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Węgrzyn E, Mejdrová I, Müller FM, Nainytė M, Escobar L, Carell T. RNA-Templated Peptide Bond Formation Promotes L-Homochirality. Angew Chem Int Ed Engl 2024; 63:e202319235. [PMID: 38407532 DOI: 10.1002/anie.202319235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
The world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D-configured and the encoded amino acids that comprise the proteins of all living species feature an all-L-configuration at the α-carbon atoms. The homochirality of α-amino acids is essential for folding of the peptides into well-defined and functional 3D structures and the homochirality of D-ribose is crucial for helix formation and base-pairing. The question of why nature uses only encoded L-α-amino acids is not understood. Herein, we show that an RNA-peptide world, in which peptides grow on RNAs constructed from D-ribose, leads to the self-selection of homo-L-peptides, which provides a possible explanation for the homo-D-ribose and homo-L-amino acid combination seen in nature.
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Affiliation(s)
- Ewa Węgrzyn
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Ivana Mejdrová
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Felix M Müller
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Milda Nainytė
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Luis Escobar
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
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2
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Yao LY, Qin L, Chen Z, Lam J, Yam VWW. Assembly of Luminescent Chiral Gold(I)-Sulfido Clusters via Chiral Self-Sorting. Angew Chem Int Ed Engl 2024; 63:e202316200. [PMID: 38009456 DOI: 10.1002/anie.202316200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
Due to the ubiquity of chirality in nature, chiral self-assembly involving self-sorting behaviors has remained as one of the most important research topics of interests. Herein, starting from a racemic mixture of SEG-based (SEG=SEGPHOS) chlorogold(I) precursors, a unique chiral butterfly-shape hexadecanuclear gold(I) cluster (Au16 ) with different ratios of RSEG and SSEG ligands is obtained via homoleptic and heterochiral self-sorting. More interestingly, by employing different chlorogold(I) precursors of opposite chirality (such as RSEG -Au2 and SBIN -Au2 (BIN=BINAP)), an unprecedented heteroleptic and heterochiral self-sorting strategy has been developed to give a series of heteroleptic chiral decanuclear gold(I) clusters (Au10 ) with propellor-shape structures. Heterochiral and heteroleptic self-sorting have also been observed between enantiomers of homoleptic chiral Au10 clusters to result in the heteroleptic chiral Au10 clusters via cluster-to-cluster transformation. Incorporation of heteroleptic ligands is found to decrease the symmetry from S4 of homoleptic meso Au10 to C2 of heteroleptic chiral Au10 clusters. The chirality has been transferred from the axial chiral ligands and stored in the heteroleptic gold(I) clusters.
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Affiliation(s)
- Liao-Yuan Yao
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
- MOE Key Laboratory of Cluster Sciences, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 8 Liangxiang East Road, Beijing, 102488, P. R. China
| | - Lin Qin
- MOE Key Laboratory of Cluster Sciences, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 8 Liangxiang East Road, Beijing, 102488, P. R. China
| | - Ziyong Chen
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Jonathan Lam
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
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3
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Demongeot J, Waku J, Cohen O. Combinatorial and frequency properties of the ribosome ancestors. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:884-902. [PMID: 38303447 DOI: 10.3934/mbe.2024037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
BACKGROUND The current ribosome has evolved from the primitive stages of life on Earth. Its function is to build proteins and on the basis of this role, we are looking for a universal common ancestor to the ribosome which could: i) present optimal combinatorial properties, and ii) have left vestiges in the current molecules composing the ribosome (rRNA or r-proteins) or helping in its construction and functioning. METHODS Genomic public databases are used for finding the nucleotide sequences of rRNAs and mRNA of r-proteins and statistical calculations are performed on the occurrence in these genes of some pentamers belonging to the RNA proposed as optimal ribosome ancestor. RESULTS After having exhibited a possible solution to the problem of an RNA capable of catalyzing peptide genesis, traces of this RNA are found in many rRNAs and mRNA of r-proteins, as well as in factors contributing to the construction of the current ribosome. CONCLUSIONS The existence of an optimal primordial RNA whose function is to facilitate the creation of peptide bonds between amino acids may have contributed to accelerate the emergence of the first vital processes. Its traces should be found in many living species inside structures structurally and functionally close to the ribosome, which is already the case in the species studied in this article.
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Affiliation(s)
- Jacques Demongeot
- AGEIS, Faculty of Medicine, University Grenoble Alpes, 38700 La Tronche, France
| | - Jules Waku
- IRD UMI 209 UMMISCO and LIRIMA, University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Olivier Cohen
- AGEIS, Faculty of Medicine, University Grenoble Alpes, 38700 La Tronche, France
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Mechanism of Chiral-Selective Aminoacylation of an RNA Minihelix Explored by QM/MM Free-Energy Simulations. Life (Basel) 2023; 13:life13030722. [PMID: 36983877 PMCID: PMC10057131 DOI: 10.3390/life13030722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/10/2023] Open
Abstract
Aminoacylation of a primordial RNA minihelix composed of D-ribose shows L-amino acid preference over D-amino acid without any ribozymes or enzymes. This preference in the amino acylation reaction likely plays an important role in the establishment of homochirality in L-amino acid in modern proteins. However, molecular mechanisms of the chiral selective reaction remain unsolved mainly because of difficulty in direct observation of the reaction at the molecular scale by experiments. For seeking a possible mechanism of the chiral selectivity, quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations of the aminoacylation reactions in a modeled RNA were performed to investigate differences in their free-energy profiles along the reactions for L- and D-alanine and its physicochemical origin. The reaction is initiated by approaching a 3′-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. The QM/MM umbrella sampling MD calculations showed that the height of the free-energy barrier for L-alanine aminoacylation reaction was 17 kcal/mol, which was 9 kcal/mol lower than that for the D-alanine system. At the transition state, the distance between the negatively charged 3′-oxygen and the positively charged amino group of L-alanine was shorter than that of D-alanine, which was caused by the chirality difference of the amino acid. These results indicate that the transition state for L-alanine is more electrostatically stabilized than that for D-alanine, which would be a plausible mechanism previously unexplained for chiral selectivity in the RNA minihelix aminoacylation.
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Demongeot J, Thellier M. Primitive Oligomeric RNAs at the Origins of Life on Earth. Int J Mol Sci 2023; 24:ijms24032274. [PMID: 36768599 PMCID: PMC9916791 DOI: 10.3390/ijms24032274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
There are several theories on the origin of life, which differ by choosing the preponderant factor of emergence: main function (autocatalysis versus replication), initial location (black smokers versus ponds) or first molecule (RNA versus DNA). Among the two last ones, the first assumes that an RNA world involving a collaboration of small RNAs with amino-acids pre-existed and the second that DNA-enzyme-lipid complexes existed first. The debate between these classic theories is not closed and the arguments for one or the other of these theories have recently fueled a debate in which the two have a high degree of likelihood. It therefore seems interesting to propose a third intermediate way, based on the existence of an RNA that may have existed before the latter stages postulated by these theories, and therefore may be the missing link towards a common origin of them. To search for a possible ancestral structure, we propose as candidate a small RNA existing in ring or hairpin form in the early stages of life, which could have acted as a "proto-ribosome" by favoring the synthesis of the first peptides. Remnants of this putative candidate RNA exist in molecules nowadays involved in the ribosomal factory, the concentrations of these relics depending on the seniority of these molecules within the translation process.
