Table 4A. Cell Biochemical Activities Used in Natural Genetic Engineering (NGE)

NGE activities



Endo- & exonucleases

Cleave nucleic acid chains or duplexes at interior (endo) or terminal (exo) positions

(Haber 1995; Khare and Eckert 2002; Gogarten and Hilario 2006; Calvin and Li 2008; Zhuang, Jiang et al. 2009; Wakamatsu, Kitamura et al. 2010; Barzel, Obolski et al. 2011; Schwartz and Heyer 2011; Cao 2012)

DNA & RNA ligases

Splice together 3’ OH and 5’ phosphate ends of nucleic acid chains

(Pascal 2008; Vago, Leva et al. 2009; Vicens and Cech 2009; Yutin and Koonin 2009; Simsek, Brunet et al. 2011)

DNA & RNA polymerases

Template-directed DNA and RNA polymerization; both precise and error-prone processes

(Goodman 2002; Fujii and Fuchs 2004; Livneh, Ziv et al. 2010; McHenry 2011; Nikitina, Tischenko et al. 2011; Werner and Grohmann 2011; Fijalkowska, Schaaper et al. 2012; Hsin and Manley 2012; Kwak, Fuda et al. 2013)

Ribonucleotide and deoxyribonucleotide terminal transferases

Template-independent addition of nucleotides to the 3’ OH end of a nucleic acid chain

(Greider and Blackburn 1985; Greider and Blackburn 1987; Fowler and Suo 2006; Martin and Keller 2007; Motea and Berdis 2010)

Reverse transcriptases

Make a DNA strand complementary to an RNA template

(Varmus 1987; Zimmerly, Moran et al. 1999; Liu, Deora et al. 2002; Simon and Zimmerly 2008; Belfort, Curcio et al. 2011; Gladyshev and Arkhipova 2011)

RNA chaperones

Hold RNA molecules in position for reverse transcription or splicing

(Mohr, Matsuura et al. 2006; Rajkowitsch and Schroeder 2007; Kim, Jung et al. 2010; Martin 2010; Batisse, Guerrero et al. 2012)

Coordinated multiprotein homologous recombination (Rec) complexes

Carry out the process of reciprocal exchange or “gene conversion”[1] between two homologous duplexes

(Kowalczykowski 2000; Szekvolgyi and Nicolas 2010; White 2011; Grabarz, Barascu et al. 2012; Krejci, Altmannova et al. 2012)

Coordinated multiprotein non-homologous end-joining (NHEJ) complexes

Join together the ends of two linear DNA molecules; generally involves “processing” the ends so they can be ligated together

(Pitcher, Wilson et al. 2005; van Gent and van der Burg 2007; Weterings and Chen 2008; Fattah, Lee et al. 2010; Mladenov and Iliakis 2011; Grabarz, Barascu et al. 2012)

Serine & tyrosine site-specific recombinases

Carry out reciprocal exchange between specific recombination sites by a series of single-strand DNA-protein transesterifications[2]

(Smith and Thorpe 2002; Poulter and Goodwin 2005; Hallet and Sherratt 2010; Rice, Mouw et al. 2010; Van Houdt, Leplae et al. 2012)

Transposases and integrases

Bind to specific sequences at the end of paired duplex regions to induce transient cleavages that are subsequently ligated into a target duplex to mobilize a segment of DNA

(Polard and Chandler 1995; Nowacki, Higgins et al. 2009; Aziz, Breitbart et al. 2010; Hallet and Sherratt 2010; Hickman, Chandler et al. 2010; Montano and Rice 2011; Yuan and Wessler 2011)

Homing endonucleases and inteins

Site-specific duplex endonucleases; sometimes encoded by self-splicing protein domains (inteins)

(Gogarten, Senejani et al. 2002; Stoddard 2005; Dassa, London et al. 2009; Raghavan and Minnick 2009; Elleuche and Poggeler 2010; Marcaida, Munoz et al. 2010; Barzel, Naor et al. 2011; Taylor and Stoddard 2012)

Retrosplicing introns

Self-splicing type II introns capable of reverse-splicing into RNA or DNA strains

(Zimmerly, Guo et al. 1995; Eickbush 1999; Mohr, Smith et al. 2000; Dickson, Huang et al. 2001; Lambowitz and Zimmerly 2004; Mohr, Matsuura et al. 2006)




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Barzel, A., U. Obolski, et al. (2011). "Home and away- the evolutionary dynamics of homing endonucleases." BMC Evol Biol 11: 324.

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Belfort, M., M. J. Curcio, et al. (2011). "Telomerase and retrotransposons: reverse transcriptases that shaped genomes." Proc Natl Acad Sci U S A 108(51): 20304-20310.

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Dickson, L., H. R. Huang, et al. (2001). "Retrotransposition of a yeast group II intron occurs by reverse splicing directly into ectopic DNA sites." Proc Natl Acad Sci U S A 98(23): 13207-13212.

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Fujii, S. and R. P. Fuchs (2004). "Defining the position of the switches between replicative and bypass DNA polymerases." Embo J 23(21): 4342-4352.

Gladyshev, E. A. and I. R. Arkhipova (2011). "A widespread class of reverse transcriptase-related cellular genes." Proc Natl Acad Sci U S A 108(51): 20311-20316.

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Hallet, B. and D. J. Sherratt (2010). "Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements." FEMS Microbiol Rev 21(2): 157-178.

Hickman, A. B., M. Chandler, et al. (2010). "Integrating prokaryotes and eukaryotes: DNA transposases in light of structure." Crit Rev Biochem Mol Biol 45(1): 50-69.

Hsin, J. P. and J. L. Manley (2012). "The RNA polymerase II CTD coordinates transcription and RNA processing." Genes Dev 26(19): 2119-2137.

