Molecular Simulation Research on Metabolic Origin and Evolution
-
摘要: 新陈代谢为生命提供了物质和能量基础,与生命起源和进化密切相关.然而,由于缺乏化石证据,代谢的起源及其影响生物进化的分子机制等重要问题尚待解决.近年来,网络扩张算法等分子模拟方法的出现为解决这些问题提供了新途径.本文综述了近年来代谢起源进化的分子模拟研究,以期为相关领域学科发展提供新思路.Abstract: Metabolism provides the material and energy basis for life and played important roles in the origin and evolution of life. However, due to the lack of fossil evidence, significant issues such as the origin of metabolism and the molecular mechanisms of metabolism affecting evolution have yet to be resolved. In recent years, the emergence of molecular simulation methods such as network expansion algorithms provides new solutions to the above issues. This article will review recent molecular simulation studies on the origin and evolution of metabolism, with a view to providing new ideas for research in related fields.
-
Key words:
- Metabolism /
- Molecular simulation /
- Phosphorus /
- Oxygen
-
[1] KAUFFMAN S A. The Origins of Order:Self-Organization andSelection in Evolution[M]. Oxford:Oxford University Press, 1993 [2] WÄCHTERSHÄUSER G. The origin of life and its methodologicalchallenge[J]. J. Theor. Biol., 1997, 187 (4):483-494 [3] KAUFFMAN S A. Investigations[M]. Oxford:Oxford UniversityPress, 2000 [4] LANIER K A, WILLIAMS L D. The origin of life:models anddata[J]. J. Mol. Evol., 2017, 84(2-3):85-92 [5] KNOLL A H, CARROLL S B. Early animal evolution:emerging viewsfrom comparative biology and geology[J]. Science, 1999,284(5423):2129-2137 [6] FALKOWSKI P G, ISOZAKI Y. The story of O[J]. Science, 2008, 322:540-542 [7] SCHWARTZ A W. Phosphorus in prebiotic chemistry[J].Philosoph. Trans. Royal Soc. B:Biol. Sci., 2006,361 (1474):1743-1749 [8] KRISHNAMURTHY R, HUD N V. Introduction:chemical evolution andthe origins of life[J]. Chem. Rev., 2020, 120(11):4613-4615 [9] KANEHISA M, GOTO S. Kegg:Kyoto encyclopedia of genes andgenomes[J]. Nucl. Acids Res., 2000, 28(1):27-30 [10] KANEHISA M, SATO Y, FURUMICHI M, et al. New approach forunderstanding genome variations in kegg[J]. Nucleic Acids Res.,2019, 47(D1):D590-D595 [11] EBENHÖH O, HANDORF T, HEINRICH R. Structural analysis ofexpanding metabolic networks[J]. Genome Inform., 2004,15(1):35-45 [12] GOLDFORD J E, HARTMAN H, SMITH T F, et al. Remnants of anancient metabolism without phosphate[J]. Cell, 2017,168(6):1126-1134 [13] NITSCHKE W, MCGLYNN S E, MILNER-WHITE E J, et al. On theantiquity of metalloenzymes and their substrates in bioenergetics[J].Biochim. Biophys. Acta:Bioenerg., 2013, 1827(8-9):871-881 [14] TIAN T, CHU X Y, YANG Y, et al. Phosphates as energysources to expand metabolic networks[J]. Life, 2019,9(2):43 [15] DE ZWART I I, MEADE S J, PRATT A J. Biomimetic phosphoryltransfer catalysed by iron (ii)-mineral precipitates[J]. Geochim.Cosmochim. Acta, 2004, 68(20):4093-4098 [16] HOLM N G, DUMONT M, IVARSSON M, et al. Alkaline fluidcirculation in ultramafic rocks and formation of nucleotide constituents:a hypothesis[J]. Geochem. Trans., 2006, 7(1):1-7 [17] DE SOUZA-BARROS F, VIEYRA A. Mineral interface in extremehabitats:a niche for primitive molecular evolution for the appearance ofdifferent forms of life