Ti plasmid

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The structure of the Ti plasmid Ti plasmid.svg
The structure of the Ti plasmid

A tumour inducing (Ti) plasmid is a plasmid found in pathogenic species of Agrobacterium , including A. tumefaciens, A. rhizogenes, A. rubi and A. vitis.

Contents

Evolutionarily, the Ti plasmid is part of a family of plasmids carried by many species of Alphaproteobacteria. Members of this plasmid family are defined by the presence of a conserved DNA region known as the repABC gene cassette, which mediates the replication of the plasmid, the partitioning of the plasmid into daughter cells during cell division as well as the maintenance of the plasmid at low copy numbers in a cell. [1] The Ti plasmids themselves are sorted into different categories based on the type of molecule, or opine, they allow the bacteria to break down as an energy source. [2]

The presence of this Ti plasmid is essential for the bacteria to cause crown gall disease in plants. [1] This is facilitated via certain crucial regions in the Ti plasmid, including the vir region, which encodes for virulence genes, and the transfer DNA (T-DNA) region, which is a section of the Ti plasmid that is transferred via conjugation into host plant cells after an injury site is sensed by the bacteria. These regions have features that allow the delivery of T-DNA into host plant cells, and can modify the host plant cell to cause the synthesis of molecules like plant hormones (e.g. auxins, cytokinins) and opines and the formation of crown gall tumours. [1]

Because the T-DNA region of the Ti plasmid can be transferred from bacteria to plant cells, it represented an exciting avenue for the transfer of DNA between kingdoms and spurred large amounts of research on the Ti plasmid and its possible uses in bioengineering.

Nomenclature and classification

The Ti plasmid is a member of the RepABC plasmid family found in Alphaproteobacteria. [3] These plasmids are often relatively large in size, ranging from 100kbp to 2Mbp. They are also often termed replicons, as their replication begins at a single site. Members of this family have a characteristic repABC gene cassette. [4] Another notable member of this family is the root inducing (Ri) plasmid carried by A. rhizogenes, which causes another plant disease known as hairy root disease. [1]

A key feature of Ti plasmids is their ability to drive the production of opines, which are derivatives of various amino acids or sugar phosphates, in host plant cells. These opines can then be used as a nutrient for the infecting bacteria, which catabolizes the respective opines using genes encoded in the Ti plasmid.

Accordingly, Ti plasmids have been classified based on the type of opine they catabolize, namely: nopaline-, octopine- or mannityl-types, which are amino acid derivatives, or agrocinopine-type, which are sugar phosphate derivatives. [1]

Historical discovery

The identification of A. tumefaciens as the cause of gall tumours in plants paved the way for insights into the molecular basis of crown gall disease. [5]

The first indication of a genetic effect on host plant cells came in 1942-1943, where plant cells of secondary tumours were found to lack any bacterial cells within. However, these tumour cells did possess the ability to produce opines metabolized by the infecting bacterial strain. [6] Crucially, the production of the respective opines occurred regardless of the plant species and occasionally only within crown gall tissues, indicating that the bacteria had transferred some genetic material to the host plant cells in order to allow opine synthesis. [5]

However, how and to what extend did DNA transfer occur remained an open question. Adding A. tumefaciens DNA alone did not cause tumors in plants, [7] while very little A. tumefaciens DNA was found to be integrated into the host plant cell genome. [8] The addition of deoxyribonucleases (DNases) to degrade DNA also failed to prevent the formation and growth of the plant tumors. [9] These suggested that little, if any, of the A. tumefaciens DNA is transferred to the host plant cell to cause disease and, if DNA is indeed transferred from the bacteria to the plant, it must occur in a protected manner.

Subsequently, oncogenic bacterial strains were found to be able to convert non-pathogenic bacteria into pathogens via the process of conjugation, where the genes responsible for virulence were transferred to the non-pathogenic cells. [10] The role of a plasmid in this pathogenic ability was further supported when large plasmids were found only in pathogenic bacteria but not avirulent bacteria. [11] Eventually, the detection of parts of bacterial plasmids in host plant cells was established, confirming that this was the genetic material responsible for the genetic effect of infection. [12]

With the identification of the Ti plasmid, many studies were carried out to determine the characteristics of the Ti plasmid and how the genetic material is transferred from the Agrobacterium to the plant host. Some notable early milestones in the studies of Ti plasmids include the mapping of a Ti plasmid in 1978 and the studying of sequence similarity between different Ti plasmids in 1981. [13] [14]

Between 1980–2000, the characterization of the T-DNA region and the 'vir' region was also pursued. Studies into the T-DNA region determined their process of transfer and identified genes allowing the synthesis of plant hormones and opines. [15] Separately, early work aimed to determine the functions of the genes encoded in the 'vir' region - these were broadly categorized into those that allowed bacterial-host interactions and those that enabled T-DNA delivery. [2]

