Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure

Korkhin, Yakov; Unligil, Ulug M; Littlefield, Otis; Nelson, Pamlea J.; Stuart, David I.; Sigler, Paul B.; Bell, Stephen D.; Abrescia, Nicola G. A.

doi:10.1371/journal.pbio.1000102

Cited by 115 publications

(144 citation statements)

References 52 publications

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“…Besides these two cases of subfunctionalization of individual subunits, the Pol II holoenzyme is responsible for mRNA transcription. The essential core components of RNA polymerase are well conserved across the tree of life (Zhang et al 1999;Cramer et al 2001;Hirata et al 2008;Korkhin et al 2009). …”

mentioning

confidence: 99%

Transcription-Independent Functions of an RNA Polymerase II Subunit, Rpb2, During Genome Rearrangement in the Ciliate, Oxytricha trifallax

et al. 2014

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The RNA polymerase II (Pol-II) holoenzyme, responsible for messenger RNA production, typically consists of 10-12 subunits. Our laboratory previously demonstrated that maternally deposited, long, noncoding, template RNAs are essential for programmed genome rearrangements in the ciliate Oxytricha trifallax. Here we show that such RNAs are bidirectionally transcribed and transported to the zygotic nucleus. The gene encoding the second-largest subunit of Pol-II, Rpb2, has undergone gene duplication, and the two paralogs, Rpb2-a and -b, display different expression patterns. Immunoprecipitation of double-stranded RNAs identified an association with Rpb2-a. Through immunoprecipitation and mass spectrometry, we show that Rpb2-a in early zygotes appears surprisingly unassociated with other Pol II subunits. A partial loss of function of Rpb2-a leads to an increase in expression of transposons and other germline-limited satellite repeats. We propose that evolutionary divergence of the Rpb2 paralogs has led to acquisition of transcription-independent functions during sexual reproduction that may contribute to the negative regulation of germline gene expression.

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mentioning

confidence: 99%

Transcription-Independent Functions of an RNA Polymerase II Subunit, Rpb2, During Genome Rearrangement in the Ciliate, Oxytricha trifallax

et al. 2014

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“…Of the twelve RNAPII subunits 10 are conserved within all archaea, whereas cren-and korarchaeota also contain an RPB8 homologue in line with the notion that these archaea are closer related to eukaryotes than euryarchaeota [2,19]. The crenarchaeal Sulfolobus RNAP harbours an additional RNAP subunit, Rpo13, which is not conserved in eukaryotic nor bacterial RNAPs [20]. Rpo13 is a largely disordered protein that interacts with the downstream DNA in a sequenceindependent fashion and may contribute to RNAP-DNA interactions during transcription initiation and/or elongation [21].…”

Section: Architecture Of Archaeal Rnapmentioning

confidence: 53%

Molecular Mechanisms of Transcription Initiation—Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation

Blombach

Smollett

Grohmann

et al. 2016

Journal of Molecular Biology

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Open complex formation is an important target for the regulation of transcription in all domains of life. We propose that TFE and the bacterial general transcription factor CarD, though structurally and evolutionary unrelated, show interesting parallels in their mechanism to enhance open complex formation. We argue that open complex formation is used as a way 3 to regulate transcription in all domains of life, and these regulatory mechanisms co-evolved with the basal transcription machinery.

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“…This protein presumably appeared at an early step in eukaryotic evolution [6,68]. This Rpo8 subunit (15.1 kDa; 132 residues) is located at peripheral positions, similar to eukaryotic Rpb8, and interacts with subunit Rpo1N, equivalent to the interaction of Rpb8 with Rpb1 in eukaryotes [69].…”

Section: Rpb8mentioning

confidence: 99%

Subunits Common to RNA Polymerases

Cuevas-Bermúdez¹,

Martínez-Fernández²,

Garrido-Godino³

et al. 2018

The Yeast Role in Medical Applications

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RNA polymerases are heteromultimeric complexes responsible of RNA synthesis. In yeast, as in the other eukaryotes, these complexes contain five common subunits (Rpb5, Rpb6, Rpb8, Rpb10 and Rpb12) that must have similar functions in the three RNA polymerases. However, some of these proteins have been shown to also have specific roles. In the last few decades, substantial progress has been made to understand the role of these common subunits in transcription, but their participation in the activity of each enzyme remains unclear. This review gives a comprehensive overview of current knowledge on the five common subunits of eukaryotic RNA pol, placing attention not only on their common roles in the activity of the RNA pols but also on describing specific roles for some of the complexes.

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Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure

Cited by 115 publications

References 52 publications

Transcription-Independent Functions of an RNA Polymerase II Subunit, Rpb2, During Genome Rearrangement in the Ciliate, Oxytricha trifallax

Transcription-Independent Functions of an RNA Polymerase II Subunit, Rpb2, During Genome Rearrangement in the Ciliate, Oxytricha trifallax

Molecular Mechanisms of Transcription Initiation—Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation

Subunits Common to RNA Polymerases

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