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Guo L, Yang G. Pioneering DNA assembling techniques and their applications in eukaryotic microalgae. Biotechnol Adv 2024; 70:108301. [PMID: 38101551 DOI: 10.1016/j.biotechadv.2023.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/12/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.
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Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China; Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; MoE Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao 266003, China.
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2
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Jailani AAK, Chattopadhyay A, Kumar P, Singh OW, Mukherjee SK, Roy A, Sanan-Mishra N, Mandal B. Accelerated Long-Fragment Circular PCR for Genetic Manipulation of Plant Viruses in Unveiling Functional Genomics. Viruses 2023; 15:2332. [PMID: 38140572 PMCID: PMC10747169 DOI: 10.3390/v15122332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular cloning, a crucial prerequisite for engineering plasmid constructs intended for functional genomic studies, relies on successful restriction and ligation processes. However, the lack of unique restriction sites often hinders construct preparation, necessitating multiple modifications. Moreover, achieving the successful ligation of large plasmid constructs is frequently challenging. To address these limitations, we present a novel PCR strategy in this study, termed 'long-fragment circular-efficient PCR' (LC-PCR). This technique involves one or two rounds of PCR with an additional third-long primer that complements both ends of the newly synthesized strand of a plasmid construct. This results in self-circularization with a nick-gap in each newly formed strand. The LC-PCR technique was successfully employed to insert a partial sequence (210 nucleotides) of the phytoene desaturase gene from Nicotiana benthamiana and a full capsid protein gene (770 nucleotides) of a begomovirus (tomato leaf curl New Delhi virus) into a 16.4 kb infectious construct of a tobamovirus, cucumber green mottle mosaic virus (CGMMV), cloned in pCambia. This was done to develop the virus-induced gene silencing vector (VIGS) and an expression vector for a foreign protein in plants, respectively. Furthermore, the LC-PCR could be applied for the deletion of a large region (replicase enzyme) and the substitution of a single amino acid in the CGMMV genome. Various in planta assays of these constructs validate their biological functionality, highlighting the utility of the LC-PCR technique in deciphering plant-virus functional genomics. The LC-PCR is not only suitable for modifying plant viral genomes but also applicable to a wide range of plant, animal, and human gene engineering under in-vitro conditions. Additionally, the LC-PCR technique provides an alternative to expensive kits, enabling quick introduction of modifications in any part of the nucleotide within a couple of days. Thus, the LC-PCR proves to be a suitable 'all in one' technique for modifying large plasmid constructs through site-directed gene insertion, deletion, and mutation, eliminating the need for restriction and ligation.
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Affiliation(s)
- A. Abdul Kader Jailani
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Plant Pathology Department, University of Florida, North Florida Research and Education Centre, Quincy, FL 32351, USA
| | - Anirudha Chattopadhyay
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
- Pulses Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar 385506, India
| | - Pradeep Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Oinam Washington Singh
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Sunil Kumar Mukherjee
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Anirban Roy
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
| | - Neeti Sanan-Mishra
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.C.); (P.K.); (O.W.S.); (S.K.M.); (A.R.)
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3
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Liu C, Song Y, Hu T, Wang S, Yi K, Wang J, Yan Q, Wei L, Zhang Z, Li H, Luo Y, Wu L, Zhang D, Meng E. Adenylate Kinase Fused to Spidroin as a Catalyst for Decreasing Leakage out of 3D-Bioprinted Hydrogels and for ATP Regeneration. Biomacromolecules 2023; 24:1662-1674. [PMID: 36913719 DOI: 10.1021/acs.biomac.2c01445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Numerous metabolic reactions and pathways use adenosine 5'-triphosphate (ATP) as an energy source and as a phosphorous or pyrophosphorous donor. Based on three-dimensional (3D)-printing, enzyme immobilization can be used to improve ATP regeneration and operability and reduce cost. However, due to the relatively large mesh size of 3D-bioprinted hydrogels soaked in a reaction solution, the lower-molecular-weight enzymes cannot avoid leaking out of the hydrogels readily. Here, a chimeric adenylate-kinase-spidroin (ADK-RC) is created, with ADK serving as the N-terminal domain. The chimera is capable of self-assembling to form micellar nanoparticles at a higher molecular scale. Although fused to spidroin (RC), ADK-RC remains relatively consistent and exhibits high activity, thermostability, pH stability, and organic solvent tolerance. Considering different surface-to-volume ratios, three shapes of enzyme hydrogels are designed, 3D bioprinted, and measured. In addition, a continuous enzymatic reaction demonstrates that ADK-RC hydrogels have higher specific activity and substrate affinity but a lower reaction rate and catalytic power compared to free enzymes in solution. With ATP regeneration, the ADK and ADK-RC hydrogels significantly increase the production of d-glucose-6-phosphate and obtain an efficient usage frequency. In conclusion, enzymes fused to spidroin might be an efficient strategy for maintaining activity and reducing leakage in 3D-bioprinted hydrogels under mild conditions.
