VIII 实 验 论 文 参 见 ： Preiner, M.; Igarashi, K.; Muchowska, K. B.; et al.(2020) A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism. Nature Ecology & Evolution, 4: 534–542。 IX Russell, M. J.; Nitschke, W.(2017). Methane: Fuel or exhaust at the emergence of life? Astrobiology, 17(10): 1053–1066. X 二氧化碳被氢气还原成甲酸，参见：Moret, S.; Dyson, P. J.; Laurenczy, G.(2014). Direct synthesis of formic acid from carbon dioxide by hydrogenation in acidic media. Nature communications, 5: 4017。 XI Herschy, B.; Whicher, A.; Camprubi, E.; et al. (2014). An origin-of-life reactor to simulate alkaline hydrothermal vents. Journal of molecular evolution, 79(5-6): 213–227;Volbeda, A.; Fontecilla-Camps J. C. (2006). Catalytic nickel–iron–sulfur clusters: from minerals to enzymes. In: Simonneaux, G.(eds). Bioorganometallic Chemistry. Topics in organometallic chemis try, 17: 57–82. Berlin, Germany:Springer. XII 实 验 论 文 ， 参 见 ： Herschy, B.; Whicher, A.; Camprubi, E.; et al.(2014). An origin-of-life reactor to simulate alkaline hy drothermal vents. Journal of molecular evolution, 79(5-6): 213–227。
XIII 在这个实验最终发表后的论文：Vasiliadou, R.; Dimov, N.; Szita, N.; et al.(2019). Possible mechanisms of CO2 reduc tion by H2 via prebiotic vectorial electrochemistry. Interface focus, 9(6)。 XIV Hudson, R.; de Graaf, R.; Rodin, M. S.; et al.( 2020). CO2 reduction driven by a pH gradient. Proceedings of the National Academy of Sciences, 117 (37): 22873-22879. XV 关于甲酰甲烷呋喃脱氢酶的催化原理：Wagner, T.; Ermler, U.; Shima, S.(2016). The methanogenic CO2 reduc ing-and-fixing enzyme is bifunctional and contains 46[4Fe-4S] clusters. Science, 354(6308): 114–117. XVI 关 于 甲 酰 甲 烷 呋 喃 脱 氢 酶 ， 参 见 ： Wagner, T.; Ermler, U.; Shima, S.(2016). The methanogenic CO2 reducing-and-fix ing enzyme is bifunctional and contains 46[4Fe-4S] clusters. Science, 354(6308): 114– 117。 XVII 关 于 钴 咕 啉 铁 硫 蛋 白 的 作 用 机 理 ， 参 见 ： Svetlitchnaia, T.; Svetlitchnyi, V.; Meyer, O.; Dobbek, H.(2006). Struc tural insights into methyltransfer reactions of a corrinoid iron–sulfur protein involved in acetyl-CoA synthesis. Proceedings of the National Academy of Sciences, 103(39): 14331-14336; Stich, T. A.; Seravalli, J.; Venkateshrao, S.; et al.(2006). Spec
troscopic studies of the corrinoid/iron-sulfur protein from Moorella thermoacetica. Journal of the American Chemical Soci ety, 128(15):5010–5020。 XVIII 关于一氧化碳脱氢/乙酰辅酶A合成酶，参见： Dobbek, H.; Svetlitchnyi, V.; Gremer, L.; et al.(2001). Crystal struc ture of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster. Science, 293(5533): 1281 –1285; Lindahl, P. A.(2009).Nickel-carbon bonds in acetyl-coenzyme a synthases/carbon monoxide dehydrogenases. Metal ions in life sciences, 6:133- 150。 XIX 关于乙酰辅酶A合成酶的铁硫簇A催化机制，参见： Hegg, E. L.(2004). Unraveling the Structure and mechanism of acetyl-coenzyme a synthase. Accounts of chemical research, 37(10): 775–783。 第十章 I 关于白烟囱假说对甲硫醇和硫代乙酸甲酯的倾向，参 见：Martin, W.; Russell, M. J.( 2007). On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical transactions of The Royal Society B Biological Sciences, 362(1486):1887–1925。
II Kitadai, N.; Maruyama, S.(2018). Origins of building blocks of life: A review. Geoscience frontiers, 9(4): 1117-1153. III Camprubi, E.; Jordan, S. F.; Vasiliadou, R.; Lane, N.(2017). Iron catalysis at the origin of life. IUBMB Life, 69(6):373-381. IV Whicher, A.; Camprubi, E.; Pinna, S.; et al. (2018) Acetyl phosphate as a primordial energy currency at the origin of life. Or igins of life and evolution of biospheres,;48(2):159–179. 第四幕 第十一章 I 关 于 天 花 病 毒 的 起 源 ， 参 见 ： Hughes, A. L.; Irausquin, S.; Friedman, R.(2010). The evolutionary biology of pox viruses. Infection, genetics and evolution, 10 (1): 50–59。 II 关于最复杂的拟菌病毒基因组，参见：Abrahão, J.; Silva, L.; Silva, L. S.; et al.(2018). Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nature communications, 9(749)。
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ribonucleotides in prebiotically plausible conditions. Nature, 459(7244): 239–242. IV Martin. W.; Russell. M. J.(2006). On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical transactions of The Royal Society B Biological Sciences, 362(1486): 1887–1925；Harrison, S.; Lane, N.; Life as a guide to prebiotic nucleotide synthesis. Nature communications, 9(5176). V Herschy, B.; Whicher, A.; Camprubi, E.; et al. (2014). An origin-of-life reactor to simulate alkaline hydrothermal vents. Journal of molecular evolution, 79(5-6):213–227. VI Baaske, P.; Weinert, F. M.; Duhr, S.; et al.( 2007). Extreme accumulation of nucleotides in simulated hydrothermal pore systems. Proceedings of the National Academy of Sciences, 104(22): 9346-9351; Mast, C. B.; Schink, S.; Gerland, U.; Braun, D.( 2013). Escalation of polymerization in a thermal gradient. Proceedings of the National Academy of Sciences, 110(20):8030-8035. VII White, H. B. 3rd.(1976). Coenzymes as fossils of an earlier metabolic state. Journal of molecular evolution, 7(2):101-104; Penny, D.( 2005). An interpretative review of the origin of life research. Biology & Philosophy, 20:633–671.
