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User:Ddelrio08/Origin of transfer

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An origin of transfer (oriT) is a short sequence ranging from 40-500 base pairs in length[1][2] that is necessary for the transfer of DNA from a gram-negative bacterial donor to recipient during bacterial conjugation[3][4][5][6]. The transfer of DNA is a critical component for antimicrobial resistance within bacterial cells[7] and the oriT structure and location within plasmid DNA is complimentary for its function in bacterial conjugation. The first oriT to be identified and cloned was on the RK2 (IncP) conjugative plasmid, which was done by Guiney and Helinski in 1979[8][9].

Structure

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oriT regions are central to the process of transferring DNA from the donor to recipient and contain several important regions that facilitate this:

  1. nic site: where the unwound plasmid DNA is cut; usually site-specific[10][11][4].
  2. An inverted repeat sequence: signals the end of replication of donor DNA and is responsible for transfer frequency, plasmid mobilization, and secondary DNA structure formation[10][3][12].
  3. AT-rich region: important for DNA strand opening and is located adjacent to the inverted repeat sequences[1][10][3][13][14][5].

The oriT is a noncoding region of the bacterial DNA[15]. Due to its important role in initiating bacterial conjugation, the oriT is both an enzymatic substrate and recognition site for the relaxase proteins[1][15][16]. Relaxosomes have oriT-specific auxiliary factors that help it to identify and bind to the oriT [1]. Upstream of the oriT nic site is a termination sequence[5].

oriTs are primarily cis-acting, which allows for a more efficient DNA transfer[14][5][17].

oriT within Plasmid DNA

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Figure 1 ▲ Region of oriT sequence on plasmid DNA.

The oriT region in plasmid DNA is the site where strands or fragments of DNA can be transferred from cell to cell during the conjugation of plasmids (see bacterial conjugation below) and the cloning of DNA.[18] The initiation of transfer and replication activities begins at the nick site specific to a region on the plasmid DNA[19]. Studies published in 1984 determined the location of these single-stranded nick sites on F plasmid DNA[19]. Researchers used gel electrophoresis to restriction map the regions of plasmid DNA and employed restriction endonucleases to further refine the DNA fragments[19]. They were able to procure a functioning oriT region at 373 base pairs and found that nic sites were dispersed over a region of 20 base pairs at the end of the oriT region[19].

Function in Bacterial Conjugation

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Further information: Bacterial conjugation
Figure 2 ▲ Two bacterial cells undergoing bacterial conjugation. (1) relaxase and helicase bind to the plasmid (F-factor) at the origin of transfer (OriT). Helicase unwinds the plasmid DNA and relaxase attaches to the transfer DNA strand. (3) Relaxase carries the transfer DNA strand through the pilus connecting the two bacterial cells. (4) The remaining strand is rewound with a complementary strand of DNA. (5) Relaxase joins the two ends of the transfer DNA into a circular plasmid. (6) Relaxase detaches from the plasmid. (7) New plasmid DNA is rewound with a complementary strand of DNA.

At the start of bacterial conjugation, a donor cell will elaborate a pilus and signal to a nearby recipient cell to get in close contact. This identification of a suitable recipient cell will begin the mating pair formation process[1][20]. This process of bringing the two cells together recruits the type IV secretion system, a protein complex that forms the transfer channel between the donor and recipient, starting the formation of the relaxation complex known as the relaxosome at the oriT[15].

A relaxase protein will nick the DNA at the oriT and begin conjugation[4][16]. The nicked DNA strand, known as the T-strand, is then transferred to the recipient cell in a 5’ to 3’ direction beginning at the oriT[4][14][5]. Synthesis of the complementary DNA and recircularization of the T-strand back at the oriT results in both the donor and recipient cells being capable of plasmid transfer[21].

Antimicrobial Resistance

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The interaction between the DNA oriT and relaxase enables antimicrobial resistance via horizontal gene transfer (Figure 1) [22]. Various oriT regions in plasmid DNA contain inverted repeats onto which relaxase proteins are able bind[6]. Major contributors of drug resistance are mobile genomic islands (MGIs), or segments in DNA that are found in similar strains of bacteria and are factors in diversification of bacteria[6][23]. MGIs provide resistance to their host cells, and through bacterial conjugation, spread this advantage to other cells[6]. With bacterial cell MGIs having their own oriT sequences and being in close proximity to relaxosome genes, they are very similar to conjugative plasmids that are responsible for the prevalence of drug resistance among bacterial cells[6].

