留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

代谢起源进化的分子模拟研究

阮耀 田恬 姜莹英 秦涛 褚欣奕 张红雨

阮耀, 田恬, 姜莹英, 秦涛, 褚欣奕, 张红雨. 代谢起源进化的分子模拟研究[J]. 空间科学学报, 2021, 41(1): 158-166. doi: 10.11728/cjss2021.01.158
引用本文: 阮耀, 田恬, 姜莹英, 秦涛, 褚欣奕, 张红雨. 代谢起源进化的分子模拟研究[J]. 空间科学学报, 2021, 41(1): 158-166. doi: 10.11728/cjss2021.01.158
RUAN Yao, TIAN Tian, JIANG Yingying, QIN Tao, CHU Xinyi, ZHANG Hongyu. Molecular Simulation Research on Metabolic Origin and Evolution[J]. Journal of Space Science, 2021, 41(1): 158-166. doi: 10.11728/cjss2021.01.158
Citation: RUAN Yao, TIAN Tian, JIANG Yingying, QIN Tao, CHU Xinyi, ZHANG Hongyu. Molecular Simulation Research on Metabolic Origin and Evolution[J]. Journal of Space Science, 2021, 41(1): 158-166. doi: 10.11728/cjss2021.01.158

代谢起源进化的分子模拟研究

doi: 10.11728/cjss2021.01.158
基金项目: 

国家自然科学基金面上项目资助(31870837)

详细信息
    作者简介:

    褚欣奕,E-mail:chuxy@webmail.hzau.edu.cn;张红雨,E-mail:zhy630@mail.hzau.edu.cn

  • 中图分类号: Q591

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.

     

  • [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
  • 加载中
计量
  • 文章访问数:  261
  • HTML全文浏览量:  7
  • PDF下载量:  75
  • 被引次数: 0
出版历程
  • 收稿日期:  2020-11-06
  • 刊出日期:  2021-01-15

目录

    /

    返回文章
    返回