VIII White, H. B. 3rd.(1976). Coenzymes as fossils of an earlier metabolic state. Journal of molecular evolution, 7(2):101-104; Graham, D. E.; White, R. H. (2002). Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Natural product reports, 19(2):133-47. 第十三章 I 关于切赫发现内含子催化剪接，参见：Abelson, J. (2017). The discovery of catalytic RNA. Nature Reviews Molecular Cell Biology, 18: 653. II Nissen, P.; Hansen, J.; Ban, N.; et al. (2000).The structural basis of ribosome activity in peptide bond synthesis. Sci ence, 289(5481): 920–929. III 关于最早提出RNA世界假说的三人的论文，参见： Woese, C. R.(1967). The genetic code: The molecular basis for genetic expression. Harper & Row, 186; Crick, F. H.(1968). The origin of the genetic code. Journal of Molecular Biolo gy, 38(3): 367–379; Orgel, L. E. (1968). Evolution of the genetic apparatus. Journal of Molecular Biology, 38(3): 381–393. IV 沃尔特·吉尔伯特提出RNA世界假说的论文，参见： Gilbert, W.(1986). Origin of life: The RNA world. Na
ture, 319(6055): 618–618. V 关于连接小段RNA的酶RNA，参见：Doudna, J. A.; Usman, N.; Szostak, J. W.(1993). Ribozyme-catalyzed primer ex tension by trinucleotides: A model for the RNA-catalyzed replication of RNA. Biochemistry, 32(8): 2111-2115. VI Wochner, A.; Attwater, J.; Coulson, A.; et al. (2011). Ribozyme-catalyzed transcription of an active ribozyme. Sci ence, 332(6026):209-212. VII 关于24-3聚合酶，参见：Horning, D. P.; Joyce, G. F.(2016). Amplification of RNA by an RNA polymerase ribozyme.Proceedings of the National Academy of Sciences, 113(35): 9786-9791。 VIII 关于酶RNA自复制组合，参见：Lincoln, T. A.; Joyce, G. F.(2009). Self-sustained replication of an RNA enzyme. Sci ence.;323(5918):1229–1232. IX 关于自催化的酶RNA三元组合，参见：Vaidya, N.; Manapat, M. L.; Chen, I.A.; et al.(2012). Spontaneous network for mation among cooperative RNA replicators. Nature, 491: 72–77. 第十四章
I 关 于 斯 皮 格 曼 怪 的 发 现 ， 参 见 ： Spiegelman, S.; Haruna, I.; Holland, I. B.;et al.(1965). The synthesis of a self-propagating and infectious nucleic acid with a purified enzyme. Proceedings of the National Academy of Sciences, 54(3):919–927。 II 重现斯皮格曼怪的论文，参见：Oehlenschläger, F.; Eigen, M.(1997). 30 Years Later – a new approach to sol spiegelman’s and leslie orgel’s in vitro EVOLUTIONARY STUDIES dedicated to leslie orgel on the occasion of his 70th birthday. Origins of life and evolution of the biosphere, 27: 437–457。 III 关于RNA干扰机制的免疫功能，参见：Stram, Y.; Kuzntzova, L. (2006). Inhibition of viruses by RNA interference. Virus Genes, 32(3): 299–306; Blevins, T.; Rajeswaran, R.; Shivaprasad, P. V.; et al.(2006). Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic acids research, 34(21): 6233–46; Cerutti, H.; Casas-Mollano, J. A.(2006). On the origin and functions of RNAmediated silencing: from protists to man. Current genetics, 50(2): 81–99. IV 关于病毒抑制宿主的RNA干扰的参考文献：Lucy, A. P.; Guo, Hui-Shan.; Li, Wan-Xiang;et al.(2000). Suppression of post-transcriptional gene silencing by a
plant viral protein localized in the nucleus. The EMBO Journal, 19(7): 1672–80。 V 迪 纳 的 论 文 参 见 ： Diener, T. O.(1989). Circular RNAs: relics of precellular evolution?. Proceedings of the National Acade my of Sciences, 86(23):9370-9374。 VI 弗洛雷斯的论文，参见：Flores, R.; Gago-Zachert, S.; Serra, P.; et al.(2014). Viroids: survivors from the RNA world? An nual review of microbiology, 68:395- 414。 VII 关于类病毒的单系群问题，参见：Elena, S. F.; Dopazo, J.; de la Peña, M.; et al.(2001). Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: A reassessment. Journal of molecular evolution, 53: 155–159。 VIII 沃森总结RNA世界假说发展状况的文献，参见： Gesteland, R. F.; Atkins, J. F.(eds.) (1993). The RNA World. NY: Cold Spring Harbor Laboratory Press. IX 关于类病毒复制机制，参见：Flores, R.; Gas, M.- E.; Molina-Serrano, D.; et al.(2009). Viroid replication: rolling-circles,enzymes and ribozymes. Viruses,1(2):317–334; Flores, R.; Hernández, C.; Martínez de Alba, A. E.; et al.(2005). Viroids and
viroid-host interactions. Annual review of phytopathology, 43:117-139. X 关于转运RNA连接酶闭合类病毒，参见：Nohales, M.- A.; Molina-Serrano, D.; Flores, R.; et al.(2012). Involvement of the chloroplastic isoform of tRNA ligase in the replication of viroids belonging to the family avsunviroidae. Journal of virolo gy, 86(15): 8269- 8276。 第十五章 I 关于RNA基因组尺寸，参见：Burrell, C. J.; Howard, C. R.; Frederick A. Murphy, F. A.( 2016). Fenner and White’s Medi cal Virology(5th Edition). Academic Press。 II 关于基因组带有RNA的大肠杆菌，参见：Mehta, A. P.; Wang, Yiyang; Reed, S. A.; et al.(2018). Bacterial Genome Con taining Chimeric DNA–RNA Sequences. Journal of the American chemical society, 140(36): 11464- 11473。 III 关于逆转录酶与RNA聚合酶的相似性，参见：Gupta. S. P. (eds.)(2019).Viral polymerases: Structures, functions and roles as antiviral drug targets. Academic Press, 1-42。
IV 关于福泰尔的DNA酶系统起源假说，参见：Forterre, P.(2001). Genomics and early cellular evolution. The origin of the DNA world. Comptes Rendus de l’Académie des Sciences-Series III-Sciences de la Vie, 324(12): 1067–1076; Forterre, P.; Filée,J.; Myllykallio, H.( 2000-2013) Origin and evolution of DNA and DNA replication machineries. In: Madame curie bioscience database [Internet]. Austin (TX): Landes Bioscience. https://www.ncbi.nlm.nih.gov/books/NBK6360/; Forterre, P.( 2005). The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie, 87(9-10):793-803; For terre, P.; Krupovic, M.(2012). The origin of virions and virocells: The escape hypothesis revisited. In: Witzany G. (eds) Viruses: Essential agents of life. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4899- 6_3。 V 关 于 内 源 性 逆 转 录 病 毒 ， 参 见 ： Voisset, C.; Blancher, A.; Perron, H.; et al.(1999). Phylogeny of a novel family of human endogenous retrovirus sequences, HERV-W, in humans and other primates. AIDS research and human retrovirus es, 15(17): 1529–1533; Lavialle, C.; Cornelis, G.; Dupressoir, A.; et al.(2013). Paleovirology of ‘syncytins’, retroviral env genes exapted for a role in placentation. Philosophical transactions of the Royal Society B Biological
Sciences, 368 (1626): 20120507; Lander, E. S.; Linton, L. M.; Birren, B.; Nusbaum, C.(2001). International Human Genome Sequencing Consortium. Initial se quencing and analysis of the human genome. Nature, 409 (6822): 860–921。 VI 关于噬菌体使用U碱基DNA，参见：Pérez‐Lago, L.; Serrano‐Heras, G.; Baños, B.; et al.(2011). Characterization of Bacillus subtilis uracil‐DNA glycosylase and its inhibition by phage φ29 protein p56. Molecular microbiology, 80(6):1657-66。 VII 关于合成5-羟甲基胞嘧啶的酶的结构，参见：Song, H. K.; Sohn, S. H.; Suh, S. W.(1999). Crystal structure of deoxy cytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing com plex. The EMBO journal, 18(5):1104‐1113。 VIII 关于5-羟甲基胞嘧啶出现在哺乳动物大脑中，参见： Kriaucionis, S.; Heintz, N.(2009). The nuclear DNA base 5-hy droxymethylcytosine is present in Purkinje neurons and the brain. Science, 324 (5929): 929–930。 IX 关于对流式PCR，参见：Braun, D.; Goddard, N. L.; Libchaber, A.(2003). Exponential DNA replication by laminar con vection. Physical review letters, 91(15):158103。
