Molecular Mechanisms Of Natural Genetic Engineering

(Hedges and Batzer 2005; Kelman and White 2005; Postberg, Heyse et al. 2008; Selmecki, Forche et al. 2010; Deem, Keszthelyi et al. 2011; Levin and Moran 2011)

DNA uptake from the environment

(Davey, Rech et al. 1989; Dubnau 1999; MacFadyen, Chen et al. 2001; Chen 2004; Meibom, Blokesch et al. 2005; Claverys, Prudhomme et al. 2006; Redfield, Findlay et al. 2006; Johnsen, Dubnau et al. 2009; Kovacs, Smits et al. 2009; Maughan and Redfield 2009; Weber-Lotfi, Ibrahim et al. 2009)

Sperm-mediated DNA transfer: (Gandolfi 1998; Chang, Qian et al. 2002; Smith and Spadafora 2005; Yanagimachi 2005; Lavitrano, Busnelli et al. 2006; Spadafora 2007; Navarro, Risco et al. 2008; Spadafora 2008; Garcia-Vazquez, Ruiz et al. 2010)

Intercellular DNA transfer

(Wolff, Malone et al. 1990; Heinemann and Sprague 1991; Sprague 1991; Wang, Goodman et al. 2002; Pappas and Winans 2003; Chung, Vaidya et al. 2006; Rocco and Churchward 2006; Simoes-Barbosa, Arganaraz et al. 2006; Richardson and Palmer 2007; Tsai, Huang et al. 2008; Lai and Lin 2009; Gillespie, Brayton et al. 2010; Hayes, Aoki et al. 2010; Hecht, Nitz et al. 2010; Snir and Trifonov 2010; Zhu and Mahato 2010; Ananiadou, Sullivan et al. 2011; Anderson and Seifert 2011; Babic, Berkmen et al. 2011; Fernandez-Gonzalez, de Paz et al. 2011; Ghinet, Bordeleau et al. 2011; Schroder, Schuelein et al. 2011)

Table III.1. Examples of intercellular and interkingdom DNA transfer
Horizontal transfer mode	Documented transfers
Uptake of environmental and liposomal DNA	Bacteria – bacteria: (Averhoff and Friedrich 2003; Claverys, Prudhomme et al. 2006; Averhoff 2009) Archaea-archaea: (Bertani and Baresi 1987; Worrell, Nagle et al. 1988); (Cline, Schalkwyk et al. 1989; Patel, Nash et al. 1994; Metcalf, Zhang et al. 1997; Soppa 2006; Almeida, Leszczyniecka et al. 2008; Berkner and Lipps 2008; Soppa, Baumann et al. 2008) Algal transfection: (Walker, Purton et al. 2005). Plant – bacteria: (Kay, Vogel et al. 2002; de Vries, Herzfeld et al. 2004) Plastid transfection: (O'Neill, Horvath et al. 1993) Mammalian cell transfection: (Wolff and Budker 2005; Khalil, Kogure et al. 2006; Kim and Eberwine 2010) and lipofection: (Felgner 1987; Zuhorn, Kalicharan et al. 2002) Plant protoplasts: (Potrykus 1990; Davey, Anthony et al. 2005)
Conjugal transfer	Bacteria – bacteria: (Hayes 1968) Archaea – archaea: (Prangishvili, Albers et al. 1998) Bacteria – archaea: (Dodsworth, Li et al. 2010) Bacteria – yeast: (Heinemann and Sprague 1989; Heinemann and Sprague 1991) Bacteria – plant: (Chilton 1983; Winans 1992; Broothaerts, Mitchell et al. 2005) Bacteria – animal: (Schroder, Schuelein et al. 2011)
Viral transduction and GTAs (gene transfer agents)	Bacteria – bacteria: (Stanton 2007; McDaniel, Young et al. 2010) Archaea-archaea: (Meile, Abendschein et al. 1990; Bertani 1999); (Zillig, Prangishvilli et al. 1996; Eiserling, Pushkin et al. 1999; Prangishvili 2003; Snyder, Stedman et al. 2003; Prangishvili and Garrett 2005; Prangishvili, Forterre et al. 2006; Prangishvili, Garrett et al. 2006) Bacteria – plant: (Chung, Vaidya et al. 2006) Animal cell – animal cell: (El-Aneed 2004) Animal cell – virus: (Filee, Pouget et al. 2008)
direct fusion of cells or protoplasts that lack a rigid outer covering.	Bacteria-bacteria: (Schaeffer, Cami et al. 1976; Hopwood, Wright et al. 1977; Patnaik, Louie et al. 2002; Dai, Ziesman et al. 2005) Mammal-mammal: (Ramos, Bonenfant et al. 2002; Trontelj, Usaj et al. 2010; Yamanaka and Blau 2010) Plant-plant: (Gamborg and Holl 1977; Binding, Krumbiegel-Schroeren et al. 1986; Nehls, Krumbiegel-Schroeren et al. 1986; Potrykus 1990; Fahleson and Glimelius 1999; Davey, Anthony et al. 2005; Poma, Limongi et al. 2006; Savitha, Sadhasivam et al. 2010)
Parasitic or endosymbiotic association	Plant – fern: (Davis, Anderson et al. 2005) Plant – plant: (Davis and Wurdack 2004) (Mower, Stefanovic et al. 2004) Bacteria – invertebrate: (Hotopp, Clark et al. 2007; Nikoh, Tanaka et al. 2008; Nikoh and Nakabachi 2009)
Undetermined mechanism	Archaea – bacteria: (Koonin, Makarova et al. 2001) Bacteria – fungus: (Belbahri, Calmin et al. 2008) Bacteria – protist: (Huang, Mullapudi et al. 2004; Stechmann, Baumgartner et al. 2006; Whitaker, McConkey et al. 2009) Archaea – protist: (Andersson, Sarchfield et al. 2005; Huang, Xu et al. 2005) Protist – protist: (Andersson 2005; Andersson, Sarchfield et al. 2005; Andersson, Hirt et al. 2006; Andersson, Sjogren et al. 2007; Andersson 2009; Andersson 2009)