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Affiliation(s)
- Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, Laboratory AGEIS EA 7407 Tools for e-Gnosis Medical, 38700 Grenoble, France
- Correspondence:
| | - Michel Thellier
- Académie des Sciences, Section Biologie Integrative, 75006 Paris, France
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6
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Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101561. [PMID: 36294996 PMCID: PMC9604999 DOI: 10.3390/life12101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The acquisition of functions via the elongation of nucleotides is an important factor in the development of the RNA world. In our previous study, we found that the introduction of complementary seven-membered kissing loops into inactive R3C ligase ribozymes revived their ligation activity. In this study, we applied the kissing complex formation-induced rearrangement of RNAs to two nonfunctional RNAs by introducing complementary seven-membered loops into each of them. By combining these two forms of RNAs, the ligase activity (derived from the R3C ligase ribozyme) as well as cleavage activity (derived from the hammerhead ribozyme) was obtained. Thus, effective RNA evolution toward the formation of a life system may require the achievement of “multiple” functions via kissing-loop interactions, as indicated in this study. Our results point toward the versatility of kissing-loop interactions in the evolution of RNA, i.e., two small nonfunctional RNAs can gain dual functions via a kissing-loop interaction.
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Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center. Life (Basel) 2022; 12:life12040573. [PMID: 35455064 PMCID: PMC9030986 DOI: 10.3390/life12040573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 12/03/2022] Open
Abstract
The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obtain peptide bond formation between aminoacyl-minihelices (primordial tRNAs, the structures composed of a coaxial stack of the acceptor stem on the T-stem of tRNA). One of the components of the PTC, P1c2UGGU (74-mer), formed a dimer and a peptide bond was formed between two aminoacyl-minihelices tethered by the dimeric P1c2UGGU. Peptide synthesis depended on both the existence of the dimeric P1c2UGGU and the sequence complementarity between the ACCA-3′ sequence of the minihelix. Thus, the tRNA-like structures derived from the PTC could have originated as a scaffold of aminoacyl-minihelices for peptide bond formation through an interaction of the CCA sequence of minihelices. Moreover, with the same origin, some would have evolved to constitute the present PTC of the ribosome, and others to function as present tRNAs.
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Roberts SJ, Liu Z, Sutherland JD. Potentially Prebiotic Synthesis of Aminoacyl-RNA via a Bridging Phosphoramidate-Ester Intermediate. J Am Chem Soc 2022; 144:4254-4259. [PMID: 35230111 PMCID: PMC9097472 DOI: 10.1021/jacs.2c00772] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Translation
according to the genetic code is made possible by selectivity
both in aminoacylation of tRNA and in anticodon/codon recognition.
In extant biology, tRNAs are selectively aminoacylated by enzymes
using high-energy intermediates, but how this might have been achieved
prior to the advent of protein synthesis has been a largely unanswered
question in prebiotic chemistry. We have now elucidated a novel, prebiotically
plausible stereoselective aminoacyl-RNA synthesis, which starts from
RNA-amino acid phosphoramidates and proceeds via phosphoramidate-ester
intermediates that subsequently undergo conversion to aminoacyl-esters
by mild acid hydrolysis. The chemistry avoids the intermediacy of
high-energy mixed carboxy-phosphate anhydrides and is greatly favored
under eutectic conditions, which also potentially allow for the requisite
pH fluctuation through the variable solubility of CO2 in
solid/liquid water.
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Affiliation(s)
- Samuel J Roberts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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9
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Trimetaphosphate-induced chiral selection between amino acid and nucleoside using 15N-31P coupling NMR. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Li D, Sun L, Ding Y, Liu M, Xie L, Liu Y, Shang L, Wu Y, Jiang HJ, Chi L, Qiu X, Xu W. Water-Induced Chiral Separation on a Au(111) Surface. ACS NANO 2021; 15:16896-16903. [PMID: 34652898 DOI: 10.1021/acsnano.1c07842] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Facing the scientific question of the origin of chirality in life, water is considered to play a crucial role in driving many biologically relevant processes in vivo. Water has been demonstrated in vitro to be related to chiral generation, amplification, and inversion, while the underlying mechanism is still not fully understood. Real-space evidence at the single-molecule level is thus urgently required to understand the role of water molecules in biomolecular chirality related issues. Herein, we choose one of the RNA bases, the biomolecule uracil (U), which self-assembles into racemic hydrogen-bonded structures. Upon water exposure, surprisingly, racemic structures could be transformed to homochiral water-involved structures, resulting in an unexpected chiral separation on the surface. The origin of chiral separation is due to preferential binding between water and the specific site of U molecules, which leads to the formation of the energetically most favorable homochiral (U-H2O-U)2 cluster as seed for subsequent chiral amplification. Such a water-driven self-assembly process may also be extended to other biologically relevant systems such as amino acids and sugars, which would provide general insights into the role that water molecules may play in the origin of homochirality in vivo.
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Affiliation(s)
- Donglin Li
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Luye Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanqi Ding
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Mengxi Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Lei Xie
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Yinfu Liu
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Lina Shang
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
| | - Yangfan Wu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People's Republic of China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Hui-Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Lifeng Chi
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People's Republic of China
| | - Xiaohui Qiu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wei Xu
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, People's Republic of China
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Horikoshi T, Noguchi H, Umehara T, Mutsuro-Aoki H, Kurihara R, Noguchi R, Hashimoto T, Watanabe Y, Ando T, Kamata K, Park SY, Tamura K. Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNA Tyr with an extra guanosine residue at the 5'-terminus. Biochem Biophys Res Commun 2021; 575:90-95. [PMID: 34461441 DOI: 10.1016/j.bbrc.2021.08.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/24/2022]
Abstract
tRNATyr of Nanoarchaeum equitans has a remarkable feature with an extra guanosine residue at the 5'-terminus. However, the N. equitans tRNATyr mutant without extra guanosine at the 5'-end was tyrosylated by tyrosyl-tRNA synthase (TyrRS). We solved the crystal structure of N. equitans TyrRS at 2.80 Å resolution. By comparing the present solved structure with the complex structures TyrRS with tRNATyr of Thermus thermophilus and Methanocaldococcus jannaschii, an arginine substitution mutant of N. equitans TyrRS at Ile200 (I200R), which is the putative closest candidate to the 5'-phosphate of C1 of N. equitans tRNATyr, was prepared. The I200R mutant tyrosylated not only wild-type tRNATyr but also the tRNA without the G-1 residue. Further tyrosylation analysis revealed that the second base of the anticodon (U35), discriminator base (A73), and C1:G72 base pair are strong recognition sites.
