Proposed ancestors of phage nucleic acid packaging motors (and cells)

Viruses

Volumn 3, Issue 7, 2011, Pages 1249-1280

  Serwer, Philip ^a  

^a UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

Abiotic ancestors; Bacteriophage structure; Biological energy transduction; Information carrying polymers; Thermal ratchet

Indexed keywords

ADENOSINE TRIPHOSPHATASE; BACTERIOPHAGE DNA; DNA; RNA;

ABIOTIC ORIGIN; ARTICLE; AUTOCATALYSIS; BACTERIOPHAGE T3; BACTERIOPHAGE T7; BIOGENESIS; CATALYSIS; COEVOLUTION; DIFFUSION; DIMERIZATION; DNA BINDING; DNA PACKAGING; DNA VIRUS; ENERGY TRANSFER; GENOME; INTERNALIZATION; MOLECULAR INTERACTION; PHAGE DNA PACKAGING MOTOR; POLYMERIZATION; RNA VIRUS; THERMODYNAMICS; VIRUS CAPSID; VIRUS ENVELOPE;

BACTERIOPHAGES; DNA PACKAGING; MODELS, MOLECULAR; MOLECULAR MOTOR PROTEINS; NUCLEIC ACIDS;

MIRIDAE;

EID: 79960790667     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3071249     Document Type: Article

References (126)

