Editing Transfer DNA

{{Short description|Type of DNA in bacterial genomes}}
[[Image:Ti plasmid.svg|thumb|350px|right|Ti plasmid with tDNA region]]
The '''transfer DNA''' (abbreviated '''T-DNA''') is the transferred [[DNA]] of the [[Ti plasmid|tumor-inducing (Ti) plasmid]] of some species of bacteria such as ''[[Agrobacterium tumefaciens]]'' and ''[[Agrobacterium rhizogenes]] (actually an Ri plasmid)''. The T-DNA is transferred from bacterium into the host plant's [[Cell nucleus|nuclear]] DNA [[genome]].<ref>{{Cite journal|last=Gelvin|first=Stanton B.|date=2017-11-27|title=Integration of Agrobacterium T-DNA into the Plant Genome|url=https://www.annualreviews.org/doi/10.1146/annurev-genet-120215-035320|journal=Annual Review of Genetics|volume=51|issue=1|pages=195–217|doi=10.1146/annurev-genet-120215-035320|pmid=28853920|issn=0066-4197|url-access=subscription}}</ref> The capability of this specialized tumor-inducing (Ti) plasmid is attributed to two essential regions required for DNA transfer to the host cell. The T-DNA is bordered by 25-base-pair repeats on each end. Transfer is initiated at the right border and terminated at the left border and requires the ''vir'' genes of the Ti plasmid.

The bacterial T-DNA is about 24,000 base pairs long<ref>{{cite journal|vauthors=Barker RF, Idler KB, Thompson DV, Kemp JD|date=November 1983|title=Nucleotide sequence of the tDNA region from theA grobacterium tumefaciens octopine Ti plasmid pTi15955|journal=Plant Molecular Biology|volume=2|issue=6|pages=335–50|doi=10.1007/BF01578595|pmid=24318453|s2cid=26118909}}</ref><ref>{{Cite journal|vauthors=Gielen J, Terryn N, Villarroel R, Van Montagu M|date=1999-08-01|title=Complete nucleotide sequence of the tDNA region of the plant tumour-inducing Agrobacterium tumefaciens Ti plasmid pTiC58|journal=Journal of Experimental Botany|volume=50|issue=337|pages=1421–1422|doi=10.1093/jxb/50.337.1421|issn=0022-0957|doi-access=free}}</ref> and contains plant-expressed [[gene]]s that code for [[enzyme]]s synthesizing [[opines]] and [[phytohormone]]s. By transferring the T-DNA into the plant genome, the bacterium essentially reprograms the plant cells to grow into a tumor and produce a unique food source for the bacteria. The synthesis of the plant hormones [[auxin]] and [[cytokinin]] by enzymes encoded in the T-DNA  enables the plant cell to overgrow, thus forming the [[crown gall tumor]]s typically induced by ''Agrobacterium tumefaciens'' infection.<ref name=":0">{{cite journal|vauthors=Hiei Y, Komari T, Kubo T|date=September 1997|title=Transformation of rice mediated by Agrobacterium tumefaciens|journal=Plant Molecular Biology|volume=35|issue=1–2|pages=205–18|doi=10.1023/a:1005847615493|pmid=9291974|s2cid=19196285}}</ref> ''Agrobacterium rhizogenes'' causes a similar infection known as [[Hairy root culture|hairy root disease]]. The [[opines]] are [[amino acid]] derivatives used by the bacterium as a source of carbon and energy. This natural process of [[horizontal gene transfer]] in plants is being utilized as a tool for fundamental and applied research in plant biology through ''Agrobacterium tumefaciens'' mediated foreign gene transformation and insertional mutagenesis.<ref>{{cite journal|vauthors=Zupan JR, Zambryski P|date=April 1995|title=Transfer of tDNA from Agrobacterium to the plant cell|journal=Plant Physiology|volume=107|issue=4|pages=1041–7|doi=10.1104/pp.107.4.1041|pmc=157234|pmid=7770515}}</ref><ref name="pmid10590158">{{cite journal|vauthors=Krysan PJ, Young JC, Sussman MR|date=December 1999|title=T-DNA as an insertional mutagen in Arabidopsis|journal=The Plant Cell|volume=11|issue=12|pages=2283–90|doi=10.1105/tpc.11.12.2283|pmc=144136|pmid=10590158}}</ref> Plant genomes can be engineered by use of ''[[Agrobacterium]]'' for the delivery of sequences hosted in [[Transfer DNA binary system|T-DNA binary vectors]].