Replication, partitioning and maintenance

The repABC gene cassette of Ti plasmids in Agrobacteria, with a schematic of their gene product and activities RepABC gene cassette of Ti plasmids.png
The repABC gene cassette of Ti plasmids in Agrobacteria, with a schematic of their gene product and activities

The replication, partitioning and maintenance of the Ti plasmid depends on the repABC gene cassette, which is mainly made up of three genes: repA, repB and repC. repA and repB each encode for proteins involved in plasmid partitioning, while repC encodes a replication initiator. [1] These genes are expressed from 4 different promoters located upstream of repA. repE encodes for a small antisense RNA and is located between repB and repC. [4] Additionally, there is a partitioning site (parS) and an origin of replication (oriV) present within the repABC cassette. [1]

Replication of the Ti plasmid

The replication of the Ti plasmid is driven by the RepC initiator protein ( P05684 ), which possesses two protein domains: an N-terminal domain (NTD) that binds to DNA and a C-terminal domain (CTD). Mutational analyses have shown that without a functional RepC protein, the Ti plasmid is unable to replicate. [4] Meanwhile, the oriV sequence is around 150 nucleotides in length and is found within the repC gene. [3] Laboratory experiments have shown that the RepC protein binds to this region, suggesting its role as the origin of replication. [16] Therefore, while the complete process behind the replication of the Ti plasmid has not been fully described, the initial step of replication would likely depend on the expression of RepC and its binding to oriV. Of note, the RepC protein only acts in cis, where it only drives the replication of the plasmid it is encoded in and not any other plasmid also present in the bacterial cell. [16]

Partitioning of the Ti plasmid

Components involved in the RepA/RepB partitioning system of Ti plasmids [1]
ComponentFunction
RepA (ParA), P05682 A weak ATPase that negatively autoregulates the expression of the repABC cassette and can form filaments to aid in the partitioning of the plasmid during cell division
RepB (ParB), P05683 A DNA binding protein that serves as an adaptor between RepA and the parS site
parSThe palindromic binding site for the ParB protein; consensus GTTNNCNGCNGNNAAC

The partitioning system of the Ti plasmid is similar to the ParA/ParB system used in other plasmids and bacterial chromosomes and is thought to act in the same way. [17] Mutations in either of the proteins RepA or RepB have resulted in a decrease in plasmid stability, indicating their role and importance in plasmid partitioning. [4] The ability of RepA to form filaments allows it to create a physical bridge along which DNA can be pulled to opposite poles of a dividing cell. Meanwhile, the RepB protein can bind specifically to the parS sequence, forming a complex with DNA that can be recognized by RepA. [1] [4] This system is particularly important for the proper partitioning of the Ti plasmid, as the plasmid is only present in few copy numbers in the bacterial cell.

Maintenance of the Ti plasmid

The Ti plasmid is maintained at low copy numbers within a bacterial cell. This is partly achieved by influencing the expression of the replication initiator RepC. [1] When bound to ADP, RepA is activated to work with RepB, acting as a negative regulator of the repABC cassette. [3] The levels of RepC is therefore kept low within a cell, preventing too many rounds of replication from occurring during each cell division cycle. Furthermore, there is a small RNA known as RepE encoded between repB and repC that lowers the expression of repC. [18] RepE is complementary to RepC and will bind with the repC mRNA to form a double-stranded molecule. This can then block the translational production of the RepC protein. [18]

Separately, the expression of the repABC cassette and hence the copy number of the Ti plasmid is also influenced via a quorum sensing system in Agrobacterium. [4] Quorum sensing systems respond to bacterial population densities by sensing a molecule, known as an autoinducer, that is produced by the bacterial cells at low levels and would build up to a threshold level when there is a high density of bacteria present. [18] In this case, the autoinducer is the N-3-oxooctanoyl-L-homoserine lactone (3-O-C8-AHL) molecule, which is sensed by a regulator known as TraR. [4] When activated, TraR will bind to regions known as tra boxes in the repABC gene cassette's promoter regions to drive expression. Therefore, a high level of population density increases the number of plasmids present within each bacterial cell, likely to support pathogenesis in the plant host. [4]

Features

Virulence operon

The composition of the vir region of octopine-type Ti plasmids Vir region of Ti plasmids.png
The composition of the vir region of octopine-type Ti plasmids

The expression of the vir region is usually repressed under normal conditions, and only becomes activated when the bacteria senses plant-derived signals from wound sites. This activation is necessary for the production of Vir proteins and the transfer of DNA and proteins into host plant cells. [1]

VirA and VirG form a two-component regulatory system within Agrobacterium. [19] This is a type of sensing and signalling system found commonly in bacteria; in this case, they act to sense plant-derived signals to drive the expression of the vir region. During the sensing, VirA, a histidine sensor kinase, will become phosphorylated before passing on this phosphate group to the response regulator VirG. [20] The activated response regulator VirG can then bind to a region of DNA known as the vir box, located upstream of each vir promoter, to activate the expression of the vir region. [1] [19] One possible downstream functions of the sensing mediated by VirA and VirG is the directional movement, or chemotaxis, of the bacteria towards plant-derived signals; this allows the Agrobacterium to move towards the wound site in plants. [21] Furthermore, with the induction of the vir region, the transfer of T-DNA can be mediated by the Vir proteins. [22]

