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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。
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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。
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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。
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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.Originsof life and evolution of biospheres, 44(4)
:299‐302。
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第十七章
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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). RNA-dependent 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。
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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。
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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。
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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。
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V 迷你螺旋起源更早，参见：Sun, F.-J.; Caetano-Anollés, 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。
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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。
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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。
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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。
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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 Bulletin, 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 AndPaleontology 50 Years After Simpson. Washington (DC): National Academies Press (US). Available from: https://www.ncbi.nlm. nih.gov/books/NBK232211/。
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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.。
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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。
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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。
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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 molecularevolution, 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。
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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。
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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 Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code.Life, 9(2): 37。
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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。
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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)。
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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。
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XIX 三重迷你螺旋假说参见：Burton, Z. F.(2020). The 3-Minihelix tRNA evolution theorem.Journal of molecular evolution, 88: 234–242。
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XX 手性选择氨酰化假说参见：Tamura, K.; Schimmel, P.(2004). Chiral-selective aminoacylation of an RNA minihelix.Science, 305(5688): 1253.
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