The Origin of Life: Look Up and Look Down

Peters, John W.; Williams, Loren Dean

doi:10.1089/ast.2012.0818

Cited by 12 publications

(10 citation statements)

References 60 publications

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“…In our view, observed biopolymer universalities and idiosyncracies support a model in which polymer synthesis by condensation cooperated with hydrolytic degradation, mediated by folding and assembly, to drive chemical evolution (Brack 1987 ; Abkevich et al 1996 ; Hud and Anet 2000 ; Peters and Williams 2012 ). In contrast to the consensus, this model suggests that early selection operated at the level of hydrolytic degradation (mitigated by folding and assembly), rather than at the level of synthesis.…”

Section: Origins Of Biopolymers—origins Of Lifesupporting

confidence: 68%

Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers

et al. 2018

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Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We observe that all three biopolymer types are pre-organized, conditionally self-complementary, chemically unstable in aqueous media yet persistent because of kinetic trapping, with chiral monomers and directional chains. All three biopolymers are synthesized by dehydration reactions that are catalyzed by molecular motors driven by hydrolysis of phosphorylated nucleosides. All three biopolymers can access specific states that protect against hydrolysis. These protected states are folded, using self-complementary interactions among recurrent folding elements within a given biopolymer, or assembled, in associations between the same or different biopolymer types. Self-association in a hydrolytic environment achieves self-preservation. Heterogeneous association achieves partner-preservation. These universal properties support a model in which life’s polymers emerged simultaneously and co-evolved in a common hydrolytic milieu where molecular persistence depended on folding and assembly. We believe that an understanding of the structure, function, and origins of any given type of biopolymer requires the context of other biopolymers.

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Section: Origins Of Biopolymers—origins Of Lifesupporting

confidence: 68%

Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers

et al. 2018

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“…Thus, Urzymes appear to be an important experimental platform from which to explore both forward [ 25 , 26 ] and backward [ 18 , 19 ] in time [ 41 ]. Moreover, they also seem to be the smallest segments that retain all three of the activities associated with faithful translation of the code [ 13 ].…”

Section: Resultsmentioning

confidence: 99%

“…Williams [ 41 , 44 , 45 ] has directed a similar effort to our own that has been devoted to reducing the size of the ribosomal 23S RNA containing the peptidyl-transferase center. Analysis of the thermodynamics of catalyzed and uncatalyzed peptide bond synthesis by that catalyst [ 22 , 23 ] shows that it is substantially more primitive, even in fully evolved ribosomes, than the active sites of the aaRS.…”

Section: Resultsmentioning

confidence: 99%

What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention

Carter

2015

Life

128

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We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code. A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA. Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene. Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily. Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. That scenario documents a path to increasing complexity that obviates the need for a single polymer to act both catalytically and as an informational molecule.

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“…In this model, protein synthesis and protein folding coevolved along with the translation system. At the earliest stages, proto-peptide synthesis cooperated with differential rates of hydrolytic degradation, mediated by folding and assembly, to drive chemical evolution (1, 63–66). This model is consistent with incremental conversion of noncoded depsipeptides (which are unstructured, in part, due to their ester bonds, below) to coded polypeptide (which can fold to well-defined functional domains).…”

Section: Discussionmentioning

confidence: 99%

Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions

Frenkel-Pinter

Haynes

Martin

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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106

105

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Numerous long-standing questions in origins-of-life research center on the history of biopolymers. For example, how and why did nature select the polypeptide backbone and proteinaceous side chains? Depsipeptides, containing both ester and amide linkages, have been proposed as ancestors of polypeptides. In this paper, we investigate cationic depsipeptides that form under mild dry-down reactions. We compare the oligomerization of various cationic amino acids, including the cationic proteinaceous amino acids (lysine, Lys; arginine, Arg; and histidine, His), along with nonproteinaceous analogs of Lys harboring fewer methylene groups in their side chains. These analogs, which have been discussed as potential prebiotic alternatives to Lys, are ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid (Orn, Dab, and Dpr). We observe that the proteinaceous amino acids condense more extensively than these nonproteinaceous amino acids. Orn and Dab readily cyclize into lactams, while Dab and Dpr condense less efficiently. Furthermore, the proteinaceous amino acids exhibit more selective oligomerization through their α-amines relative to their side-chain groups. This selectivity results in predominantly linear depsipeptides in which the amino acids are α-amine−linked, analogous to today’s proteins. These results suggest a chemical basis for the selection of Lys, Arg, and His over other cationic amino acids for incorporation into proto-proteins on the early Earth. Given that electrostatics are key elements of protein−RNA and protein−DNA interactions in extant life, we hypothesize that cationic side chains incorporated into proto-peptides, as reported in this study, served in a variety of functions with ancestral nucleic acid polymers in the early stages of life.

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The Origin of Life: Look Up and Look Down

Cited by 12 publications

References 60 publications

Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers

Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers

What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention

Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions

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