X 关 于 用 乙 醛 等 小 分 子 从 头 合 成 DNA 单 体 ， 参 见 ： Teichert, J. S.; Kruse, F. M.; Trapp, O.(2019). Direct prebiotic pathway to DNA nucleosides. Angewandte chemie, 58(29)。 XI 关于真核细胞RNA催化机制，参见：Torrents, E. (2014). Ribonucleotide reductases: essential enzymes for bacterial life. Frontiers in cellular and infection microbiology, 4:52。 XII 关于RNR制造自由基，参见：Kang, G.; Taguchi, A. T.; Stubbe, J.; Drennan, C. L.(2020). Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex. Science, 368(6489): 424-427。 XIII 关于RNR自由基攻击核糖，参见：Cerqueira, N. M.; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.(2006). Dehydra tion of ribonucleotides catalyzed by ribonucleotide reductase: the role of the enzyme. Biophysical journal, 90(6):2109‐2119。 XIV 关于RNR类型，参见：Tomtera, A. B.; Zoppellaroa, G.; Andersena, N. H.; et al.(2013). Ribonucleotide reductase class I with diferent radical generating clusters, Coordination chemistry reviews, 257(1): 3- 26。
XV 关于RNR进化关系，参见：Poole, A. M.; Logan, D. T.; Sjöberg, B.-M.(2002). The evolution of ribonucleotide reduc tase: much ado about oxygen. Journal of molecular evolution, 55(2): 180–196。 XVI 福泰尔关于RNR的病毒起源，参见：Forterre, P.; Filée, J.; Myllykallio, H.( 2000-2013) Origin and evolution of DNA and DNA replication machineries. In: Madame curie bioscience database [Internet]. Austin (TX): Landes Bioscience. https://www.ncbi.nlm.nih.gov/books/NBK6360/。 第十六章 I 克里克的论文文献：Crick F.H. The origin of the genetic code. J. Mol. Biol. 1968;38:367–379. doi: 10.1016/0022-2836(68) 90392-6. II 标准密码子第一位的规律，参见：Wong, J. T.(1975). A co-evolution theory of the genetic code. Proceedings of the National Academy of Sciences, 72 (5): 1909-1912; Taylor, F. J. R.; Coates, D. (1989). The code within the codons. BioSys tems, 22(3): 177–187; Umbarger, H. E.(1978). Amino acid biosynthesis and its regulation. Annual review of biochemis try, 47: 533–606; Danmaliki, G. I.; Liu, P. B.; Hwang, P. M.(2017). Stereoselective deuteration in aspartate, asparagine,
lysine, and methionine amino acid residues using fumarate as a carbon source for Escherichia coli in D2O. Biochemistry, 56(45):6015-6029。 III 关于氨基酸侧链疏水性，参见：Wimley, W. C.; Creamer, T. P.; White, S. H.(1996). Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry, 35 (16): 5109– 5124。 IV 库宁总结影响力最大的三个标准遗传密码起源假说，参 见：Koonin, E. V.; Novozhilov, A. S.(2009). Origin and evolu tion of the genetic code: the universal enigma. IUBMB Life, 61(2):99‐111。 V 伽莫夫的论文，参见：GAMOW, G. (1954). Possible relation between deoxyribonucleic acid and protein structures. Na ture, 173, 318。 VI 立体化学假说，参见：GAMOW, G. (1954). Possible relation between deoxyribonucleic acid and protein structures.Nature, 173, 318; Pelc, S.; Welton, M. (1966). Stereochemical relationship between coding triplets and amino-acids. Na ture, 209: 868–870)； Ellington, A. D.; Khrapov, M.; Shaw, C. A.(2006). The scene of a frozen accident. RNA, 6(4):485‐498。
VII 错误最小化假说，参见：Woese, C. R.(1965). On the evolution of the genetic code. PNAS, 54(6):1546- 52；Sonneborn,T. M.(1965). Degeneracy of the genetic code: extent, nature, and genetic implications. Evolving genes and proteins, 377–397;Epstein, C. J. (1966). Role of the amino-acid “code” and of selection for conformation in the evolution of proteins. Na ture, 210(5031):25-8。 VIII 关 于 突 变 参 考 文 献 ： Suzanne Clancy (2008). Genetic mutation. Nature education, 1 (1): 187； Wellstein, A.; Pitschner,H. F.(1988). Complex doseresponse curves of atropine in man explained by diferent functions of M1- and M2-cholinoceptors. Naunyn-Schmiedeberg’s Archives of Pharmacology, 338 (1): 19–27。 IX 标准遗传密码优越性，参见：Woese, C. R.; Dugre, D. H.; Saxinger, W. C.; et al.(1966). The molecular basis for the ge netic code. Proceedings of the National Academy of Sciences, 55(4): 966-74; Freeland, S. J.; Hurst, L. D.(1998). The genetic code is one in a million. Journal of molecular evolution, 47(3):238-48。 X 协 同 进 化 假 说 ， 参 见 ： Wong, J. T.(1975). A coevolution theory of the genetic code. Proceedings of the National Academy of Sciences, 72(5):1909‐1912;
Wong, J. T.(2005). Coevolution theory of the genetic code at age thirty. Bioes says, 27(4):416-25。 XI 协 同 进 化 假 说 争 议 参 见 ： Ronneberg, T. A.; Landweber, L. F.; Freeland, S. J.(2000). Testing a biosynthetic theory of the genetic code: fact or artifact? Proceedings of the National Academy of Sciences, 97(25): 13690-5。 XII 标准遗传密码始于甘氨酸，参见：Lei, L.; Burton, Z. F.(2020). Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code. Life(Basel), 10(3):21。 XIII 密码子催化假说参见：Copley, S. D.; Smith, E.; Morowitz, H. J.(2005). A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proceedings of the National Academy of Sciences, 102 (12): 4442-4447。 XIV GADV 蛋 白 质 世 界 假 说 参 见 ： Kenji, I.(2005). Possible steps to the emergence of life: The [GADV] ‐protein world hy pothesis. The Chemical Record, 5(2): 107-118; Kenji, I.(2014). [GADV]-protein world hypothesis on the origin of life. Origins of life and evolution of biospheres, 44(4):299‐302。
第十七章 I 缺少特定类型aaRS的氨酰转运RNA合成方式参见：Ibba, M.; Söll, D.(2001). The renaissance of aminoacyl-tRNA syn thesis. EMBO Reports, 2(5): 382‐387; Bailly, M.; Blaise, M.; Lorber, B.;et al.(2007). The transamidosome: a dynamic ribonu cleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis. Molecular cell, 28(2): 228‐239; Yuan,J.; Palioura, S.; Salazar, J. C.; et al.(2006). RNAdependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proceedings of the National Academy of Sciences, 103(50):18923‐ 18927; Sauerwald, A.; Zhu, W.; Major, T. A.; et al. (2005). RNA-dependent cysteine biosynthesis in archaea. Science, 307(5717): 1969‐1972。 II 修改标准遗传密码，参见：Mandell, D. J.; Lajoie, M. J.; Mee, M. T.; et al.(2015). Biocontainment of genetically modified organisms by synthetic protein design. Nature, 518 (7537): 55–60; Zhang, Y.; Ptacin, J.; Fischer, E.; et al.(2017). A semi-syn thetic organism that stores and retrieves increased genetic information. Nature, 551: 644–647。 III 转 运 RNA 的 内 含 子 参 见 ： Randau, L.; Söll, D. (2008). Transfer RNA genes in pieces. EMBO Reports,
9(7):623‐628;Fu jishima, K.; Kanai, A.(2014). tRNA gene diversity in the three domains of life. Frontiers in genetics, 5:142。 IV 转 运 RNA 内 在 相 似 性 参 见 ： Tang, T. H.; Rozhdestvensky, T. S.; d’Orval, B. C.; et al. (2002). RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic acids research, 30, 921–930; Widmann, J.;Gi ulio, M. D.; Yarus, M.; Knight, R.(2005). tRNA creation by hairpin duplication. Journal of molecular evolution, 61, 524–530。 V 迷 你 螺 旋 起 源 更 早 ， 参 见 ： Sun, F.-J.; CaetanoAnollés, G. (2007). The origin and evolution of tRNA inferred from phy logenetic analysis of structure. Journal of Molecular Evolution, 66(1): 21–35; Fujishima, K.; Sugahara, J.; Tomita, M.; Kanai,A. (2008). Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5’and 3’ tRNA halves. PLoS ONE, 3: e1622。 VI 迷你螺旋独立结合aaRS参见：Frugier, M.; Florentz, C.; Giegé, R.(1994). Eficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide. The EMBO Journal, 13: 2218–2226; Saks, M.E.;Sampson, J.R.