Khare, V. and K. A. Eckert (2002). "The proofreading 3'-->5' exonuclease activity of DNA polymerases: a kinetic barrier to translesion DNA synthesis." Mutat Res 510(1-2): 45-54.

Kim, W. Y., H. J. Jung, et al. (2010). "The Arabidopsis U12-type spliceosomal protein U11/U12-31K is involved in U12 intron splicing via RNA chaperone activity and affects plant development." Plant Cell 22(12): 3951-3962.

Kowalczykowski, S. C. (2000). "Initiation of genetic recombination and recombination-dependent replication." Trends Biochem Sci 25(4): 156-165.

Krejci, L., V. Altmannova, et al. (2012). "Homologous recombination and its regulation." Nucleic Acids Res 40(13): 5795-5818.

Kwak, H., N. J. Fuda, et al. (2013). "Precise maps of RNA polymerase reveal how promoters direct initiation and pausing." Science 339(6122): 950-953.

Lambowitz, A. M. and S. Zimmerly (2004). "Mobile group II introns." Annu. Rev. Genet. 38: 1-35.

Liu, M., R. Deora, et al. (2002). "Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage." Science 295(5562): 2091-2094.

Livneh, Z., O. Ziv, et al. (2010). "Multiple two-polymerase mechanisms in mammalian translesion DNA synthesis." Cell Cycle 9(4): 729-735.

Marcaida, M. J., I. G. Munoz, et al. (2010). "Homing endonucleases: from basics to therapeutic applications." Cell Mol Life Sci 67(5): 727-748.

Martin, G. and W. Keller (2007). "RNA-specific ribonucleotidyl transferases." Rna 13(11): 1834-1849.

Martin, S. L. (2010). "Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1." RNA Biol 7(6): 706-711.

McHenry, C. S. (2011). "Bacterial replicases and related polymerases." Curr Opin Chem Biol 15(5): 587-594.

Mladenov, E. and G. Iliakis (2011). "Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways." Mutat Res 711(1-2): 61-72.

Mohr, G., D. Smith, et al. (2000). "Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences." Genes Dev 14(5): 559-573.

Mohr, S., M. Matsuura, et al. (2006). "A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone." Proc Natl Acad Sci U S A 103(10): 3569-3574.

Montano, S. P. and P. A. Rice (2011). "Moving DNA around: DNA transposition and retroviral integration." Curr Opin Struct Biol 21(3): 370-378.

Motea, E. A. and A. J. Berdis (2010). "Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase." Biochim Biophys Acta 1804(5): 1151-1166.

Nikitina, T. V., L. I. Tischenko, et al. (2011). "Recent insights into regulation of transcription by RNA polymerase III and the cellular functions of its transcripts." Biol Chem 392(5): 395-404.

Nowacki, M., B. P. Higgins, et al. (2009). "A functional role for transposases in a large eukaryotic genome." Science 324(5929): 935-938.

Pascal, J. M. (2008). "DNA and RNA ligases: structural variations and shared mechanisms." Curr Opin Struct Biol 18(1): 96-105.

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Polard, P. and M. Chandler (1995). "Bacterial transposases and retroviral integrases." Mol Microbiol 15(1): 13-23.

Poulter, R. T. and T. J. Goodwin (2005). "DIRS-1 and the other tyrosine recombinase retrotransposons." Cytogenet Genome Res 110(1-4): 575-588.

Raghavan, R. and M. F. Minnick (2009). "Group I introns and inteins: disparate origins but convergent parasitic strategies." J Bacteriol 191(20): 6193-6202.

Rajkowitsch, L. and R. Schroeder (2007). "Dissecting RNA chaperone activity." Rna 13(12): 2053-2060.

Rice, P. A., K. W. Mouw, et al. (2010). "Orchestrating serine resolvases." Biochem Soc Trans 38(2): 384-387.

Schwartz, E. K. and W. D. Heyer (2011). "Processing of joint molecule intermediates by structure-selective endonucleases during homologous recombination in eukaryotes." Chromosoma 120(2): 109-127.

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Simsek, D., E. Brunet, et al. (2011). "DNA Ligase III Promotes Alternative Nonhomologous End-Joining during Chromosomal Translocation Formation." PLoS Genet 7(6): e1002080.

Smith, M. C. and H. M. Thorpe (2002). "Diversity in the serine recombinases." Mol Microbiol 44(2): 299-307.

Stoddard, B. L. (2005). "Homing endonuclease structure and function." Q Rev Biophys 38(1): 49-95.

Szekvolgyi, L. and A. Nicolas (2010). "From meiosis to postmeiotic events: homologous recombination is obligatory but flexible." FEBS J 277(3): 571-589.

Taylor, G. K. and B. L. Stoddard (2012). "Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms." Nucleic Acids Res 40(12): 5189-5200.

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Weterings, E. and D. J. Chen (2008). "The endless tale of non-homologous end-joining." Cell Res 18(1): 114-124.

White, M. F. (2011). "Homologous recombination in the archaea: the means justify the ends." Biochem Soc Trans 39(1): 15-19.

Yuan, Y. W. and S. R. Wessler (2011). "The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies." Proc Natl Acad Sci U S A 108(19): 7884-7889.

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Zimmerly, S., J. V. Moran, et al. (1999). "Group II intron reverse transcriptase in yeast mitochondria. Stabilization and regulation of reverse transcriptase activity by the intron RNA." J Mol Biol 289(3): 473-490.

[1] Gene conversion occurs when only a small segment of one molecule is substituted for the corresponding region of the homologous molecule without altering the linkages of flanking regions.

[2] The OH groups of a serine or tyrosine residue in the recombinase form a transient phosphodiester linkage with a DNA strand 5’ phosphate group.