1
|
Kumar P, Sankaranarayanan R. When Paul Berg meets Donald Crothers: an achiral connection through protein biosynthesis. Nucleic Acids Res 2024; 52:2130-2141. [PMID: 38407292 PMCID: PMC10954443 DOI: 10.1093/nar/gkae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
Outliers in scientific observations are often ignored and mostly remain unreported. However, presenting them is always beneficial since they could reflect the actual anomalies that might open new avenues. Here, we describe two examples of the above that came out of the laboratories of two of the pioneers of nucleic acid research in the area of protein biosynthesis, Paul Berg and Donald Crothers. Their work on the identification of D-aminoacyl-tRNA deacylase (DTD) and 'Discriminator hypothesis', respectively, were hugely ahead of their time and were partly against the general paradigm at that time. In both of the above works, the smallest and the only achiral amino acid turned out to be an outlier as DTD can act weakly on glycine charged tRNAs with a unique discriminator base of 'Uracil'. This peculiar nature of glycine remained an enigma for nearly half a century. With a load of available information on the subject by the turn of the century, our work on 'chiral proofreading' mechanisms during protein biosynthesis serendipitously led us to revisit these findings. Here, we describe how we uncovered an unexpected connection between them that has implications for evolution of different eukaryotic life forms.
Collapse
Affiliation(s)
- Pradeep Kumar
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Rajan Sankaranarayanan
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| |
Collapse
|
2
|
Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F. The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity. Nucleic Acids Res 2020; 48:6170-6183. [PMID: 32266934 PMCID: PMC7293025 DOI: 10.1093/nar/gkaa221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
Collapse
Affiliation(s)
- Ketty Pernod
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Laure Schaeffer
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Johana Chicher
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg - Esplanade, CNRS FRC1589, Université de Strasbourg, 2, allée Konrad Roentgen Descartes, F-67084 Strasbourg, France
| | - Eveline Hok
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Christian Rick
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Eric Westhof
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Michael Ryckelynck
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| |
Collapse
|