The virB operon is the largest operon in the vir region, encoding for 11 VirB proteins involved in the transfer process of T-DNA and bacterial proteins into host plant cells (see transfer apparatus below). [23] [24]

The virC operon encodes for two proteins: VirC1 and VirC2. These proteins influence the pathogenesis of the Agrobacterium towards different plant hosts, and mutations can reduce but not remove the virulence of the bacteria. [25] Both the virC and virD operons can be repressed by a chromosomally encoded protein known as Ros. [26] [27] Ros binds to a region of DNA that overlaps with the binding site of the VirG regulator, and therefore competes with VirG to control their expression levels. [26] [27] Functionally, VirC1 and VirC2 promote the assembly of a relaxosome complex during the conjugative transfer of T-DNA from the bacteria to the host plant cell. [28] This is an energy-dependent process mediated via their NTPase activity, and occurs as they bind to a region of DNA known as overdrive. [28] As a result, they act to increase the amount of T-DNA strands produced. Following the production of the DNA strand to be transferred (transfer strand, T-strand), the VirC proteins can also help to direct the transfer strand to the transfer apparatus. [28]

The virD operon encodes for 4 proteins: VirD1-D4. [29] VirD1 and VirD2 are involved in the processing of T-DNA during conjugation to produce the T-strand; this is the single-stranded DNA molecule that is transported to the host plant cell (see transfer apparatus below). [30] During the processing, VirD1 will act as a topoisomerase to unwind the DNA strands. [30] VirD2, a relaxase, will then nick one of the DNA strands and remain bound to the DNA as it is transferred to the recipient cell. [31] [32] Within the recipient cell, VirD2 will also work together with VirE2 to direct the transferred DNA to the recipient cell's nucleus. There are suggestions that VirD2 may be phosphorylated and dephosphorylated by different proteins, affecting its ability to deliver DNA. [33] Conversely, little is known about VirD3, and mutational analyses have not provided any support for its role in the virulence of Agrobacterium. [34] Finally, VirD4 is a crucial part of the conjugation process, serving as a coupling factor that recognizes and transfers the T-strand to the transport channel. [35]

The virE operon encodes for 2 proteins: VirE1 and VirE2. [36] VirE2 is an effector protein translocated together with the T-strand into host plant cells. There, it binds to the T-strand to direct its delivery to the nucleus of the host plant cell. [37] [38] Part of this activity involves the presence of nuclear localization sequences within the protein, which marks the protein and the associated DNA for entry into the nucleus. It also protects the T-strand from nuclease attack. [39] There is some speculation regarding the role of VirE2 as a protein channel, allowing DNA to move through the plant cytoplasmic membrane. [40] On the other hand, VirE1 may be involved in promoting the transfer of the VirE2 protein into the host plant cell. [41] It binds to the ssDNA-binding domain of VirE2, therefore preventing the VirE2 protein from prematurely binding to the T-strand within the bacterial cell. [42]

virF is a host specificity factor found in some but not all types of Ti plasmids; for example, octopine-type Ti plasmids possess virF but nopaline-types do not. [43] [44] The ability of A. tumefaciens to induce crown gall tumours in certain plant species but not others has been attributed to the presence or absence of this virF gene. [43] [44]

The virH operon encodes for 2 proteins: VirH1 and VirH2. [45] A bioinformatics study of the amino acid sequences of the VirH protein showed similarities between them and a superfamily of proteins known as cytochrome P450 enzymes. [46] VirH2 was then discovered to metabolize certain phenolic compounds detected by VirA. [45]

Transfer DNA (T-DNA)

The T-DNA of Agrobacterium is approximately 15-20 kbp in length and will become integrated into the host plant genome upon its transfer via a process known as recombination. This process utilizes preexisting gaps in the host plant cell's genome to allow the T-DNA to pair with short sequences in the genome, priming the process of DNA ligation, where the T-DNA is permanently joint to the plant genome. [37] The T-DNA region is flanked at both ends by 24bp sequences.

