The ancient heart of the ribosomal large subunit: a response to Caetano-Anolles - PubMed (original) (raw)
Comment
. 2015 Apr;80(3-4):166-70.
doi: 10.1007/s00239-015-9678-8. Epub 2015 Apr 16.
Affiliations
- PMID: 25877522
- DOI: 10.1007/s00239-015-9678-8
Comment
The ancient heart of the ribosomal large subunit: a response to Caetano-Anolles
Anton S Petrov et al. J Mol Evol. 2015 Apr.
Abstract
Our recent Accretion Model of ribosomal evolution uses insertion fingerprints and a "trunk-branch" formalism to recapitulate the building up of common core rRNA of the Large Ribosomal Subunit. The Accretion Model is a conservative and natural extension of a method developed by Bokov and Steinberg (Nature 457:977-80, 2009), which confirms the correctness of lower resolution models by Fox and others. In each of these models, the LSU originates with the peptidyl transferase center (PTC), consistent with expectations that the ribosome is the source of defined-sequence functional proteins. In an adjacent note, Caetano-Anolles (J Mol Evol 80:162-165, 2015) disparages the Accretion Model, because it controverts the 'Growth Inferred by Genothermal Ordering' (GIGO) model. GIGO analyzes secondary structures, assigns the origin of the ribosome to a region outside of the PTC, and assumes or deduces that (i) large protein enzymes of defined amino acid sequence predate ribosomal synthesis of proteins, (ii) proteins directly replicate by non-ribosomal mechanisms, (iii) rRNA unfailingly increases in thermodynamic stability over time, and (iv) the Woese and Fox canonical tree of life is mis-rooted. Much of the specific GIGO critique of the Accretion Model is based on confusion about the three-dimensional nature of RNA and trunk-branch polymorphism; the Accretion Model incorporates several types of trunk-branch relationships.
Comment on
- Evolution of the ribosome at atomic resolution.
Petrov AS, Bernier CR, Hsiao C, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG, Harvey SC, Fox GE, Wartell RM, Hud NV, Williams LD. Petrov AS, et al. Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10251-6. doi: 10.1073/pnas.1407205111. Epub 2014 Jun 30. Proc Natl Acad Sci U S A. 2014. PMID: 24982194 Free PMC article. - Ancestral Insertions and Expansions of rRNA do not Support an Origin of the Ribosome in Its Peptidyl Transferase Center.
Caetano-Anollés G. Caetano-Anollés G. J Mol Evol. 2015 Apr;80(3-4):162-5. doi: 10.1007/s00239-015-9677-9. Epub 2015 Apr 12. J Mol Evol. 2015. PMID: 25864085 Free PMC article.
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