1. Alberts, B.; Miake-Lye, R. Unscrambling the puzzle of biological machines: The importance of the details. Cell 1992, 68, 415-420.
2. Córdova, N.J.; Ermentrout, B.; Oster, G.F. Dynamics of single-motor molecules: The thermal ratchet model. Proc. Natl. Acad. Sci. U. S. A. 1992, 89, 339-343.
3. Ishii, Y.; Taniguchi, Y.; Iwaki, M.; Yanagida, T. Thermal fluctuations biased for directional motion in molecular motors. BioSystems 2008, 93, 34-38.
4. Mickler, M.; Schleiff, E.; Hügel, T. From biological towards artificial molecular motors. Chemphyschem 2008, 9, 1503-1509.
5. Howard, J. Motor proteins as nanomachines: The roles of thermal fluctuations in generating force and motion. Séminaire Poincaré 2009, 12, 33-44.
6. Iwaki, M.; Iwane, A.H.; Shimokawa, T.; Cooke, R.; Yanagida, T. Brownian search-and-catch mechanism for myosin-VI steps. Nat. Chem. Biol. 2009, 5, 430-405.
7. Hänggi, P.; Marchesoni, F. Artificial Brownian motors: Controlling transport on the nanoscale. Rev. Mod. Phys. 2009, 81, 387-442.
8. Spirin, A.S. The Ribosome as a conveying thermal ratchet machine. J. Biol. Chem. 2009, 284, 21103-21119.
9. Aathavan, K.; Politzer, A.T.; Kaplan, A.; Moffitt, J.R.; Chemla, Y.R.; Grimes, S.; Jardine, P.J.; Anderson, D.L.; Bustamante, C. Substrate interactions and promiscuity in a viral DNA packaging motor. Nature 2009, 461, 669-673.
10. Simpson, A.A.; Tao, Y.; Leiman, P.G.; Badasso, M.O.; He, Y.; Jardine, P.J.; Olson, N.H.; Morais, M.C.; Grimes, S.; Anderson, D.L., et al. Structure of the bacteriophage phi29 DNA packaging motor. Nature 2000, 408, 745-750.
11. Rao, V.B.; Feiss, M. The bacteriophage DNA packaging motor. Annu. Rev. Genet. 2008, 42, 647-681.
12. Lee, T.J.; Schwartz, C.; Guo, P. Construction of bacteriophage phi29 DNA packaging motor and its applications in nanotechnology and therapy. Ann. Biomed. Eng. 2009, 37, 2064-2081.
13. Sun, S.; Kondabagil, K.; Draper, B.; Alam, T.I.; Bowman, V.D.; Zhang, Z.; Hegde, S.; Fokine, A.; Rossmann, M.G.; Rao, V.B. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 2008, 135, 1251-1262.
14. Yu, J.; Moffitt, J.; Hetherington, C.L.; Bustamante, C.; Oster, G. Mechanochemistry of a viral DNA packaging motor. J. Mol. Biol. 2010, 400, 186-203.
15. Ray, K.; Sabanayagam, C.R.; Lakowicz, J.R.; Black, L.W. DNA crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y-DNA substrate. Virology 2010, 398, 224-232.
16. Lebedev, A.A.; Krause, M.H.; Isidro, A.L.; Vagin, A.A.; Orlova, E.V.; Turner, J.; Dodson, E.J.; Tavares, P.; Antson, A.A. Structural framework for DNA translocation via the viral portal protein. EMBO J. 2007, 26, 1984-1994.
17. Oliveira, L.; Cuervo, A.; Tavares, P. Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein. J. Biol. Chem. 2010, 285, 7366-7373.
18. Serwer, P. A Hypothesis for Bacteriophage DNA Packaging Motors. Viruses 2010, 2, 1821-1843.
19. Higgins, C.F. Multiple molecular mechanisms for multidrug resistance transporters. Nature 2007, 446, 749-757.
20. Linton, K.J. Structure and function of ABC transporters. Physiology 2007, 22, 122-130.
21. Gutmann, D.A.; Ward, A.; Urbatsch, I.L.; Chang, G.; van Veen, H.W. Understanding polyspecificity of multidrug ABC transporters: Closing in on the gaps in ABCB1. Trends Biochem. Sci. 2010, 35, 36-42.
22. Kurakin, A. Self-organization versus watchmaker: Ambiguity of molecular recognition and design charts of cellular circuitry. J. Mol. Recognit. 2007, 20, 205-214.
23. Kurakin, A. Order without design. Theor. Biol. Med. Modell. 2010, 7, 12.
24. Sheaffer, A.K.; Newcomb, W.W.; Gao, M.; Yu, D.; Weller, S.K.; Brown, J.C.; Tenney, D.J. Herpes simplex virus DNA cleavage and packaging proteins associate with the procapsid prior to its maturation. J. Virol. 2001, 75, 687-698.