(1996). Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNASer acceptor stem by E. coli seryl-tRNA synthetase. The EMBO Journal, 15: 2843 –2849。 VII 迷你螺旋的非经典碱基对决定aaRS的结合能力参见： McClain, W. H.; Foss, K.(1988). Changing the identity of a tRNA by introducing a G-U wobble pair near the 3’ acceptor end. Science, 240(4853): 793-6; Schimmel, P.; Ribas de Pouplana,L.(1995). Transfer RNA: from minihelix to genetic code. Cell, 81(7): 983-6。 VIII aaRS 的 3’ 端 域 比 反 密 码 子 域 更 古 老 ， 参 见 ： Shimizu, M.; Asahara, H.; Tamura, K.; Hasegawa, T.; Himeno, H.(1992).The role of anticodon bases and the discriminator nucleotide in the recognition of some E. coli tRNAs by their aminoacyl-tRNA synthetases. Journal of molecular evolution, 35(5): 436-43; Francklyn, C.; Schimmel, P.(1990). Enzymatic aminoacylation of an eight-base-pair microhelix with histidine. Proceedings of the National Academy of Sciences, 87(21): 8655– 8659。 IX 基因组标签假说参见：Weiner, A. M.; Maizels, N. (1999). The genomic tag hypothesis: modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein
synthesis. Biological Bulle tin, 196(3):327-8; discussion 329-30; 2, Phylogeny from Function: The Origin of tRNA Is in Replication, not Translation, In:National Academy of Sciences (US); Fitch, W. M.; Ayala, F. J.(editors)(1995). Tempo And Mode In Evolution: Genetics And Paleontology 50 Years After Simpson. Washington (DC): National Academies Press (US). Available from: https://www.ncbi.nlm. nih.gov/books/NBK232211/。 X 转 运 RNA 在 三 域 中 的 多 样 性 参 见 ： Fujishima, K.; Kanai, A.(2014). tRNA gene diversity in the three domains of life. Frontiers in Genetics, 5: 142.。 XI CCA 添 加 酶 给 病 毒 添 加 CCA 尾 ， 参 见 ： Hema, M.; Gopinath, K.; Kao, C.(2005). Repair of the tRNA-like CCA se quence in a multipartite positive-strand RNA virus. Journal of virology, 79(3): 1417‐1427。 XII 两种CCA添加酶，参见：Neuenfeldt, A.; Just, A.; Betat, H.; Mörl. M.(2008). Evolution of tRNA nucleotidyltransfer ases: A small deletion generated CC-adding enzymes. Proceedings of the National Academy of Sciences, 105 (23): 7953-7958;Bralley, P.; Chang, S. A.; Jones, G. H.(2005). A phylogeny of bacterial RNA nucleotidyltransferases: bacillus halodurans con tains
Two tRNA nucleotidyltransferases. Journal of bacteriology, 187 (17) : 5927-5936。 XIII 忒修斯的船假说参见：White, H. B. 3rd.(1976). Coenzymes as fossils of an earlier metabolic state. Journal of molecular evolution, 7(2):101‐104; Graham, D. E.; White, R. H.(2002). Elucidation of methanogenic coenzyme biosyntheses: from spec troscopy to genomics. Natural product reports, 19(2): 133-47。 XIV 剪接体进化自内含子参见：Seetharaman, M.; Eldho, N. V.; Padgett, R. A.; Dayie, K. T.(2006). Structure of a self-splic ing group II intron catalytic efector domain 5: parallels with spliceosomal U6 RNA. RNA, 12 (2): 235–47; Valadkhan, S.(2010). Role of the snRNAs in spliceosomal active site. RNA Biology, 7 (3): 345– 53。 XV aaRS进化关系与协同进化假说的匹配参见：Kim, Y.; Opron, K.; Burton, Z.F.(2019). A tRNA- and AnticodonCentric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code. Life, 9(2): 37。 XVI 多肽催化氨基酸连接转运RNA假说参见：Chatterjee, S.; Yadav, S.(2019). The origin of prebiotic information system in the peptide/RNA world: a simulation model of the evolution of translation and
the genetic code. Life, 9(1): 25; Kunnev, D.;Gospodinov, A.(2018). Possible emergence of sequence specific RNA aminoacylation via peptide intermediary to initiate dar winian evolution and code through origin of life. Life, 8(4):44。 XVII 蛋白质自我复制参见：Rout, S. K.; Friedmann, M. P.; Riek, R.; Greenwald. J.(2018). A prebiotic template-directed pep tide synthesis based on amyloids. Nature communications, 9 (1)。 XVIII 双 发 夹 假 说 参 见 ： Di Giulio, M.(2004). The origin of the tRNA molecule: implications for the origin of protein synthe sis. Journal of theoretical biology, 226(1): 89‐93; Chatterjee, S.; Yadav, S. (2019). The origin of prebiotic information system in the peptide/RNA world: a simulation model of the evolution of translation and the genetic code. Life, 9(1):25。 XIX 三重迷你螺旋假说参见：Burton, Z. F.(2020). The 3-Minihelix tRNA evolution theorem. Journal of molecular evolu tion, 88: 234–242。 XX 手性选择氨酰化假说参见：Tamura, K.; Schimmel, P. (2004). Chiral-selective aminoacylation of an RNA minihelix. Sci ence, 305(5688): 1253.
XXI 甘氨酸起始假说参见：Bernhardt, H. S.; Tate, W. P.(2008). Evidence from glycine transfer RNA of a frozen accident at the dawn of the genetic code. Biology direct, 3:53; Bernhardt, H. S.; Tate, W. P. (2010). The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stabilityenhancing binding partners to tRNA? Biology direct, 5:16。 XXII 受体臂折叠假说参见：Puglisi, E. V.; Puglisi, J. D.; Williamson, J. R.; RajBhandary, U. L.(1994). NMR analysis of tRNA acceptor stem microhelices: discriminator base change afects tRNA conformation at the 3’ end. Proceedings of the Na tional Academy of Sciences, 91(24): 11467‐11471。 XXIII 芜菁黄花叶病毒争夺缬氨酸参见：Colussi, T. M.; Costantino, D. A.; Hammond, J. A.; Ruehle, G. M.; Nix, J.C.; Kieft, J. S.(2014). The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. Na ture, 511(7509): 366‐369。 XXIV 芜菁黄花叶病毒结合其他氨基酸参见：Dreher, T. W.(2009). Role of tRNA-like structures in controlling plant virus replication. Virus research, 139(2): 217‐ 229; Tsai, C. H.; Dreher, T. W.(1991). Turnip yellow mosaic virus RNAs with anti codon loop substitutions
that result in decreased valylation fail to replicate eficiently. Journal of virology, 65(6): 3060‐ 3067;Wientges, J.; Putz, J.; Giege, R.; Florentz, C.; Schwienhorst, A.(2000). Selection of viral RNA-derived tRNA-like structures with improved valylation activities. Biochemistry, 39: 6207–18; Dreher, T. W.; Tsai, C. H.; Skuzeski, J. M.(1996). Aminoacyla tion identity switch of turnip yellow mosaic virus RNA from valine to methionine results in an infectious virus. Proceedings of the National Academy of Sciences, 93:12212–6。 XXV 转 运 RNA 样 结 构 加 快 翻 译 速 度 参 见 ： Osman,T.; Hemenway, C. L.; Buck, K. W.(2000). Role of the 3’tRNA-Like Structure in Tobacco Mosaic Virus MinusStrand RNA Synthesis by the Viral RNA-Dependent RNA Polymerase In Vitro. Jour nal of virology, 74(24): 11671-11680; Gallie, D. R.; Feder, J. N.; Schimke, R. T.; Walbot, V.(1991). Functional analysis of the tobacco mosaic virus tRNA-like structure in cytoplasmic gene regulation, Nucleic acids research, 19(18): 5031– 5036。 XXVI 病毒转运RNA样结构只凭假结就可以结合aaRS，参 见：Schimmel, P.; Alexander. R.(1998). Diverse RNA sub strates for aminoacylation: Clues to origins?