Applications

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Further information: Diatom

Conjugation allows for the transfer of target genes to many recipients, including yeast[24], mammalian cells[25][26], and diatoms[27].

Diatoms could be useful plasmid hosts as they have the potential to autotrophically produce biofuels and other chemicals[27]. There are some methods for genetic transfer for diatoms, but they are slow compared to bacterial conjugation. By designing plasmids for the diatoms P. tricornutum and T. pseudonana based on sequences for yeast and developing a method for conjugation from E. coli to the diatoms, researchers hope to advance genetic manipulation in diatoms[27].

One of the main problems in using bacterial conjugation in genetic engineering is that certain selectable markers on the plasmids generate bacteria that have resistance to antibiotics like ampicillin and kanamycin[28].

A 2017 study on mobile genomic islands revealed that MGIs are able to integrate themselves into the genome of the receiving bacterial cells by themselves via int, a gene that that codes for the integrase enzyme. After the OriT of the MGI are processed by the relaxosomes encoded by integrative and conjugative elements (ICE), the MGI are able to enter the genome of the receiver cells and allow for the multiformity of bacteria that leads to antimicrobial resistance[29]

See also

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References

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  1. ^ a b c d e De La Cruz, Fernando; Frost, Laura S.; Meyer, Richard J.; Zechner, Ellen L. (2010-01). "Conjugative DNA metabolism in Gram-negative bacteria". FEMS Microbiology Reviews. 34 (1): 18–40. doi:10.1111/j.1574-6976.2009.00195.x. ISSN 1574-6976. {{cite journal}}: Check date values in: |date= (help)
  2. ^ Frost, L. S. (2009-01-01), Schaechter, Moselio (ed.), "Conjugation, Bacterial", Encyclopedia of Microbiology (Third Edition), Oxford: Academic Press, pp. 517–531, doi:10.1016/b978-012373944-5.00007-9, ISBN 978-0-12-373944-5, retrieved 2021-12-03
  3. ^ a b c Kiss, János; Szabó, Mónika; Hegyi, Anna; Douard, Gregory; Praud, Karine; Nagy, István; Olasz, Ferenc; Cloeckaert, Axel; Doublet, Benoît (2019). "Identification and Characterization of oriT and Two Mobilization Genes Required for Conjugative Transfer of Salmonella Genomic Island 1". Frontiers in Microbiology. 10: 457. doi:10.3389/fmicb.2019.00457. ISSN 1664-302X. PMC 6414798. PMID 30894848.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  4. ^ a b c d Howard, Michael T.; Nelson, William C.; Matson, Steven W. (1995-11). "Stepwise Assembly of a Relaxosome at the F Plasmid Origin of Transfer". Journal of Biological Chemistry. 270 (47): 28381–28386. doi:10.1074/jbc.270.47.28381. ISSN 0021-9258. {{cite journal}}: Check date values in: |date= (help)CS1 maint: unflagged free DOI (link)
  5. ^ a b c d e Lanka, Erich; Wilkins, Brian M. (1995-06-01). "Dna processing reactions in bacterial conjugation". Annual Review of Biochemistry. 64 (1): 141–169. doi:10.1146/annurev.bi.64.070195.001041. ISSN 0066-4154.
  6. ^ a b c d e Kiss, János; Szabó, Mónika; Hegyi, Anna; Douard, Gregory; Praud, Karine; Nagy, István; Olasz, Ferenc; Cloeckaert, Axel; Doublet, Benoît (2019). "Identification and Characterization of oriT and Two Mobilization Genes Required for Conjugative Transfer of Salmonella Genomic Island 1". Frontiers in Microbiology. 10: 457. doi:10.3389/fmicb.2019.00457. ISSN 1664-302X. PMC 6414798. PMID 30894848.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  7. ^ Gyles, C.; Boerlin, P. (2014-03-01). "Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease". Veterinary Pathology. 51 (2): 328–340. doi:10.1177/0300985813511131. ISSN 0300-9858.