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Affiliation(s)
- Tatsuya Horikoshi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiroki Noguchi
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Takuya Umehara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiromi Mutsuro-Aoki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryodai Kurihara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryohei Noguchi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Takahiro Hashimoto
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Yuki Watanabe
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kenichi Kamata
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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12
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Wu LF, Su M, Liu Z, Bjork SJ, Sutherland JD. Interstrand Aminoacyl Transfer in a tRNA Acceptor Stem-Overhang Mimic. J Am Chem Soc 2021; 143:11836-11842. [PMID: 34283595 PMCID: PMC8397310 DOI: 10.1021/jacs.1c05746] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Protein-catalyzed aminoacylation
of the 3′-overhang of tRNA
by an aminoacyl-adenylate could not have taken place prior to the
advent of genetically coded peptide synthesis, and yet the latter
process has an absolute requirement for aminoacyl-tRNA. There must
therefore have been an earlier nonprotein-catalyzed means of generating
aminoacyl-tRNA. Here, we demonstrate efficient interstrand aminoacyl
transfer from an aminoacyl phosphate mixed anhydride at the 5′-terminus
of a tRNA acceptor stem mimic to the 2′,3′-diol terminus
of a short 3′-overhang. With certain five-base 3′-overhangs,
the transfer of an alanyl residue is highly stereoselective with the l-enantiomer being favored to the extent of ∼10:1 over
the d-enantiomer and is much more efficient than the transfer
of a glycyl residue. N-Acyl-aminoacyl residues are
similarly transferred from a mixed anhydride with the 5′-phosphate
to the 2′,3′-diol but with a different dependence of
efficiency and stereoselectivity on the 3′-overhang length
and sequence. Given a prebiotically plausible and compatible synthesis
of aminoacyl phosphate mixed anhydrides, these results suggest that
RNA molecules with acceptor stem termini resembling modern tRNAs could
have been spontaneously aminoacylated, in a stereoselective and chemoselective
manner, at their 2′,3′-diol termini prior to the onset
of protein-catalyzed aminoacylation.
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Affiliation(s)
- Long-Fei Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Meng Su
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Samuel J Bjork
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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13
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Ying J, Ding R, Liu Y, Zhao Y. Prebiotic Chemistry in Aqueous Environment: A Review of Peptide Synthesis and Its Relationship with Genetic Code. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianxi Ying
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Yan Liu
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
| | - Yufen Zhao
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
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14
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Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay. Biosystems 2021; 208:104481. [PMID: 34245865 DOI: 10.1016/j.biosystems.2021.104481] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 12/19/2022]
Abstract
The Rodin-Ohno hypothesis postulates that two classes of aminoacyl-tRNA synthetases were encoded complementary to double-stranded DNA. Particularly, Geobacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS, belonging to class I) and Escherichia coli histidyl-tRNA synthetase (HisRS, belonging to class II) show high complementarity of the middle base of the codons in the mRNA sequence encoding each ATP binding site. Here, for the reported 46-residue peptides designed from the three-dimensional structures of TrpRS and HisRS, amino acid activation analysis was performed using the malachite green assay, which detects the pyrophosphate departing from ATP in the forward reaction of the first step of tRNA aminoacylation. A maltose-binding protein fusion with the 46 residues of TrpRS (TrpRS46mer) exhibited high activation capacity for several amino acids in the presence of ATP and amino acids, but the activity of an alanine substitution mutant of the first histidine in the HIGH motif (TrpRS46merH15A) was largely reduced. In contrast, pyrophosphate release by HisRS46mer in the histidine activation step was lower than that in the case of TrpRS46mer. Both HisRS46mer and the alanine mutant at the 113th arginine (HisRS46merR113A) showed slightly higher levels of pyrophosphate release than the maltose-binding protein alone. These results do not rule out the Rodin-Ohno hypothesis, but may suggest the necessity of establishing unique evolutionary models from different perspectives.
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15
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Chu XY, Zhang HY. Protein Homochirality May Be Derived from Primitive Peptide Synthesis by RNA. ASTROBIOLOGY 2021; 21:628-635. [PMID: 33600215 DOI: 10.1089/ast.2020.2324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Homochirality is a feature of life, but its origin is still disputed. Recent theories indicate that the origin of homochirality coincided with that of the RNA world, but proteins have not yet been incorporated into the story. Ribosome is considered a living fossil that survived the RNA world and records the oldest interaction between RNA and proteins. Inspired by several ribosome-related findings, we propose a hypothesis as follows: the substrate chirality preference of some primitive peptide synthesis ribozymes can mediate the chirality transmission from RNA to protein. In return, the chiral preference of protective peptide-RNA interaction can bring these ribozymes an evolutionary advantage and facilitate the expansion of enantiomeric excess in peptides. Monte Carlo simulation results show that this system's chemistry model is plausible. This model can be further tested through investigation of the chirality preference for the interactions between d/l-ribose-composed rRNA homologs and l/d-amino acid-composed peptides.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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16
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Liu Z, Wu LF, Xu J, Bonfio C, Russell DA, Sutherland JD. Harnessing chemical energy for the activation and joining of prebiotic building blocks. Nat Chem 2020; 12:1023-1028. [PMID: 33093680 DOI: 10.1038/s41557-020-00564-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/21/2020] [Indexed: 11/09/2022]
Abstract
Life is an out-of-equilibrium system sustained by a continuous supply of energy. In extant biology, the generation of the primary energy currency, adenosine 5'-triphosphate and its use in the synthesis of biomolecules require enzymes. Before their emergence, alternative energy sources, perhaps assisted by simple catalysts, must have mediated the activation of carboxylates and phosphates for condensation reactions. Here, we show that the chemical energy inherent to isonitriles can be harnessed to activate nucleoside phosphates and carboxylic acids through catalysis by acid and 4,5-dicyanoimidazole under mild aqueous conditions. Simultaneous activation of carboxylates and phosphates provides multiple pathways for the generation of reactive intermediates, including mixed carboxylic acid-phosphoric acid anhydrides, for the synthesis of peptidyl-RNAs, peptides, RNA oligomers and primordial phospholipids. Our results indicate that unified prebiotic activation chemistry could have enabled the joining of building blocks in aqueous solution from a common pool and enabled the progression of a system towards higher complexity, foreshadowing today's encapsulated peptide-nucleic acid system.
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Affiliation(s)
- Ziwei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Long-Fei Wu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Jianfeng Xu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Claudia Bonfio
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - David A Russell
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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17
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Mutsuro-Aoki H, Hamachi K, Kurihara R, Tamura K. Aminoacylation of short hairpin RNAs through kissing-loop interactions indicates evolutionary trend of RNA molecules. Biosystems 2020; 197:104206. [PMID: 32640271 DOI: 10.1016/j.biosystems.2020.104206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022]
Abstract
The unique G3:U70 base pair in the acceptor stem of tRNAAla has been shown to be a critical recognition site by alanyl-tRNA synthetase (AlaRS). The base pair resides on one of the arms of the L-shaped structure of tRNA (minihelix) and the genetic code has likely evolved from a primordial tRNA-aaRS (aminoacyl-tRNA synthetase) system. In terms of the evolution of tRNA, incorporation of a G:U base pair in the structure would be important. Here, we found that two independent short hairpin RNAs change their conformation through kissing-loop interactions, finally forming a minihelix-like structure, in which the G3:U70 base pair is incorporated. The RNA system can be properly aminoacylated by the minimal Escherichia coli AlaRS variant with alanylation activity (AlaRS442N). Thus, characteristic structural features produced via kissing-loop interactions may provide important clues into the evolution of RNA.