on earth[J]. Comp. Biochem. Physiol.Part C:Toxicol. Pharmacol., 2007, 146(1/2):10-21 [18] MARTIN W, RUSSELL M J. On the origin of biochemistry at analkaline hydrothermal vent[J]. Philosoph. Trans. Royal Soc. B:Biol. Sci., 2007, 362(1486):1887-1926 [19] ZABINSKI R F, TONEY M D. Metal ion inhibition of nonenzymaticpyridoxal phosphate catalyzed decarboxylation and transamination[J].J. Am. Chem. Soc., 2001, 123(2):193-198 [20] NELSON D L, LEHNINGER A L, COX M M. Lehninger Principles ofBiochemistry[M]. New York:Macmillan, 2008 [21] MAHEEN G, WANG Y, WANG Y, et al. Mimicking the prebioticacidic hydrothermal environment:One-pot prebiotic hydrothermal synthesisof glucose phosphates[J]. Heteroatom Chem., 2011,22(2):186-191 [22] KELLER M A, TURCHYN A V, RALSER M. Non-enzymatic glycolysis andpentose phosphate pathway-like reactions in a plausible a rchean ocean[J].Mol. Syst. Biol., 2014, 10(4):725 [23] COGGINS A J, POWNER M W. Prebiotic synthesis of phosphoenolpyruvate by α-phosphorylation-controlled triose glycolysis[J].Nature Chemistry, 2017, 9(4):310 [24] PASCAL R, POITEVIN F, BOITEAU L. Energy sources for prebioticchemistry and early life:Constraints and availability[C]//Proceedings ofthe Origins of Life and Evolution of Biospheres. Netherlands:Springer, 2009:260-261 [25] ANBAR A D, DUAN Y, LYONS T W, et al. A whiff of oxygenbefore the great oxidation event?[J]. Science, 2007,317(5846):1903-1906 [26] KATO Y, SUZUKI K, NAKAMURA K, et al. Hematite formation byoxygenated groundwater more than 2.76 billion years ago[J]. EarthPlanet. Sci. Lett., 2009, 278(1/2):40-49 [27] HOASHI M, BEVACQUA D C, OTAKE T, et al. Primary haematiteformation in an oxygenated sea 3.46 billion years ago[J]. Nat.Geosci., 2009, 2(4):301-306 [28] BAUDOUIN-CORNU P, THOMAS D. Oxygen at life's boundaries[J].Nature, 2007, 445(7123):35-36 [29] HOLLAND H. Early life on earth[C]//Proceedings of the NobelSymposium. New York:Columbia University Press, 1994:237-244 [30] RAYMOND J, BLANKENSHIP R E. Biosynthetic pathways, genereplacement and the antiquity of life[J]. Geobiology, 2004,2(4):199-203 [31] CATLING D C, GLEIN C R, ZAHNLE K J, et al. Why O2 isrequired by complex life on habitable planets and the concept of planetary"oxygenation time"[J]. Astrobiology, 2005, 5(3):415-438 [32] HEDGES S B, CHEN H, KUMAR S, et al. A genomic timescalefor the origin of eukaryotes[J]. BMC Evol. Biol., 2001,1(1):1-10 [33] BROCKS J J, LOGAN G A, BUICK R, et al. Archean molecularfossils and the early rise of eukaryotes[J]. Science, 1999,285(5430):1033-1036 [34] FALKOWSKI P G, KATZ M E, MILLIGAN A J, et al. The rise ofoxygen over the past 205 million years and the evolution of large placentalmammals[J]. Science, 2005, 309(5744):2202-2204 [35] RAYMOND J, SEGRÉ D. The effect of oxygen on biochemicalnetworks and the evolution of complex life[J]. Science, 2006,311(5768):1764-1767 [36] SUMMONS R E, BRADLEY A S, JAHNKE L L, et al. Steroids,triterpenoids and molecular oxygen[J]. Philosoph. Trans. Royal Soc.B:Biol. Sci., 2006, 361 (1470):951-968 [37] CHEN L L, WANG G Z, ZHANG H Y. Sterol biosynthesis andprokaryotes-to-eukaryotes evolution[J]. Biochem. Biophys. Res.Commun., 