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Mmbando GS. Recent Advances in Antibiotic-Free Markers; Novel Technologies to Enhance Safe Human Food Production in the World. Mol Biotechnol 2022. [DOI: 10.1007/s12033-022-00609-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
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Yang FJ, Chen CN, Chang T, Cheng TW, Chang NC, Kao CY, Lee CC, Huang YC, Hsu JC, Li J, Lu MJ, Chan SP, Wang J. phiC31 integrase for recombination mediated single copy insertion and genome manipulation in C. elegans. Genetics 2021; 220:6428549. [PMID: 34791215 DOI: 10.1093/genetics/iyab206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 11/02/2021] [Indexed: 11/14/2022] Open
Abstract
C. elegans benefits from a large set of tools for genome manipulation. Yet, the precise single-copy insertion of very large DNA constructs (>10 kb) and the generation of inversions are still challenging. Here, we adapted the phiC31 integrase system for C. elegans. We generated an integrated phiC31 integrase expressing strain flanked by attP sites that serves as a landing pad for integration of transgenes by recombination mediated cassette exchange (RCME). This strain is unc-119(-) so RMCE integrants can be produced simply by injection of a plasmid carrying attB sites flanking unc-119(+) and the gene(s) of interest. Additionally, phiC31 integrase is removed concomitantly with integration, eliminating the need to outcross away the integrase. Integrations were obtained for insert sizes up to ∼33.4 kb. Taking advantage of this integration method we establish a dual color fluorescent operon reporter system able to study post-transcriptional regulation of mRNA. Last, we show that large chromosomal segments can be inverted using phiC31 integrase. Thus, the phiC31 integrase system should be a useful addition to the C. elegans toolkit.
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Affiliation(s)
- Fang-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chiao-Nung Chen
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tiffany Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ting-Wei Cheng
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ni-Chen Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Yi Kao
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Chi Lee
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ching Huang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jung-Chen Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jengyi Li
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Meiyeh J Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Peng Chan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
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Pathak B, Srivastava V. Recombinase-mediated integration of a multigene cassette in rice leads to stable expression and inheritance of the stacked locus. Plant Direct 2020; 4:e00236. [PMID: 32760877 PMCID: PMC7391932 DOI: 10.1002/pld3.236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 05/03/2023]
Abstract
Efficient methods for multigene transformation are important for developing novel crop varieties. Methods based on random integrations of multiple genes have been successfully used for metabolic engineering in plants. However, efficiency of co-integration and co-expression of the genes could present a bottleneck. Recombinase-mediated integration into the engineered target sites is arguably a more efficient method of targeted integration that leads to the generation of stable transgenic lines at a high rate. This method has the potential to streamline multigene transformation for metabolic engineering and trait stacking in plants. Therefore, empirical testing of transgene(s) stability from the multigene site-specific integration locus is needed. Here, the recombinase technology based on Cre-lox recombination was evaluated for developing multigenic lines harboring constitutively-expressed and inducible genes. Targeted integration of a five genes cassette in the rice genome generated a precise full-length integration of the cassette at a high rate, and the resulting multigenic lines expressed each gene reliably as defined by their promoter activity. The stable constitutive or inducible expression was faithfully transmitted to the progeny, indicating inheritance-stability of the multigene locus. Co-localization of two distinctly inducible genes by heat or cold with the strongly constitutive genes did not appear to interfere with each other's expression pattern. In summary, high rate of co-integration and co-expression of the multigene cassette installed by the recombinase technology in rice shows that this approach is appropriate for multigene transformation and introduction of co-segregating traits. SIGNIFICANCE STATEMENT Recombinase-mediated site-specific integration approach was found to be highly efficacious in multigene transformation of rice showing proper regulation of each gene driven by constitutive or inducible promoter. This approach holds promise for streamlining gene stacking in crops and expressing complex multigenic traits.
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Affiliation(s)
- Bhuvan Pathak
- Department of Crop, Soil & Environmental SciencesUniversity of ArkansasFayettevilleARUSA
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental SciencesUniversity of ArkansasFayettevilleARUSA
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
- Department of HorticultureUniversity of ArkansasFayettevilleARUSA
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Abstract
Background Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate. Intuitively, one may hypothesize that those synonymous mutations which increase the tAI values are favored by natural selection. Results We use the maize (Zea mays) genome to test our assumption. The first supporting evidence is that the tAI-increasing synonymous mutations have higher fixed-to-polymorphic ratios than the tAI-decreasing ones. Next, the DAF (derived allele frequency) or MAF (minor allele frequency) of the former is significantly higher than the latter. Moreover, similar results are obtained when we investigate CAI (codon adaptation index) instead of tAI. Conclusion The synonymous mutations in the maize genome are not strictly neutral. The tAI-increasing mutations are positively selected while those tAI-decreasing ones undergo purifying selection. This selection force might be weak but should not be automatically ignored.
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Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.
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