 

Intercellular RNA transfer

(Lotvall and Valadi 2007; Smalheiser 2007; Lai and Lin 2009; Westwood, Roney et al. 2009; Eldh, Ekstrom et al. 2010; Rudzinski and Aminabhavi 2010; Shim and Kwon 2010; Zhu and Mahato 2010; Zomer, Vendrig et al. 2010; Diken, Kreiter et al. 2011; Shegokar, Al Shaal et al. 2011; Yuan, Naguib et al. 2011)

            Exosomes: (Boss and Renne 2010; Mathivanan, Ji et al. 2010; Pegtel, Cosmopoulos et al. 2010; Pegtel, van de Garde et al. 2011; Ramachandran and Palanisamy 2011)

            Viral packaging of cell RNAs: (Jorgensen, Nielsen et al. 2009; Amen and Griffiths 2011)

Intercellular protein (and prion) transfer

(Maruyama and Hartl 1991; Hunter 2006; Smalheiser 2007; Eggenberger, Birtalan et al. 2009; Gousset, Schiff et al. 2009; Gousset and Zurzolo 2009; Chen, Bruce et al. 2010; Afanasieva, Kushnirov et al. 2011; Dubey and Ben-Yehuda 2011; Dupont, Prochiantz et al. 2011; Eggenberger, Mink et al. 2011; Lindgren and Langel 2011; Beringue, Herzog et al. 2012)

            Type I-VI and nanotube transfer/secretion systems: (Ball, Durand et al. 2002; Cascales and Christie 2003; Delepelaire 2004; Filloux 2004; Jacob-Dubuisson, Fernandez et al. 2004; Christie, Atmakuri et al. 2005; Cianciotto 2005; Angkawidjaja and Kanaya 2006; Buttner and Bonas 2006; Cornelis 2006; Desvaux, Cooper et al. 2006; Dautin and Bernstein 2007; Juhas, Crook et al. 2008; Krehenbrink and Downie 2008; Rossier, Dao et al. 2008; Senf, Tommassen et al. 2008; Alvarez-Martinez and Christie 2009; Boyer, Fichant et al. 2009; Deakin and Broughton 2009; Durand, Verger et al. 2009; Filloux 2009; Pukatzki, McAuley et al. 2009; Tseng, Tyler et al. 2009; Bleves, Viarre et al. 2010; Marlovits and Stebbins 2010; Masi and Wandersman 2010; Rego, Chandran et al. 2010; Salacha, Kovacic et al. 2010; Ananiadou, Sullivan et al. 2011; Dubey and Ben-Yehuda 2011; Ficht 2011; Filloux 2011)