Proceedings of the National Academy of Sciences, 95(18): 10351-10353。 XXVII 粉红面包霉菌逆转录质粒参见：Kuiper，M. T.； Lambowitz, A. M.(1988). A novel reverse transcriptase activity associated with mitochondrial plasmids of neurospora. Cell, 55(4): 693-704; Chen, B.; Lambowitz, A. M.(1997). De novo and DNA primer-mediated initiation of cDNA synthesis by the mauriceville retroplasmid reverse transcriptase involve recognition of a 3’ CCA sequence. Journal of molecular biology, 271(3): 311- 32。 XXVIII 关于逆转录质粒的自我剪切参见：Saville, B. J.; Collins, R. A.(1990). A site-specific self-cleavage reaction per formed by a novel RNA in Neurospora mitochondria. Cell, 61(4): 685-696。 XXIX 逆转录质粒的逆转录酶逆转录转运RNA参见：Chiang, C. C.; Lambowitz, A. M.(1997). The Mauriceville ret roplasmid reverse transcriptase initiates cDNA synthesis de novo at the 3’ end of tRNAs. Molecular and cellular biolo gy, 17(8): 4526‐4535。 第十八章
I 肽基转移酶中心的精确结构和催化原理参见：Yonath, A.(2002). High-resolution structures of large ribosomal sub units from mesophilic eubacteria and halophilic archaea at various functional States. Current protein and peptide sci ence, 3(1): 67‐78; Agmon, I.; Bashan, A.; Zarivach, R.; Yonath, A.(2005). Symmetry at the active site of the ribosome: struc tural and functional implications. Biological chemistry, 386(9): 833‐844。 II 肽基转移酶中心与转运RNA的相似性参见：Agmon, I. (2009). The dimeric proto-ribosome: Structural details and possi ble implications on the origin of life. International journal of molecular sciences, 10(7): 2921‐2934。 III 原始蛋白质翻译系统自发组织假说参见：Agmon, I. (2018). Hypothesis: spontaneous advent of the prebiotic translation system via the accumulation of L-shaped RNA elements. International journal of molecular sciences, 19(12): 4021。 IV RNA自组织通用模块参见：Jaeger, L.; Chworos, A. (2006). The architectonics of programmable RNA and DNA nano structures. Current opinion in structural biology, 16(4):531‐543。 V 阿格蒙的L形模块自发组织成蛋白质翻译系统假说参见： Agmon, I.(2009). The dimeric proto-ribosome: Structural
details and possible implications on the origin of life. International journal of molecular sciences, 10(7): 2921‐2934; Agmon,I.(2018). Hypothesis: spontaneous advent of the prebiotic translation system via the accumulation of L-shaped RNA elements. International journal of molecular sciences, 19(12): 4021。 VI 转运信使RNA参见：Giudice, E.; Macé, K.; Gillet, R.(2014). Trans-translation exposed: understanding the structures and functions of tmRNA-SmpB. Frontiers in Microbiology, 5:113。 VII 雷纳尔德·吉莱的信使RNA起源假说参见：Macé, K.; Gillet, R.(2016). Origins of tmRNA: the missing link in the birth of protein synthesis? Nucleic Acids Research, 44(17): 8041–8051; Guyomar, C.; Gillet, R.(2019). When transfer‐messenger RNA scars reveal its ancient origins. Annals of the New York Academy of Sciences, 1447: 80-87。 第五幕 第十九章
I 费托合成反应制造脂肪酸参见：McCollom, T. M.; Seewald, J. S.(2007). Abiotic synthesis of organic compounds in deep sea hydrothermal environments. Chemical Reviews, 107(2): 382–401; McCollom, T. M.; Seewald, J. S.(2006). Carbon isotope composition of organic compounds produced by abiotic synthesis under hydrothermal conditions. Earth and planetary science letters, 243(1–2): 74-84; McCollom, T.M.; Ritter, G.; Simoneit, B.R.T.(1999). Lipid Synthesis under hydrothermal conditions by Fischer-Tropsch-Type reactions. Origins of life and evolution of biospheres, 29(2): 153–166。 II 脂肪酸与氨基酸混合物的原始细胞膜参见：Cornell, C. E.; Black, R. A.; Xue, M.; et al.(2019). Prebiotic amino acids bind to and stabilize prebiotic fatty acid membranes. Proceedings of the National Academy of Sciences, 116(35): 17239-17244。 III 尼克·莱恩的脂肪酸与类异戊二烯混合物的原始细胞 膜参见：Jordan, S.F.; Rammu, H.; Zheludev, I. N.; et al.(2019).Promotion of protocell self-assembly from mixed amphiphiles at the origin of life. Nature ecology & evolution, 3: 1705–1714。 IV 杰克·绍斯塔克用柠檬酸稳定原始细胞膜参见： O’Flaherty, D. K.; Kamat, N. P.; Mirza, F. N.; et al.
(2018). Copying of Mixed-Sequence RNA Templates inside Model Protocells. Journal of the American Chemical Society, 140(15):5171‐5178; Adamala, K.; Szostak, J. W.(2013). Nonenzymatic template-directed RNA synthesis inside model protocells. Science, 342(6162): 1098‐ 1100。 V 杰克·绍斯塔克的原始细胞分裂实验参见：Hanczyc, M. M.; Fujikawa, S. M.; Szostak, J. W.(2003). Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science, 302(5645): 618-622; Zhu, T. F.; Szostak, J. W.(2009). Coupled growth and division of model protocell membranes. Journal of the American Chemical Society, 131(15): 5705‐5713; Budin, I.; Debnath, A.; Szostak, J. W.(2012). Concentration-driven growth of model protocell membranes. Journal of the American Chemical Society, 134(51): 20812‐20819。 VI 杰克·绍斯塔克用肽把RNA吸附在原始细胞膜上的实验 参见：Kamat, N.P.; Tobé, S.; Hill, I. T.; Szostak, J. W.(2015).Electrostatic Localization of RNA to Protocell Membranes by Cationic Hydrophobic Peptides. Angewandte chemie international edition, 54(40): 11735‐11739。 VII 杰克·绍斯塔克发现RNA自我复制能够促进原始细胞膜 扩增，参见：Chen, I. A.; Roberts, R. W.; Szostak, J. W.