25. Baker, M.L.; Jiang, W.; Rixon, F.J.; Chiu, W. Common ancestry of herpesviruses and tailed DNA bacteriophages. J. Virol. 2005, 79, 14967-14970.
26. Johnson, J.E.; Chiu, W. DNA packaging and delivery machines in tailed bacteriophages. Curr. Opin. Struct. Biol. 2007, 17, 237-243.
27. Krupovic, M.; Bamford, D. Virus evolution: How far does the double barrel viral lineage extend? Nat. Rev. 2008, 6, 941-948.
28. Koonin, E.V.; Yutin, N. Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology 2009, 53, 284-292.
29. Jiang, W.; Baker, M.L.; Jakana, J.; Weigele, P.R; King, J.; Chiu, W. Backbone structure of the infectious epsilon 15 virus capsid revealed by electron cryomicroscopy. Nature 2008, 451, 1130-1134.
30. Black, L.W. DNA packaging and cutting by phage terminases: Control in phage T4 by a synaptic mechanism. Bioessays 1995, 17, 1025-1030.
31. Sheaffer, A.K.; Newcomb, W.W.; Gao, M.; Yu, D.; Weller, S.K.; Brown, J.C.; Tenney, D.J. Herpes simplex virus DNA cleavage and packaging proteins associate with the procapsid prior to its maturation. J. Virol. 2001, 75, 687-698.
32. Serwer, P.; Hayes, S.J.; Zaman, S.; Lieman, K.; Rolando, M.; Hardies, S.C. Improved isolation of undersampled bacteriophages: Finding of distant terminase genes. Virology 2004, 329, 412-424.
33. Iyer, L.M.; Makarova, K.S.; Koonin, E.V.; Aravind, L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: Implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res. 2004, 32, 5260-5279.
34. Ponchon, L.; Boulanger, P.; Labesse, G.; Letellier, L. The endonuclease domain of bacteriophage terminases belongs to the resolvase/integrase/ribonuclease H superfamily: A bioinformatics analysis validated by a functional study on bacteriophage T5. J. Biol. Chem. 2006, 281, 5829-5836.
35. Burroughs, A.M.; Iyer, L.M.; Aravind, L. Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems. Genome Dyn. 2007, 3, 48-65.
36. Agirrezabala, X.; Martin-Benito, J.; Valle, M.; Gonzalez, J.M.; Valencia, A.; J. Valpuesta, J.M.; Carrascosa, J.L. Structure of the connector of bacteriophage T7 at 8Å resolution: Structural homologies of a basic component of a DNA translocating machinery. J. Mol. Biol. 2005, 347, 895-902.
37. Newcomb, W.W.; Juhas, R.M.; Thomsen, D.R.; Homa, F.L.; Burch, A.D.; Weller, S.K.; Brown, J.C. The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid. J. Virol. 2001, 75, 10923-10932.
38. Newcomb, W.W.; Cockrell, S.K.; Homa, F.L.; Brown, J.C. Polarized DNA injection from the herpesvirus capsid. J. Mol. Biol. 2009, 392, 885-894.
39. Bamford, D.H.; Burnett, R.M.; Stuart D.I. Evolution of viral structure. Theor. Popul. Biol. 2002, 61, 461-470.
40. Martin, W.; Russell, M.J. On the origins of cells: A hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos. Trans. R. Soc. Lond. B 2003, 358, 59-85.
41. Kutschera, U.; Niklas, K.J. The modern theory of biological evolution: An expanded synthesis. Naturwissenschaften 2004, 91, 255-276.
42. Catalano, C.E. The terminase enzyme from bacteriophage lambda: A DNA-packaging machine. Cell. Mol. Life Sci. 2000, 57, 128-148.
43. Petrov, A.S.; Harvey, S.C. Packaging double-helical DNA into viral capsids: Structures, forces, and energetics. Biophys. J. 2008, 95, 497-502.
44. Sun, S.; Rao, V.B.; Rossmann, M.G. Genome packaging in viruses. Curr. Opin. Struct. Biol. 2010, 20, 114-120.
45. Serwer, P.; Wright, E.T.; Hakala, K.; Weintraub, S.T.; Su, M.; Jiang, W. DNA packaging-associated hyper-capsid expansion of bacteriophage T3. J. Mol. Biol. 2010, 397, 361-374.
46. Serwer, P. Models of bacteriophage DNA packaging motors. J. Struct. Biol. 2003, 141, 179-188.
47. Smith, D.E.; Tans, S.J.; Smith, S.B.; Grimes, S.; Anderson, D.L.; Bustamante, C. The bacteriophage straight phi29 portal motor can package DNA against a large internal force. Nature 2001, 413, 748-752.
