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Duan L, Zhang S, Yang Y, Wang Q, Lan Q, Wang Y, Xu W, Jin W, Li L, Chen R. A feasible method for detecting unknown GMOs via a combined strategy of PCR-based suppression subtractive hybridization and next-generation sequencing. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Simple innovative adaptor to improve genome walking with convenient PCR. J Genet Eng Biotechnol 2020; 18:64. [PMID: 33083895 PMCID: PMC7575660 DOI: 10.1186/s43141-020-00082-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 09/30/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Various polymerase chain reaction (PCR)-based methods have been applied for the development of genome walking (GW) technique. These methods which could be based on the application of restriction enzymes or primers have various efficiencies to identify the unknown nucleotide sequences. The present study was conducted to design a new innovative double-strand adaptor using MAP30 gene sequence of Momordica charantia plant as a model to improve genome walking with convenient PCR. RESULTS The adaptor was designed using multiple restriction sites of Hind III, BamH I, EcoR I, and Bgl II enzymes with no restriction site in a known sequence of the MAP30 gene. In addition, no modification was required to add phosphate, amine, or other groups to the adaptor, since restriction enzyme digestion of double-strand adaptor provided the 5' phosphate group. Here, preparation of the phosphate group in the genomic DNA of the plant digestion with restriction enzymes was performed followed by ligation with digested adaptor containing 5' phosphate group. CONCLUSION PCR was done to amplify the unknown sequence using MAP30 gene-specific primer and adaptor primer. Results confirmed the ability of the technique for successful identification of the sequence. Consequently, a newly designed adaptor in the developed technique reduced the time and cost of the method compared to the conventional genome walking; also, cloning and culturing of bacterial steps could be eliminated.
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Cyclic Digestion and Ligation-Mediated PCR Used for Flanking Sequence Walking. Sci Rep 2020; 10:3434. [PMID: 32103092 PMCID: PMC7044209 DOI: 10.1038/s41598-020-60411-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/12/2020] [Indexed: 11/12/2022] Open
Abstract
Ligation-mediated PCR (LM-PCR) is a classical method for isolating flanking sequences; however, it has a common limitation of reduced success rate owing to the circularization or multimerization of target restriction fragments including the known sequence. To address this limitation, we developed a novel LM-PCR method, termed Cyclic Digestion and Ligation-Mediated PCR (CDL-PCR). The novelty of this approach involves the design of new adapters that cannot be digested after being ligated with the restriction fragment, and cyclic digestion and ligation may be manipulated to block the circularization or multimerization of the target restriction fragments. Moreover, to improve the generality and flexibility of CDL-PCR, an adapter precursor sequence was designed, which could be digested to prepare 12 different adapters at low cost. Using this method, the flanking sequences of T-DNA insertions were obtained from transgenic rice and Arabidopsis thaliana. The experimental results demonstrated that CDL-PCR is an efficient and flexible method for identifying the flanking sequences in transgenic rice and Arabidopsis thaliana.
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Zhu J, Zhu Q, Gong R, Xu Q, Cai M, Jiang T, Zhou X, Zhou M, Zhang Y. PiggyBac transposon-mediated mutagenesis and application in yeast Komagataella phaffii. Biotechnol Lett 2018; 40:1365-1376. [PMID: 30003383 DOI: 10.1007/s10529-018-2592-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/10/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Around one-fourth of the Komagataella phaffii genes encode hypothetical proteins with unknown functions. However, lack of powerful tools for genetic screening in K. phaffii significantly limits the functional analysis of these unknown genes. Transposon mutagenesis has been utilized as an insertional mutagenesis tool in many other organisms and would be extremely valuable if it could be applied in K. phaffii. RESULTS In this study, we investigated in K. phaffii the transposition activity and efficiency of piggyBac (PB) transposon, a DNA transposon from the cabbage looper moth Trichoplusia ni through the integrated-plasmid system. We also designed a binary-plasmid system which could generate stable mutants. Finally we evaluated the quality of this mutagenesis system by a simple screening for functional genes involved in K. phaffii carbon catabolite repression. CONCLUSIONS Our results demonstrate that PB-mediated mutagenesis could be a feasible and useful tool for functional gene screening in K. phaffii.
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Affiliation(s)
- Jinxiang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Qiaoyun Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ruiqing Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Qin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Tianyi Jiang
- Roche R&D Center (China) Ltd., Shanghai, People's Republic of China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, People's Republic of China
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Košir AB, Arulandhu AJ, Voorhuijzen MM, Xiao H, Hagelaar R, Staats M, Costessi A, Žel J, Kok EJ, Dijk JPV. ALF: a strategy for identification of unauthorized GMOs in complex mixtures by a GW-NGS method and dedicated bioinformatics analysis. Sci Rep 2017; 7:14155. [PMID: 29074984 PMCID: PMC5658351 DOI: 10.1038/s41598-017-14469-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/09/2017] [Indexed: 12/27/2022] Open
Abstract
The majority of feed products in industrialised countries contains materials derived from genetically modified organisms (GMOs). In parallel, the number of reports of unauthorised GMOs (UGMOs) is gradually increasing. There is a lack of specific detection methods for UGMOs, due to the absence of detailed sequence information and reference materials. In this research, an adapted genome walking approach was developed, called ALF: Amplification of Linearly-enriched Fragments. Coupling of ALF to NGS aims for simultaneous detection and identification of all GMOs, including UGMOs, in one sample, in a single analysis. The ALF approach was assessed on a mixture made of DNA extracts from four reference materials, in an uneven distribution, mimicking a real life situation. The complete insert and genomic flanking regions were known for three of the included GMO events, while for MON15985 only partial sequence information was available. Combined with a known organisation of elements, this GMO served as a model for a UGMO. We successfully identified sequences matching with this organisation of elements serving as proof of principle for ALF as new UGMO detection strategy. Additionally, this study provides a first outline of an automated, web-based analysis pipeline for identification of UGMOs containing known GM elements.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Alfred J Arulandhu
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
- Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV, Wageningen, The Netherlands
| | | | - Hongmei Xiao
- College of Food Science and Technology, Nanjing Agricultural University, Jiangsu, 210095, P. R. China
| | - Rico Hagelaar
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Martijn Staats
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | | | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Esther J Kok
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Jeroen P van Dijk
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands.
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Wang Q, Shi N, Shang Y, Liu X, Fu W, Zhao Y, Pan D, Xu W, Lin X. Comprehensive molecular characterization of a transgenic pig expressing hCD46 gene. Gene 2017; 626:376-385. [DOI: 10.1016/j.gene.2017.05.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
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Arulandhu AJ, van Dijk JP, Dobnik D, Holst-Jensen A, Shi J, Zel J, Kok EJ. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs). Anal Bioanal Chem 2016; 408:4575-93. [PMID: 27086015 DOI: 10.1007/s00216-016-9513-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/11/2016] [Accepted: 03/22/2016] [Indexed: 01/04/2023]
Abstract
With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples.
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Affiliation(s)
- Alfred J Arulandhu
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Jeroen P van Dijk
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - David Dobnik
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106, Oslo, Norway
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Center for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Life Sciences Building, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jana Zel
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Esther J Kok
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands.
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