(2004).The emergence of competition between model protocells. Science, 305(5689):1474‐1476。 VIII 杰克·绍斯塔克发现磷脂促进原始细胞膜吸收胶束， 参见：Budin, I.; Szostak, J. W.(2011). Physical efects underlying the transition from primitive to modern cell membranes. Proceedings of the National Academy of Sciences, 108(13): 5249‐5254。 IX 脂肪酸合成参考文献：Dijkstra, Albert J., R. J. Hamilton, and Wolf Hamm. “Fatty Acid Biosynthesis.” Trans Fatty Acids. Oxford: Blackwell Pub., 2008. 12. Print. X 古 菌 合 成 类 异 戊 二 烯 细 胞 膜 ， 参 见 ： Jain, S.; Caforio, A.; Driessen, A. J.(2014). Biosynthesis of archaeal membrane ether lipids. Frontiers in microbiology, 5: 641。 第二十章 I 人工合成铁硫蛋白参见：Mutter, A. C.; Tyryshkin, A. M.; Campbell, I. J.; et al.(2019). De novo design of symmetric ferre doxins that shuttle electrons in vivo. Proceedings of the National Academy of Sciences, 116(29): 14557-14562。
II 能量转换氢化酶结构参见：Schoelmerich, M. C.; Müller, V.(2019). Energy conservation by a hydrogenasedependent che miosmotic mechanism in an ancient metabolic pathway. Proceedings of the National Academy of Sciences, 116(13): 6329-6334;Shafaat, H. S.; Rüdiger, O.; Ogata, H.; Lubitz, W.(2013). [NiFe] hydrogenases: A common active site for hydrogen metabolism under diverse conditions. Biochimica et Biophysica Acta (BBA) – Bioenergetics, 1827(8–9): 986-1002。 III 尼克·莱恩和威廉·马丁关于原始细胞膜的能量代 谢，参见：Lane, N.; Martin, W. F.(2012). The origin of membrane bioenergetics. Cell, 151(7): 1406‐1416。 IV 能量转换氢化酶工作机制参考文献：Kurkin, S.; Meuer, J.; Koch, J.; et al.(2002). The membrane-bound [NiFe]-hy drogenase (Ech) from Methanosarcina barkeri: unusual properties of the iron–sulphur clusters. European journal of bio chemistry, 269(24): 6101-6111; Forzi, L.; Koch, J.; Guss, A. M.; et al.(2005). Assignment of the [4Fe–4S] clusters of Ech hydrogenase from Methanosarcina barkeri to individual subunits via the characterization of site-directed mutants. FEBS jour nal, 272(18): 4741-4753。
V 白烟囱假说对钠离子参与能量代谢的研究参见：Martin, W. F.; Sousa, F. L.; Lane, N. (2014). Energy at life’s origin. Sci ence, 344(6188): 1092–1093。 VI 钠离子梯度驱动物质能量代谢参见：Pisa, K. Y.; Weidner, C.; Maischak, H.; Kavermann, H.; Müller, V. (2007). The coupling ion in the methanoarchaeal ATP synthases: H+ vs. Na+ in the A1Ao ATP synthase from the archaeon Methanosarcina mazei Gö1. FEMS microbiology letters, 277(1): 56–63; Schiel-Bengelsdorf, B. M.; Dürre, P.(2012). Pathway engineering and synthetic biology using acetogens. FEBS letters, 586(15): 2191– 2198。 VII 逆向转运蛋白参见：Swartz, T. H.; Ikewada, S.; Ishikawa, O.; et al.(2005). The Mrp system: a giant among monovalent cation/proton antiporters? Extremophiles, 9(5): 345–354; Efremov, R. G.; Sazanov, L. A.(2012). The coupling mechanism of respiratory complex I--a structural and evolutionary perspective. Biochimica et biophysica acta, 1817(10):1785‐1795。 VIII 原 始 海 洋 盐 度 参 见 ： Knauth, L. P.(2005). Temperature and salinity history of the Precambrian ocean: implications for the course of microbial evolution. Palaeogeography, Palaeoclimatology, Palaeoecology, 219(1-2): 53–69; Marty, B.; Avice,G.;
Bekaert, D. V.; Broadley, M. W.(2018). Salinity of the Archaean oceans from analysis of fluid inclusions in quartz. Comptes Rendus Geoscience, 350(4): 154–163。 IX Maden, B. E. H.; Monro, R. E.(1968). RibosomeCatalyzed peptidyl transfer: efects of cations and pH value. European Journal of Biochemistry, 6(2): 309– 316. X Mulkidjanian, A. Y.; Bychkov,A. Y.; Dibrova, D. V.; et al.(2012). Origin of first cells at terrestrial, anoxic geothermal fields.Proceedings of the National Academy of Sciences, 109 (14) E821-E830. 第二十一章 I 尤金·库宁的ATP合酶起源图景参见：Mulkidjanian, A.; Makarova, K.; Galperin, M.; et al.(2007). Inventing the dynamo machine: the evolution of the F-type and Vtype ATPases. Nature Reviews Microbiology, 5(11): 892– 899。 II 六元环解旋酶的结构和作用参见：Patel, S. S.; Picha, K. M.(2000). Structure and Function of Hexameric Helicases. Annu al review of biochemistry, 69(1): 651– 697。
III ρ因子与ATP合酶进化同源，参见：Dombroski, A. J.; Platt, T.(1988). Structure of rho factor: an RNAbinding domain and a separate region with strong similarity to proven ATP-binding domains. Proceedings of the National Academy of Scienc es, 85(8): 2538‐ 2542。 IV ρ因子工作机制参见：Adelman, J. L.; Jeong, Y. J.; Liao, J. C.; et al.(2006). Mechanochemistry of transcription termina tion factor Rho. Molecular cell, 22(5): 611‐621。 V TrwB参见：Tato, I.; Zunzunegui, S.; de la Cruz, F.; et al.(2005). TrwB, the coupling protein involved in DNA transport during bacterial conjugation, is a DNA-dependent ATPase. Proceedings of the National Academy of Scienc es, 102(23):8156‐8161; Cabezon, E.; de la Cruz, F.(2006). TrwB: An F1-ATPase-like molecular motor involved in DNA trans port during bacterial conjugation. Research in microbiology, 157(4); 299– 305。 VI DNA移位酶与接合质粒参见：Lawley, T. D.; Klimke, W. A.; Gubbins, M. J.; Frost, L. S.(2003). F factor conjugation is a true type IV secretion system, FEMS microbiology letters, 224(1): 1–15; Arutyunov, D.; Frost, L. S.(2013). F conjugation:Back to the
beginning. Plasmid, 70 (1): 18–32; Klümper, U.; Droumpali, A.; Dechesne, A.; Smets, B. F.(2014). Novel assay to measure the plasmid mobilizing potential of mixed microbial communities. Frontiers in microbiology, 5:730; Gonzalez-Perez,B.; Lucas, M.; Cooke, L.; et al. (2007). Analysis of DNA processing reactions in bacterial conjugation by using suicide oligo nucleotides. The EMBO journal, 26(16): 3847-57; Fernández-González, E.; de Paz, H. D.; Alperi, A.; et al.(2011). Transfer of R388 derivatives by a pathogenesis-associated type IV secretion system into both bacteria and human cells. Journal of bacteri ology, 193(22): 6257‐6265。 VII TrwK与TrwB进化同源参见：Arechaga, I.; Peña, A.; Zunzunegui, S.; et al.(2008). ATPase Activity and Oligomeric State of TrwK, the VirB4 Homologue of the Plasmid R388 Type IV Secretion System. Journal of bacteriology, 190(15): 5472-9;Peña, A.; Ripoll-Rozada, J.; Zunzunegui, S.; et al.(2011). Autoinhibitory Regulation of TrwK, an Essential VirB4 ATPase in Type IV Secretion Systems. The journal of biological chemistry, 286(19): 17376-82。 VIII TrwB 与 TrwK 可 以 混 用 参 见 ： Waksman, G.(2019). From conjugation to T4S systems in Gram‐negative bacteria: a mechanistic biology perspective. EMBO
