title: Evolution of the ribosome at atomic resolution.
abstract: The origins and evolution of the ribosome, 3-4 billion years ago, remain imprinted in the biochemistry of extant life and in the structure of the ribosome. Processes of ribosomal RNA (rRNA) expansion can be "observed" by comparing 3D rRNA structures of bacteria (small), yeast (medium), and metazoans (large). rRNA size correlates well with species complexity. Differences in ribosomes across species reveal that rRNA expansion segments have been added to rRNAs without perturbing the preexisting core. Here we show that rRNA growth occurs by a limited number of processes that include inserting a branch helix onto a preexisting trunk helix and elongation of a helix. rRNA expansions can leave distinctive atomic resolution fingerprints, which we call "insertion fingerprints." Observation of insertion fingerprints in the ribosomal common core allows identification of probable ancestral expansion segments. Conceptually reversing these expansions allows extrapolation backward in time to generate models of primordial ribosomes. The approach presented here provides insight to the structure of pre-last universal common ancestor rRNAs and the subsequent expansions that shaped the peptidyl transferase center and the conserved core. We infer distinct phases of ribosomal evolution through which ribosomal particles evolve, acquiring coding and translocation, and extending and elaborating the exit tunnel.
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332; anton.petrov@biology.gatech.edu loren.williams@chemistry.gatech.edu.
authors: Anton S
authors: AS
authors: Petrov
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;
authors: Chad R
authors: CR
authors: Bernier
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan;
authors: Chiaolong
authors: C
authors: Hsiao
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;
authors: Ashlyn M
authors: AM
authors: Norris
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;
authors: Nicholas A
authors: NA
authors: Kovacs
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;
authors: Chris C
authors: CC
authors: Waterbury
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;Department of Biology and Biochemistry, University of Houston, Houston, TX 77204; and.
authors: Victor G
authors: VG
authors: Stepanov
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Biology, Georgia Institute of Technology, Atlanta, GA 30332.
authors: Stephen C
authors: SC
authors: Harvey
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;Department of Biology and Biochemistry, University of Houston, Houston, TX 77204; and.
authors: George E
authors: GE
authors: Fox
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Biology, Georgia Institute of Technology, Atlanta, GA 30332.
authors: Roger M
authors: RM
authors: Wartell
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;
authors: Nicholas V
authors: NV
authors: Hud
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332;School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332; anton.petrov@biology.gatech.edu loren.williams@chemistry.gatech.edu.
authors: Loren Dean
authors: LD
authors: Williams
mesh_terms: D000818:Animals; D001105:Archaea / Q000737:chemistry / Q000235:genetics; D001419:Bacteria / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005658:Fungi / Q000737:chemistry / Q000235:genetics; D006801:Humans; D015394:Molecular Structure; D010802:Phylogeny; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics*; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics*
chemical_list: D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012331:RNA, Fungal; D016053:RNA, Protozoan; D012335:RNA, Ribosomal
keywords: C value; RNA evolution; origin of life; phylogeny; translation