48. Oram, M.; Sabanayagam, C.; Black, L.W. Modulation of the packaging reaction of bacteriophage t4 terminase by DNA structure. J. Mol. Biol. 2008, 381, 61-72.
49. Mindich, L. Packaging, replication and recombination of the segmented genomes of bacteriophage 6 and its relatives. Virus Res. 2004, 101, 83-92.
50. Kainov, D.E.; Tuma, R.; Mancini, E.J. Hexameric molecular motors: P4 packaging ATPase unravels the mechanism. Cell. Mol. Life Sci. 2006, 63, 1095-1105.
51. Butcher, S.J.; Dokland, T.; Ojala, P.M.; Bamford, D.H.; Fuller S.D. Intermediates in the assembly pathway of the double-stranded RNA virus phi6. EMBO J. 1997, 16, 4477-4487.
52. Karhu, N.J.; Ziedaite, G.; Bamford, D.H.; Bamford, J.K.H. Efficient DNA packaging of bacteriophage PRD1 requires the unique vertex protein P6. J. Virol. 2007, 81, 2970-2979.
53. Butcher, S.J.; Bamford, D.H.; Fuller, S.D. DNA packaging orders the membrane of bacteriophage PRD1. EMBO J. 1995, 14, 6078-6086.
54. Gold, T. The deep, hot biosphere. Proc. Natl. Acad. Sci. U. S. A. 1992, 89, 6045-6049.
55. Gold, T. The Deep Hot Biosphere; Springer: New York, NY, USA, 1999.
56. Koonin, E.V. On the origin of cells and viruses: Primordial virus world scenario. Ann. N. Y. Acad. Sci. 2009, 1178, 47-64.
57. Nitschke, W.; Russell, M.J. Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/W, Co, S and Se, forced life to emerge. J. Mol. Evol. 2009, 69, 481-496.
58. Vetsigian, K.; Woese, C.; Goldenfeld, N. Collective evolution and the genetic code. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 10696-10701.
59. Woese, C.R.; Goldenfeld, N. How the microbial world saved evolution from the scylla of molecular biology and the charybdis of the modern synthesis. Microbiol. Mol. Biol. Rev. 2009, 73, 14-21.
60. Van der Put, P.J. The Inorganic Chemistry of Materials: How to Make Things out of Elements; Academic Press: San Diego, CA, USA, 2001; Chapter 4.3.2, pp. 123-126.
61. Mori, T. Novel physical properties of rare earth higher borides. J. Phys. Conf. Ser. 2009, 176, 012036.
62. Pauling, L.; Marsh, R.E. The structure of chlorine hydrate. Proc. Natl. Acad. Sci. U. S. A. 1952, 38, 112-118.
63. Sloan, E.D., Jr. Clathrate Hydrates of Natural Gases, 2nd ed.; Marcel Dekker, Inc.: New York, NY, USA, 1998.
64. Zhang, J.; Hawtin, R.W.; Yang, Y.; Nakagava, E.; Rivero, M.; Choi, S.K.; Rodger, P.M. Molecular dynamics study of methane hydrate formation at a water/methane interface. J. Phys. Chem. B 2008, 112, 10608-10618.
65. Pauling, L. General Chemistry; W.H. Freeman and Co.: New York, NY, USA, 1970; Chapter 12.
66. Tielrooij, K.J.; Garcia-Araez, N.; Bonn, M.; Bakker, H.J. Cooperativity in ion hydration. Science 2010, 328, 1006-1009.
67. Glasby, G.P. Abiogenic origin of hydrocarbons: An historical overview. Resour. Geol. 2006, 56, 85-98.
68. Greenwood, N.N.; Earnshaw, A. Chemistry of the Elements; Pergamon: Oxford, UK, 1984, pp. 318-322.
69. Kauffman, S. At Home in the Universe: The Search for the Laws of Self-Organization and Complexity; Oxford University Press: Oxford, UK, 1995.
70. Vlassov, A.V.; Kazakov, S.A.; Johnston, B.H.; Landweber, L.F. The RNA world on ice: A new scenario for the emergence of RNA information. J. Mol. Evol. 2005, 61, 264-273.
71. Forterre, P. The two ages of the RNA world, and the transition to the DNA world: A story of viruses and cells. Biochemie 2005, 87, 793-803.
72. Goldenfeld, N; Woese, C. Biology's next revolution. Nature 2007, 445, 369.
73. Cech, T.R. Evolution of biological catalysis: Ribozyme to RNA enzyme. Cold Spring Harbor Symp. Quant. Biol. 2009, 74, 11-16.
74. Pace, N.R. Origin of life-Facing up to the physical setting. Cell 1991, 65, 531-533.
75. Serwer, P. Buoyant density sedimentation of macromolecules in sodium iothalamate density gradients. J. Mol. Biol. 1975, 92, 433-448.