Reports, 20(2): e47012; Christie, P.(2017). Structural biology: Loading T4SS sub strates. Nature microbiology, 2(9): 17125。 IX 古菌鞭毛参见：Wallden, K.; Rivera-Calzada, A.; Waksman, G.(2010). Type IV secretion systems: versatility and diversity in function. Cellular Microbiology, 12(9): 1203–12; Ghosh, A.; Albers, S. V. (2011). Assembly and function of the archaeal flagellum. Biochemical society transactions, 39(1):64‐ 69; Ng, S. Y. M.; Chaban, B.; Jarrell, K. F.(2006). Archaeal flagella,bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. Journal of molecular microbiology and biotechnology, 11(3–5): 167–91; Thomas, N. A.; Bardy, S. L.; Jarrell, K. F.(2001). The archaeal flagellum: a diferent kind of prokaryotic motility structure, FEMS microbiology reviews, 25(2): 147–174. XIII 型 分 泌 系 统 与 ATP 合 酶 同 源 参 见 ： Diepold, A.; Armitage, J. P.(2015). Type III secretion systems: the bacterial flagel lum and the injectisome. Philosophical transactions of the royal society b biological sciences, 370(1679):20150020; Erhardt, M.;Namba, K.; Hughes, K. T.(2010). Bacterial nanomachines: the flagellum and type III injectisome. Cold Spring Harbor perspec tives in biology, 2(11):a000299。
XI 与氢离子结合能力是ATP合酶转动方向的决定因素参 见 ： Cross, R. L.; Müller, V.(2004). The evolution of A-,F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio. FEBS letters, 576(1-2):1‐4。 XII 能量转换氢化酶就是复合物I的进化原型，参见： Efremov, R. G.; Sazanov, L. A.(2012). The coupling mechanism of respiratory complex I--a structural and evolutionary perspective. Biochimica et Biophysica Acta, 1817(10):1785‐1795; Hed derich R.(2004). Energyconverting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I. Journal of bioenergetics and biomembranes, 36(1): 65‐75; Schoelmerich, M. C.; Müller, V.(2020). Energyconverting hydrogenases: the link between H2 metabolism and energy conservation. Cellular and molecular life sciences, 77, 1461–1481; Moparthi, V. K.;Hägerhäll, C. (2011). The evolution of respiratory chain complex I from a smaller last common ancestor consisting of 11 protein subunits. Journal of molecular evolution, 72(5- 6):484‐497。 第二十二章 I 发 现 电 子 分 歧 参 见 ： Li, F.; Hinderberger, J.; Seedorf, H.; et al.(2008). Coupled ferredoxin and
crotonyl coenzyme A (CoA) reduction with NADH catalyzed by the Butyryl-CoA Dehydrogenase/Etf Complex from clostridium kluyveri. Journal of Bacteriology, 190(3): 843-850; Kaster, A.-k.; Moll, J.; Parey, K.; Thauer. R. K.(2011).Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proceedings of the National Academy of Sciences, 108(7): 2981-2986。 II 威廉·马丁与尼克·莱恩的电子传递链起源图景参见： Lane, N.; Martin, W. F.(2012). The origin of membrane bio energetics. Cell, 151(7):1406-1416; Kulkarni, G.; Mand, T. D.; William W. Metcalf, W. W.(2009). Energy conservation viahydrogen cycling in the methanogenic archaeon methanosarcina barkeri. Proceedings of the National Academy of Sciences, 106(37): 15915-15920; Sousa, F. L.; Thiergart, T.; Landan, G.; et al.(2013). Early bioenergetic evolution. Philosophical transactions of The Royal Society B Biological Sciences, 368(1622): 20130088; Sojo, V.; Pomiankowski, A.; Lane, N.(2014). A bioenergetic basis for membrane divergence in archaea and bacteria [published correction appears in PLoS Biol, 2015 Mar, 13(3): e1002102]. PLoS Biology, 12(8): e1001926; Sojo, V.; Herschy, B.; Whicher, A.; Camprubí, E.; Lane, N.(2016). The Origin of Life in Alkaline Hydrothermal Vents. Astrobiology, 16(2): 181-97。
III Sauer, U.; Canonaco, F.; Heri, S.; Perrenoud, A.; Fischer, E.(2004). The soluble and membrane-bound transhydroge nases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. Journal of biological chemistry, 279(8): 6613-6619. D; Bennett, B.; Kimball, E.; Gao, M.; et al.(2009). Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nature chemical biology, 5(8): 593–599。 IV 产甲烷古菌与产乙酸细菌共生吗，参见：Schuchmann, K.; Müller, V.(2016). Energetics and Application of Heterotrophy in Acetogenic Bacteria. Applied and environmental microbiology, 82(14): 4056-4069。 V 威廉·马丁提出的产甲烷古菌与产乙酸细菌内共生成为 真核生物祖先的假说，参见：Martin, W. F.; Garg, S.; Zimorski,V.(2015). Endosymbiotic theories for eukaryote origin. Philosophical transactions of The Royal Society B Biological Sciences, 370(1678):20140330。 VI 细菌和古菌的复制体的差异参见：Leipe, D. D.; Aravind, L.; Koonin, E. V.(1999). Did DNA replication evolve twice in dependently?. Nucleic Acids Research, 27(17): 3389-3401; Bleichert, F.; Botchan, M. R.; Berger, J. M.(2017). Mechanisms for initiating cellular DNA replication. Science, 355(6327): eaah6317。
VII 帕特里克·福泰尔的DNA复制系统起源图景参见： Forterre P, Filée J, Myllykallio H. Origin and Evolution of DNA and DNA Replication Machineries. In: Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-2013. Available from: https://www.ncbi.nlm.nih.gov/books/NBK6360/; Forterre, P.; Gadelle, D.(2009). Phylogenomics of DNA to poisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic acids research, 37(3): 679-692。 VIII 腺病毒的DNA复制机制参见：Pacesa, M.(2016). Purification of Recombinant Adenoviral Hexon Proteins for Genera tion of Virus-specific Antibodies & Nextgeneration Sequencing of Adenoviral Genomes. 10.13140/RG.2.2.20211.53282; Salas, M.; Holguera, I.; Redrejo-Rodríguez, M.; De Vega, M.(2016). DNA-Binding Proteins Essential for Protein-Primed Bacterio phage Φ29 DNA Replication. Frontiers in molecular biosciences, 3. https://doi.org/10.3389/fmolb.2016.00037。 IX 病毒用六元环的移位酶把DNA装入衣壳粒，参见： Patel, S. S.; Picha, K. M.(2000). Structure and Function of Hex americ Helicases. Annual review of biochemistry, 69(1): 651–697; Happonen, L. J.; Oksanen, E.; Liljeroos, L.;et al.(2013). The Structure
of the NTPase that powers DNA packaging into sulfolobus turreted icosahedral Virus 2. Journal of Virology, 87(15): 8388-8398。 X 病 毒 的 冈 崎 片 段 参 见 ： Miller, E.; Kutter, E.; Mosig, G.; et al.(2003). Bacteriophage T4 Genome. Microbiology and molecular biology reviews, 67(1): 86- 156; Nelson, S.; Kumar, R.; Benkovic, S.(2008). RNA primer handof in bacteriophage T4 DNA replication: The role of single-stranded DNA-binding protein and polymerase accessory proteins. The Journal of biological chemistry, 283(33): 22838-46。 XI 病毒与细胞用来复制DNA的酶的亲缘关系参见：Filée, J.; Forterre, P.; Sen-Lin, T.; Laurent, J.(2002). Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. Journal of molecular evolution, 54(6):763- 773; Villarreal, L. P.; DeFilippis, V. R.(2000). A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. Journal of virology, 74(15): 7079-7084。 XII 核黄素依赖型电子分歧酶参见：Wagner, T.; Koch, J.; Ermler, U.; Shima, D.(2017). Methanogenic heterodisulfide reduc tase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science,
357(6352): 699-703; Kai, S.; Chowdhury, N. P.; Müller, V.(2018). Complex Multimeric [FeFe] Hydrogenases: biochemistry, physiology and new opportunities for the hydrogen economy. Frontiers in microbiology, 04 December , https://doi.org/10.3389/fmicb.2018.02911。 XIII 古菌的甲基转移酶参见：Deobald, D.; Adrian, L.; Schöne, C.; et al.(2018). Identification of a unique Radical SAM methyltransferase required for the sp3-Cmethylation of an arginine residue of methyl-coenzyme M reductase. Scientific re ports, 8(1): 7404。 XIV 几种铁硫蛋白的结构相似性参见：Poehlein, A.; Schmidt, S.; Kaster, A. K.; et al.(2012). An Ancient Pathway Com bining Carbon Dioxide Fixation with the Generation and Utilization of a Sodium Ion Gradient for ATP Synthesis. PLOS ONE, 7(3): e33439; Schuchmann, K.; Chowdhury, N. P.; Müller, V.(2018). Complex Multimeric [FeFe] Hydrogenases: Bio chemistry, Physiology and New Opportunities for the Hydrogen Economy. Frontiers in microbiology, 9: 2911; Schuchmann,K.; Vonck, J.; Müller, V.(2016), A bacterial hydrogen‐dependent CO2 reductase forms filamentous structures. FEBS Jour nal, 283(7): 1311-1322; Schwarz, F. M.; Schuchmann, K.; Müller, V.(2018). Hydrogenation of CO2 at ambient pressure cata lyzed by a highly active thermostable biocatalyst. Biotechnology for biofuels, 11, 237。
