Abstract
Inserts and insert sites in transgenic, papaya ringspot virus (PRSV)-resistant commercial papaya Rainbow and SunUp, were characterized as part of a petition to Japan to allow import of fresh fruit of these cultivars from the U.S. and to provide data for a larger study aimed at understanding the global impact of DNA transformation on whole genome structure. The number and types of inserts were determined by Southern analysis using probes spanning the entire transformation plasmid and their sequences determined from corresponding clones or sequence reads from the whole-genome shotgun (WGS) sequence of SunUp papaya. All the functional transgenes, coding for the PRSV coat protein (CP), neophosphotransferase (nptII) and β-glucuronidase (uidA) were found in a single 9,789 basepair (bp) insert. Only two other inserts, one consisting of a 290 bp nonfunctional fragment of the nptII gene and a 1,533 bp plasmid-derived fragment containing a nonfunctional 222 bp segment of the tetA gene were detected in Rainbow and SunUp. Detection of the same three inserts in samples representing transgenic generations five to eight (R5 to R8) suggests that the three inserts are stably inherited. Five out of the six genomic DNA segments flanking the three inserts were nuclear plastid sequences (nupts). From the biosafety standpoint, no changes to endogenous gene function based on sequence structure of the transformation plasmid DNA insertion sites could be determined and no allergenic or toxic proteins were predicted from analysis of the insertion site and flanking genomic DNA.
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Abbreviations
- bp:
-
base pair
- CP:
-
coat protein
- DSB:
-
double-stranded break
- ELISA:
-
enzyme-linked immunosorbent assay
- FAO:
-
Food and Agriculture Organization (of the United Nations)
- GE:
-
genetically engineered
- GUS:
-
β-glucuronidase
- IUIS:
-
International Union of Immunological Societies
- kb:
-
kilobase pair
- MAR:
-
matrix attachment regions
- NHEJ:
-
nonhomologous end joining
- nupt-DNA:
-
nuclear plastid DNA
- nupts:
-
nuclear plastid sequence
- numts:
-
nuclear mitochondrial sequence
- ORF:
-
open reading frame
- PCR:
-
polymerase chain reaction
- PDR:
-
pathogen-derived resistance
- PTGS:
-
post-transcriptional gene silencing
- PRSV:
-
Papaya ringspot virus
- SDAP:
-
Structural Database for Allergenic Proteins
- T-DNA:
-
transferred DNA
- Topo I:
-
Topoisomerase I
- Topo II:
-
Topoisomerase II
- WGS:
-
whole-genome shotgun
- WHO:
-
World Health Organization
References
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zheng Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:10.1093/nar/25.17.3389
Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F et al (2002) T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep 3:1152–1157. doi:10.1093/embo-reports/kvf237
Dai S, Zheng P, Marmey P, Zhang S, Tian W et al (2001) Comparative analysis of transgenic rice plants obtained by Agrobacterium-mediated transformation and particle bombardment. Mol Breed 7:25–33. doi:10.1023/A:1009687511633
Drescher A, Ruf S, Calsa T Jr, Carrer H, Bock R (2000) The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J 22:97–104. doi:10.1046/j.1365-313x.2000.00722.x
FAO/WHO (2001) Evaluation of allergenicity of genetically modified foods. Report of a joint FAO/WHO expert consultation on allergenicity of foods derived from biotechnology. Available at: http://www.who.int/foodsafety/publications/biotech/en/ec_jan2001.pdf.