2007, 363(4):885-888 [38] JIANG Y Y, KONG D X, QIN T, et al. How does oxygen risedrive evolution——Clues from oxygen-dependent biosynthesis of nuclearreceptor ligands[J]. Biochem. Biophys. Res. Commun., 2010,391(2):1158-1160 [39] KONG D X, GUO M Y, XIAO Z H, et al. Historical variationof structural novelty in a natural product library[J]. Chem.Biodivers., 2011, 8(11):1968-1977 [40] JIANG Y Y, KONG D X, QIN T, et al. The impact of oxygenon metabolic evolution:a chemoinformatic investigation[J]. PLoSComput. Biol., 2012, 8(3):e1002426 [41] CAETANO-ANOLLÉS G, WANG M, CAETANO-ANOLLÉS D, et al.The origin, evolution and structure of the protein world[J].Biochem. J., 2009, 417(3):621-637 [42] MA B G, CHEN L, JI H F, et al. Characters of very ancientproteins[J]. Biochem. Biophys. Res. Commun., 2008,366(3):607-611 [43] CAETANO-ANOLLÉS G, YAFREMAVA L S, GEE H, et al. Theorigin and evolution of modern metabolism[J]. Int. J. Biochem. CellBiol., 2009, 41(2):285-297 [44] ANDREEVA A, HOWORTH D, CHANDONIA J M, et al. Data growthand its impact on the scop database:new developments[J]. Nucl.Acids Res., 2007, 36(1):D419-D425 [45] WINSTANLEY H F, ABELN S, DEANE C M. How old is your fold[J].Bioinformatics, 2005, 21(1):449-458 [46] ABELN S, DEANE C M. Fold usage on genomes and protein foldevolution[J]. Proteins:Struct., Funct., Bioinform., 2005,60(4):690-700 [47] CAETANO ANOLLÉS G, CAETANO ANOLLÉS D. An evolutionarilystructured universe of protein architecture[J]. Genome Res.,2003, 13(7):1563-1571 [48] CAETANO ANOLLES G, CAETANO ANOLLES D. Universal sharing patternsin proteomes and evolution of protein fold architecture and life[J].J. Mol. Evol., 2005, 60(4):484-498 [49] WANG M, BOCA S M, KALELKAR R, et al. A phylogenomicreconstruction of the protein world based on a genomic census of proteinfold architecture[J]. Complexity, 2006, 12(1):27-40 [50] WANG M, JIANG Y Y, KIM K M, et al. A universal molecularclock of protein folds and its power in tracing the early history ofaerobic metabolism and planet oxygenation[J]. Mol. Biol. Evol.,2011, 28(1):567-582 [51] SESSIONS A L, DOUGHTY D M, WELANDER P V, et al. Thecontinuing puzzle of the great oxidation event[J]. Curr. Biol.,2009, 19(14):R567-R574 [52] HART S, SCHLARB-RIDLEY B, BENDALL D, et al. Terminaloxidases of cyanobacteria[J]. Biochem. Soc. Trans., 2005, 33(4):832-835 [53] KIM K M, QIN T, JIANG Y Y, et al. Protein domain structureuncovers the origin of aerobic metabolism and the rise of planetaryoxygen[J]. Structure, 2012, 20(1):67-76 [54] JI H F, CHEN L, ZHANG H Y. Organic cofactors participated morefrequently than transition metals in redox reactions of primitiveproteins[J]. Bioessays, 2008, 30(8):766-771 [55] ZHU G, GOLDING G B, DEAN A M. The selective cause of an ancientadaptation[J]. Science, 2005, 307(5713):1279-1282 [56] BENNER S A, RICARDO A. Planetary systems biology[J]. Mol.Cell, 2005, 17(4):471-472 [57] ALCOTT L J, MILLS B J, POULTON S W. Stepwise earth oxygenationis an inherent property of global biogeochemical cycling[J].Science, 2019, 366(6471):1333-1337
点击查看大图
计量
- 文章访问数: 535
- HTML全文浏览量: 58
- PDF下载量: 87
- 被引次数: 0