Within the host plant cell's genome, the T-DNA of Agrobacterium is expressed to produce two main groups of proteins. [1] One group is responsible for the production of plant growth hormones. As these hormones are produced, there will be an increase in the rate of cell division and therefore the formation of crown gall tumors. [47] The second group of proteins are responsible for driving the synthesis of opines in the host plant cells. The specific opines produced depends on the type of the Ti plasmid but not on the plant host. These opines cannot be utilized by the plant host, and will instead be exported out of the plant cell where it can be taken up by the Agrobacterium cells. The bacteria possess genes in other regions of the Ti plasmid that allows the catabolism of opines. [1]

Transfer apparatus

Transfer apparatuses encoded within the Ti plasmid have to achieve two objectives: allow the conjugative transfer of the Ti plasmid between bacteria and allow the delivery of the T-DNA and certain effector proteins into host plant cells. These are achieved by the Tra/Trb system and the VirB/VirD4 system respectively, which are members of the type IV secretion system (T4SS). [47]

For the Ti plasmid and T-DNA to be transferred via conjugation, they must first be processed by different proteins, such as the relaxase enzyme (TraA/VirD2) and the DNA transfer and replication (Dtr) proteins. Together, these proteins will recognize and bind to a region known as the origin of transfer (oriT) in the Ti plasmid to form the relaxosome complex. For the T-DNA, a nick will be created at the T-DNA's border sequence, and the nicked T-strand will be transported to the cell membrane, where the rest of the transfer machinery is present. [31]

Within the VirB/VirD4 system, the VirD2 relaxase is aided by the accessory factors VirD1, VirC1 and VirC2 while it processes the DNA substrate. [48] Furthermore, the VirD2 relaxase and the VirC proteins will contribute to the delivery of the DNA strand to the VirD4 receptor at the cell membrane. [28] This receptor is an essential component of T4SSs, and is thought to energize and mediate the transfer of the DNA into the translocation channel between two cells. [49] The table below summarizes the proteins encoded in the virB operon that makes up the translocation channel of the VirB/VirD4 system. [1]

Protein(s)Function
VirB4, VirB11ATPases that provide the energy for DNA transfer [50] [51]
VirB3, VirB6, VirB8Subunits of a putative inner membrane translocase [50] [52] [53]
VirB7, VirB9, VirB10Forms a core complex that stabilizes the channel subunits [50] [54]
VirB2The major pilin subunit of the conjugative pilus [50]
VirB1, VirB5Minor components of the conjugative pilus [55] [56]

Uses in bioengineering

The ability of Agrobacterium to deliver DNA into plant cells opened new doors for plant genome engineering, allowing the production of genetically modified plants (transgenic plants). [57] Proteins involved in mediating the transfer of T-DNA will first recognize the border sequences of the T-DNA region. Therefore, it is possible for scientists to use T-DNA border sequences to flank any desired sequence of interest - such a product can then be inserted into a plasmid and introduced into Agrobacterium cells. [58] There, the border sequences will be recognized by the transfer apparatus of A. tumefaciens and delivered in a standard manner into the target plant cell. [1] Moreover, by leaving behind only the border sequences of the T-DNA, the resulting product will edit the plant genome without causing any tumours in plants. [59] This method has been used to modify several crop plants, including rice, [60] barley [61] and wheat. [62] Further work have since extended the targets of A. tumefaciens to include fungi and human cell lines. [63] [64]

