RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life

Meyer, McCauley O.; Yamagami, Ryota; Choi, S.K.; Keating, Christine D.; Bevilacqua, Philip C.

doi:10.1101/2023.02.27.530264

Cited by 3 publications

(3 citation statements)

References 102 publications

(111 reference statements)

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“…Library preparation generally followed previously reported protocols from our lab (67)(68)(69). See the Supplementary Materials and Methods for details.…”

Section: Chita Library Preparationmentioning

confidence: 99%

“…After transcription, 3′cleavage fragments and uncleaved full-length ribozymes, which are of similar length, were selected via denaturing PAGE (Figure 1B, red enclosure). To prepare the RNA for sequencing, we employed a similar library preparation to protocols previously reported from our lab (67)(68)(69). We utilized the shared 3′-terminal hydroxyl of the 3'-cleavage fragments and full-length ribozymes to ligate on an adenylated reverse transcription primer.…”

Section: Development Of Cleavage High-throughput Assay (Chita)mentioning

confidence: 99%

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Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

McKinley,

Meyer,

Sebastian

et al. 2024

Preprint

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Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed CHiTA (Cleavage High-Throughput Assay), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymesen massein a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1, 600 previously reported putative twisters and ∼1, 000 new candidate twisters. The new candidates were identified computationally in ∼1, 000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs.GRAPHICAL ABSTRACT

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“…Library preparation generally followed previously reported protocols from our lab (67)(68)(69). See the Supplementary Materials and Methods for details.…”

Section: Chita Library Preparationmentioning

confidence: 99%

Section: Development Of Cleavage High-throughput Assay (Chita)mentioning

confidence: 99%

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

McKinley,

Meyer,

Sebastian

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Meyer et al [94] performed Next-Generation Sequencing (NGS) experiments in membraneless compartments called complex coacervates. They characterized the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments.…”

Section: Organic Composomes and Various Organic Metabolism-first Modelsmentioning

confidence: 99%

Why is Abiogenesis Such a Tough Nut to Crack?

Abel

2023

Preprint

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The latest life-origin literature is reviewed, along with grouping and classification of the most enduring models of abiogenesis. New trends are identified in origin-of-life thought. Astrobiology continues to deal mostly with inorganic and very elementary organic reactions in extreme environments. Nonequilibrium thermodynamics has received a great deal of attention. Attempts have been made to relate Bejan’s Constructal Law to life and abiogenesis. RNA World preclusions only seem to have grown, while ribozyme/peptide models have expanded. The biosemiotic movement and code biology is gaining influence in refining a more complete description of life. Prof James Tour at Rice University in a fourteen-lecture series lists a number of synthetic biochemical hurtles remaining that still need to be overcome. But the need for some sort of informational recipe, instruction, steering and control now seems to be the most prominent area of focus and concern. Even a protometabolism needed active selection and controls rather than mere constraints or law. The latest literature still does not elucidate how protometabolism was orchestrated in an inanimate, pre-evolutionary environment.

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Biomolecular condensates – extant relics or evolving microcompartments?

Rangachari

2023

Commun Biol

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Unprecedented discoveries during the past decade have unearthed the ubiquitous presence of biomolecular condensates (BCs) in diverse organisms and their involvement in a plethora of biological functions. A predominant number of BCs involve coacervation of RNA and proteins that demix from homogenous solutions by a process of phase separation well described by liquid-liquid phase separation (LLPS), which results in a phase with higher concentration and density from the bulk solution. BCs provide a simple and effective means to achieve reversible spatiotemporal control of cellular processes and adaptation to environmental stimuli in an energy-independent manner. The journey into the past of this phenomenon provides clues to the evolutionary origins of life itself. Here I assemble some current and historic discoveries on LLPS to contemplate whether BCs are extant biological hubs or evolving microcompartments. I conclude that BCs in biology could be extant as a phenomenon but are co-evolving as functionally and compositionally complex microcompartments in cells alongside the membrane-bound organelles.

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RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life

Cited by 3 publications

References 102 publications

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

Why is Abiogenesis Such a Tough Nut to Crack?

Biomolecular condensates – extant relics or evolving microcompartments?

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