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Affiliation(s)
- Changjun Liu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Yanmin Song
- Department of Emergency Medicine, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Tianhao Hu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Shan Wang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Ke Yi
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Jianjie Wang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Qing Yan
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Li'an Wei
- Changsha Sanjiang Smart Technology Co., Ltd., Changsha 410026, Hunan, P. R. China
| | - Zheyang Zhang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Huimin Li
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Yutao Luo
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Lei Wu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Dongyi Zhang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Er Meng
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China.,Key Laboratory of Genetic Improvement and Multiple Utilization of Economic Crops in Hunan Province, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China.,Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
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Liu C, Yan Q, Yi K, Hu T, Wang J, Zhang Z, Li H, Luo Y, Zhang D, Meng E. A secretory system for extracellular production of spider neurotoxin huwentoxin-I in Escherichia coli. Prep Biochem Biotechnol 2022; 53:914-922. [PMID: 36573266 DOI: 10.1080/10826068.2022.2158473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Due to their advantages in structural stability and versatility, cysteine-rich peptides, which are secreted from the venom glands of venomous animals, constitute a naturally occurring pharmaceutical arsenal. However, the correct folding of disulfide bonds is a challenging task in the prokaryotic expression system like Escherichia coli due to the reducing environment. Here, a secretory expression plasmid pSE-G1M5-SUMO-HWTX-I for the spider neurotoxin huwentoxin-I (HWTX-I) with three disulfides as a model of cysteine-rich peptides was constructed. By utilizing the signal peptide G1M5, the fusion protein 6 × His-SUMO-HWTX-I was successfully secreted into extracellular medium of BL21(DE3). After enrichment using cation-exchange chromatography and purification utilizing the Ni-NTA column, 6 × His-SUMO-HWTX-I was digested via Ulp1 kinase to release recombinant HWTX-I (rHWTX-I), which was further purified utilizing RP-HPLC. Finally, both impurities with low and high molecular weights were completely removed. The molecular mass of rHWTX-I was identified as being 3750.8 Da, which was identical to natural HWTX-I with three disulfide bridges. Furthermore, by utilizing whole-cell patch clamp, the sodium currents of hNav1.7 could be inhibited by rHWTX-I and the IC50 value was 419 nmol/L.
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Affiliation(s)
- Changjun Liu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Genetic Improvement and Multiple Utilization of Economic Crops in Hunan Province, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-polluted Soils, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Qing Yan
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Ke Yi
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Tianhao Hu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Jianjie Wang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Zheyang Zhang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Huimin Li
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Yutao Luo
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Dongyi Zhang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Er Meng
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Genetic Improvement and Multiple Utilization of Economic Crops in Hunan Province, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-polluted Soils, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
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Wang W, Zheng G, Lu Y. Recent Advances in Strategies for the Cloning of Natural Product Biosynthetic Gene Clusters. Front Bioeng Biotechnol 2021; 9:692797. [PMID: 34327194 PMCID: PMC8314000 DOI: 10.3389/fbioe.2021.692797] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial natural products (NPs) are a major source of pharmacological agents. Most NPs are synthesized from specific biosynthetic gene clusters (BGCs). With the rapid increase of sequenced microbial genomes, large numbers of NP BGCs have been discovered, regarded as a treasure trove of novel bioactive compounds. However, many NP BGCs are silent in native hosts under laboratory conditions. In order to explore their therapeutic potential, a main route is to activate these silent NP BGCs in heterologous hosts. To this end, the first step is to accurately and efficiently capture these BGCs. In the past decades, a large number of effective technologies for cloning NP BGCs have been established, which has greatly promoted drug discovery research. Herein, we describe recent advances in strategies for BGC cloning, with a focus on the preparation of high-molecular-weight DNA fragment, selection and optimization of vectors used for carrying large-size DNA, and methods for assembling targeted DNA fragment and appropriate vector. The future direction into novel, universal, and high-efficiency methods for cloning NP BGCs is also prospected.