  8. ^ Guiney, Donald G.; Helinski, Donald R. (1979-10-01). "The DNa-protein relaxation complex of the plasmid RK2: Location of the site-specific nick in the region of the proposed origin of transfer". Molecular and General Genetics MGG. 176 (2): 183–189. doi:10.1007/BF00273212. ISSN 1432-1874.
  9. ^ Guiney, Donald G.; Helinski, Donald R. (1979-10-01). "The DNa-protein relaxation complex of the plasmid RK2: Location of the site-specific nick in the region of the proposed origin of transfer". Molecular and General Genetics MGG. 176 (2): 183–189. doi:10.1007/BF00273212. ISSN 1432-1874.
  10. ^ a b c Francia, M. Victoria; Varsaki, Athanasia; Garcillán-Barcia, M. Pilar; Latorre, Amparo; Drainas, Constantin; de la Cruz, Fernando (2004-02). "A classification scheme for mobilization regions of bacterial plasmids". FEMS Microbiology Reviews. 28 (1): 79–100. doi:10.1016/j.femsre.2003.09.001. ISSN 1574-6976. {{cite journal}}: Check date values in: |date= (help)
  11. ^ Zhang, Shuyu; Meyer, Richard (1997). "The relaxosome protein MobC promotes conjugal plasmid mobilization by extending DNA strand separation to the nick site at the origin of transfer". Molecular Microbiology. 25 (3): 509–516. doi:10.1046/j.1365-2958.1997.4861849.x. ISSN 1365-2958.
  12. ^ Scherzinger, Eberhard; Lurz, Rudi; Otto, Sabine; Dobrinski, Beate (1992). "In vitrocleavage of double- and single-stranded DNA by plasmid RSF1010-encoded mobilization proteins". Nucleic Acids Research. 20 (1): 41–48. doi:10.1093/nar/20.1.41. ISSN 0305-1048. PMC 310323. PMID 1738602.{{cite journal}}: CS1 maint: PMC format (link)
  13. ^ Coupland, George M.; Brown, Anthony M. C.; Willetts, Neil S. (1987-06-01). "The origin of transfer (oriT) of the conjugative plasmid R46: Characterization by deletion analysis and DNA sequencing". Molecular and General Genetics MGG. 208 (1): 219–225. doi:10.1007/BF00330445. ISSN 1432-1874.
  14. ^ a b c Fu, Y H; Tsai, M M; Luo, Y N; Deonier, R C (1991-02-01). "Deletion analysis of the F plasmid oriT locus". Journal of Bacteriology. 173 (3): 1012–1020. doi:10.1128/jb.173.3.1012-1020.1991. PMC 207219. PMID 1991706.{{cite journal}}: CS1 maint: PMC format (link)
  15. ^ a b c Zrimec, Jan; Lapanje, Aleš (2018-01-29). "DNA structure at the plasmid origin-of-transfer indicates its potential transfer range". Scientific Reports. 8 (1): 1820. doi:10.1038/s41598-018-20157-y. ISSN 2045-2322.
  16. ^ a b Byrd, Devon R.; Matson, Steven W. (1997). "Nicking by transesterification: the reaction catalysed by a relaxase". Molecular Microbiology. 25 (6): 1011–1022. doi:10.1046/j.1365-2958.1997.5241885.x. ISSN 1365-2958.
  17. ^ Lee, Catherine A.; Grossman, Alan D. (2007-10-15). "Identification of the Origin of Transfer (oriT) and DNA Relaxase Required for Conjugation of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis". Journal of Bacteriology. 189 (20): 7254–7261. doi:10.1128/JB.00932-07. PMC 2168444. PMID 17693500.{{cite journal}}: CS1 maint: PMC format (link)
  18. ^ Karcher, SUSAN J. (1995-01-01), Karcher, SUSAN J. (ed.), "2 - RECOMBINANT DNA CLONING", Molecular Biology, San Diego: Academic Press, pp. 45–134, doi:10.1016/b978-012397720-5.50036-0, ISBN 978-0-12-397720-5, retrieved 2021-10-28