Similar plasmids

Root-inducing (Ri) plasmid

Symbiotic (sym) plasmids of Rhizobia

See also

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References

  1. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Gordon JE, Christie PJ (December 2014). "The Agrobacterium Ti Plasmids". Microbiology Spectrum. 2 (6). doi: 10.1128/microbiolspec.PLAS-0010-2013 . PMC   4292801 . PMID   25593788.
  2. 1 2 Hooykaas PJ, Beijersbergen AG (1994). "The virulence system of Agrobacterium tumefaciens". Annual Review of Phytopathology. 32 (1): 157–181. doi:10.1146/annurev.py.32.090194.001105.
  3. 1 2 3 Pinto UM, Pappas KM, Winans SC (November 2012). "The ABCs of plasmid replication and segregation". Nature Reviews. Microbiology. 10 (11): 755–65. doi:10.1038/nrmicro2882. PMID   23070556. S2CID   6518175.
  4. 1 2 3 4 5 6 7 8 Cevallos MA, Cervantes-Rivera R, Gutiérrez-Ríos RM (July 2008). "The repABC plasmid family". Plasmid. 60 (1): 19–37. doi:10.1016/j.plasmid.2008.03.001. PMID   18433868.
  5. 1 2 Kado CI (2014). "Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens". Frontiers in Microbiology. 5 (340): 340. doi: 10.3389/fmicb.2014.00340 . PMC   4124706 . PMID   25147542.
  6. ↑ Petit A, Delhaye S, Tempé J, Morel G (1970). "Recherches sur les guanidines des tissues de Crown gall. Mise en evidence d'une relation biochimique spécifique entre les souches d'Agrobacterium tumefaciens et les tumeurs qu'elles induisent". Physiol. Vég. 8: 205–213.
  7. ↑ Kado CI, Lurquin PF (1976). "Studies on Agrobacterium tumefaciens. V. Fate of exogenously added bacterial DNA in Nicotiana tabacum". Physiological Plant Pathology. 8 (1): 73–82. doi:10.1016/0048-4059(76)90009-6.
  8. ↑ Drlicá KA, Kado CI (September 1974). "Quantitative estimation of Agrobacterium tumefaciens DNA in crown gall tumor cells". Proceedings of the National Academy of Sciences of the United States of America. 71 (9): 3677–81. Bibcode:1974PNAS...71.3677D. doi: 10.1073/pnas.71.9.3677 . PMC   433839 . PMID   4530329.
  9. ↑ Braun AC, Wood HN (November 1966). "On the inhibition of tumor inception in the crown-gall disease with the use of ribonuclease A". Proceedings of the National Academy of Sciences of the United States of America. 56 (5): 1417–22. Bibcode:1966PNAS...56.1417B. doi: 10.1073/pnas.56.5.1417 . PMC   219988 . PMID   5230302.
  10. ↑ Kerr A (1971). "Acquisition of virulence by non-pathogenic isolates of Agrobacterium radiobacter". Physiological Plant Pathology. 1 (3): 241–246. doi:10.1016/0048-4059(71)90045-2.
  11. ↑ Zaenen I, Van Larebeke N, Van Montagu M, Schell J (June 1974). "Supercoiled circular DNA in crown-gall inducing Agrobacterium strains". Journal of Molecular Biology. 86 (1): 109–27. doi:10.1016/s0022-2836(74)80011-2. PMID   4854526.
  12. ↑ Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW (June 1977). "Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis". Cell. 11 (2): 263–71. doi:10.1016/0092-8674(77)90043-5. PMID   890735. S2CID   7533482.
  13. ↑ Chilton MD, Montoya AL, Merlo DJ, Drummond MH, Nutter R, Gordon MP, Nester EW (February 1978). "Restriction endonuclease mapping of a plasmid that confers oncogenicity upon Agrobacterium tumefaciens strain B6-806". Plasmid. 1 (2): 254–69. doi:10.1016/0147-619x(78)90043-4. PMID   748950.
  14. ↑ Engler G, Depicker A, Maenhaut R, Villarroel R, Van Montagu M, Schell J (October 1981). "Physical mapping of DNA base sequence homologies between an octopine and a nopaline Ti plasmid of Agrobacterium tumefaciens". Journal of Molecular Biology. 152 (2): 183–208. doi:10.1016/0022-2836(81)90239-4. PMID   6276566.
  15. ↑ Zambryski P, Tempe J, Schell J (January 1989). "Transfer and function of T-DNA genes from agrobacterium Ti and Ri plasmids in plants". Cell. 56 (2): 193–201. doi:10.1016/0092-8674(89)90892-1. PMID   2643473. S2CID   19393909.
  16. 1 2 Pinto UM, Flores-Mireles AL, Costa ED, Winans SC (September 2011). "RepC protein of the octopine-type Ti plasmid binds to the probable origin of replication within repC and functions only in cis". Molecular Microbiology. 81 (6): 1593–606. doi: 10.1111/j.1365-2958.2011.07789.x . PMID   21883520.
  17. ↑ Bignell C, Thomas CM (September 2001). "The bacterial ParA-ParB partitioning proteins". Journal of Biotechnology. 91 (1): 1–34. doi:10.1016/S0168-1656(01)00293-0. PMID   11522360.