Mutator trans-lesion polymerases and point mutations

(Maenhaut-Michel, Janel-Bintz et al. 1992; Wagner, Gruz et al. 1999; Godoy, Gizatullin et al. 2000; Napolitano, Janel-Bintz et al. 2000; Fuchs, Koffel-Schwartz et al. 2001; Pham, Rangarajan et al. 2001; Goodman 2002; Wagner, Etienne et al. 2002; Fuchs, Fujii et al. 2004; Tippin, Pham et al. 2004; Schlacher, Pham et al. 2006; Yamada, Nunoshiba et al. 2006; Fuchs and Fujii 2007; Fujii and Fuchs 2007; Godoy, Jarosz et al. 2007; Sundin and Weigand 2007; Cohen, Godoy et al. 2009; Jiang, Karata et al. 2009; Koskiniemi and Andersson 2009; Waters, Minesinger et al. 2009; Garcia-Villada and Drake 2010; Koskiniemi, Hughes et al. 2010; Patel, Jiang et al. 2010; Benson, Norton et al. 2011; Herr, Ogawa et al. 2011; Herr, Williams et al. 2011; Sladewski, Hetrick et al. 2011)

Homology-dependent recombination (HR)

(Myers and Stahl 1994; Takahashi and Norden 1994; Kuzminov 1999; Jakupciak and Wells 2000; Kowalczykowski 2000; Seitz, Haseltine et al. 2001; Lusetti and Cox 2002; Rong and Golic 2003; Miyazaki, Bressan et al. 2004; Nishant and Rao 2006; Pacher, Schmidt-Puchta et al. 2007; Argueso, Westmoreland et al. 2008; Dillingham and Kowalczykowski 2008; Frankenberg-Schwager, Becker et al. 2008; Karboul, Mazza et al. 2008; Naranjo and Corredor 2008; San Filippo, Sung et al. 2008; Wang and Maier 2008; Beucher, Birraux et al. 2009; Handa, Morimatsu et al. 2009; Lisby and Rothstein 2009; Hicks, Kim et al. 2010; Hoang, Tan et al. 2010; Manthey and Bailis 2010; Szekvolgyi and Nicolas 2010; Wahls and Davidson 2010; Daniel, Lange et al. 2011; Grey, Sommermeyer et al. 2011; Holloman 2011; Lange, Pan et al. 2011; Tang, Dominska et al. 2011)

Microhomology-dependent and single-strand annealing (SSA) break repair

(Wu, Sugiyama et al. 2006; Yamada-Inagawa, Klar et al. 2007; Frankenberg-Schwager, Becker et al. 2008; Hastings, Ira et al. 2009; Manthey, Naik et al. 2009; Letsolo, Rowson et al. 2010; Pannunzio, Manthey et al. 2010; Pannunzio, Manthey et al. 2010; Yu and McVey 2010; Chiarle, Zhang et al. 2011; Glover, Jun et al. 2011)

Non-homologous end-joining (NHEJ)

(Wilson and Lieber 1999; Dudasova, Dudas et al. 2004; Pitcher, Wilson et al. 2005; Bowater and Doherty 2006; Meaburn, Misteli et al. 2007; Pacher, Schmidt-Puchta et al. 2007; Pitcher, Brissett et al. 2007; Bennardo, Cheng et al. 2008; Chan, Galli et al. 2008; Frankenberg-Schwager, Becker et al. 2008; Malyarchuk, Castore et al. 2008; McVey and Lee 2008; Schulte-Uentrop, El-Awady et al. 2008; Wu, Topper et al. 2008; Yano and Chen 2008; Brissett and Doherty 2009; Mahaney, Meek et al. 2009; Mimitou and Symington 2009; Yano, Morotomi-Yano et al. 2009; Yano, Morotomi-Yano et al. 2009; Rupnik, Lowndes et al. 2010; Williams, Lees-Miller et al. 2010; Garcia, Phelps et al. 2011; Lowden, Flibotte et al. 2011; Mladenov and Iliakis 2011; Ogiwara and Kohno 2011; Stracker and Petrini 2011)

