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The Legend of ATP: From Origin of Life to Precision Medicine. Metabolites 2022; 12:metabo12050461. [PMID: 35629965 PMCID: PMC9148104 DOI: 10.3390/metabo12050461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 02/05/2023] Open
Abstract
Adenosine triphosphate (ATP) may be the most important biological small molecule. Since it was discovered in 1929, ATP has been regarded as life’s energy reservoir. However, this compound means more to life. Its legend starts at the dawn of life and lasts to this day. ATP must be the basic component of ancient ribozymes and may facilitate the origin of structured proteins. In the existing organisms, ATP continues to construct ribonucleic acid (RNA) and work as a protein cofactor. ATP also functions as a biological hydrotrope, which may keep macromolecules soluble in the primitive environment and can regulate phase separation in modern cells. These functions are involved in the pathogenesis of aging-related diseases and breast cancer, providing clues to discovering anti-aging agents and precision medicine tactics for breast cancer.
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Chu XY, Zhang HY. Cofactors as Molecular Fossils To Trace the Origin and Evolution of Proteins. Chembiochem 2020; 21:3161-3168. [PMID: 32515532 DOI: 10.1002/cbic.202000027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Due to their early origin and extreme conservation, cofactors are valuable molecular fossils for tracing the origin and evolution of proteins. First, as the order of protein folds binding with cofactors roughly coincides with protein-fold chronology, cofactors are considered to have facilitated the origin of primitive proteins by selecting them from pools of random amino acid sequences. Second, in the subsequent evolution of proteins, cofactors still played an important role. More interestingly, as metallic cofactors evolved with geochemical variations, some geochemical events left imprints in the chronology of protein architecture; this provides further evidence supporting the coevolution of biochemistry and geochemistry. In this paper, we attempt to review the molecular fossils used in tracing the origin and evolution of proteins, with a special focus on cofactors.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
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Kang SK, Chen BX, Tian T, Jia XS, Chu XY, Liu R, Dong PF, Yang QY, Zhang HY. ATP selection in a random peptide library consisting of prebiotic amino acids. Biochem Biophys Res Commun 2015; 466:400-5. [PMID: 26365351 DOI: 10.1016/j.bbrc.2015.09.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
Abstract
Based upon many theoretical findings on protein evolution, we proposed a ligand-selection model for the origin of proteins, in which the most ancient proteins originated from ATP selection in a pool of random peptides. To test this ligand-selection model, we constructed a random peptide library consisting of 15 types of prebiotic amino acids and then used cDNA display to perform six rounds of in vitro selection with ATP. By means of next-generation sequencing, the most prevalent sequence was defined. Biochemical and biophysical characterization of the selected peptide showed that it was stable and foldable and had ATP-hydrolysis activity as well.
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Affiliation(s)
- Shou-Kai Kang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Bai-Xue Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Tian Tian
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xi-Shuai Jia
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xin-Yi Chu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Rong Liu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Peng-Fei Dong
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qing-Yong Yang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hong-Yu Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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Role of Everlasting Triplet Expansions in Protein Evolution. J Mol Evol 2010; 72:232-9. [DOI: 10.1007/s00239-010-9425-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 12/01/2010] [Indexed: 02/05/2023]
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The origin of the genetic code and of the earliest oligopeptides. Res Microbiol 2009; 160:481-6. [PMID: 19524038 DOI: 10.1016/j.resmic.2009.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 05/26/2009] [Accepted: 05/27/2009] [Indexed: 11/22/2022]
Abstract
Reconstruction of the earliest proteins in the ancient binary alphabet [glycine family G, alanine family A] leads to repeats of G alternating with repeats of A. In addition, omnipresent motifs can be assembled in two of the earliest genes involved in energy supply, crucial for Life, i.e. ATP/GTP binding and ATPase activity. They are an almost perfect match to the alternating G and A and are complementary to each other.
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Ma BG, Chen L, Ji HF, Chen ZH, Yang FR, Wang L, Qu G, Jiang YY, Ji C, Zhang HY. Characters of very ancient proteins. Biochem Biophys Res Commun 2007; 366:607-11. [PMID: 18073136 DOI: 10.1016/j.bbrc.2007.12.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 12/04/2007] [Indexed: 11/25/2022]
Abstract
Tracing the characters of very ancient proteins represents one of the biggest challenges in the study of origin of life. Although there are no primitive protein fossils remaining, the characters of very ancient proteins can be traced by molecular fossils embedded in modern proteins. In this paper, first the prior findings in this area are outlined and then a new strategy is proposed to address the intriguing issue. It is interesting to find that various molecular fossils and different protein datasets lead to similar conclusions on the features of very ancient proteins, which can be summarized as follows: (i) the architectures of very ancient proteins belong to the following folds: P-loop containing nucleoside triphosphate hydrolases (c.37), TIM beta/alpha-barrel (c.1), NAD(P)-binding Rossmann-fold domains (c.2), Ferredoxin-like (d.58), Flavodoxin-like (c.23) and Ribonuclease H-like motif (c.55); (ii) the functions of very ancient proteins are related to the metabolisms of purine, pyrimidine, porphyrin, chlorophyll and carbohydrates; (iii) a certain part of very ancient proteins need cofactors (such as ATP, NADH or NADPH) to work normally.
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Affiliation(s)
- Bin-Guang Ma
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
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Sobolevsky Y, Frenkel ZM, Trifonov EN. Combinations of Ancestral Modules in Proteins. J Mol Evol 2007; 65:640-50. [DOI: 10.1007/s00239-007-9032-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 07/30/2007] [Accepted: 08/17/2007] [Indexed: 11/30/2022]
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Affiliation(s)
- Eviatar Nevo
- Institute of Evolution and the International Graduate Center of Evolution, University of Haifa
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