Literature DB >> 30700721

Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates.

Raghav R Poudyal1,2, Rebecca M Guth-Metzler3,4, Andrew J Veenis5,6, Erica A Frankel5,6,7, Christine D Keating8, Philip C Bevilacqua9,10,11.   

Abstract

Membraneless compartments, such as complex coacervates, have been hypothesized as plausible prebiotic micro-compartments due to their ability to sequester RNA; however, their compatibility with essential RNA World chemistries is unclear. We show that such compartments can enhance key prebiotically-relevant RNA chemistries. We demonstrate that template-directed RNA polymerization is sensitive to polycation identity, with polydiallyldimethylammonium chloride (PDAC) outperforming poly(allylamine), poly(lysine), and poly(arginine) in polycation/RNA coacervates. Differences in RNA diffusion rates between PDAC/RNA and oligoarginine/RNA coacervates imply distinct biophysical environments. Template-directed RNA polymerization is relatively insensitive to Mg2+ concentration when performed in PDAC/RNA coacervates as compared to buffer, even enabling partial rescue of the reaction in the absence of magnesium. Finally, we show enhanced activities of multiple nucleic acid enzymes including two ribozymes and a deoxyribozyme, underscoring the generality of this approach, in which functional nucleic acids like aptamers and ribozymes, and in some cases key cosolutes localize within the coacervate microenvironments.

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Year:  2019        PMID: 30700721      PMCID: PMC6353945          DOI: 10.1038/s41467-019-08353-4

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  48 in total

1.  General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme.

Authors:  S Nakano; D M Chadalavada; P C Bevilacqua
Journal:  Science       Date:  2000-02-25       Impact factor: 47.728

2.  The liquid drop nature of nucleoli.

Authors:  John F Marko
Journal:  Nucleus       Date:  2012-03-01       Impact factor: 4.197

3.  NUPACK: Analysis and design of nucleic acid systems.

Authors:  Joseph N Zadeh; Conrad D Steenberg; Justin S Bois; Brian R Wolfe; Marshall B Pierce; Asif R Khan; Robert M Dirks; Niles A Pierce
Journal:  J Comput Chem       Date:  2011-01-15       Impact factor: 3.376

4.  The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics.

Authors:  Shana Elbaum-Garfinkle; Younghoon Kim; Krzysztof Szczepaniak; Carlos Chih-Hsiung Chen; Christian R Eckmann; Sua Myong; Clifford P Brangwynne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-26       Impact factor: 11.205

5.  Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters.

Authors:  Timothy J Nott; Timothy D Craggs; Andrew J Baldwin
Journal:  Nat Chem       Date:  2016-05-16       Impact factor: 24.427

6.  Reversible generation of coacervate droplets in an enzymatic network.

Authors:  Karina K Nakashima; Jochem F Baaij; Evan Spruijt
Journal:  Soft Matter       Date:  2018-01-17       Impact factor: 3.679

7.  Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme.

Authors:  B M Chowrira; A Berzal-Herranz; J M Burke
Journal:  Biochemistry       Date:  1993-02-02       Impact factor: 3.162

8.  Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution.

Authors:  Grigory S Filonov; Jared D Moon; Nina Svensen; Samie R Jaffrey
Journal:  J Am Chem Soc       Date:  2014-11-05       Impact factor: 15.419

9.  Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis.

Authors:  Ryota Yamagami; Jamie L Bingaman; Erica A Frankel; Philip C Bevilacqua
Journal:  Nat Commun       Date:  2018-06-01       Impact factor: 14.919

10.  Compartmentalised RNA catalysis in membrane-free coacervate protocells.

Authors:  Björn Drobot; Juan M Iglesias-Artola; Kristian Le Vay; Viktoria Mayr; Mrityunjoy Kar; Moritz Kreysing; Hannes Mutschler; T-Y Dora Tang
Journal:  Nat Commun       Date:  2018-09-07       Impact factor: 14.919

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  46 in total

1.  Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary.

Authors:  Omar A Saleh; Byoung-Jin Jeon; Tim Liedl
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-29       Impact factor: 11.205

2.  Chemical-mediated translocation in protocell-based microactuators.

Authors:  Ning Gao; Mei Li; Liangfei Tian; Avinash J Patil; B V V S Pavan Kumar; Stephen Mann
Journal:  Nat Chem       Date:  2021-06-24       Impact factor: 24.427

3.  Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes.

Authors:  Ryota Yamagami; Ruochuan Huang; Philip C Bevilacqua
Journal:  Biochemistry       Date:  2019-09-12       Impact factor: 3.162

4.  Lipid sponge droplets as programmable synthetic organelles.

Authors:  Ahanjit Bhattacharya; Henrike Niederholtmeyer; Kira A Podolsky; Rupak Bhattacharya; Jing-Jin Song; Roberto J Brea; Chu-Hsien Tsai; Sunil K Sinha; Neal K Devaraj
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-21       Impact factor: 11.205

5.  Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates.

Authors:  Raghav R Poudyal; Christine D Keating; Philip C Bevilacqua
Journal:  ACS Chem Biol       Date:  2019-06-07       Impact factor: 5.100

6.  Mechanistic dissection of increased enzymatic rate in a phase-separated compartment.

Authors:  William Peeples; Michael K Rosen
Journal:  Nat Chem Biol       Date:  2021-05-25       Impact factor: 15.040

Review 7.  The role of liquid-liquid phase separation in regulating enzyme activity.

Authors:  Brian G O'Flynn; Tanja Mittag
Journal:  Curr Opin Cell Biol       Date:  2021-01-24       Impact factor: 8.382

8.  Measuring the activity and structure of functional RNAs inside compartments formed by liquid-liquid phase separation.

Authors:  Raghav R Poudyal; McCauley O Meyer; Philip C Bevilacqua
Journal:  Methods Enzymol       Date:  2020-07-10       Impact factor: 1.600

9.  Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.

Authors:  Yei-Chen Lai; Ziwei Liu; Irene A Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-25       Impact factor: 11.205

10.  Non-associative phase separation in an evaporating droplet as a model for prebiotic compartmentalization.

Authors:  Wei Guo; Andrew B Kinghorn; Yage Zhang; Qingchuan Li; Aditi Dey Poonam; Julian A Tanner; Ho Cheung Shum
Journal:  Nat Commun       Date:  2021-05-27       Impact factor: 14.919

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