Site-specific recombination

(Murray 1987; Goodwin and Poulter 2001; Radman-Livaja, Shaw et al. 2003; Goodwin, Poulter et al. 2004; Groth and Calos 2004; Draper, Cesar et al. 2005; Kobryn and Chaconas 2005; Poulter and Goodwin 2005; Cesar and Llosa 2007; Piednoel and Bonnivard 2009; Rajeev, Malanowska et al. 2009; Rowe-Magnus 2009; Rice, Mouw et al. 2010; Smith, Brown et al. 2010; Vanhooff, Normand et al. 2010; Agundez, Machon et al. 2011; Kojima and Jurka 2011)

Integrons

(Hall and Stokes 1993; Vaisvila, Morgan et al. 2001; Fluit and Schmitz 2004; Gillings, Holley et al. 2005; Labbate, Case et al. 2009)

DNA Transpsosons

(McClintock 1987; Georgiev, Tikhomirova et al. 1997; Kempken and Kuck 1998; Haren, Ton-Hoang et al. 1999; Berger and Haas 2001; Duval-Valentin, Marty-Cointin et al. 2004; Gueguen, Rousseau et al. 2005; Liu, Crellin et al. 2005; Kapitonov and Jurka 2006; Menzel, Dechyeva et al. 2006; Pomerantseva, Biryukova et al. 2006; Brillet, Bigot et al. 2007; Wicker, Sabot et al. 2007; Brazelton and Baross 2009; Aziz, Breitbart et al. 2010; Claeys Bouuaert and Chalmers 2010; Ivics and Izsvak 2010; Ling and Cordaux 2010; Marquez and Pritham 2010; Momose, Abe et al. 2010; Munoz-Lopez and Garcia-Perez 2010; Pajunen, Rasila et al. 2010; Bardaji, Anorga et al. 2011; Demattei, Hedhili et al. 2011; Flutre, Duprat et al. 2011; Kojima and Jurka 2011; Montano and Rice 2011; Novick, Smith et al. 2011; Siddique, Buisine et al. 2011; Thomas, Sorourian et al. 2011)

LTR retrotransposons and retroviruses

(Errede, Company et al. 1985; Company and Errede 1987; Company and Errede 1988; Errede and Ammerer 1989; Haren, Ton-Hoang et al. 1999; Martin, Herniou et al. 1999; Goodwin and Poulter 2001; Tam, Hughes et al. 2002; Gifford and Tristem 2003; Goodwin, Poulter et al. 2004; Gifford, Kabat et al. 2005; Lewinski and Bushman 2005; Poulter and Goodwin 2005; Kejnovsky, Kubat et al. 2006; Katzourakis, Tristem et al. 2007; Morrish, Garcia-Perez et al. 2007; Delelis, Carayon et al. 2008; Eiden 2008; Faye, Arnaud et al. 2008; Gifford, Katzourakis et al. 2008; Hizi 2008; Zolotukhin, Schneider et al. 2008; Blomberg, Benachenhou et al. 2009; Cordaux and Batzer 2009; Gilbert, Maxfield et al. 2009; Jaratlerdsiri, Rodriguez-Zarate et al. 2009; Katzourakis, Gifford et al. 2009; Piednoel and Bonnivard 2009; Goldstone, Yap et al. 2010; Hou, Rajagopal et al. 2010; Kozak 2010; Silverman, Nguyen et al. 2010; van der Kuyl, Cornelissen et al. 2010; Yan, Liu et al. 2010; Dewannieux, Vernochet et al. 2011; Flutre, Duprat et al. 2011; Montano and Rice 2011; Neumann, Navratilova et al. 2011; Paprotka, Delviks-Frankenberry et al. 2011)

