No Genome is an Island Extra References 8


8. The Virosphere as an Evolutionary R & D Sector


·      8.A. DNA Spreading.


o   Phage as sources of environmental DNA. Phage-encapsulated DNA can be taken up by bacteria (Claverys, Prudhomme et al. 2006; Seitz and Blokesch 2013), archaea (Lipscomb, Stirrett et al. 2011; Atomi, Imanaka et al. 2012), and yeast (Mitrikeski 2015). Environmental reservoirs for antibiotic resistance DNA determinants, particularly in soils associated with intensive agriculture (Colomer-Lluch, Jofre et al. 2011; Anand, Bera et al. 2016).


o   Role of phages in horizontal transfers: (Muniesa, Colomer-Lluch et al. 2013; Balcazar 2014; Bobay, Touchon et al. 2014; Touchon, Bernheim et al. 2016; Harrison and Brockhurst 2017)


o   Marine viruses modify metazoan hosts. Solar-powered sea slugs (Mujer, Andrews et al. 1996; Pierce, Maugel et al. 1999; Green, Li et al. 2000; Mondy and Pierce 2003; Pierce, Massey et al. 2003)


o   Tripartite symbioses between insects, bacteria and phage. (Moran, Degnan et al. 2005; Bordenstein, Marshall et al. 2006)


·      8.B. Vector Role of Viruses, GTAs, VLPs and Giant Viruses from Evolutionary “Melting Pots.”


o   Protist “Melting Pots” and Vector Role of Viruses, GTAs, VLPs and Giant Viruses (NCLDVs). (Boyer, Yutin et al. 2009; Moliner, Fournier et al. 2010; Slimani, Pagnier et al. 2013; Shterzer and Mizrahi 2015; Wang and Wu 2017)


o   NCLDVs (Van Etten and Meints 1999; La Scola, Audic et al. 2003; Filee, Siguier et al. 2007; Ogata and Claverie 2007; Moreira and Brochier-Armanet 2008; Claverie, Grzela et al. 2009; Schroeder, Park et al. 2009; Colson and Raoult 2010; Filee and Chandler 2010; Fischer, Allen et al. 2010; Forterre 2010; Raoult 2010; Raoult and Boyer 2010; Thomas and Greub 2010; Desnues, La Scola et al. 2012; Filée and Chandler 2012; Jeudy, Abergel et al. 2012; Merhej and Raoult 2012; Nasir, Kim et al. 2012; Yoosuf, Yutin et al. 2012; Yutin and Koonin 2012; Boughalmi, Saadi et al. 2013; Claverie 2013; Claverie and Abergel 2013; Colson, Pagnier et al. 2013; Yutin, Colson et al. 2013; Katzourakis and Aswad 2014; Maumus, Epert et al. 2014; Piacente, De Castro et al. 2014; Yutin, Wolf et al. 2014; Abergel, Legendre et al. 2015; Blanc, Gallot-Lavallee et al. 2015; Filee 2015; Koonin, Krupovic et al. 2015; Legendre, Lartigue et al. 2015; Sun, Feschotte et al. 2015; Aherfi, Colson et al. 2016; Fischer and Hackl 2016; Wilhelm, Coy et al. 2016; Colson, La Scola et al. 2017)


·      8.C. Adaptive lysogenic conversion of bacteria (Brussow, Canchaya et al. 2004; Casas, Miyake et al. 2006; Casas and Maloy 2011; Fortier and Sekulovic 2013; Harrison and Brockhurst 2017):


o   Corynebacterium diptheria (Groman 1953; Groman 1953; Groman 1955; Groman and Eaton 1955; Groman and Memmer 1958)

o   Vibrio cholerae (Waldor and Mekalanos 1996; Das 2014; Wang, Pang et al. 2015)

o   Pseudomonas aeruginosa (Vaca-Pacheco, Paniagua-Contreras et al. 1999; Davies, James et al. 2016; Saucedo-Mora, Castaneda-Tamez et al. 2017)

o   Clostridium botulinum as well as other Clostridium infections (Fortier 2017; Fortier 2018)

o   Escherichia coli (Eichhorn, Heidemanns et al. 2018)

o   Burkholderia cenocepacia (Roszniowski, McClean et al. 2018)

o   Enterococcus faecium (Rigvava, Kusradze et al. 2018)

o   Staphylococcus aureus/MRSA (Lee and Park 2016; Kraushaar, Hammerl et al. 2017)

o   Wolbachia (insect endosymbiont) (Bordenstein and Bordenstein 2016; LePage, Metcalf et al. 2017; Lindsey, Bhattacharya et al. 2018)

o   Aphid endosymbiont (Degnan and Moran 2008)

o   Plant pathogen Ralstonia solanacearum (Askora, Kawasaki et al. 2017).