XV 十二种核黄素依赖型电子分歧酶的进化关系参见： Poudel, S.; Dunham, E. C.; Lindsay, M. R.; et al. (2018). Origin and Evolution of Flavin-Based Electron Bifurcating Enzymes. Frontiers in microbiology, 9:1762。 终章 I 用原子力显微镜看到了有机化学反应中的化学键变化， 参见：de Oteyza, D. G.; Gorman, P.; Chen, Y.-C.;et al. (2013).Direct imaging of covalent bond structure in single-molecule chemical reactions. Science, 340(6139):1434-7。 II 基金观察到的最远的天体，参见：Klotz, I.(March 3, 2016). “Hubble Spies Most Distant, Oldest Galaxy Ever”. Seeker. Discovery, Inc. Retrieved February 5, 2020。 III 木星卫星的轨道共振产生了强烈的潮汐作用参见： Tyler, R. H.(2008). Strong ocean tidal flow and heating on moons of the outer planets. Nature, 456(7223): 770– 772。 IV 钻探木卫二的计划参见：Powell, J.; Powell, J.; Maise, G.; Paniagua, J.(2005). NEMO: A mission to search for and return to Earth possible life forms on
Europa. Acta astronautica, 57: 579–593; Weiss, P.; Yung, K. L.; Ng,T. C.; et al.(2008). Study of a thermal drill head for the exploration of subsurface planetary ice layers. Planetary and space science, 56: 1280– 1292; Weiss, P.; Yung, K. L.; Kömle, N.; et al.(2011). Thermal drill sampling system onboard high-velocity impactors for exploring the subsurface of Europa. Advances in space research, 48(4): 743。 V 土卫二海洋参见：Platt, J.; Bell, B.(2014-04-03). NASA space assets detect ocean inside saturn moon. NASA。 VI 土卫二的白烟囱参见：Waite, J. H; Glein, C. R; Perryman, R. S; et al.(2017). Cassini finds molecular hydrogen in the En celadus plume: Evidence for hydrothermal processes. Science, 356 (6334): 155–159。 VII 土卫二喷出物蕴含的有机物参见：Cassini Tastes Organic Material at Saturn’s Geyser Moon. NASA, March 26, 2008. Retrieved March 26, 2008; Postberg, F.; Khawaja, N.; Abel, B.; et al.(2018). Macromolecular organic compounds from the depths of Enceladus. Nature, 558(7711): 564–568。 VIII 银河系中的类地行星参见：Overbye, D.(4 November 2013). Far-Of Planets Like the Earth Dot the Galaxy. New York Times; Petigura, Erik A.; Howard, A. W.; Marcy
G. W.(2013). Prevalence of Earth-size planets orbiting Sun-like stars. Proceed ings of the National Academy of Sciences, 110(48):19273-8; Khan, A. Milky Way may host billions of Earth-size planets. Los Angeles Times. 4 November 2013。 IV 格 利 泽 832c 参 见 ： Wall, M. （ June 25, 2014 ） . Nearby Alien Planet May Be Capable of Supporting Life. space.com,re trieved June 26, 2014。 幕后 增章一 I 一 个 规 律 参 见 ： Nelson, P.; Masel, J.(2017). Intercellular competition and the inevitability of multicellular aging. Proceed ings of the National Academy of Sciences, 114(49): 12982–87; Wagner, G. P. (2017). The power of negative [theoretical] results. Proceedings of the National Academy of Sciences, 114 (49): 12851–52。 II 超过1万岁的南极海绵：Susanne Gatti (2002) “The Role of Sponges in High-Antarctic Carbon and Silicon Cycling - a Modelling Approach” . Ber. Polarforsch. Meeresforsch. 434. ISSN 1618-3193。
III 发 现 了 四 千 岁 的 珊 瑚 ： https://www.nature.com/news/2009/090323/full/news.2009. 185.html IV 关于外肛动物门的群落，参见：Ruppert, E. E.; Fox, R. S.; Barnes, R. D.(2004). Lophoporata. Invertebrate Zoology (7 ed.), 829–845。关于帚虫，参见：Emig, C. C. (2003). Phylum: Phoronida (PDF). In: Grzimek, B.; Kleiman, D. G.; Hutchins,M.(eds.) Grzimek’s Animal Life Encyclopedia 2. Protostomes (2 ed.), Thompson Gale, 491–495, Retrieved 2011-03-01。 V 关于苔藓虫，参见：Ruppert, E. E.; Fox, R. S.; Barnes, R. D.(2004). Lophoporata. Invertebrate Zoology (7 ed.), 829–845。 VI 关于海鞘群落，参见：Munday, R.; Rodriguez, D.; Di Maio, A.; et al.(2015). Aging in the colonial chordate, Botryllus schlosseri. Invertebrate reproduction and development, 59(sup1):45–50。 VII 仅 就 海 鞘 的 衰 老 而 言 ， 参 见 ： Sköld, H. N.; Asplund, M. E.; Wood, C. A.; Bishop, J. D. D.(2011). Telomerase deficiency in a colonial ascidian after prolonged asexual propagation. Journal of Experimental Zoology Part B Molecular and Develop mental Evolution, 316(4): 276-83; Brown, F. D.; Keeling, E. L.; Le, A. D.; Swalla, B. J.(2009). Whole body regeneration in a
colonial ascidian, Botrylloides violaceus. Journal of Experimental Zoology Part B Molecular and Developmental Evolution, 312(8): 885-900; Sköld, H. N., Asplund, M. E.; Wood, C. A.; Bishop, J. D.(2011). Telomerase deficiency in a colonial ascidian after prolonged asexual propagation. Journal of Experimental Zoology Part B Molecular and Developmental Evolu tion, 316(4): 276-283; Rinkevich, B. (2017). Senescence in Modular Animals. In: Sheferson, R.; Jones, O.; SalgueroGómez,R.(Eds.). The Evolution of Senescence in the Tree of Life. Cambridge: Cambridge University Press, 220- 237; Laird, D. J.; Weiss man, I.(2004). Telomerase maintained in self-renewing tissues during serial regeneration of the urochordate Botryllus schlosseri. Developmental biology, 273(2):185-94。 VIII 涡虫寿命重置参见：Tan, T. C. J.; Rahman, R.; Jaber-Hijazi, F.; et al.(2012). Telomere maintenance and telomerase activi ty are diferentially regulated in asexual and sexual worms. Proceedings of the National Academy of Sciences, 109(11): 4209-14;Mouton, S.; Grudniewska, M.; Glazenburg, L.; et al.(2018). Resilience to aging in the regeneration‐capable flatworm Mac rostomum lignano. Aging Cell. 17:e12739。 海星寿命重置参见：Garcia-Cisneros, A.; Pérez-Portela, R.; Almroth, B.; et al.(2015). Long telomeres are associated with clonality in wild populations of the
fissiparous starfish Coscinasterias tenuispina. Heredity, 115: 437–443; Varney, R. M.;Po mory, C. M.; Janosik, A. M.(2017). Telomere elongation and telomerase expression in regenerating arms of the starfish Luidia clathrata (Asteroidea: Echinodermata). Marine biology, 164, 195. https://doi.org/10.1007/s00227-017-3230-x。 IX 细菌利用外来DNA修复自己的DNA：Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM (Sep tember 1994). “Biochemistry of homologous recombination in Escherichia coli”. Microbiological Reviews. 58 (3): 401–65.doi:10.1128/MMBR.58.3.401- 465.1994. PMC 372975. PMID 7968921；Cromie GA (August 2009). “Phylogenetic ubiquity and shufling of the bacterial RecBCD and AddAB recombination complexes”. Journal of Bacteriology. 191 (16): 5076– 84.doi:10.1128/JB.00254-09. PMC 2725590. PMID 19542287；Morimatsu K, Kowalczykowski SC (May 2003). “RecFOR pro teins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair”. Molecular Cell. 11 (5): 1337 –47. doi:10.1016/S1097-2765(03)00188-6. PMID 12769856。 X 关于细菌的衰老：Moseley, J. B. (2013). “Cellular Aging: Symmetry Evades Senescence”. Current Biology.