Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

Yagi, Sota; Padhi, Aditya K.; Vucinic, Jelena; Barbe, Sophie; Schiex, Thomas; Nakagawa, Reiko; Simoncini, David; Zhang, Kam Y. J.; Tagami, Shunsuke

doi:10.1021/jacs.1c05367

Cited by 25 publications

(41 citation statements)

References 56 publications

(82 reference statements)

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“…We now report the observation of PA dimers and evidence of transient α-helical folding in aqueous buffer. These results agree well with the growing appreciation that oligomers are a key intermediate in the evolution of structured domains, particularly of symmetric and repetitive protein architectures. − The stability of the dimer, however, is modest ( K d of 233 ± 134 μM), indicating that the PA peptide exists on the cusp of foldability . The PA peptide, therefore, represents an evolutionary intermediate just prior to the emergence of an independently folding protein domain.…”

Section: Discussionsupporting

confidence: 82%

“…Probing the relationship between defined oligomeric states, folding, and phase separation is of fundamental importance to our understanding of protein evolution. Oligomeric states are now recognized as a defining feature in the early evolution of symmetric and repetitive protein architectures, including the β-trefoil, the β-propeller, , the double-ψ β-barrel, and the P-Loop NTPases . It is through oligomerization that short peptides can achieve structures of sufficient complexity and stability to execute biological functions.…”

Section: Introductionmentioning

confidence: 99%

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Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

et al. 2022

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Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance spectroscopy (EPR) to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron–electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif revealed the presence of dimers, even in the absence of RNA. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. DEER measurements of spin-diluted, doubly labeled peptides in solution indicated transient α-helical character. The distance distributions between spin labels in the dimer and the signatures of α-helical folding are consistent with the symmetric (HhH) 2 -Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.

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Section: Discussionsupporting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

et al. 2022

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“…We now report the observation of PA dimers and evidence of transient α-helical folding in aqueous buffer. These results agree well with the growing appreciation that oligomers are a key intermediate in the evolution of structured domains, particularly of symmetric and repetitive protein architectures 9,10,[12][13][14]51 . The stability of the dimer, however, is modest (Kd of 233 ± 134 µM), indicating that the PA peptide exists on the cusp of foldability.…”

Section: Coacervates As a Cradle For Protein Evolutionsupporting

confidence: 88%

“…Oligomeric states are now recognized as a defining feature in the early evolution of symmetric and repetitive protein architectures 9 , including the β-trefoil 10 the β-propeller 11,12 , the double-ψ β-barrel 13 , and the P-Loop NTPases 14 . It is through oligomerization that short peptides can achieve structures of sufficient complexity and stability to execute biological functions.…”

Section: Introductionmentioning

confidence: 99%

Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Seal

Weil-Ktorza

Despotović

et al. 2022

Preprint

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Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance (EPR) spectroscopy to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif reveals the presence of dimers, even in the absence of RNA, and transient α-helical character. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. The distance distributions between spin labels are consistent with the symmetric (HhH)2-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.

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“…Prebiotic peptide ligation in water, recently reported by Canavelli et al 24 , might have supported the transition from short peptides into functional proteins by allowing protein folding to occur in the same aqueous environment. We have recently reconstructed the ancient β-barrel fold at the core of proteinaceous RNA polymerase by the homodimerization of a peptide with only seven amino acid types 57 . Valine and lysine are the two richest amino acid types and together constitute more than half of the peptide (eight lysine and fourteen valine residues in the 43 a.a. peptide), suggesting that its ancestors (like K 2 V 6 ) might have both captured RNA and enhanced RNA polymerization by ribozymes.…”

Section: Discussionmentioning

confidence: 99%

Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion

Holliger

Tagami

2022

Nat Commun

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Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg2+-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K2V6: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl2, while enhancing it significantly at 400 mM MgCl2. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.

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Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

Cited by 25 publications

References 56 publications

Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion

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