is currently misannotated as a pseudogene due to an early stop codon which is actually the separation between subunits B’’ and H, the upstream CDS (protein P0CX06) [74]. The true rpoB2 TSS was detected by our dRNA-Seq analysis as an iTSS (TSS_10473_3) inside the longer misannotated CDS and the ‘isoform’ has pI and MW values consistent with the true RpoB2 (Fig.…”

Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal “Shock” Reveal Generic and Specific Metal Responses

“…Zn 2ϩ triggered the downregulation of the RNA polymerase protruding stalk ORFs; EЉ (Msed_2240) was downregulated by both LD and HD Zn 2ϩ , while E= (Msed_2241) and F (Msed_0062) were downregulated by HD Zn 2ϩ (82). Evidence suggests that the structure is a target for transcription factor binding, aiding in RNA polymerase recruitment and the activation of transcription machinery (82). Thus, the downregulation of these subunits would effectively stall transcription during Zn 2ϩ exposure.…”

“…Further, HD Zn 2ϩ caused the downregulation of three translation elongation factors (Msed_0084, Msed_0209, Msed_2208) and one translation initiation factor (Msed_2243) (see Table S1 in the supplemental material). Zn 2ϩ triggered the downregulation of the RNA polymerase protruding stalk ORFs; EЉ (Msed_2240) was downregulated by both LD and HD Zn 2ϩ , while E= (Msed_2241) and F (Msed_0062) were downregulated by HD Zn 2ϩ (82). Evidence suggests that the structure is a target for transcription factor binding, aiding in RNA polymerase recruitment and the activation of transcription machinery (82).…”

Isolation and Characterization of Pyrimidine Auxotrophs from the Hyperthermophilic Archaeon Sulfolobus acidocaldarius DSM 639

“…It grows optimally at 77℃ and pH 3 under aerobic and heterotrophic conditions. Many studies of the replication [3], transcription [13][14][15], and translation [11,18,24] in archaea have been carried out, but in vivo experiments were for a long time hampered by the lack of appropriate genetic system [1,20,22]. Nevertheless, various genetic tools and methods have been reported especially in halophilic archaea [7,19].…”