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Affiliation(s)
- Hiromi Mutsuro-Aoki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Kokoro Hamachi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryodai Kurihara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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18
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Arutaki M, Kurihara R, Matsuoka T, Inami A, Tokunaga K, Ohno T, Takahashi H, Takano H, Ando T, Mutsuro-Aoki H, Umehara T, Tamura K. G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases. J Mol Evol 2020; 88:501-509. [DOI: 10.1007/s00239-020-09945-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/28/2020] [Indexed: 11/25/2022]
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19
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Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life. BIOLOGY 2020; 9:biology9050088. [PMID: 32344921 PMCID: PMC7285048 DOI: 10.3390/biology9050088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/06/2020] [Accepted: 04/19/2020] [Indexed: 11/17/2022]
Abstract
(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singular docosameric RNA molecule, we call the ALPHA sequence. Then, we searched for any relics of the peptides made from ALPHA in sequences deposited in the different public databases. (3) Results: Sequence matching between ALPHA and sequences from organisms among the earliest forms of life on Earth were found at high statistical relevance. We hypothesize that the frequency of appearance of relics from ALPHA sequence in present genomes has a functional necessity. (4) Conclusions: Given the fitness of ALPHA as a supportive sequence of the framework of all existing theories, and the evolution of Archaea and giant viruses, it is anticipated that the unique properties of this singular archetypal ALPHA sequence should prove useful as a model matrix for future applications, ranging from synthetic biology to DNA computing.
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20
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RNA Aptamers for a tRNA-Binding Protein from Aeropyrum pernix with Homologous Counterparts Distributed Throughout Evolution. Life (Basel) 2020; 10:life10020011. [PMID: 32024042 PMCID: PMC7175363 DOI: 10.3390/life10020011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/15/2020] [Accepted: 01/28/2020] [Indexed: 12/02/2022] Open
Abstract
In the present in vitro selection study, we isolated and characterized RNA aptamers for a tRNA-binding protein (Trbp) from an extremophile archaeon Aeropyrum pernix. Trbp-like structures are frequently found not only in aminoacyl-tRNA synthetases but also in diverse types of proteins from different organisms. They likely arose early in evolution and have played important roles in evolution through interactions with key RNA structures. RNA aptamers specific for A. pernix Trbp were successfully selected from a pool of RNAs composed of 60 nucleotides, including a random 30-nucleotide region. From the secondary structures, we obtained a shortened sequence composed of 21 nucleotides, of which the 3′-terminal single stranded CA nucleotides are essential for binding. This may be related to the initial evolutionary role of the universal CCA-3′ terminus of tRNA in the interaction with Trbp-like structures.
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21
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Kuncha SK, Kruparani SP, Sankaranarayanan R. Chiral checkpoints during protein biosynthesis. J Biol Chem 2019; 294:16535-16548. [PMID: 31591268 DOI: 10.1074/jbc.rev119.008166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein chains contain only l-amino acids, with the exception of the achiral glycine, making the chains homochiral. This homochirality is a prerequisite for proper protein folding and, hence, normal cellular function. The importance of d-amino acids as a component of the bacterial cell wall and their roles in neurotransmission in higher eukaryotes are well-established. However, the wider presence and the corresponding physiological roles of these specific amino acid stereoisomers have been appreciated only recently. Therefore, it is expected that enantiomeric fidelity has to be a key component of all of the steps in translation. Cells employ various molecular mechanisms for keeping d-amino acids away from the synthesis of nascent polypeptide chains. The major factors involved in this exclusion are aminoacyl-tRNA synthetases (aaRSs), elongation factor thermo-unstable (EF-Tu), the ribosome, and d-aminoacyl-tRNA deacylase (DTD). aaRS, EF-Tu, and the ribosome act as "chiral checkpoints" by preferentially binding to l-amino acids or l-aminoacyl-tRNAs, thereby excluding d-amino acids. Interestingly, DTD, which is conserved across all life forms, performs "chiral proofreading," as it removes d-amino acids erroneously added to tRNA. Here, we comprehensively review d-amino acids with respect to their occurrence and physiological roles, implications for chiral checkpoints required for translation fidelity, and potential use in synthetic biology.
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Affiliation(s)
- Santosh Kumar Kuncha
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India.,Academy of Scientific and Innovative Research, CSIR-CCMB Campus, Hyderabad, Telangana 500007, India
| | - Shobha P Kruparani
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
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22
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Ando T, Takahashi S, Tamura K. Principles of chemical geometry underlying chiral selectivity in RNA minihelix aminoacylation. Nucleic Acids Res 2019; 46:11144-11152. [PMID: 30321374 PMCID: PMC6265448 DOI: 10.1093/nar/gky909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/02/2018] [Indexed: 02/05/2023] Open
Abstract
The origin of homochirality in L-amino acid in proteins is one of the mysteries of the evolution of life. Experimental studies show that a non-enzymatic aminoacylation reaction of an RNA minihelix has a preference for L-amino acid over D-amino acid. The reaction initiates by approaching of a 3'-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. Here, employing molecular dynamics simulations, we examined the possible mechanisms that determine this chiral selectivity. The simulation system adopted a geometry required for the chemical reaction to occur more frequently with L-alanine than that with D-alanine. For L-alanine, the structure with this geometry was formed by a combination of stable dihedral angles along alanyl phosphate backbone with a canonical RNA structure, where the methyl group of alanine was placed on the opposite side of the approaching 3'-hydroxyl group with respect to the carbonyl plane. For D-alanine, the methyl group and the 3'-hydroxyl group were placed on the same side with respect to the carbonyl plane, which significantly decreased its ability to approach 3'-oxygen close to the carbonyl carbon compared to L-alanine. The mechanism suggested herein can explain experimentally observed chiral preferences.
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Affiliation(s)
- Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Shunichi Takahashi
- Department of Applied Electronics, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Koji Tamura
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.,Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
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23
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Demongeot J, Norris V. Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins. Life (Basel) 2019; 9:E51. [PMID: 31216720 PMCID: PMC6617141 DOI: 10.3390/life9020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 01/02/2023] Open
Abstract
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included "infinite" proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon's synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences.
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Affiliation(s)
- Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, AGEIS EA 7407 Tools for e-Gnosis Medical, 38700 La Tronche, France.
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Université de Rouen, 76821 Mont-Saint-Aignan CEDEX, France.
