Archaeal RNA polymerase arrests transcription at DNA lesions

Abstract

Transcription elongation is not uniform and transcription is often hindered by protein-bound factors or DNA lesions that limit translocation and impair catalysis. Despite the high degree of sequence and structural homology of the multi-subunit RNA polymerases (RNAP), substantial differences in response to DNA lesions have been reported. Archaea encode only a single RNAP with striking structural conservation with eukaryotic RNAP II (Pol II). Here, we demonstrate that the archaeal RNAP from Thermococcus kodakarensis is sensitive to a variety of DNA lesions that pause and arrest RNAP at or adjacent to the site of DNA damage. DNA damage only halts elongation when present in the template strand, and the damage often results in RNAP arresting such that the lesion would be encapsulated with the transcription elongation complex. The strand-specific halt to archaeal transcription elongation on modified templates is supportive of RNAP recognizing DNA damage and potentially initiating DNA repair through a process akin to the well-described transcription-coupled DNA repair (TCR) pathways in Bacteria and Eukarya.

The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex

“…In Bacteria, Mfd acts as the transcription repair coupling factor and terminates TECs stalled at bulky DNA lesions while concurrently recruiting bacterial nucleotide excision repair (NER) enzymes to the site of damage. NER or the transcription-coupled repair (TCR) subpathway have not been explicitly demonstrated in Archaea, although tantalizing evidence implies NER may be active in diverse archaeal clades ( 16 , 52 , 60 – 62 ). Eta-mediated transcription termination resembles Mfd-mediated termination, and deletion of both factors from their respective organisms results in sensitivity of cells to ultraviolet-induced DNA damage ( 16 , 63 ).…”

Key Concepts and Challenges in Archaeal Transcription

“…It appears therefore likely that archaea might utilise TCR, but decisive experimental evidence is still sparse. While Thermococcus RNAP appears to be an efficient DNA-damage sensor [123], the components mediating TCR in bacteria and eukaryotes, MfD/UvrD and CSA/B, respectively, do not to have obvious homologues in archaea. A hallmark feature of transcription coupled-repair is the efficient discrimination between the transcribed and the non-transcribed strand that is reflected in different rates of repair.…”

Haloferax volcanii —a model archaeon for studying DNA replication and repair

“…The crenarchaeon S. solfataricus does not favour repair of transcribed strands suggesting that the system for TCR in this species (if present) is no faster than that of GG-NER [ 315 , 316 ]. However, the RNAP of euryarchaeon T. kodakarensis has been shown to pause at a variety of DNA lesions suggesting damage recognition by the RNAP itself, akin to mechanisms of TCR in other domains of life [ 317 ]. To date, no homologues of bacterial TRCF have been identified in archaea [ 255 ].…”