== Mechanism of transformation in nature ==
The infection process of T-DNA into the host cell and integration into its nucleus involve multiple steps. First, the bacteria multiply in the wound sap before infection and then attach to the plant cell walls. The bacterial virulence genes' expression of approximately 10 [[operon]]s is activated by perception of phenolic compounds such as [[acetosyringone]] emitted by wounded plant tissue and follows cell-cell contact. Then this process proceeds with the [[Macromolecule|macromolecular]] [[Translocation (genetics)|translocation]] from ''Agrobacterium'' to cytoplasm of host cell, transmission of T-DNA along with associated proteins (called '''T-complex''') to the host cell nucleus followed by disassembly of the T-complex, stable integration of T-DNA into host plant [[genome]], and eventual expression of the transferred [[gene]]s. The integration of T-DNA into a host genome involves the formation of a single-stranded nick in the DNA at the right border of the Ti plasmid. This nick creates a region of single stranded DNA from the left border of the T-DNA gene over to the right border which was cut. Then, single stranded binding proteins attach to the single stranded DNA. DNA synthesis displaces the single stranded region and then a second nick at the left border region releases the single stranded T-DNA fragment. Further this fragment can  be incorporated into a host genome.<ref name="pmid24166430">{{cite journal|vauthors=Lacroix B, Citovsky V|author-link2=Vitaly Citovsky|date=2013|title=The roles of bacterial and host plant factors in Agrobacterium-mediated genetic transformation|journal=The International Journal of Developmental Biology|volume=57|issue=6–8|pages=467–81|doi=10.1387/ijdb.130199bl|pmid=24166430|doi-access=free|pmc=9478875}}</ref>

''Agrobacterium'' has been known to evolve a control system that uses plant host factors and cellular processes for several pathways of host-plant defense response to invade the host cell nucleus. For the integration of T-DNA into the target host genome, ''Agrobacterium'' carries out multiple interactions with host-plant factors.<ref name="pmid24166430" /> To interact with host plant proteins many ''Agrobacterium'' virulence proteins encoded by vir genes. ''Agrobacterium'' ''vir'' gene expression occurs via the VirA-VirG sensor that results in generation of a mobile single-stranded T-DNA copy (T-strand).  A processed form of VirB2 is the major component of the T-complex that is required for transformation. VirD2 is the protein that caps the 5′ end of the transferred T-strand by covalent attachment and is transported to the host cell cytoplasm.<ref>{{cite journal|vauthors=Koukolíková-Nicola Z, Raineri D, Stephens K, Ramos C, Tinland B, Nester EW, Hohn B|date=February 1993|title=Genetic analysis of the virD operon of Agrobacterium tumefaciens: a search for functions involved in transport of T-DNA into the plant cell nucleus and in T-DNA integration|journal=Journal of Bacteriology|volume=175|issue=3|pages=723–31|doi=10.1128/jb.175.3.723-731.1993|pmc=196211|pmid=8380800}}</ref><ref>{{Cite journal|last=Arya|first=Aditya|date=February 2017|title=Agrobacterium Pathology and Ti Plasmid based Vector Design.|journal=High Value Notes|volume=4|issue=1|pages=1–24|doi=10.13140/RG.2.2.18345.49769/1|name-list-style=vanc}}</ref> VirE2 is the single-stranded DNA binding protein that presumably coats the T- strand in the host cytoplasm by [[cooperative binding]]. It is then directed into the nucleus via interactions with the host cell proteins such as importin a, bacterial VirE3, and dynein-like proteins. Several other bacterial virulence effectors like VirB5, VirB7 (the minor components of the T-complex), VirD5, VirE2, VirE3, and VirF that may also interact with proteins of host plant cells.<ref>{{cite journal|vauthors=Gelvin SB|date=March 2003|title=Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool|journal=Microbiology and Molecular Biology Reviews|volume=67|issue=1|pages=16–37, table of contents|doi=10.1128/mmbr.67.1.16-37.2003|pmc=150518|pmid=12626681}}</ref>

== Uses in biotechnology ==
''Agrobacterium''-mediated T-DNA transfer is widely used as a tool in [[biotechnology]]. For more than two decades, ''Agrobacterium tumefaciens'' has been exploited for introducing genes into plants for basic research as well as for commercial production of [[transgenic crops]].<ref>{{cite journal|vauthors=Oltmanns H, Frame B, Lee LY, Johnson S, Li B, Wang K, Gelvin SB|date=March 2010|title=Generation of backbone-free, low transgene copy plants by launching T-DNA from the Agrobacterium chromosome|journal=Plant Physiology|volume=152|issue=3|pages=1158–66|doi=10.1104/pp.109.148585|pmc=2832237|pmid=20023148}}</ref> In [[genetic engineering]], the tumor-promoting and opine-synthesis genes are removed from the T-DNA and replaced with a gene of interest and/or a selection marker, which is required to establish which plants have been successfully transformed. Examples of selection markers include neomycin phosphotransferase, hygromycin B phosphotransferase (which both phosphorylate antibiotics) and [[phosphinothricin acetyltransferase]] (which acetylates and deactivates [[phosphinothricin]], a potent inhibitor of [[glutamine synthetase]]) or a [[herbicide]] formulations such as Basta or Bialophos.<ref name="pmid18250230">{{cite journal|vauthors=Lee LY, Gelvin SB|date=February 2008|title=tDNA binary vectors and systems|journal=Plant Physiology|volume=146|issue=2|pages=325–32|doi=10.1104/pp.107.113001|pmc=2245830|pmid=18250230}}</ref> Another selection system that can be employed is usage of metabolic markers such as phospho-mannose isomerase.<ref>{{Cite journal|vauthors=Todd R, Tague BW|date=2001-12-01|title=Phosphomannose isomerase: A versatile selectable marker forArabidopsis thaliana germ-line transformation|journal=Plant Molecular Biology Reporter|language=en|volume=19|issue=4|pages=307–319|doi=10.1007/bf02772829|s2cid=46196053|issn=0735-9640}}</ref> ''Agrobacterium'' is then used as a vector to transfer the engineered T-DNA into the plant cells where it integrates into the plant genome. This method can be used to generate [[transgenic plant]]s carrying a foreign gene. ''Agrobacterium tumefaciens'' is capable of transferring foreign DNA to both [[monocotyledons]] and [[dicotyledonous]] plants efficiently while taking care of critically important factors like the genotype of plants, types and ages of tissues inoculated, kind of vectors, strains of ''Agrobacterium'', selection marker genes and selective agents, and various conditions of tissue culture.<ref name=":0" />