  18. 1 2 3 Chai Y, Winans SC (June 2005). "A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid". Molecular Microbiology. 56 (6): 1574–85. doi: 10.1111/j.1365-2958.2005.04636.x . PMID   15916607. S2CID   20348880.
  19. 1 2 Winans SC (October 1991). "An Agrobacterium two-component regulatory system for the detection of chemicals released from plant wounds". Molecular Microbiology. 5 (10): 2345–50. doi:10.1111/j.1365-2958.1991.tb02080.x. PMID   1791750. S2CID   21209713.
  20. ↑ Huang Y, Morel P, Powell B, Kado CI (February 1990). "VirA, a coregulator of Ti-specified virulence genes, is phosphorylated in vitro". Journal of Bacteriology. 172 (2): 1142–4. doi: 10.1128/jb.172.2.1142-1144.1990 . PMC   208549 . PMID   2298696.
  21. ↑ Shaw CH, Ashby AM, Brown A, Royal C, Loake GJ, Shaw CH (May 1988). "virA and virG are the Ti-plasmid functions required for chemotaxis of Agrobacterium tumefaciens towards acetosyringone". Molecular Microbiology. 2 (3): 413–7. doi:10.1111/j.1365-2958.1988.tb00046.x. PMID   3398775. S2CID   8536451.
  22. ↑ Stachel SE, Zambryski PC (August 1986). "virA and virG control the plant-induced activation of the T-DNA transfer process of A. tumefaciens". Cell. 46 (3): 325–33. doi:10.1016/0092-8674(86)90653-7. PMID   3731272. S2CID   37938846.
  23. ↑ Ward JE, Akiyoshi DE, Regier D, Datta A, Gordon MP, Nester EW (April 1988). "Characterization of the virB operon from an Agrobacterium tumefaciens Ti plasmid". The Journal of Biological Chemistry. 263 (12): 5804–14. doi: 10.1016/S0021-9258(18)60637-4 . PMID   3281947.
  24. ↑ Vergunst AC, Schrammeijer B, den Dulk-Ras A, de Vlaam CM, Regensburg-Tuïnk TJ, Hooykaas PJ (November 2000). "VirB/D4-dependent protein translocation from Agrobacterium into plant cells". Science. 290 (5493): 979–82. Bibcode:2000Sci...290..979V. doi:10.1126/science.290.5493.979. PMID   11062129.
  25. ↑ Close TJ, Tait RC, Rempel HC, Hirooka T, Kim L, Kado CI (June 1987). "Molecular characterization of the virC genes of the Ti plasmid". Journal of Bacteriology. 169 (6): 2336–44. doi: 10.1128/jb.169.6.2336-2344.1987 . PMC   212055 . PMID   3584058.
  26. 1 2 Cooley MB, D'Souza MR, Kado CI (April 1991). "The virC and virD operons of the Agrobacterium Ti plasmid are regulated by the ros chromosomal gene: analysis of the cloned ros gene". Journal of Bacteriology. 173 (8): 2608–16. doi: 10.1128/jb.173.8.2608-2616.1991 . PMC   207827 . PMID   2013576.
  27. 1 2 D'Souza-Ault MR, Cooley MB, Kado CI (June 1993). "Analysis of the Ros repressor of Agrobacterium virC and virD operons: molecular intercommunication between plasmid and chromosomal genes". Journal of Bacteriology. 175 (11): 3486–90. doi: 10.1128/jb.175.11.3486-3490.1993 . PMC   204748 . PMID   8501053.
  28. 1 2 3 4 Atmakuri K, Cascales E, Burton OT, Banta LM, Christie PJ (May 2007). "Agrobacterium ParA/MinD-like VirC1 spatially coordinates early conjugative DNA transfer reactions". The EMBO Journal. 26 (10): 2540–51. doi:10.1038/sj.emboj.7601696. PMC   1868908 . PMID   17505518.
  29. ↑ Porter SG, Yanofsky MF, Nester EW (September 1987). "Molecular characterization of the virD operon from Agrobacterium tumefaciens". Nucleic Acids Research. 15 (18): 7503–17. doi:10.1093/nar/15.18.7503. PMC   306264 . PMID   3658701.
  30. 1 2 Ghai J, Das A (May 1989). "The virD operon of Agrobacterium tumefaciens Ti plasmid encodes a DNA-relaxing enzyme". Proceedings of the National Academy of Sciences of the United States of America. 86 (9): 3109–13. Bibcode:1989PNAS...86.3109G. doi: 10.1073/pnas.86.9.3109 . PMC   287074 . PMID   2541431.
  31. 1 2 Zechner EL, Lang S, Schildbach JF (April 2012). "Assembly and mechanisms of bacterial type IV secretion machines". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 367 (1592): 1073–87. doi: 10.1098/rstb.2011.0207 . PMC   3297438 . PMID   22411979.
  32. ↑ Yanofsky MF, Porter SG, Young C, Albright LM, Gordon MP, Nester EW (November 1986). "The virD operon of Agrobacterium tumefaciens encodes a site-specific endonuclease". Cell. 47 (3): 471–7. doi:10.1016/0092-8674(86)90604-5. PMID   3021341. S2CID   40721668.
  33. ↑ Tao Y, Rao PK, Bhattacharjee S, Gelvin SB (April 2004). "Expression of plant protein phosphatase 2C interferes with nuclear import of the Agrobacterium T-complex protein VirD2". Proceedings of the National Academy of Sciences of the United States of America. 101 (14): 5164–9. Bibcode:2004PNAS..101.5164T. doi: 10.1073/pnas.0300084101 . PMC   387391 . PMID   15047887.