76. Martin, W.; Baross, J.; Kelley, D.; Russell, M.J. Hydrothermal vents and the origin of life. Nat. Rev. Microbiol. 2008, 6, 805-814.
77. Serwer P.; Hayes, S.J.; Thomas, J.A.; Demeler, B.; Hardies, S.C. Isolation of novel large and aggregating bacteriophages. Methods Mol. Biol. 2009, 501, 55-66.
78. Serwer, P.; Wang, H. Single-particle light microscopy of bacteriophages. J. Nanosci. Nanotechnol. 2005, 5, 2014-2028.
79. Pais-Correia, A.-M.; Sachse, M.; Guadagnini, S.; Robbiati, V.; Lasserre, R.; Gessain, A.; Gout, O.; Alcover, A.; Thoulouze, M.-I. Biofilm-like extracellular viral assemblies mediate HTLV-1 cell-to-cell transmission at virological synapses. Nat. Med. 2010, 16, 83-89.
80. Wächtershäuser, G. On the chemistry and evolution of the pioneer organism. Chem. Biodiversity 2007, 4, 584-602.
81. Serwer, P. Evolution and the complexity of bacteriophages. Virol. J. 2007, 4, 30.
82. Moreau, H.; Piganeau, G.; Desdevises, Y.; Cooke, R.; Derelle, E.; Grimsley, N. Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer. J. Virol. 2010, 84, 12555-12563.
83. Filee, J.; Chandler, M. Gene exchange and the origin of giant viruses. Intervirology 2010, 53, 354-361.
84. Liu, H.; Fu, Y.; Jiang, D.; Li, G.; Xie, J.; Cheng, J.; Peng, Y.; Ghabrial, S.A.; Yi, X. Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J. Virol. 2010, 84, 11876-11887.
85. Baker, T.S.; Newcomb, W.W.; Olson, N.H.; Cowsert, L.M.; Olson, C.; Brown, J.C. Structures of bovine and human papillomaviruses. Analysis by cryoelectron microscopy and three-dimensional image reconstruction. Biophys. J. 1991, 60, 1445-1456.
86. Belnap, D.M.; Olson, N.H.; Cladel, N.M.; Newcomb, W.W.; Brown, J.C.; Kreider, J.W.; Christensen, N.D.; Baker, T.S. Conserved features in papillomavirus and polyomavirus capsids. J. Mol. Biol. 1996, 259, 249-263.
87. Ben-nun-Shaul, O.; Bronfeld, H.; Reshef, D.; Schueler-Furman, O.; Oppenheim, A. The SV40 capsid is stabilized by a conserved pentapeptide hinge of the major capsid protein VP1. J. Mol. Biol. 2009, 386, 1382-1391.
88. Prangishvili, D.; Forterre, P.; Garrett, R.A. Viruses of the archaea: A unifying view. Nat. Rev. Microbiol. 2006, 4, 837-848.
89. Bize, A.; Peng, X.; Prokofeva, M.; Maclellan, K.; Lucas, S.; Forterre, P.; Garrett, R.A.; Bonch-Osmolovskaya, E.A.; Prangishvili, D. Viruses in acidic geothermal environments of the Kamchatka Peninsula. Res. Microbiol. 2008, 159, 358-366.
90. Prangishvili, D.; Garrett, R.A.; Koonin, E.V. Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life. Virus Res. 2006, 117, 52-67
91. Huet, A.; Conway, J.F.; Letellier, L.; Boulanger, P. In vitro assembly of the T = 13 procapsid of bacteriophage T5 with its scaffolding domain. J. Virol. 2010, 84, 9350-9358.
92. Dokland, T. Scaffolding proteins and their role in viral assembly. Cell. Mol. Life Sci. 1999, 56, 580-603.
93. Johnson, J.E. Multi-disciplinary studies of viruses: The role of structure in shaping the questions and answers. J. Struct. Biol. 2008, 163, 246-253.
94. Fane, B.A.; Prevelige, P.E., Jr. Mechanism of scaffolding-assisted viral assembly. Adv. Protein Chem. 2003, 64, 259-299.
95. Bândea, C.I. A new theory on the origin and the nature of viruses. J. Theor. Biol. 1983, 105, 591-602.
96. Forterre, P. Defining life: The virus viewpoint. Origins Life Evol. Biospheres 2010, 40, 151-160.
97. Summers, W.C. Félix d'Herelle and the Origins of Molecular Biology; Yale University Press: New Haven, CT, USA, 1999.
98. D'Herelle, F. The Bacteriophage and Its Clinical Application; Charles C. Thomas: Springfield, IL, USA, 1933; Translated to English.
99. Forterre, P. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain. Proc. Natl. Acad. Sci. U. S. A. 103, 3669-3674.
100. Cue, D.; Feiss, M. Genetic evidence that recognition of cos Q, the signal for termination of phage lambda DNA packaging, depends on the extent of head filling. Genetics 1997, 147, 7-17.