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24
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Ikehara K. The Origin of tRNA Deduced from Pseudomonas aeruginosa 5' Anticodon-Stem Sequence : Anticodon-stem loop hypothesis. ORIGINS LIFE EVOL B 2019; 49:61-75. [PMID: 31077036 DOI: 10.1007/s11084-019-09573-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/28/2019] [Indexed: 10/26/2022]
Abstract
The riddle of the origin of life is unsolved as yet. One of the best ways to solve the riddle would be to find a vestige of the first life from databases of DNA and/or protein of modern organisms. It would be, especially, important to know the origin of tRNA, because it mediates between genetic information and the amino acid sequence of a protein. Here I attempt to find a vestige of the origin and evolution of tRNA from base sequences of Pseudomonas aeruginosa tRNA gene. It was first perceived that 5' anticodon (AntiC) stem sequences of P. aeruginosa tRNA for translation of G-start codon (GNN) are intimately and mutually related. Then, mutual relations among all of the forty-two 5' AntiC stem sequences of P. aeruginosa tRNA were examined. These relationships imply that P. aeruginosa tRNA originated from four anticodon stem-loops (AntiC-SL) translating GNC codons to the corresponding four amino acids, Gly, Ala, Asp and Val (where N is G, C, A, or T). In contrast to the case of AntiC-stem sequence, a mutual relation map could not be drawn with D-, T- and acceptor-stem sequences of P. aeruginosa tRNA. Thus I conclude that the four AntiC-SLs were the first primeval tRNAs.
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Affiliation(s)
- Kenji Ikehara
- G&L Kyosei Institute, Koharu Bld. 202, Hokkeji 153-4, Nara, 630-8001, Japan.
- The International Institute for Advanced Studies of Japan, Kizugawadai 9-3, Kizugawa, Kyoto, 619-0225, Japan.
- Professor Emeritus of Nara Women's University, Nara, Japan.
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25
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Liu Z, Mariani A, Wu L, Ritson D, Folli A, Murphy D, Sutherland J. Tuning the reactivity of nitriles using Cu(ii) catalysis - potentially prebiotic activation of nucleotides. Chem Sci 2018; 9:7053-7057. [PMID: 30310625 PMCID: PMC6137443 DOI: 10.1039/c8sc02513d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022] Open
Abstract
A synergistic system was established involving activating nucleotides with nitriles using Cu(ii) and protecting RNA degradation by byproducts of alpha-aminonitriles.
During the transition from prebiotic chemistry to biology, a period of solution-phase, non-enzymatic activation of (oligo)nucleotides must have occurred, and accordingly, a mechanism for phosphate activation must have existed. Herein, we detail results of an investigation into prebiotic phosphate activation chemistry using simple, prebiotically available nitriles whose reactivity is increased by Cu2+ ions. Furthermore, although Cu2+ ions are known to catalyse the hydrolysis of phosphodiester bonds, we found this deleterious activity to be almost completely suppressed by inclusion of amino acids or dipeptides, which may suggest a productive relationship between protein and RNA from the outset.
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Affiliation(s)
- Ziwei Liu
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Angelica Mariani
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Longfei Wu
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Dougal Ritson
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Andrea Folli
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , UK
| | - Damien Murphy
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , UK
| | - John Sutherland
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
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26
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27
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Macé K, Gillet R. Origins of tmRNA: the missing link in the birth of protein synthesis? Nucleic Acids Res 2016; 44:8041-51. [PMID: 27484476 PMCID: PMC5041485 DOI: 10.1093/nar/gkw693] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 12/20/2022] Open
Abstract
The RNA world hypothesis refers to the early period on earth in which RNA was central in assuring both genetic continuity and catalysis. The end of this era coincided with the development of the genetic code and protein synthesis, symbolized by the apparition of the first non-random messenger RNA (mRNA). Modern transfer-messenger RNA (tmRNA) is a unique hybrid molecule which has the properties of both mRNA and transfer RNA (tRNA). It acts as a key molecule during trans-translation, a major quality control pathway of modern bacterial protein synthesis. tmRNA shares many common characteristics with ancestral RNA. Here, we present a model in which proto-tmRNAs were the first molecules on earth to support non-random protein synthesis, explaining the emergence of early genetic code. In this way, proto-tmRNA could be the missing link between the first mRNA and tRNA molecules and modern ribosome-mediated protein synthesis.
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Affiliation(s)
- Kevin Macé
- Université de Rennes 1, CNRS UMR 6290 IGDR, Translation and Folding Team, 35042 Rennes cedex, France
| | - Reynald Gillet
- Université de Rennes 1, CNRS UMR 6290 IGDR, Translation and Folding Team, 35042 Rennes cedex, France Institut Universitaire de France
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28
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Tamura K. Origins and Early Evolution of the tRNA Molecule. Life (Basel) 2015; 5:1687-99. [PMID: 26633518 PMCID: PMC4695843 DOI: 10.3390/life5041687] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 11/16/2022] Open
Abstract
Modern transfer RNAs (tRNAs) are composed of ~76 nucleotides and play an important role as "adaptor" molecules that mediate the translation of information from messenger RNAs (mRNAs). Many studies suggest that the contemporary full-length tRNA was formed by the ligation of half-sized hairpin-like RNAs. A minihelix (a coaxial stack of the acceptor stem on the T-stem of tRNA) can function both in aminoacylation by aminoacyl tRNA synthetases and in peptide bond formation on the ribosome, indicating that it may be a vestige of the ancestral tRNA. The universal CCA-3' terminus of tRNA is also a typical characteristic of the molecule. "Why CCA?" is the fundamental unanswered question, but several findings give a comprehensive picture of its origin. Here, the origins and early evolution of tRNA are discussed in terms of various perspectives, including nucleotide ligation, chiral selectivity of amino acids, genetic code evolution, and the organization of the ribosomal peptidyl transferase center (PTC). The proto-tRNA molecules may have evolved not only as adaptors but also as contributors to the composition of the ribosome.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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29
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Tamura K. Beyond the Frozen Accident: Glycine Assignment in the Genetic Code. J Mol Evol 2015; 81:69-71. [PMID: 26289730 DOI: 10.1007/s00239-015-9694-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
tRNA with a terminal UCCA-3' forms a structure in which the 3'-sequence folds back. The adenine of glycyl-AMP can base-pair with the uridine of the UCCA-3' region, which places the glycine residue in close proximity to the 3'-terminal adenosine of tRNA, possibly enabling the transfer of glycine from glycyl-AMP to tRNA. Thus, the UCCA-3'-containing tRNA (as seen in eubacterial tRNA(Gly)s) would possess an intrinsic property of glycylation by glycyl-AMP. This model provides a new perspective on the origins of the glycine assignment in the genetic code, beyond the "frozen accident" hypothesis.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan. .,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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30
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Kurihara E, Uchida S, Umehara T, Tamura K. Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis. BIOLOGY 2014; 3:452-65. [PMID: 25256424 PMCID: PMC4192621 DOI: 10.3390/biology3030452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/14/2014] [Accepted: 07/22/2014] [Indexed: 11/17/2022]
Abstract
The R3C ligase ribozyme is an artificial ligase ribozyme produced by modification of the ribozyme that lacks cytidine. Here, we attempted to modify the original R3C ribozyme (73 nucleotides) by reducing the number of nucleotides while maintaining the maximum possible catalytic efficiency. By partially deleting both the "grip" (P4 + P5) and "hammer" (P3) stem-loops, we found the critical border to retain activity comparable to that of full-length R3C. The three-way junction structure was necessary to maintain enzymatic function and the stability of the "grip" (P4 + P5) stem had a large influence on the catalytic activity of R3C. The final minimized ribozyme we obtained comprised ~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA. Our findings suggest that the autocatalytic function in ribozymes is indeed possible to obtain using sequence lengths achievable with prebiotic synthesis.