  34. ↑ Vogel AM, Das A (August 1992). "The Agrobacterium tumefaciens virD3 gene is not essential for tumorigenicity on plants". Journal of Bacteriology. 174 (15): 5161–4. doi: 10.1128/jb.174.15.5161-5164.1992 . PMC   206339 . PMID   1629176.
  35. ↑ Kumar RB, Das A (March 2002). "Polar location and functional domains of the Agrobacterium tumefaciens DNA transfer protein VirD4". Molecular Microbiology. 43 (6): 1523–32. doi:10.1046/j.1365-2958.2002.02829.x. PMID   11952902. S2CID   43167663.
  36. ↑ Winans SC, Allenza P, Stachel SE, McBride KE, Nester EW (January 1987). "Characterization of the virE operon of the Agrobacterium Ti plasmid pTiA6". Nucleic Acids Research. 15 (2): 825–37. doi:10.1093/nar/15.2.825. PMC   340470 . PMID   3547330.
  37. 1 2 Gelvin SB (2012). "Traversing the Cell: Agrobacterium T-DNA's Journey to the Host Genome". Frontiers in Plant Science. 3: 52. doi: 10.3389/fpls.2012.00052 . PMC   3355731 . PMID   22645590.
  38. ↑ Das A (May 1988). "Agrobacterium tumefaciens virE operon encodes a single-stranded DNA-binding protein". Proceedings of the National Academy of Sciences of the United States of America. 85 (9): 2909–13. Bibcode:1988PNAS...85.2909D. doi: 10.1073/pnas.85.9.2909 . PMC   280112 . PMID   2452439.
  39. ↑ Schrammeijer B, Beijersbergen A, Idler KB, Melchers LS, Thompson DV, Hooykaas PJ (June 2000). "Sequence analysis of the vir-region from Agrobacterium tumefaciens octopine Ti plasmid pTi15955". Journal of Experimental Botany. 51 (347): 1167–9. doi: 10.1093/jexbot/51.347.1167 . PMID   10948245.
  40. ↑ Dumas F, Duckely M, Pelczar P, Van Gelder P, Hohn B (January 2001). "An Agrobacterium VirE2 channel for transferred-DNA transport into plant cells". Proceedings of the National Academy of Sciences of the United States of America. 98 (2): 485–90. Bibcode:2001PNAS...98..485D. doi: 10.1073/pnas.011477898 . PMC   14613 . PMID   11149937.
  41. ↑ Sundberg C, Meek L, Carroll K, Das A, Ream W (February 1996). "VirE1 protein mediates export of the single-stranded DNA-binding protein VirE2 from Agrobacterium tumefaciens into plant cells". Journal of Bacteriology. 178 (4): 1207–12. doi: 10.1128/jb.178.4.1207-1212.1996 . PMC   177787 . PMID   8576060.
  42. ↑ Sundberg CD, Ream W (November 1999). "The Agrobacterium tumefaciens chaperone-like protein, VirE1, interacts with VirE2 at domains required for single-stranded DNA binding and cooperative interaction". Journal of Bacteriology. 181 (21): 6850–5. doi:10.1128/JB.181.21.6850-6855.1999. PMC   94155 . PMID   10542192.
  43. 1 2 Jarchow E, Grimsley NH, Hohn B (December 1991). "virF, the host-range-determining virulence gene of Agrobacterium tumefaciens, affects T-DNA transfer to Zea mays". Proceedings of the National Academy of Sciences of the United States of America. 88 (23): 10426–30. Bibcode:1991PNAS...8810426J. doi: 10.1073/pnas.88.23.10426 . PMC   52941 . PMID   11607242.
  44. 1 2 Melchers LS, Maroney MJ, den Dulk-Ras A, Thompson DV, van Vuuren HA, Schilperoort RA, Hooykaas PJ (February 1990). "Octopine and nopaline strains of Agrobacterium tumefaciens differ in virulence; molecular characterization of the virF locus". Plant Molecular Biology. 14 (2): 249–59. doi:10.1007/BF00018565. PMID   2101693. S2CID   8736045.
  45. 1 2 Kalogeraki VS, Zhu J, Eberhard A, Madsen EL, Winans SC (November 1999). "The phenolic vir gene inducer ferulic acid is O-demethylated by the VirH2 protein of an Agrobacterium tumefaciens Ti plasmid". Molecular Microbiology. 34 (3): 512–22. doi: 10.1046/j.1365-2958.1999.01617.x . PMID   10564493.
  46. ↑ Kanemoto RH, Powell AT, Akiyoshi DE, Regier DA, Kerstetter RA, Nester EW, et al. (May 1989). "Nucleotide sequence and analysis of the plant-inducible locus pinF from Agrobacterium tumefaciens". Journal of Bacteriology. 171 (5): 2506–12. doi: 10.1128/jb.171.5.2506-2512.1989 . PMC   209927 . PMID   2708311.
  47. 1 2 Zhu J, Oger PM, Schrammeijer B, Hooykaas PJ, Farrand SK, Winans SC (July 2000). "The bases of crown gall tumorigenesis". Journal of Bacteriology. 182 (14): 3885–95. doi: 10.1128/jb.182.14.3885-3895.2000 . PMC   94570 . PMID   10869063.
  48. ↑ De Vos G, Zambryski P (1989). "Expression of Agrobacterium nopaline-specific VirD1, VirD2, and VirC1 proteins and their requirement for T-strand production in E. coli". Molecular Plant-Microbe Interactions. 2 (2): 43–52. doi:10.1094/mpmi-2-043. PMID   2520160.
