51
|
Curtin SJ, Anderson JE, Starker CG, Baltes NJ, Mani D, Voytas DF, Stupar RM. Targeted mutagenesis for functional analysis of gene duplication in legumes. Methods Mol Biol 2013; 1069:25-42. [PMID: 23996306 DOI: 10.1007/978-1-62703-613-9_3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Assessment of gene function oftentimes requires mutant populations that can be screened by forward or reverse genetic analysis. The situation becomes more complicated in polyploidy or paleopolyploid genomes that have two or more copies for most genes. Here we describe a method for engineering zinc-finger nucleases (ZFNs) for the purpose of creating targeted mutations in the paleopolyploid soybean genome. ZFNs are recombinant proteins composed of an engineered zinc-finger array fused to a nonspecific cleavage domain. When engineered to recognize a specific nucleotide sequence, the cleavage domain will generate highly mutagenic DNA double-strand breaks frequently resulting in insertions and deletions at the target locus. Depending on the number of target sites present within the genome, this method has the capacity to target either single- or multi-copy gene families. In this chapter, we describe an inexpensive, rapid, and user-friendly approach for ZFN assembly and application in soybean based on the previously described context-dependent assembly method.
Collapse
Affiliation(s)
- Shaun J Curtin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | | | | | | | | | | | | |
Collapse
|
52
|
Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF. Transcription activator-like effector nucleases enable efficient plant genome engineering. PLANT PHYSIOLOGY 2013; 161:20-7. [PMID: 23124327 PMCID: PMC3532252 DOI: 10.1104/pp.112.205179] [Citation(s) in RCA: 276] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/21/2012] [Indexed: 05/17/2023]
Abstract
The ability to precisely engineer plant genomes offers much potential for advancing basic and applied plant biology. Here, we describe methods for the targeted modification of plant genomes using transcription activator-like effector nucleases (TALENs). Methods were optimized using tobacco (Nicotiana tabacum) protoplasts and TALENs targeting the acetolactate synthase (ALS) gene. Optimal TALEN scaffolds were identified using a protoplast-based single-strand annealing assay in which TALEN cleavage creates a functional yellow fluorescent protein gene, enabling quantification of TALEN activity by flow cytometry. Single-strand annealing activity data for TALENs with different scaffolds correlated highly with their activity at endogenous targets, as measured by high-throughput DNA sequencing of polymerase chain reaction products encompassing the TALEN recognition sites. TALENs introduced targeted mutations in ALS in 30% of transformed cells, and the frequencies of targeted gene insertion approximated 14%. These efficiencies made it possible to recover genome modifications without selection or enrichment regimes: 32% of tobacco calli generated from protoplasts transformed with TALEN-encoding constructs had TALEN-induced mutations in ALS, and of 16 calli characterized in detail, all had mutations in one allele each of the duplicate ALS genes (SurA and SurB). In calli derived from cells treated with a TALEN and a 322-bp donor molecule differing by 6 bp from the ALS coding sequence, 4% showed evidence of targeted gene replacement. The optimized reagents implemented in plant protoplasts should be useful for targeted modification of cells from diverse plant species and using a variety of means for reagent delivery.
Collapse
Affiliation(s)
| | | | - Xiaohong Li
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chendu 610054, People’s Republic of China (Y.Z.); Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (Y.Z., X.L., J.A.B., Y.Q., C.G.S., D.F.V.); Cellectis Plant Sciences, St. Paul, Minnesota 55114 (F.Z., D.F.V.); and Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (A.J.B.)
| | - Joshua A. Baller
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chendu 610054, People’s Republic of China (Y.Z.); Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (Y.Z., X.L., J.A.B., Y.Q., C.G.S., D.F.V.); Cellectis Plant Sciences, St. Paul, Minnesota 55114 (F.Z., D.F.V.); and Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (A.J.B.)
| | - Yiping Qi
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chendu 610054, People’s Republic of China (Y.Z.); Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (Y.Z., X.L., J.A.B., Y.Q., C.G.S., D.F.V.); Cellectis Plant Sciences, St. Paul, Minnesota 55114 (F.Z., D.F.V.); and Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (A.J.B.)
| | - Colby G. Starker
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chendu 610054, People’s Republic of China (Y.Z.); Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (Y.Z., X.L., J.A.B., Y.Q., C.G.S., D.F.V.); Cellectis Plant Sciences, St. Paul, Minnesota 55114 (F.Z., D.F.V.); and Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (A.J.B.)
| | - Adam J. Bogdanove
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chendu 610054, People’s Republic of China (Y.Z.); Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (Y.Z., X.L., J.A.B., Y.Q., C.G.S., D.F.V.); Cellectis Plant Sciences, St. Paul, Minnesota 55114 (F.Z., D.F.V.); and Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (A.J.B.)
| | - Daniel F. Voytas
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chendu 610054, People’s Republic of China (Y.Z.); Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (Y.Z., X.L., J.A.B., Y.Q., C.G.S., D.F.V.); Cellectis Plant Sciences, St. Paul, Minnesota 55114 (F.Z., D.F.V.); and Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 (A.J.B.)
| |
Collapse
|
53
|
Abstract
Recent advances in genome engineering provide newfound control over a plant's genetic material. It is now possible for most bench scientists to alter DNA in living plant cells in a variety of ways, including introducing specific nucleotide substitutions in a gene that change a protein's amino acid sequence, deleting genes or chromosomal segments, and inserting foreign DNA at precise genomic locations. Such targeted DNA sequence modifications are enabled by sequence-specific nucleases that create double-strand breaks in the genomic loci to be altered. The repair of the breaks, through either homologous recombination or nonhomologous end joining, can be controlled to achieve the desired sequence modification. Genome engineering promises to advance basic plant research by linking DNA sequences to biological function. Further, genome engineering will enable plants' biosynthetic capacity to be harnessed to produce the many agricultural products required by an expanding world population.
Collapse
Affiliation(s)
- Daniel F Voytas
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|