Fermín GA (2002) Use, application, and technology transfer of native and synthetic genes to engineer single and multiple transgenic viral resistance. Ph.D. Thesis, Cornell University, Geneva, p 293
Gonsalves D (1998) Control of papaya ringspot virus in papaya: A case study. Annu Rev Phytopathol 36:415–437. doi:10.1146/annurev.phyto.36.1.415
Gonsalves D, Ferreira S (2003) Transgenic papaya: A case for managing risks of Papaya ringspot virus in Hawaii. OnlinePlant Health Progress doi:10.1094/PHP-2003-1113-1003-RV
Gonsalves D, Gonsalves C, Ferreira S, Pitz K, Fitch M, et al (2004) Transgenic virus resistant papaya: From hope to reality for controlling papaya ringspot virus in Hawaii. APSnet feature story for July, 2004 Online at: http://www.apsnet.org/online/feature/ringspot
Gonsalves D (2006) Transgenic papaya: Development, release, impact, and challenges. Adv Virus Res 67:317–354. doi:10.1016/S0065-3527(06)67009-7
Gonsalves D, Vegas A, Prasartsee V, Drew R, Suzuki JY et al (2006) Developing papaya to control Papaya ringspot virus by transgenic resistance, intergeneric hybridization, and tolerance breeding. In: Janick J (ed) Plant breeding reviews. John Wiley and Sons, Inc., Hoboken, pp 35–73
Gonsalves D, Ferreira SA, Suzuki JY, Tripathi S (2008) Papaya. In: Kole C, Hall TC (eds) Tropical and subtropical fruits and nuts. Compendium of transgenic crop plants, vol. 5. Wiley-Blackwell, Oxford West Sussex Hoboken, pp 131-162
Gonsalves D, Suzuki JY, Tripathi S, Ferreira SA (2008) Papaya ringspot virus. In: Mahy BWJ, van Regenmortel MHV (eds) Encyclopedia of virology. Elsevier Ltd, Oxford, pp 1–8
Gorbunova V, Levy AA (1997) Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucleic Acids Res 25:4650–4657. doi:10.1093/nar/25.22.4650
Gorbunova V, Levy AA (1999) How plants make ends meet: DNA double-strand break repair. Trends Plant Sci 4:263–269. doi:10.1016/S1360-1385(99)01430-2
Guo X, Ruan S, Hu W, Cai D, Fan L (2008) Chloroplast DNA insertions into the nuclear genome of rice: the genes, sites and ages of insertion involved. Funct Integr Genomics 8:101–108. doi:10.1007/s10142-007-0067-2
Heck GR, Armstrong CL, Astwood JD, Behr CF, Bookout JT et al (2005) Development and characterization of a CP4 EPSPS-based glyphosate-tolerant corn event. Crop Sci 45:329–339
Huang CY, Ayliffe MA, Timmis JN (2004) Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco. Proc Natl Acad Sci USA 101:9710–9715. doi:10.1073/pnas.0400853101
Huang CY, Grünheit N, Ahmadinejad N, Timmis JN, Martin W (2005) Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Plant Physiol 138:1723–1733. doi:10.1104/pp.105.060327
Ivanciuc O, Schein CH, Braun W (2002) Data mining of sequences and 3D structures of allergenic proteins. Bioinformatics 18:1358–1364. doi:10.1093/bioinformatics/18.10.1358
Ivanciuc O, Schein CH, Braun W (2003) SDAP: Database and computational tools for allergenic proteins. Nucleic Acids Res 31:359–362. doi:10.1093/nar/gkg010
Kleter GA, Peijnenburg AACM (2002) Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE-binding linear epitopes of allergens. BMC Struct Biol 2:1–11. doi:10.1186/1472-6807-2-8
Knoop V, Unseld M, Marienfeld J, Brandt P, Sunkel S et al (1996) copia-, gypsy- and LINE-Like retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana. Genetics 142:579–585
Kohli A, Leech M, Vain P, Laurie DA, Christou P (1998) Transgene organization in rice engineered through direct DNA transfer supports a two-phase integration mechanism mediated by the establishment of integration hot spots. Proc Natl Acad Sci USA 95:7203–7208. doi:10.1073/pnas.95.12.7203
