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Michael Yarus

Publications and source records attributed to Michael Yarus.

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On an RNA-membrane protogenome

Selected ribonucleotide sequences bind well to zwitterionic phospholipid bilayer membranes, though randomized RNAs do not. There are no evident repeated sequences in selected membrane binding RNAs. This implies small and varied motifs responsible for membrane affinity. Such subsequences have been partially defined. Bound RNAs require divalents like Mg2+ and/or Ca2+, preferring more ordered phospholipids: gel, ripple or rafted membranes, in that order. RNAs also bind and stabilize bilayers that are bent or sharply deformed. In contrast, RNA binding without divalents extends to negatively charged membranes formed from simpler anionic phospholipids, and to plausibly prebiotic fatty acid bilayers. RNA-membranes also retain RNA function, such as base pairing, passive transport of tryptophan, specific affinity for peptide side chains, like arginine, and catalysis by ribozymic ligase. Multiple membrane-bound RNAs with biochemical functions, linked by specific base-pairing are readily constructed. Given these experimental facts, genetic effects seem plausible. RNA functions often reside in few nucleotides, and are easily joined in a small RNA. Base-paired groups of these can evolve to be purposeful, joining related RNA functions. Such RNA groups permit complex genome functions, but require only replication of short RNAs. RNA-membranes facilitate accurate RNA segregation at cell division, and quickly evolve by appending new base-paired functions. Thus, ancient RNA-membranes could act as a protogenome, supporting orderly encoded RNA expression, inheritance and evolution before DNA and the DNA genome.

q-bio.BM

Near-ideal selection for the Standard Genetic Code

Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit quantitative assumptions, delivers the SGC (Standard Genetic Code). The pathway and evidence for it is summarized below, striving for a clearer, more complete account than was possible during its construction. Beginning with experimental amino acid-RNA interactions, code assignments are fused, codes divide and an early coding crescendo is tested for homogeneous assignments, which are then selected for independent survival in a near-empty biotic world. During escape from the site of origin and diaspora, a near-complete SGC becomes dominant by supporting proficient division. Crescendo, escape and diaspora together comprise a near-ideal least selection for a Standard Genetic Code that specifically served LUCA, likely a free-living anaerobic thermophilic microbe. Selection during diaspora conceivably made persistence across gigayears feasible.

q-bio.PE

Familiar biological, chemical and physical events credibly evolve the Standard Genetic Code

The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide transition (RNPT), finally code escape and diaspora. An index of evolutionary plausibility based on least selection takes simultaneous account of speed and accuracy of evolution, identifying favored evolutions. Combining RNA world specificities allowed convergence of early coding to SGC assignments. Secondly, this was sufficient to launch a post-RNA-world RNPT. The RNPT allowed biosynthesis of complex amino acids, depending heavily on late code fusions between coexisting independent codes. Thirdly, escape from fluctuating, but highly-evolved codes of the RNPT applied a near-ideal selection for fastest-evolving and most accurate/useful genetic codes. Concurrently, a code and its microbial carrier suited to a free-living existence necessarily evolved. The established unity of life on Earth likely traces to SGC ascendancy during escape from the RNPT, and code diaspora.

q-bio.PE