  19. ^ a b c d Thompson, R.; Taylor, L.; Kelly, K.; Everett, R.; Willetts, N. (1984-05). "The F plasmid origin of transfer: DNA sequence of wild-type and mutant origins and location of origin-specific nicks". The EMBO journal. 3 (5): 1175–1180. ISSN 0261-4189. PMC 557491. PMID 6329741. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  20. ^ Arutyunov, Denis; Frost, Laura S. (2013-07-01). "F conjugation: Back to the beginning". Plasmid. Special Issue based on the International Society for Plasmid Biology Meeting: Santander 2012. 70 (1): 18–32. doi:10.1016/j.plasmid.2013.03.010. ISSN 0147-619X.
  21. ^ Frost, L S; Ippen-Ihler, K; Skurray, R A (1994-06). "Analysis of the sequence and gene products of the transfer region of the F sex factor". Microbiological Reviews. 58 (2): 162–210. ISSN 0146-0749. PMID 7915817. {{cite journal}}: Check date values in: |date= (help)
  22. ^ Zrimec, Jan (2020). "Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens". MicrobiologyOpen. 9 (12): e1129. doi:10.1002/mbo3.1129. ISSN 2045-8827. PMC 7755788. PMID 33111499.{{cite journal}}: CS1 maint: PMC format (link)
  23. ^ Carraro, Nicolas; Rivard, Nicolas; Burrus, Vincent; Ceccarelli, Daniela (2017-03-04). "Mobilizable genomic islands, different strategies for the dissemination of multidrug resistance and other adaptive traits". Mobile Genetic Elements. 7 (2): 1–6. doi:10.1080/2159256X.2017.1304193. ISSN 2159-256X. PMC 5397120. PMID 28439449.{{cite journal}}: CS1 maint: PMC format (link)
  24. ^ Heinemann, Jack A.; Sprague, George F. (1989-07). "Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast". Nature. 340 (6230): 205–209. doi:10.1038/340205a0. ISSN 1476-4687. {{cite journal}}: Check date values in: |date= (help)
  25. ^ Kunik, Talya; Tzfira, Tzvi; Kapulnik, Yoram; Gafni, Yedidya; Dingwall, Colin; Citovsky, Vitaly (2001-02-13). "Genetic transformation of HeLa cells by Agrobacterium". Proceedings of the National Academy of Sciences. 98 (4): 1871–1876. doi:10.1073/pnas.98.4.1871. ISSN 0027-8424. PMID 11172043.
  26. ^ Waters, Virginia L. (2001-12). "Conjugation between bacterial and mammalian cells". Nature Genetics. 29 (4): 375–376. doi:10.1038/ng779. ISSN 1546-1718. {{cite journal}}: Check date values in: |date= (help)
  27. ^ a b c Karas, Bogumil J.; Diner, Rachel E.; Lefebvre, Stephane C.; McQuaid, Jeff; Phillips, Alex P. R.; Noddings, Chari M.; Brunson, John K.; Valas, Ruben E.; Deerinck, Thomas J.; Jablanovic, Jelena; Gillard, Jeroen T. F. (2015-04-21). "Designer diatom episomes delivered by bacterial conjugation". Nature Communications. 6 (1): 6925. doi:10.1038/ncomms7925. ISSN 2041-1723. PMC 4411287. PMID 25897682.{{cite journal}}: CS1 maint: PMC format (link)
  28. ^ Lopatkin, Allison J.; Meredith, Hannah R.; Srimani, Jaydeep K.; Pfeiffer, Connor; Durrett, Rick; You, Lingchong (2017-11-22). "Persistence and reversal of plasmid-mediated antibiotic resistance". Nature Communications. 8 (1): 1689. doi:10.1038/s41467-017-01532-1. ISSN 2041-1723. PMC 5698434. PMID 29162798.{{cite journal}}: CS1 maint: PMC format (link)
  29. ^ Carraro, Nicolas; Rivard, Nicolas; Burrus, Vincent; Ceccarelli, Daniela (2017-03-04). "Mobilizable genomic islands, different strategies for the dissemination of multidrug resistance and other adaptive traits". Mobile Genetic Elements. 7 (2): 1–6. doi:10.1080/2159256X.2017.1304193. ISSN 2159-256X. PMC 5397120. PMID 28439449.{{cite journal}}: CS1 maint: PMC format (link)
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