Breaking the mold: structures of the RNA polymerase I transcription complex reveal a new path for initiation

Jackobel, Ashleigh J.; Han, Yanping; He, Yuan; Knutson, Bruce A.

doi:10.1080/21541264.2017.1416268

Cited by 7 publications

(8 citation statements)

References 37 publications

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“…In Figure 1 (A), a model for a LUCA tRNAome is shown based on comparison of maps and the relatedness of encoded amino acids. Some of the LUCA tRNAome assignments are based on information in an accompanying paper [ 17 ]. The model for LUCA gives an indication of lineages that appear most conserved.…”

Section: Resultsmentioning

confidence: 99%

“…IM2 , for instance, the lineage tRNA Ala /tRNA Val →tRNA Ile →tRNA Phe →tRNA Tyr is indicated. Based on amino acid relatedness and positions in the codon-anticodon table, however, tRNA Leu →tRNA Phe →tRNA Tyr might be a more reasonable model [ 17 ]. We posit that tRNA Asn may originally be derived from tRNA Asp , similar to tRNA Gln being apparently derived from tRNA Glu , as might be expected based on amino acid similarity.…”

Section: Resultsmentioning

confidence: 99%

“…Restrictions against an overly inflexible 3 nt code may partly explain negative selection against adenine in the anticodon wobble position. Converting tRNA wobble adenine→inosine allows pairing with mRNA codon adenine, cytidine and uridine, increasing ambiguity of mRNA interpretation [ 12 , 13 ] Evolution of the adenine→inosine modification, therefore, provides evidence for positive selection for ambiguity at the tRNA wobble anticodon position, in order to match tRNAs with a larger set of cognate synonymous codons in mRNAs [ 17 ].…”

Section: Resultsmentioning

confidence: 99%

“…For one thing, multiple essential wobble contacts that rely on non-Watson-Crick base pairs would be disallowed. Also, ambiguity at the wobble anticodon position was likely necessary for early stage evolution of the genetic code, and wobble ambiguity remains positively selected [ 17 ]. To our knowledge, the structural explanations for degrees of freedom in pairing at the wobble position are not fully known.…”

Section: Introductionmentioning

confidence: 99%

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Rooted tRNAomes and evolution of the genetic code

et al. 2018

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We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Rooted tRNAomes and evolution of the genetic code

et al. 2018

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“…We then found that this region has DNAbinding activity, and that mutagenesis of the helices, alone or in combination, inhibited DNA-binding by PAF53 1-222 , Interestingly, the structure of the linker has not always been clearly discerned in structures of Pol I (104), possibly due to dynamics in its interactions with core Pol I or the template. It has been proposed that the linker spans the active site cleft and may in fact play a role in the narrowing of the cleft in the process of proceeding from initiation to escape (104,112). We are determining the role of the HTH in transcription, e.g.…”

Section: As Shown Inmentioning

confidence: 99%

Inducible degron-dependent depletion of the RNA polymerase I associated factor PAF53 demonstrates it is essential for cell growth and allows for the analysis of functional domains

Rothblum

McNamar

et al. 2019

Preprint

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Our knowledge of the mechanism of rDNA transcription has benefitted from the combined application of genetic techniques in yeast, and progress on the biochemistry of the various components of yeast rDNA transcription. Nomura’s laboratory derived a system in yeast for screening for mutants essential for ribosome biogenesis. Such systems have allowed investigators to not only determine if a gene was essential, but to analyze domains of the proteins for different functions in rDNA transcription in vivo. However, because there are significant differences in both the structures and components of the transcription apparatus and the patterns of regulation between mammals and yeast, there are significant deficits in our understanding of mammalian rDNA transcription. We have developed a system combining CRISPR/Cas9 and an inducible degron that allows us to combine a “genetics-like” approach to studying mammalian rDNA transcription with biochemistry. Using this system, we show that the mammalian homologue of yeast A49, PAF53, is required for rDNA transcription and mitotic growth. Further, we have been able to study the domains of the protein required for activity. We have found that while the C-terminal, DNA-binding domain (tWH) was necessary for complete function, the heterodimerization and linker domains were also essential. Analysis of the linker identified a putative DNA-binding domain. We have confirmed that the helix-turn-helix (HTH) of the linker constitutes a second DNA-binding domain within PAF53 and that the HTH is essential for PAF53 function.

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Structural Studies of Eukaryotic RNA Polymerase I Using Cryo-Electron Microscopy

Pilsl

Engel

2022

Ribosome Biogenesis

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Technical advances have pushed the resolution limit of single-particle cryo-electron microscopy (cryo-EM) throughout the past decade and made the technique accessible to a wide range of samples. Among them, multisubunit DNA-dependent RNA polymerases (Pols) are a prominent example. This review aims at briefly summarizing the architecture and structural adaptations of Pol I, highlighting the importance of cryo-electron microscopy in determining the structures of transcription complexes.

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Breaking the mold: structures of the RNA polymerase I transcription complex reveal a new path for initiation

Cited by 7 publications

References 37 publications

Rooted tRNAomes and evolution of the genetic code

Rooted tRNAomes and evolution of the genetic code

Inducible degron-dependent depletion of the RNA polymerase I associated factor PAF53 demonstrates it is essential for cell growth and allows for the analysis of functional domains

Structural Studies of Eukaryotic RNA Polymerase I Using Cryo-Electron Microscopy

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