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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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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。
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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。
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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 & Next-generation 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。
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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。
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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。
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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。
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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。
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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-C-methylation of an arginine residue of methyl-coenzyme M reductase.Scientific reports, 8(1): 7404。
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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.PLOSONE, 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 Journal, 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。
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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。
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终章
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