Kohli A, Twyman RM, Abranches R, Wegel E, Stoger E et al (2003) Transgene integration, organization and interaction in plants. Plant Mol Biol 52:247–258. doi:10.1023/A:1023941407376
Kohli A, Christou P (2008) Stable transgenes bear fruit. Nat Biotechnol 26:653–654. doi:10.1038/nbt0608-653
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12. doi:10.1186/gb-2004-1185-1182-R1112, doi:10.1186/gb-2004-5-2-r12
Liebich I, Bode J, Frisch M, Wingender D (2002) S/MARt DB: a database on scaffold/matrix attached regions. Nucleic Acids Res 30:372–374. doi:10.1093/nar/30.1.372
Liere K, Maliga P (2001) Plastid RNA polymerases in higher plants. In: Anderson B, Aro EM (eds) Regulation of Photosynthesis. Kluwer Academic Publishers, Dordrecht, pp 29–49
Ling K, Namba S, Gonsalves C, Slightom JL, Gonsalves D (1991) Protection against detrimental effects of potyvirus infection in transgenic tobacco plants expressing the papaya ringspot virus coat protein gene. Bio/Technol 9:752–758
Liu X, Baird V (2001) Rapid amplification of genome DNA ends by NlaIII partial digestion and polynucleotide tailing. Plant Mol Biol Rep 19:261–267. doi:10.1007/BF02772898
Liu YG, Mitsukawa N, Oosumi T, Whittier RF (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junction by thermal assymetric interlaced PCR. Plant J 8:457–463. doi:10.1046/j.1365-313X.1995.08030457.x
Lius S, Manshardt RM, Fitch MMM, Slightom JL, Sanford JC et al (1997) Pathogen-derived resistance provides papaya with effective protection against papaya ringspot virus. Mol Breed 3:161–168. doi:10.1023/A:1009614508659
Makarevitch I, Somers DA (2006) Association of Arabidopsis topoisomerase IIA cleavage sites with functional genomic elements and T-DNA loci. Plant J 48:697–709. doi:10.1111/j.1365-313X.2006.02915.x
Manshardt RM (1998) ‘UH Rainbow’ papaya. University of Hawaii College of Tropical Agriculture and Human Resources New Plants for Hawaii-1, p2
Martin W (2003) Gene transfer from organelles to the nucleus: Frequent and in big chunks. Proc Natl Acad Sci USA 100:8612–8614. doi:10.1073/pnas.1633606100
Matsuo M, Ito Y, Yamauchi R, Obokata J (2005) The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. Plant Cell 17:665–675. doi:10.1105/tpc.104.027706
Ming R, Moore PH, Zee F, Abbey CA, Ma H et al (2001) Construction and characterization of a papaya BAC library as a foundation for molecular dissection of a tree-fruit genome. Theor Appl Genet 102:892–899. doi:10.1007/s001220000448
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996. doi:10.1038/nature06856
NASS (2007) Papaya acreage survey 2007 results. In: National Agricultural Statistical Service, pp 1–8
Pawlowski WP, Somers DA (1998) Transgenic DNA integrated into the oat genome is frequently interspersed by host DNA. Proc Natl Acad Sci USA 95:12106–12110
Purcifull D, Edwardson J, Hiebert E, Gonsalves D (1984) Papaya ringspot virus. CMI/AAB Descriptions of plant viruses No 292 (No 84 Revised, July 1984) 8 pp CAB International, Wallingford, UK
Richly E, Leister D (2004) NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs. Mol Biol Evol 21:1972–1980. doi:10.1093/molbev/msh210
Ruf S, Kössel H, Bock R (1997) Targeted inactivation of a tobacco intron-containing open reading frame reveals a novel chloroplast-encoded photosystem I-related gene. J Cell Biol 139:95–102. doi:10.1083/jcb.139.1.95
Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8019. doi:10.1073/pnas.81.24.8014
Sawasaki T, Takahashi M, Goshima N, Morikawa H (1998) Structures of transgene loci in transgenic Arabidopsis plants obtained by particle bombardment: Junction regions can bind to nuclear matrices. Gene 218:27–35. doi:10.1016/S0378-1119(98)00388-6
Shahmuradov IA, Akbarova YY, Solovyev VV, Aliyev JA (2003) Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Plant Mol Biol 52:923–934