·      8.D. Viral modification of host genomes for adaptive innovation.


o   RNA viruses. (Horie, Kobayashi et al. 2013) (Belyi, Levine et al. 2010) Integrated viral cDNA copies often provide an adaptive benefit in the form of protection against superinfection by the cognate viruses. (Parrish, Fujino et al. 2015) (Fujino, Horie et al. 2014) (Kanda, Tristem et al. 2013).


o   Marine cyanophages (viruses that infect cyanobacteria) carry sequences encoding photosynthesis proteins, and viruses from deep-sea hydrothermal vent microbiomes encode enzymes in a wide range of cellular metabolic pathways that have nothing to do with virus replication but can be adaptive for prokaryotic cells living in such an isolated environment. (Puxty, Millard et al. 2015; Fridman, Flores-Uribe et al. 2017; He, Li et al. 2017).


o   The polydnavirus family of insect viruses (so named because their genomes are composed of multiple small DNA circles) (Webb, Fisher et al. 2009).A more complex set of nested holobiont relationships. These viruses reproduce themselves by a symbiotic association with parasitic wasps (Strand and Burke 2013). The viral genome is integrated into that of the wasp, and virus reproduction only occurs in the wasp ovary. When the wasp injects its egg into the body cavity of an insect host, such as a caterpillar, the virus accompanies the egg and infects host cells. This infection does not lead to polydnavirus reproduction, but polydnavirus genome expression affects the host (caterpillar) immune system and suppresses attacks on the parasitic wasp egg and larvae, thereby facilitating growth of a mature wasp, carrying integrated polydnavirus DNA, inside the parasitized insect. In this way, the integrated virus and the parasitic wasp have a piggy-back symbiotic relationship at the expense of the doubly infected insect host.


·      8.E. Endogenous retroviruses (ERVs) in mammalian evolution


o   Pluripotency and stem cells. (Peaston, Evsikov et al. 2004; Macfarlan, Gifford et al. 2012; Santoni, Guerra et al. 2012; Fort, Hashimoto et al. 2014; Goke, Lu et al. 2015; Izsvak, Wang et al. 2016). HERV-H transcripts appear to function as long non-coding RNAs (lncRNAs) in the maintenance of the pluripotent state (Kelley and Rinn 2012) (Lu, Sachs et al. 2014) (Durruthy-Durruthy, Sebastiano et al. 2016).


o   Placenta. (Harris 1991; Lyden, Johnson et al. 1994; Blackburn 1995; Venables, Brookes et al. 1995; Harris 1998; Langat, Johnson et al. 1998; Blond, Lavillette et al. 2000; Mi, Lee et al. 2000; Bieche, Laurent et al. 2003; Bonnaud, Bouton et al. 2004; Mallet, Bouton et al. 2004; Muir, Lever et al. 2004; Prudhomme, Oriol et al. 2004; Rote, Chakrabarti et al. 2004; Dupressoir, Marceau et al. 2005; Dunlap, Palmarini et al. 2006; Carter and Mess 2007; Malassine, Blaise et al. 2007; Mangeney, Renard et al. 2007; Mess and Carter 2007; Rawn and Cross 2008; Asher, Bennett et al. 2009; Dupressoir, Vernochet et al. 2009; Gimenez, Montgiraud et al. 2009; Heidmann, Vernochet et al. 2009; Noorali, Rotar et al. 2009; Stoye 2009; Black, Arnaud et al. 2010; Dupressoir, Vernochet et al. 2011; Macaulay, Weeks et al. 2011; Cornelis, Heidmann et al. 2012; Dupressoir, Lavialle et al. 2012; Emera and Wagner 2012; Haig 2012; Malik 2012; Chuong 2013; Chuong, Rumi et al. 2013; Cornelis, Heidmann et al. 2013; Esnault, Cornelis et al. 2013; Lee, Nolan et al. 2013; Ruebner, Strissel et al. 2013; Cornelis, Vernochet et al. 2015; Pavlicev, Hiratsuka et al. 2015; Denner 2016)





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