The same procedure of T-DNA transfer can be used to disrupt genes via [[insertional mutagenesis]].<ref name="pmid10590158" /> Not only does the inserted T-DNA sequence create a mutation but its insertion also 'tags'<ref>{{cite journal|vauthors=Liu YG, Shirano Y, Fukaki H, Yanai Y, Tasaka M, Tabata S, Shibata D|date=May 1999|title=Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=96|issue=11|pages=6535–40|bibcode=1999PNAS...96.6535L|doi=10.1073/pnas.96.11.6535|pmc=26917|pmid=10339623|doi-access=free}}</ref> the affected gene, thus allowing for its isolation as T-DNA flanking sequences. A reporter gene can be linked to the right end of the T-DNA to be transformed along with a plasmid replicon and a selectable antibiotic (such as [[hygromycin]])-resistance gene and can explicit approximately 30% of average efficiency having successful T-DNA inserts induced [[gene fusion]]s in ''Arabidopsis thaliana''.<ref name="pmid2554318">{{cite journal|vauthors=Koncz C, Martini N, Mayerhofer R, Koncz-Kalman Z, Körber H, Redei GP, Schell J|date=November 1989|title=High-frequency T-DNA-mediated gene tagging in plants|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=86|issue=21|pages=8467–71|bibcode=1989PNAS...86.8467K|doi=10.1073/pnas.86.21.8467|pmc=298303|pmid=2554318|doi-access=free}}</ref>

[[Reverse genetics]] involves testing the presumed function of a gene that is known by disrupting it and then looking for the effect of that induced mutation on the organismal phenotype.  T-DNA tagging mutagenesis involves screening of populations by T-DNA insertional mutations. Collections of known T-DNA mutations provide resources to study the functions of individual genes, as developed for the model plant ''[[Arabidopsis thaliana]]''.<ref>{{cite journal |vauthors=Alonso, JM, etal|title=Genome-wide insertional mutagenesis of Arabidopsis thaliana |journal=Science |date=2003 |volume=301 |issue=5633 |pages=653–657 |doi=10.1126/science.1086391 |pmid=12893945 |bibcode=2003Sci...301..653A |url=https://doi.org/10.1126/science.1086391|url-access=subscription }}</ref><ref name="pmid28217003">{{cite journal|vauthors=Ben-Amar A, Daldoul S, Reustle GM, Krczal G, Mliki A|date=December 2016|title=Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics|journal=Current Genomics|volume=17|issue=6|pages=460–475|doi=10.2174/1389202917666160520102827|pmc=5282599|pmid=28217003}}</ref>  Examples of T-DNA insertion mutations in ''Arabidopsis thaliana'' include those associated many classes of phenotypes including seedling-lethals, size variants, pigment variants, embryo-defectives, reduced-fertility, and morphologically or physiologically aberrant plants.<ref>{{cite journal|last=Feldmann|first=Kenneth A.|date=1991-07-01|title=T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum|journal=The Plant Journal|language=en|volume=1|issue=1|pages=71–82|doi=10.1111/j.1365-313x.1991.00071.x|issn=1365-313X|name-list-style=vanc|doi-access=free}}</ref>

== See also ==
* [[Transfer DNA binary system]]

== References ==
{{Reflist}}

== Further reading ==
{{refbegin}}
* {{cite book|title=Biology of Plants|vauthors=Raven PH, Evert RF, Eichhorn SE|date=2005|publisher=W.H. Freeman and Company Publishers|isbn=0-7167-1007-2|edition=7th|location=New York}}
{{refend}}

{{DEFAULTSORT:T-Dna}}
[[Category:Biotechnology]]
[[Category:Bacterial plant pathogens and diseases]]
[[Category:DNA mobile genetic elements]]