Non-LTR retrotransposons (SINEs, LINEs and retrotransposed RNAs)

(Bhattacharya, Bakre et al. 2002; Ohshima, Hattori et al. 2003; Dewannieux and Heidmann 2005; Ohshima and Okada 2005; Zingler, Willhoeft et al. 2005; Ding, Lin et al. 2006; Simoes-Barbosa, Arganaraz et al. 2006; Garcia-Perez, Doucet et al. 2007; Luo and Li 2007; Nishihara and Okada 2008; Dong, Poulter et al. 2009; Khazina and Weichenrieder 2009; Kroutter, Belancio et al. 2009; Fujii 2010; Konkel and Batzer 2010; Flutre, Duprat et al. 2011)

            LINE: (Picard 1976; Fawcett, Lister et al. 1986; Sezutsu, Nitasaka et al. 1995; Pickeral, Makalowski et al. 2000; Yu, Zingler et al. 2001; Gilbert, Lutz-Prigge et al. 2002; Moran and Gilbert 2002; Morrish, Gilbert et al. 2002; Lutz, Vincent et al. 2003; Kale, Moore et al. 2005; Kulpa and Moran 2005; Martin, Cruceanu et al. 2005; Martin, Li et al. 2005; Zingler, Willhoeft et al. 2005; Babushok and Kazazian 2007; Garcia-Perez 2007; Garcia-Perez, Doucet et al. 2007; Gogvadze, Barbisan et al. 2007; Goodier, Zhang et al. 2007; Morrish, Garcia-Perez et al. 2007; Perrin, Ballestar et al. 2007; Perrin, Ballestar et al. 2007; Ramos, He et al. 2007; Repanas, Zingler et al. 2007; Yamamoto, Toyota et al. 2008; Dong, Poulter et al. 2009; Suzuki, Yamaguchi et al. 2009; Bao and Jurka 2010; Beck, Collier et al. 2010; Belancio, Roy-Engel et al. 2010; Doucet, Hulme et al. 2010; Doucet, Hulme et al. 2010; Han 2010; Kojima 2010; Rouchka, Montoya-Durango et al. 2010; Yoshitake, Aoyagi et al. 2010; Khazina, Truffault et al. 2011; Thompson and Christensen 2011)

            Alu: (Yu, Zingler et al. 2001; Kolomietz, Meyn et al. 2002; Ricci, Regis et al. 2003; Athanasiadis, Rich et al. 2004; McNeil 2004; Callinan, Wang et al. 2005; Zingler, Willhoeft et al. 2005; Chen, Ferec et al. 2007; Bennett, Keller et al. 2008; Wallace, Wagstaff et al. 2008; Srikanta, Sen et al. 2009; Srikanta, Sen et al. 2009)

            SVA: (Ostertag, Goodier et al. 2003; Wang, Xing et al. 2005; Bantysh and Buzdin 2009; Damert, Raiz et al. 2009; Hancks, Ewing et al. 2009; Hancks and Kazazian 2010; Hancks, Goodier et al. 2011; Raiz, Damert et al. 2011)

RNA processing and retroelements

(Merendino, Perron et al. 2006; Mougel, Houzet et al. 2009; Galligan, Marchetti et al. 2011)

            Diversity-generating retroelements (DGRs) (Doulatov, Hodes et al. 2004; Medhekar and Miller 2007; Guo, Tse et al. 2008; Miller, Le Coq et al. 2008; Guo, Tse et al. 2011)

Retroinserting group II introns

(Lazowska, Meunier et al. 1994; Zimmerly, Moran et al. 1999; Centron and Roy 2002; Dai and Zimmerly 2002; Podar, Mullineaux et al. 2002; Dai and Zimmerly 2003; Mohr and Lambowitz 2003; Munoz-Adelantado, San Filippo et al. 2003; Schafer, Gan et al. 2003; Odom, Shenkenberg et al. 2004; Noah, Park et al. 2006; Nisa-Martinez, Jimenez-Zurdo et al. 2007; Stabell, Tourasse et al. 2007; Simon, Clarke et al. 2008; Tourasse and Kolsto 2008; Valles, Halanych et al. 2008; Kroeger, Watkins et al. 2009; Zhuang, Mastroianni et al. 2009; Mullineux, Costa et al. 2010; Pyle 2010; Tourasse, Stabell et al. 2010; Chillon, Martinez-Abarca et al. 2011; Huang, Shaikh et al. 2011; Leclercq, Giraud et al. 2011)