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Affiliation(s)
- Eri Kurihara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Sayuri Uchida
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Takuya Umehara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
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Rouch DA. Evolution of the first genetic cells and the universal genetic code: a hypothesis based on macromolecular coevolution of RNA and proteins. J Theor Biol 2014; 357:220-44. [PMID: 24931677 DOI: 10.1016/j.jtbi.2014.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022]
Abstract
A qualitative hypothesis based on coevolution of protein and nucleic acid macromolecules was developed to explain the evolution of the first genetic cells, from the likely organic chemical-rich environment of early earth, through to the Last Universal Common Ancestor (LUCA). The evolution of the first genetic cell was divided into three phases, proto-genetic cells I, II and III, and the transition to each milestone is described, based on development of chemical cross-catalysis, bio-cross-catalysis, and the universal genetic code, respectively. Selection of macromolecular properties of both peptides and nucleic acids, in response to environmental factors, was likely to be a key aspect of early evolution. The development of hereditable nucleic acids with various key functions; translation, transcription and replication, is described. These functions are envisaged to have coevolved with protein enzymes, from simple organic precursors. Genetically heritable nucleotides may have developed after the local earth environment had cooled below 63 °C. Around this temperature G-C bases would have been preferentially utilized for nucleotide synthesis. Under these conditions RNA type nucleotides were then likely selected from a range of different types of nucleotide backbones through template-based synthesis. Initial development of the genetic coding system was simplified by the availability of proto-messenger RNA sequences that contained only G and C bases, and the need to encode only four amino acids. The step-wise addition of further amino acids to the code was predicted to parallel the growing metabolic complexity of the proto-genetic cell. On completion of this evolutionary process the proto-genetic cell is envisaged to have become the LUCA, the last common ancestor of bacteria, eukaryote and archaea domains. Key issues addressed by the model include: (a) the transition from non-hereditable random sequences of peptides and nucleic acids to specific proteins coded by hereditable nucleotide sequences, (b) the origin of homochiral amino acids and sugars, and (c) the mutation limits on the sizes of early nucleic acid genomes. The first genome was limited to a size of about 200 base pairs.
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Affiliation(s)
- Duncan A Rouch
- Biotechnology and Environmental Biology, RMIT University, PO Box 71, Bundoora, Melbourne, Vic 3083, Australia.
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Xu J, Appel B, Balke D, Wichert C, Müller S. RNA aminoacylation mediated by sequential action of two ribozymes and a nonactivated amino acid. Chembiochem 2014; 15:1200-9. [PMID: 24764272 DOI: 10.1002/cbic.201300741] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Indexed: 01/29/2023]
Abstract
In the transition from the RNA world to the modern DNA/protein world, RNA-catalyzed aminoacylation might have been a key step towards early translation. A number of ribozymes capable of aminoacylating their own 3' termini have been developed by in vitro selection. However, all of those catalysts require a previously activated amino acid-typically an aminoacyl-AMP-as substrate. Here we present two ribozymes connected by intermolecular base pairing and carrying out the two steps of aminoacylation: ribozyme 1 loads nonactivated phenylalanine onto its phosphorylated 5' terminus, thereby forming a high-energy mixed anhydride. Thereafter, a complex of ribozymes 1 and 2 is formed by intermolecular base pairing, and the "activated" phenylalanine is transferred from the 5' terminus of ribozyme 1 to the 3' terminus of ribozyme 2. This kind of simple RNA aminoacylase complex was engineered from previously selected ribozymes possessing the two required activities. RNA aminoacylation with a nonactivated amino acid as described here is advantageous to RNA world scenarios because initial amino acid activation by an additional reagent (in most cases, ATP) and an additional ribozyme would not be necessary.
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Affiliation(s)
- Jiacui Xu
- Ernst Moritz Arndt Universität Greifswald, Institut für Biochemie, Felix Hausdorff Strasse 4, 17487 Greifswald (Germany); Current address: Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706 (USA)
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Metalloporphyrin Symmetry in Chiral Recognition and Enantioselective Catalysis. Symmetry (Basel) 2014. [DOI: 10.3390/sym6020210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Hamachi K, Hayashi H, Shimamura M, Yamaji Y, Kaneko A, Fujisawa A, Umehara T, Tamura K. Glycols modulate terminator stem stability and ligand-dependency of a glycine riboswitch. Biosystems 2013; 113:59-65. [PMID: 23721735 DOI: 10.1016/j.biosystems.2013.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The Bacillus subtilis glycine riboswitch comprises tandem glycine-binding aptamers and a putative terminator stem followed by the gcvT operon. Gene expression is regulated via the sensing of glycine. However, we found that the riboswitch behaves in a "glycine-independent" manner in the presence of polyethylene glycol (PEG) and ethylene glycol. The effect is related to the formation of a terminator stem within the expression platform under such conditions. The results revealed that increasing PEG stabilized the structure of the terminator stem. By contrast, the addition of ethylene glycol destabilized the terminator stem. PEG and ethylene glycol have opposite effects on transcription as well as on stable terminator stem formation. The glycine-independency of the riboswitch and the effects of such glycols might shed light on the evolution of riboswitches.
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Affiliation(s)
- Kokoro Hamachi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
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Abstract
Proteins, the main players in current biological systems, are produced on ribosomes by sequential amide bond (peptide bond) formations between amino-acid-bearing tRNAs. The ribosome is an exquisite super-complex of RNA-proteins, containing more than 50 proteins and at least 3 kinds of RNAs. The combination of a variety of side chains of amino acids (typically 20 kinds with some exceptions) confers proteins with extraordinary structure and functions. The origin of peptide bond formation and the ribosome is crucial to the understanding of life itself. In this article, a possible evolutionary pathway to peptide bond formation machinery (proto-ribosome) will be discussed, with a special focus on the RNA minihelix (primordial form of modern tRNA) as a starting molecule. Combining the present data with recent experimental data, we can infer that the peptidyl transferase center (PTC) evolved from a primitive system in the RNA world comprising tRNA-like molecules formed by duplication of minihelix-like small RNA.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510 Japan.
