Liu, L. N.

Zeng, Z. P.

Zhao, Y. F.

赵玉芬

Origins of Life and Evolution of Biospheres

Xiamen University Institutional Repository

A Synthetic Protocell Model with a Self-Encoded SystemTetsuya Yomo1,21Department of Bioinformatics Engineering, Graduate School of Information Science andTechnology, Osaka University, Japan; 2Exploratory Research for Advanced Technology(ERATO), Japan Science and Technology Agency (JST)In all living systems, the genome is replicated by proteins encoded within the genome itself,which is an essential reaction for the sustentation and evolution in biological systems. Tomimic such universal process, we constructed a simplified system comprised of a minimalset of biological components in which the genetic information is replicated by a self-encoded replicase. In this system, designated as the RNA–protein self-replication system,the catalytic subunit of replicase is synthesized from the template RNA that encodes itself,the replicase subsequently replicates the template RNA used for its own production.This synthetic self-replicating system is one of the simplest systems available, consistingof just 144 gene products, which is comparable to the hypothetical minimal cell withapproximately 150 gene products. It was further encapsulated within a microcompartmentbounded by a lipid bilayer, so called liposome, resulting in a compartmentalized self-replicating system. The information and the function for its replication are encoded ondifferent molecules and are compartmentalized into the microenvironment for evolvability.Successful construction of this in liposome self-replicating system shows a significant steptoward synthetic life, as well as provides a further insight to the protomodel of cellular life.Luisi, P. L., Ferri, F. and Stano, P. (2006) Approaches to semi-synthetic minimal cells: areview. Naturwissenschaften 93, 1–13.Shimizu, Y. et al. (2001) Cell-free translation reconstituted with purified components. Nat.Biotechnol. 19, 751–755.Sunami, T. et al. (2006) Femtoliter compartment in liposomes for in vitro selection ofproteins. Anal. Biochem. 357, 128–136.Szostak, J. W., Bartel, D. P. and Luisi, P. L. (2001) Synthesizing life. Nature 409, 387–390.E-mail: yomo@ist.osaka-u.ac.jpA Novel Evolution Concept of Protein Phosphorylation MechanismZeng Zhiping, Liu Linna, Zhao YufenDepartment of Chemistry, the Key Laboratory for Chemical Biology of Fujian Province,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005,People’s Republic of ChinaProtein phosphorylation controls many cellular processes, but its mechanism is still adebatable subject, especially for protein kinases. According to the chemical property ofN-phosphoamino acids, we deduce a novel three-step covalent mechanism (Ni et al.,2005), which is much different from ‘in-line phosphorus transfer’ mechanism (Valief etal., 2003).It is known that human contains 518 kinds of protein kinases to regulate the cell’s signal.Among them, more than 80% are the serine, threonine and tyrosine kinases with thehydroxyl group as the receptors phosphotransferases with a alcohol group as acceptor (E.COrig Life Evol Biosph (2009) 39:179–392 3312.7.1.X).While in the literature, there are phosphotransferases with a nitrogenous group asacceptor (E.C 2.7.3.X) and phosphotransferases with a carboxyl group as acceptor (E.C2.7.2.X). Therefore, it might be a reasonable approach to illuminate the kinases catalyzingthe phosphoryl transfer mechanism by comparison of these three types of kinases.These three types of kinases, catalyze the γ-P of the ATP transfer to their correspondingsubstrates with three different phosphoryl groups of receptors, namely the HO-receptor,H2N-receptor and the HOOC-receptor (see figure 1).By the thermodynamical data, it seems that the carboxyl mixed anhydride 1, easy tohydrolysis, contain much higher energy than the phosphoamide bond 2 (617 kJ mol−1),which in turn is higher than the phosphoester bond 3 (597 kJ mol−1) (Lange).In this paper, by the evolution investigation, the Ser/Thr kinases phosphoryl transfermechanism might go through the combination of the P-NH-residues and the P-OOC-residues mechanism. since the key catalytic residues of Ser/Thr kinases are Lys and Asp, itwas proposed that the γ-P of the ATP is not directly transfer to the substrate, but might beproceeded by γ-P-Lys and γ-P-Asp high-energy intermediates and then finally phosphor-ylate the substrate.Lange’s Chemistry Handbook Version 15th. section 4. properties of atoms, radicals, andbonds.Ni, F., et al., Analysis of the phosphoryl transfer mechanism of c-AMP dependent proteinkinase (PKA) by penta-coodinate phosphoric transition state theory. Current Protein &Peptide Science, 2005. 6(5): p. 437–442.Valiev, M., et al., The Role of the Putative Catalytic Base in the Phosphoryl TransferReaction in a Protein Kinase: First-Principles Calculations. Journal of the AmericanChemical Society, 2003. 125(33): p. 9926–9927.E-mail: zengzhiping@xmu.edu.cn332 Orig Life Evol Biosph (2009) 39:179–392

A Novel Evolution Concept of Protein Phosphorylation Mechanism

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A Novel Evolution Concept of Protein Phosphorylation Mechanism

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