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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.Science, 344(6188): 1092–1093。
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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。
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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。
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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.ComptesRendus Geoscience, 350(4): 154–163。
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IX Maden, B. E. H.; Monro, R. E.(1968). Ribosome-Catalyzed peptidyl transfer: efects of cations and pH value.EuropeanJournal of Biochemistry, 6(2): 309–316.
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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.
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第二十一章
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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 V-type ATPases. Nature Reviews Microbiology, 5(11): 892–899。
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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.Annual review of biochemistry, 69(1): 651–697。
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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 RNA-binding domain and a separate region with strong similarity to proven ATP-binding domains.Proceedings of the National Academy of Sciences, 85(8): 2538‐2542。
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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。
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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 Sciences, 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。
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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 bacteriology, 193(22): 6257‐6265。
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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。
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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。
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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 microbiologyand 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.
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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 perspectives in biology,2(11)
:a000299。
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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。
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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). Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I.Journal ofbioenergetics and biomembranes, 36(1): 65‐75; Schoelmerich, M. C.; Müller, V.(2020). Energy-converting 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。
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第二十二章
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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。
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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.Philosophicaltransactions 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 inPLoS 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。
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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。
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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。
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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。
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