title: Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene.
abstract: Aminoacyl-tRNA synthetases (aaRS) catalyze both chemical steps that translate the universal genetic code. Rodin and Ohno offered an explanation for the existence of two aaRS classes, observing that codons for the most highly conserved Class I active-site residues are anticodons for corresponding Class II active-site residues. They proposed that the two classes arose simultaneously, by translation of opposite strands from the same gene. We have characterized wild-type 46-residue peptides containing ATP-binding sites of Class I and II synthetases and those coded by a gene designed by Rosetta to encode the corresponding peptides on opposite strands. Catalysis by WT and designed peptides is saturable, and the designed peptides are sensitive to active-site residue mutation. All have comparable apparent second-order rate constants 2.9-7.0E-3 M(-1) s(-1) or ∼750,000-1,300,000 times the uncatalyzed rate. The activities of the two complementary peptides demonstrate that the unique information in a gene can have two functional interpretations, one from each complementary strand. The peptides contain phylogenetic signatures of longer, more sophisticated catalysts we call Urzymes and are short enough to bridge the gap between them and simpler uncoded peptides. Thus, they directly substantiate the sense/antisense coding ancestry of Class I and II aaRS. Furthermore, designed 46-mers achieve similar catalytic proficiency to wild-type 46-mers by significant increases in both kcat and Km values, supporting suggestions that the earliest peptide catalysts activated ATP for biosynthetic purposes.
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Luis
authors.initials: L
authors.lastname: Martinez-Rodriguez
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Ozgün
authors.initials: O
authors.lastname: Erdogan
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Mariel
authors.initials: M
authors.lastname: Jimenez-Rodriguez
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Katiria
authors.initials: K
authors.lastname: Gonzalez-Rivera
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Tishan
authors.initials: T
authors.lastname: Williams
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Violetta
authors.initials: V
authors.lastname: Weinreb
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Martha
authors.initials: M
authors.lastname: Collier
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Srinivas Niranj
authors.initials: SN
authors.lastname: Chandrasekaran
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Xavier
authors.initials: X
authors.lastname: Ambroggio
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260.
authors.forename: Brian
authors.initials: B
authors.lastname: Kuhlman
authors.affiliation: From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260 carter@med.unc.edu.
authors.forename: Charles W
authors.initials: CW
authors.lastname: Carter
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D049148:Aminoacylation; D055162:Biocatalysis; D020134:Catalytic Domain; D003062:Codon / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D015870:Gene Expression; D005815:Genetic Code; D007700:Kinetics; D008969:Molecular Sequence Data; D009154:Mutation; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D003062:Codon; D010455:Peptides; D011994:Recombinant Proteins; D000255:Adenosine Triphosphate; D000604:Amino Acyl-tRNA Synthetases
keywords: ATP; Rodin-Ohno hypothesis; amino acid activation; aminoacyl tRNA synthetase; chemical biology; enzyme catalysis; gene structure; origin of life; protein design; sense/antisense genetic coding