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Umehara T, Kitagawa T, Nakazawa Y, Yoshino H, Nemoto R, Tamura K. RNA tetraplex as a primordial peptide synthesis scaffold. Biosystems 2012; 109:145-50. [PMID: 22465151 DOI: 10.1016/j.biosystems.2012.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/02/2012] [Accepted: 03/08/2012] [Indexed: 11/29/2022]
Abstract
Peptide bond formation at the peptidyl transferase center on the ribosome is a crucial phenomenon in life systems. In this study, we conceptually propose possible roles of the RNA tetraplex as a scaffold for two aminoacyl minihelices that enable peptide bond formation. The basic rationale of this model is that "parallel" complementary templates composed of only 10-mer nucleotides can position two amino acids in close proximity, which is conceptually and essentially similar to the situation observed in ribosomes. Using supportive experimental data, we discuss the origin and evolution of peptide bond formation in early biological systems.
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Affiliation(s)
- Takuya Umehara
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Mutuality in Discrete and Compositional Information: Perspectives for Synthetic Genetic Codes. Cognit Comput 2011. [DOI: 10.1007/s12559-011-9116-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Guimarães RC. Metabolic basis for the self-referential genetic code. ORIGINS LIFE EVOL B 2011; 41:357-71. [PMID: 21057876 DOI: 10.1007/s11084-010-9226-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 10/08/2010] [Indexed: 11/30/2022]
Abstract
An investigation of the biosynthesis pathways producing glycine and serine was necessary to clarify an apparent inconsistency between the self-referential model (SRM) for the formation of the genetic code and the model of coevolution of encodings and of amino acid biosynthesis routes. According to the SRM proposal, glycine was the first amino acid encoded, followed by serine. The coevolution model does not state precisely which the first encodings were, only presenting a list of about ten early assignments including the derivation of glycine from serine-this being derived from the glycolysis intermediate glycerate, which reverses the order proposed by the self-referential model. Our search identified the glycine-serine pathway of syntheses based on one-carbon sources, involving activities of the glycine decarboxylase complex and its associated serine hydroxymethyltransferase, which is consistent with the order proposed by the self-referential model and supports its rationale for the origin of the genetic code: protein synthesis was developed inside an early metabolic system, serving the function of a sink of amino acids; the first peptides were glycine-rich and fit for the function of building the early ribonucleoproteins; glycine consumption in proteins drove the fixation of the glycine-serine pathway.
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Affiliation(s)
- Romeu Cardoso Guimarães
- Departamento Biologia Geral, Universidad Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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Tamura K. Molecular basis for chiral selection in RNA aminoacylation. Int J Mol Sci 2011; 12:4745-57. [PMID: 21845109 PMCID: PMC3155382 DOI: 10.3390/ijms12074745] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 06/29/2011] [Accepted: 07/18/2011] [Indexed: 12/21/2022] Open
Abstract
The chiral-selective aminoacylation of an RNA minihelix is a potential progenitor to modern tRNA-based protein synthesis using l-amino acids. This article describes the molecular basis for this chiral selection. The extended double helical form of an RNA minihelix with a CCA triplet (acceptor of an amino acid), an aminoacyl phosphate donor nucleotide (mimic of aminoacyl-AMP), and a bridging nucleotide facilitates chiral-selective aminoacylation. Energetically, the reaction is characterized by a downhill reaction wherein an amino acid migrates from a high-energy acyl phosphate linkage to a lower-energy carboxyl ester linkage. The reaction occurs under the restriction that the nucleophilic attack of O, from 3′-OH in the terminal CCA, to C, from C=O in the acyl phosphate linkage, must occur at a Bürgi-Dunitz angle, which is defined as the O–C=O angle of approximately 105°. The extended double helical form results in a steric hindrance at the side chain of the amino acid leading to chiral preference combined with cation coordinations in the amino acid and the phosphate oxygen. Such a system could have developed into the protein biosynthetic system with an exclusively chiral component (l-amino acids) via (proto) ribosomes.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Rodin AS, Szathmáry E, Rodin SN. On origin of genetic code and tRNA before translation. Biol Direct 2011; 6:14. [PMID: 21342520 PMCID: PMC3050877 DOI: 10.1186/1745-6150-6-14] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 02/22/2011] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental veto on "foresight evolution", 2) modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3) the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. RESULTS The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code) the anticodon(2-3)/codon(1-2) tetramers to their anticodon(1-2)/codon(2-3) counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other) needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator) to the eventual 76 base-long cloverleaf-shaped molecule. CONCLUSION Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ''fit'' the (likely already defined) genetic code, rather than the opposite way around. Coding triplets in this primal pre-translational code were likely similar to the anticodons, with second and third nucleotides being more important than the less specific first one. Later, when the code was expanding in co-evolution with the translation apparatus, the importance of 2-3 nucleotides of coding triplets "transferred" to the 1-2 nucleotides of their complements, thus distinguishing anticodons from codons. This evolutionary primacy of anticodons in genetic coding makes the hypothesis of primal stereo-chemical affinity between amino acids and cognate triplets, the hypothesis of coding coenzyme handles for amino acids, the hypothesis of tRNA-like genomic 3' tags suggesting that tRNAs originated in replication, and the hypothesis of ancient ribozymes-mediated operational code of tRNA aminoacylation not mutually contradicting but rather co-existing in harmony.
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Affiliation(s)
- Andrei S Rodin
- Human Genetics Center, School of Public Health, University of Texas, Houston, TX 77225, USA
- Collegium Budapest (Institute for Advanced Study), Szentháromság u. 2, H-1014 Budapest, Hungary
| | - Eörs Szathmáry
- Collegium Budapest (Institute for Advanced Study), Szentháromság u. 2, H-1014 Budapest, Hungary
- Parmenides Center for the Study of Thinking, Kirchplatz 1, D-82049 Munich/Pullach, Germany
- Institute of Biology, Eötvös University, 1c Pázmány Péter sétány, H-1117 Budapest, Hungary
| | - Sergei N Rodin
- Collegium Budapest (Institute for Advanced Study), Szentháromság u. 2, H-1014 Budapest, Hungary
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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Illangasekare M, Turk R, Peterson GC, Lladser M, Yarus M. Chiral histidine selection by D-ribose RNA. RNA (NEW YORK, N.Y.) 2010; 16:2370-2383. [PMID: 20940341 PMCID: PMC2995399 DOI: 10.1261/rna.2385310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 08/27/2010] [Indexed: 05/30/2023]
Abstract
The invariant choice of L-amino acids and D-ribose RNA for biological translation requires explanation. Here we study this chiral choice using mixed, equimolar D-ribose RNAs having 15, 18, 21, 27, 35, and 45 contiguous randomized nucleotides. These are used for simultaneous affinity selection of the smallest bound and eluted RNAs using equal amounts of L- and D-His immobilized on an achiral glass support, with racemic histidine elution. The experiment as a whole therefore determines whether RNA containing D-ribose binds L-histidine or D-histidine more easily (that is, by using a site that is more abundant/requires fewer nucleotides). The most prevalent/smallest RNA sites are reproducibly and repeatedly selected and there is a four- to sixfold greater abundance of L-histidine sites. RNA's chiral D-ribose therefore yields a more frequent fit to L-histidine. Accordingly, a D-ribose RNA site for L-His is smaller by the equivalent of just over one conserved nucleotide. The most prevalent L-His site also performs better than the most frequent D-His site-but rarer D-ribose RNAs can bind D-His with excellent affinity and discrimination. The prevalent L-His site is one we have selected before under very different conditions. Thus, selection is again reproducible, as is the recurrence of cognate coding triplets in these most probable L-His sites. If our selected RNA population were equilibrated with racemic His, we calculate that L-His would participate in seven of eight His:RNA complexes, or more. Thus, if D-ribose RNA were first chosen biologically, translational L-His usage could have followed.