  49. ↑ Gomis-Rüth FX, Solà M, de la Cruz F, Coll M (2004). "Coupling factors in macromolecular type-IV secretion machineries". Current Pharmaceutical Design. 10 (13): 1551–65. doi:10.2174/1381612043384817. PMID   15134575.
  50. 1 2 3 4 Christie PJ, Atmakuri K, Krishnamoorthy V, Jakubowski S, Cascales E (2005). "Biogenesis, architecture, and function of bacterial type IV secretion systems". Annual Review of Microbiology. 59: 451–85. doi:10.1146/annurev.micro.58.030603.123630. PMC   3872966 . PMID   16153176.
  51. ↑ Peña A, Matilla I, Martín-Benito J, Valpuesta JM, Carrascosa JL, de la Cruz F, et al. (November 2012). "The hexameric structure of a conjugative VirB4 protein ATPase provides new insights for a functional and phylogenetic relationship with DNA translocases". The Journal of Biological Chemistry. 287 (47): 39925–32. doi: 10.1074/jbc.M112.413849 . PMC   3501061 . PMID   23035111.
  52. ↑ Mossey P, Hudacek A, Das A (June 2010). "Agrobacterium tumefaciens type IV secretion protein VirB3 is an inner membrane protein and requires VirB4, VirB7, and VirB8 for stabilization". Journal of Bacteriology. 192 (11): 2830–8. doi: 10.1128/JB.01331-09 . PMC   2876495 . PMID   20348257.
  53. ↑ Jakubowski SJ, Krishnamoorthy V, Cascales E, Christie PJ (August 2004). "Agrobacterium tumefaciens VirB6 domains direct the ordered export of a DNA substrate through a type IV secretion System". Journal of Molecular Biology. 341 (4): 961–77. doi:10.1016/j.jmb.2004.06.052. PMC   3918220 . PMID   15328612.
  54. ↑ Chandran V, Fronzes R, Duquerroy S, Cronin N, Navaza J, Waksman G (December 2009). "Structure of the outer membrane complex of a type IV secretion system". Nature. 462 (7276): 1011–5. Bibcode:2009Natur.462.1011C. doi:10.1038/nature08588. PMC   2797999 . PMID   19946264.
  55. ↑ Zupan J, Hackworth CA, Aguilar J, Ward D, Zambryski P (September 2007). "VirB1* promotes T-pilus formation in the vir-Type IV secretion system of Agrobacterium tumefaciens". Journal of Bacteriology. 189 (18): 6551–63. doi: 10.1128/JB.00480-07 . PMC   2045169 . PMID   17631630.
  56. ↑ Schmidt-Eisenlohr H, Domke N, Angerer C, Wanner G, Zambryski PC, Baron C (December 1999). "Vir proteins stabilize VirB5 and mediate its association with the T pilus of Agrobacterium tumefaciens". Journal of Bacteriology. 181 (24): 7485–92. doi: 10.1128/JB.181.24.7485-7492.1999 . PMC   94205 . PMID   10601205.
  57. ↑ Hernalsteens JP, Van Vliet F, De Beuckeleer M, Depicker A, Engler G, Lemmers M, Holsters M, Van Montagu M, Schell J (1980). "The Agrobacterium tumefaciens Ti plasmid as a host vector system for introducing foreign DNA in plant cells". Nature. 287 (5783): 654–656. Bibcode:1980Natur.287..654H. doi:10.1038/287654a0. S2CID   4333703.
  58. ↑ Gelvin SB (March 2003). "Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool". Microbiology and Molecular Biology Reviews. 67 (1): 16–37, table of contents. doi: 10.1128/mmbr.67.1.16-37.2003 . PMC   150518 . PMID   12626681.
  59. ↑ Zambryski P, Joos H, Genetello C, Leemans J, Montagu MV, Schell J (1983). "Ti plasmid vector for the introduction of DNA into plant cells without alteration of their normal regeneration capacity". The EMBO Journal. 2 (12): 2143–50. doi:10.1002/j.1460-2075.1983.tb01715.x. PMC   555426 . PMID   16453482.
  60. ↑ Chan MT, Lee TM, Chang HH (1992). "Transformation of indica rice (Oryza sativa L.) mediated by Agrobacterium tumefaciens". Plant and Cell Physiology. 33 (5): 577–583. doi:10.1093/oxfordjournals.pcp.a078292.
  61. ↑ Tingay S, McElroy D, Kalla R, Fieg S, Wang M, Thornton S, Brettell R (1997). "Agrobacterium tumefaciens-mediated barley transformation". The Plant Journal. 11 (6): 1369–1376. doi: 10.1046/j.1365-313X.1997.11061369.x .
  62. ↑ Cheng M, Fry JE, Pang S, Zhou H, Hironaka CM, Duncan DR, et al. (November 1997). "Genetic Transformation of Wheat Mediated by Agrobacterium tumefaciens". Plant Physiology. 115 (3): 971–980. doi: 10.1104/pp.115.3.971 . PMC   158560 . PMID   12223854.
  63. ↑ Tzfira T, Citovsky V (2007). Agrobacterium: from biology to biotechnology. Springer Science & Business Media.
  64. ↑ Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V (February 2001). "Genetic transformation of HeLa cells by Agrobacterium". Proceedings of the National Academy of Sciences of the United States of America. 98 (4): 1871–6. Bibcode:2001PNAS...98.1871K. doi: 10.1073/pnas.98.4.1871 . PMC   29349 . PMID   11172043.
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