101. Catalano, C.E. The terminase enzyme from bacteriophage lambda: A DNA-packaging machine. Cell. Mol. Life Sci. 2000, 57, 128-148.
102. Maluf, N.K.; Gaussier, H.; Bogner, E.; Feiss, M.; Catalano, C.E. Assembly of bacteriophage lambda terminase into a viral DNA maturation and packaging machine. Biochemistry 2006, 45, 15259-15268.
103. Hashimoto, C.; Fujisawa, H. Packaging and transduction of non-T3 DNA by bacteriophage T3. Virology 1988, 166, 432-439.
104. Son, M.; Serwer, P. Role of exonuclease in the specificity of bacteriophage T7 DNA packaging. Virology 1992, 190, 824-833.
105. Serwer, P.; Watson, R.H.; Hayes, S.J. Detection and characterization of agarose-binding, capsid-like particles produced during assembly of a bacteriophage T7 procapsid. J. Virol. 1982, 42, 583-594.
106. Serwer, P.; Watson, R.H. Function of an internal bacteriophage T7 core during assembly of a T7 procapsid. J. Virol. 1982, 42, 595-601.
107. Bazinet, C.; King, J. Initiation of P22 procapsid assembly in vivo. J. Mol. Biol. 1988, 202, 77-86.
108. Dokland, T. Freedom and restraint: Themes in virus capsid assembly. Structure 2000, 8, R157-R162.
109. Johnson, J.E. Virus particle maturation: Insights into elegantly programmed nanomachines. Curr. Opin. Struct. Biol. 2010, 20, 210-216.
110. Katen, S.; Zlotnick, A. The thermodynamics of virus capsid assembly. Methods Enzymol. 2009, 455, 395-417.
111. Ackermann, H.-W.; Kropinski, A.M. Curated list of prokaryote viruses with fully sequenced genomes. Res. Microbiol. 2007, 158, 555-566.
112. Cherwa, J.E., Jr; Fane, B.A. Complete virion assembly with scaffolding proteins altered in the ability to perform a critical conformational switch. J. Virol. 2009, 83, 7391-7396.
113. Aksyuk, A.A.; Rossmann, M.G. Bacteriophage assembly. Viruses 2011, 3, 172-203.
114. Uchiyama, A.; Fane, B.A. Identification of an interacting coat-external scaffolding protein domain required for both the initiation of phiX174 procapsid morphogenesis and the completion of DNA packaging. J. Virol. 2005, 79, 6751-6756.
115. Strauss, S.K.; Scott, W.R.; Symmons, M.F.; Marvin, D.A. On the structures of filamentous bacteriophage Ff (fd, f1, M13). Eur. Biophys. J. 2008, 37, 521-527.
116. Forrey, C.; Muthukumar, M. Langevin dynamics simulations of genome packing in bacteriophage. Biophys. J. 2006, 91, 25-41.
117. Casjens, S.; Wyckoff, E.; Hayden, M.; Sampson, L.; Eppler, K.; Randall, S.; Moreno, E.T.; Serwer, P. Bacteriophage P22 portal protein is part of the gauge that regulates packing density of intravirion DNA. J. Mol. Biol. 1992, 224, 1055-1074.
118. Isidro, A.; Henriques, A.O.; Tavares, P. The portal protein plays essential roles at different steps of the SPP1 DNA packaging process. Virology 2004, 322, 253-263.
119. Zheng, H.; Olia, A.S.; Gonen, M.; Andrews, S.; Cingolani, G.; Gonen, T. A conformational switch in bacteriophage p22 portal protein primes genome injection. Mol. Cell. 2008, 29, 376-383.
120. Kudryavtsev, N. Against the organic hypothesis of the origin of petroleum. Pet. Econ. 1951, 9, 17-29.
121. Herndon, J.M. Enhanced prognosis for abiotic natural gas and petroleum resources. Curr. Sci.2006, 91, 596-598.
122. Orgel, L.E. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol. 2004, 39, 99-123.
123. Orgel, L.E. The implausibility of metabolic cycles on the prebiotic Earth. PLoS Biol. 2008, 6, e18.
124. De Duve, C. Chemistry and selection. Chem. Biodiversity 2007, 4, 574-583.
125. Woese, C.R. On the evolution of cells. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 8742-8747.
126. Bândea, C.I. A unifying scenario on the origin and evolution of cellular and viral domains. Nature Precedings 2009, available online: http://hdl.handle.net/10101/npre.2009.3888.1 (accessed on 12 July 2011).