Table
4A. Cell Biochemical Activities Used in Natural
Genetic Engineering (NGE)
NGE
activities
Functions
References
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”
(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
(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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