Somers DA, Makarevitch I (2004) Transgene integration in plants: poking or patching holes in promiscuous genomes. Curr Opin Biotechnol 15:126–131. doi:10.1016/j.copbio.2004.02.007
Souza MT Jr, Tennant PF, Gonsalves D (2005) Influence of coat protein transgene copy number on resistance in transgenic line 63-1 against Papaya ringspot virus isolates. HortScience 40:2083–2087
Sugiura M (1992) The chloroplast genome. Plant Mol Biol 18:149–168. doi:10.1007/BF00015612
Sugiura M, Hirose T, Sugita M (1998) Evolution and mechanism of translation in chloroplasts. Annu Rev Genet 32:437–459. doi:10.1146/annurev.genet.32.1.437
Suzuki JY, Tripathi S, Gonsalves D (2007) Virus-resistant transgenic papaya: Commercial development and regulatory and environmental issues. In: Punja SK, De Boer SH, Sanfaçon H (eds) Biotechnology and plant disease managment. CAB International, Wallingford, pp 436–461
Szabados L, Kovács I, Oberschall A, Ábrahám E, Kerekes I et al (2002) Distribution of 1,000 sequenced T-DNA tags in the Arabidopsis genome. Plant J 32:233–242. doi:10.1046/j.1365-313X.2002.01417.x
Takano M, Egawa H, Ikeda J, Wakasa K (1997) The structure of integration sites in transgenic rice. Plant J 11:353–361. doi:10.1046/j.1365-313X.1997.11030353.x
Tatusova TA, Madden TL (1999) Blast 2 sequences—a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250. doi:10.1111/j.1574-6968.1999.tb13575.x
Tennant P, Fermin G, Fitch MM, Manshardt RM, Slightom JL et al (2001) Papaya ringspot virus resistance of transgenic Rainbow and SunUp is affected by gene dosage, plant development, and coat protein homology. Eur J Plant Pathol 107:645–653. doi:10.1023/A:1017936226557
Tennant P, Souza MT Jr, Gonsalves D, Fitch MM, Manshardt RM et al (2005) Line 63-1: a new virus-resistant transgenic papaya. HortScience 40:1196–1199
Tennant PF, Gonsalves C, Ling KS, Fitch M, Manshardt R et al (1994) Differential protection against papaya ringspot virus isolates in coat protein gene transgenic papaya and classically cross-protected papaya. Phytopathology 84:1359–1366. doi:10.1094/Phyto-84-1359
Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123–135. doi:10.1038/nrg1271
Toyoshima Y, Onda Y, Shiina T, Nakahira Y (2005) Plastid transcription in higher plants. Crit Rev Plant Sci 24:59–81. doi:10.1080/07352680590910438
Tripathi S, Suzuki J, Gonsalves D (2006) Development of genetically engineered resistant papaya for Papaya ringspot virus in a timely manner—A comprehensive and successful approach. In: Ronald P (ed) Plant-Pathogen interactions: Methods and protocols. The Humana, New Jersey, pp 197–240
Van Droogenbroeck B, Maertens I, Haegeman A, Kyndt T, O’Brien C et al (2005) Maternal inheritance of cytoplasmic organelles in intergeneric hybrids of Carica papaya L. and Vasconcellea spp. (Caricaceae Dumort., Brassicales). Euphytica 143:161–168. doi:10.1007/s10681-005-3156-0
Vergunst AC, Hooykaas PJJ (1999) Recombination in the plant genome and its application in biotechnology. Crit Rev Plant Sci 18:1–31. doi:10.1016/S0735-2689(99)00385-8
Wilson AK, Latham JR, Steinbrecher RA (2006) Transformation-induced mutations in transgenic plants: Analysis and biosafety implications. In: Biotechnology and genetic engineering review. Lavoisier/Intercept, Cachan, pp 209–234
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Suzuki, J.Y., Tripathi, S., Fermín, G.A. et al. Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop. Tropical Plant Biol. 1, 293–309 (2008). https://doi.org/10.1007/s12042-008-9023-0
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DOI: https://doi.org/10.1007/s12042-008-9023-0