Agrobacterium T-DNA insertion in plant chromosomes

(Zupan and Zambryski 1995; Zupan, Muth et al. 2000; Pelczar, Kalck et al. 2004; Tzfira and Citovsky 2006; Muller, Atkinson et al. 2007; Boyko, Matsuoka et al. 2009; Lacroix and Citovsky 2009)

Inteins, group I introns and homing endonucleases

(Gimble 2000; Pietrokovski 2001; Ko, Choi et al. 2002; Perler 2002; Stoddard 2005; Tourasse and Kolsto 2008; Bonocora and Shub 2009; Dassa, London et al. 2009; Edgell 2009; Nielsen and Johansen 2009; Singh, Tripathi et al. 2009; Marcaida, Munoz et al. 2010; Callahan, Topilina et al. 2011; Edgell, Chalamcharla et al. 2011)

Amplifications

(Von Hoff 1991; Hastings, Slack et al. 2004; Hersh, Ponder et al. 2004; Roth and Andersson 2004; Kejnovsky, Kubat et al. 2006; Slack, Thornton et al. 2006; Hastings 2007; Pritham and Feschotte 2007; Raman and Stopfer 2008; Andersson and Hughes 2009; Tanaka and Yao 2009; Brewer, Payen et al. 2011)

Fragile sites

(Le Beau 1986; Yunis 1987; Moriarty and Webster 2003; Ishii and Furukawa 2004; Arlt, Durkin et al. 2006; Glover 2006; O'Keefe and Richards 2006; Durkin and Glover 2007; Ruiz-Herrera and Robinson 2007; Pichiorri, Ishii et al. 2008; Burrow, Williams et al. 2009; Di Rienzi, Collingwood et al. 2009; Gericke 2010)

Topoisomerases and helicases

(Lippert, Kim et al. 2011; Mischo, Gomez-Gonzalez et al. 2011; Takahashi, Burguiere-Slezak et al. 2011)

Synthetic in vivo genetic engineering

(Aagaard, Leviev et al. 1996; Reilly and Silva 1996; Guo, Karberg et al. 2000; Kolkman and Stemmer 2001; Court, Sawitzke et al. 2002; Lyznik, Gordon-Kamm et al. 2003; Poteete, Fenton et al. 2004; Jones, Kierlin et al. 2005; Rawsthorne, Turner et al. 2006; Cui and Davis 2007; Yao and Lambowitz 2007; Abalakina, Tokmakova et al. 2008; Mueller, Coleman et al. 2009; Pedersen and Phillips 2009; Pennisi 2009; Arber 2010; Grabundzija, Irgang et al. 2010; Ivics and Izsvak 2010; Marton, Zuker et al. 2010; van Boxtel and Cuppen 2010; Wei, Shi et al. 2010; Akhverdyan, Gak et al. 2011; Carroll 2011; Cui, Ji et al. 2011; Esvelt, Carlson et al. 2011; Hockemeyer, Wang et al. 2011; Huang, Ashton et al. 2011; Miller, Tan et al. 2011; Nern, Pfeiffer et al. 2011; Turan, Galla et al. 2011; Venken, Schulze et al. 2011; Zhang, Cong et al. 2011)

Genome Biology, Volume 8 Supplement 1, 2007, “Transposons in vertebrate functional genomics”: http://genomebiology.com/supplements/8/S1

 

Somatic cell diversification by movement of transposable elements

(Sheen, Sherry et al. 2000; Lutz, Vincent et al. 2003; Garcia-Perez 2007; Beck, Collier et al. 2010; Belancio, Roy-Engel et al. 2010; Singer, McConnell et al. 2010; St Laurent, Hammell et al. 2010; Baillie, Barnett et al. 2011)

 

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