Abstract
Techniques for genetic manipulation of the filamentous fungus Rhizopus have been hampered due to a lack of understanding regarding the recombination and replication mechanisms that affect the fate of introduced DNA. The ability to target chromosomal integration of a plasmid has been difficult because DNA transformed into Rhizopus rarely integrates and is autonomously replicated in a high molecular weight concatenated arrangement (i.e., series or chain). Linearization of the plasmid prior to transformation at a site having homology with the genomic DNA yields the highest frequency of integration, but repair of the double-strand break by end-joining is still the predominant event. We recently attempted to circumvent replication of the plasmid by introducing frameshift mutations in pyrG, the R. oryzae orotidine-5′-monophosphate decarboxylase gene used for selection of the vector. It was hypothesized that autonomous replication of the mutated plasmids would be incapable of restoring prototrophic growth, since the genomic pyrG also contained a mutation. However, homologous integration of the plasmid results in duplication of the pyrG gene, which can create a functional copy of pyrG if both the genomic and plasmid mutations are paired on the same duplicate copy. While this event was detected in one of the isolates, it represented less than 8% of the total transformants. The majority of transformants contained plasmid replicating autonomously in a concatenated arrangement. Sequence analysis showed that prototrophic growth was restored by repairing the non-functional pyrG sequence in the plasmid, while the genomic pyrG gene was unaltered. Frequent transfer of the genomic pyrG mutation to the plasmid suggests that gene conversion is likely occurring by recombination pathways involving break-induced replication or synthesis-dependent strand annealing.
Similar content being viewed by others
References
Allers T, Lichten M (2001) Differential timing and control of noncrossover and crossover recombination during meiosis. Cell 106:47–57
Benito EP, Campuzano V, Lopez-Matas MA, De Vicente JI, Eslava AP (1995) Isolation, characterization, and transformation, by autonomous replication, of Mucor circinelloides OMPdecase-deficient mutants. Mol Gen Genet 248:126–135
Collins I, Newlon CS (1994) Meiosis-specific formation of joint DNA molecules containing sequences from homologous chromosomes. Cell 76:65–75
Frank-Vaillant M, Marcand S (2002) Transient stability of DNA ends allows nonhomologous end joining to precede homologous recombination. Mol Cell 10:1189–1199
Gilbert DM (2001) Making sense of eukaryotic DNA replication origins. Science 294:96–100
Hastings PJ (1988) Recombination in the eukaryotic nucleus. Bioessays 9:61–64
Heeswijck R van (1986) Autonomous replication of plasmids in Mucor transformants. Carlsberg Res Commun 51:433–443
Heyer WD, Ehmsen KT, Solinger JA (2003) Holliday junctions in the eukaryotic nucleus: resolution in sight? Trends Biochem Sci 28:548–557
Hinnen A, Hicks JB, Fink GR (1978) Transformation of yeast. Proc Natl Acad Sci USA 75:1929–1933
Holliday R (1964) A mechanism for gene conversion in fungi. Genet Res 5:282–304
Hunter N, Kleckner N (2001) The single-end invasion: an asymmetric intermediate at the double-strand break to double-Holliday junction transition of meiotic recombination. Cell 106:59–70
Ira G, Malkova A, Liberi G, Foiani M, Haber JE (2003) Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast. Cell 115:401–411
Kraus E, Leung WY, Haber JE (2001) Break-induced replication: a review and an example in budding yeast. Proc Natl Acad Sci USA 98:8255–8262
Lewis LK, Resnick MA (2000) Tying up loose ends: nonhomologous end-joining in Saccharomyces cerevisiae. Mutat Res 451:71–89
Lieber MR (1999) The biochemistry and biological significance of nonhomologous DNA end joining: an essential repair process in multicellular eukaryotes. Genes Cells 4:77–85
Lin FL, Sperle K, Sternberg N (1984) Model for homologous recombination during transfer of DNA into mouse L cells: role for DNA ends in the recombination process. Mol Cell Biol 4:1020–1034
Lin FL, Sperle K, Sternberg N (1985) Recombination in mouse L cells between DNA introduced into cells and homologous chromosomal sequences. Proc Natl Acad Sci USA 82:1391–1395
Lushnikov AY, Bogdanov A, Lyubchenko YL (2003) DNA recombination: Holliday junction dynamics and branch migration. J Biol Chem 278:43130–43134
McGill C, Shafer B, Strathern J (1989) Coconversion of flanking sequences with homothallic switching. Cell 57:459–467
Merker JD, Dominska M, Petes T (2003) Patterns of heteroduplex formation associated with the initiation of meitic recombination in the yeast Saccharomyces cerevisiae Genetics 165:47–63
Nassif N, Penney J, Pal S, Engels WR, Gloor GB (1994) Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair. Mol Cell Biol 14:1613–1625
Orr-Weaver TL, Szostak JW (1983) Yeast recombination: the association between double-strand gap repair and crossing-over. Proc Natl Acad Sci USA 80:4417–4421
Paques F, Haber JE (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 63:349–404
Prado F, Aguilera A (2003) Control of cross-over by single-strand DNA resection. Trends Genet 19:428–431
Prado F, Cortes-Ledesma F, Huertas P, Aguilera A (2003) Mitotic recombination in Saccharomyces cerevisiae. Curr Genet 42:185–198
Ray A, Langer M (2002) Homologous recombination: ends as the means. Trends Plant Sci 7:435–440
Revuelta JL, Jayaram M (1986) Transformation of Phycomyces blakesleeanus to G-418 resistance by an autonomously replicating plasmid. Proc Natl Acad Sci USA 83:7344–7347
Sandoval A, Labhart P (2002) Joining of DNA ends bearing non-matching 3′-overhangs. DNA Repair 1:397–410
Schwacha A, Kleckner N (1994) Identification of joint molecules that form frequently between homologs but rarely between sister chromatids during yeast meiosis. Cell 76:51–63
Skory CD (2002) Homologous recombination and double-strand break repair in the transformation of Rhizopus oryzae. Mol Genet Genomics 268:397–406
Sun H, Treco D, Szostak JW (1991) Extensive 3′-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site. Cell 64:1155–1161
Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW (1983) The double-strand-break repair model for recombination. Cell 33:25–35
Wostemeyer J, Burmester A, Weigel C (1987) Neomycin resistance as a dominantly selectable marker for transformation of the zygomycete Absidia glauca. Curr Genet 12:625–627
Yanai K, Horiuchi H, Takagi M, Yano K (1990) Preparation of protoplasts of Rhizopus niveus and their transformation with plasmid DNA. Agric Biol Chem 54:2689–2696
Author information
Authors and Affiliations
Corresponding author
Additional information
USDA: Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.
Rights and permissions
About this article
Cite this article
Skory, C.D. Repair of plasmid DNA used for transformation of Rhizopus oryzae by gene conversion. Curr Genet 45, 302–310 (2004). https://doi.org/10.1007/s00294-004-0494-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00294-004-0494-8