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Affiliation(s)
- Mali Illangasekare
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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Active centrum hypothesis: the origin of chiral homogeneity and the RNA-world. Biosystems 2010; 103:1-12. [PMID: 20851736 DOI: 10.1016/j.biosystems.2010.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 09/06/2010] [Accepted: 09/06/2010] [Indexed: 11/22/2022]
Abstract
I propose a hypothesis on the origin of chiral homogeneity of bio-molecules based on chiral catalysis. The first chiral active centre may have formed on the surface of complexes comprising metal ions, amino acids, other coenzymes and oligomers (short RNAs). The complexes must have been dominated by short RNAs capable of self-reproduction with ligation. Most of the first complexes may have catalysed the production of nucleotides. A basic assumption is that such complexes can be assembled from their components almost freely, in a huge variety of combinations. This assumption implies that "a few" components can constitute "a huge" number of active centre types. Moreover, an experiment is proposed to test the performance of such complexes in vitro. If the complexes were built up freely from their elements, then Darwinian evolution would operate on the assembly mechanism of complexes. For the production of complexes, first their parts had to appear by forming a proper three-dimensional structure. Three possible re-building mechanisms of the proper geometric structure of complexes are proposed. First, the integration of RNA parts of complexes was assisted presumably by a pre-intron. Second, the binding of RNA parts of a complex may give rise to a "polluted" RNA world. Third, the pairing of short RNA parts and their geometric conformation may have been supported by a pre-genetic code. Finally, an evolutionary step-by-step scenario of the origin of homochirality and a "polluted" RNA world is also introduced based on the proposed combinatorial complex chemistry. Homochirality is evolved by Darwinian selection whenever the efficiency of the reflexive autocatalysis of a dynamical combinatorial library increases with the homochirality of the active centres of reactions cascades and the homochirality of the elements of the dynamical combinatorial library. Moreover, the potential importance of phospholipid membrane is also discussed.
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Abstract
The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.
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Affiliation(s)
- George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.
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Nicolas I, Chevance S, Maux PL, Simonneaux G. Chiral recognition of amines and amino acid derivatives by optically active ruthenium Halterman porphyrins in organic solvents and water. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.05.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Experimental Test of L- and D-Amino Acid Binding to L- and D-Codons Suggests that Homochirality and Codon Directionality Emerged with the Genetic Code. Symmetry (Basel) 2010. [DOI: 10.3390/sym2021180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Banik SD, Nandi N. Orientation and distance dependent chiral discrimination in the first step of the aminoacylation reaction: integrated molecular orbital and semi-empirical method (ONIOM) based calculation. Colloids Surf B Biointerfaces 2009; 74:468-76. [PMID: 19682871 DOI: 10.1016/j.colsurfb.2009.07.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 07/14/2009] [Accepted: 07/14/2009] [Indexed: 11/17/2022]
Abstract
Aminoacylation is a vital step in natural biosynthesis process of peptide and is the key step in correlating the realm of protein with the RNA world. Incorrect aminoacylation might lead to misacylation of d-amino acid in the tRNA which might cause synthesis of a hetero-peptide rather than natural homopeptide leading to the altered functionality of the peptide. However, the accuracy of this process is remarkable and leads to the attachment of the correct enantiomer of the amino acid with their cognate tRNA. Thus, the chiral discrimination is stringent. In the present work, we presented a combined ONIOM (ab initio/semi-empirical) study of the chiral discrimination in the first step of aminoacylation reaction based on a model of crystal structure of the oligomeric complex of histidyl-tRNA synthetase (HisRS) from Escherichia coli complexed with ATP and histidinol and histidyl-adenylate. The study reveals that the molecular mechanism of the chiral discrimination involves the amino acid, ATP as well as surrounding residues of the synthetase. Several factors are noted to be responsible for discrimination and explain the high level of stereospecificity of the process. The chirality of the amino acid of the substrate and its (principally) electrostatic interaction with the ATP is important for discrimination. The distance and orientational changes involved in the approach of the d-His towards the ATP is energetically unfavorable. The charge distributions on the His and ATP are important for the discrimination. Removal of the charges in the model drastically reduces the discrimination. Restricted nature of the mutual orientation within the cavity of the active site where the His and ATP are located during the change in orientation for the approach to form the adenylate makes the resultant interaction profile as different for l-His and d-His also influences chiral discrimination. The analysis of the transition state structure revealed that alteration of the chirality of the His destabilize the transition state by removing the favorable electrostatic interaction between the Glu-83 and NH(3)(+) group of the His substrate. The proximity of the surrounding residues as present in the active site of the synthetase with the His and ATP (the separation is of nanometer range) has influence of discrimination. The study provides a molecular mechanism of the retention of biological homochirality.
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Affiliation(s)
- S Dutta Banik
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
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Nandi N. Chiral discrimination in the confined environment of biological nanospace: reactions and interactions involving amino acids and peptides. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350902999682] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Human D-Tyr-tRNATyr deacylase contributes to the resistance of the cell to D-amino acids. Biochem J 2008; 417:85-94. [DOI: 10.1042/bj20080617] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DTD (D-Tyr-tRNATyr deacylase) is known to be able to deacylate D-aminoacyl-tRNAs into free D-amino acids and tRNAs and therefore contributes to cellular resistance against D-amino acids in Escherichia coli and yeast. We have found that h-DTD (human DTD) is enriched in the nuclear envelope region of mammalian cells. Treatment of HeLa cells with D-Tyr resulted in nuclear accumulation of tRNATyr. D-Tyr treatment and h-DTD silencing caused tRNATyr downregulation. Furthermore, inhibition of protein synthesis by D-Tyr treatment and h-DTD silencing were also observed. D-Tyr, D-Asp and D-Ser treatment inhibited mammalian cell viability in a dose-dependent manner; overexpression of h-DTD decreased the inhibition rate, while h-DTD-silenced cells became more sensitive to the D-amino acid treatment. Our results suggest that h-DTD may play an important role in cellular resistance against D-amino acids by deacylating D-aminoacyl tRNAs at the nuclear pore. We have also found that m-DTD (mouse DTD) is specifically enriched in central nervous system neurons, its nuclear envelope localization indicates that D-aminoacyl-tRNA editing may be vital for the survival of neurons under high concentration of D-amino acids.
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