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Affiliation(s)
- Wenfang Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guosong Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, China.,Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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6
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Bao SH, Jiang H, Zhu LY, Yao G, Han PG, Wan XK, Wang K, Song TY, Liu CJ, Wang S, Zhang ZY, Zhang DY, Meng E. A dynamic and multilocus metabolic regulation strategy using quorum-sensing-controlled bacterial small RNA. Cell Rep 2021; 36:109413. [PMID: 34289355 DOI: 10.1016/j.celrep.2021.109413] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 03/30/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Metabolic regulation strategies have been developed to redirect metabolic fluxes to production pathways. However, it is difficult to screen out target genes that, when repressed, improve yield without affecting cell growth. Here, we report a strategy using a quorum-sensing system to control small RNA transcription, allowing cell-density-dependent repression of target genes. This strategy is shown with convenient operation, dynamic repression, and availability for simultaneous regulation of multiple genes. The parameters Ai, Am, and RA (3-oxohexanoyl-homoserine lactone [AHL] concentrations at which half of the maximum repression and the maximum repression were reached and value of the maximum repression when AHL was added manually, respectively) are defined and introduced to characterize repression curves, and the variant LuxRI58N is identified as the most suitable tuning factor for shake flask culture. Moreover, it is shown that dynamic overexpression of the Hfq chaperone is the key to combinatorial repression without disruptions on cell growth. To show a broad applicability, the production titers of pinene, pentalenene, and psilocybin are improved by 365.3%, 79.5%, and 302.9%, respectively, by applying combinatorial dynamic repression.
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Affiliation(s)
- Shao-Heng Bao
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Ling-Yun Zhu
- College of Arts and Sciences, National University of Defense Technology, Changsha, PRC
| | - Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Peng-Gang Han
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Xiu-Kun Wan
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Kang Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Tian-Yu Song
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Chang-Jun Liu
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC
| | - Shan Wang
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC
| | - Zhe-Yang Zhang
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC
| | - Dong-Yi Zhang
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC; College of Arts and Sciences, National University of Defense Technology, Changsha, PRC.
| | - Er Meng
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC.
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Alternative Seamless Cloning Strategies in Fusing Gene Fragments Based on Overlap-PCR. Mol Biotechnol 2021; 63:221-231. [PMID: 33439452 DOI: 10.1007/s12033-020-00298-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Gene fragment swapping and site-directed mutagenesis are commonly required in dissecting functions of gene domains. While there are many approaches for seamless fusion of different gene fragments, new methods are yet to be developed to offer higher efficiency, better simplicity, and more affordability. In this study, we showed that in most cases overlap-PCR was highly effective in creating site-directed mutagenesis, gene fragment deletion, and substitutions using RUS1 and RUS2 as example. While for cases where the overlap-PCR approach is not feasible due to complex secondary structure of gene fragments, a unique restriction site can be generated at the overlapped region of the primers through synonymous mutations. Then different gene fragments can be seamlessly fused through traditional restriction digestion and subsequent ligation. In conclusion, while the classical overlap-PCR is not feasible, the modified overlap-PCR approaches can provide effective and alternative ways to seamlessly fuse different gene fragments.
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8
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Tao CC, Yang Y, Li F, Qiao L, Wu Y, Sun XD, Zhang YY, Li CL. Cloning short DNA into plasmids by one-step PCR. Thorac Cancer 2020; 11:3409-3415. [PMID: 33015950 PMCID: PMC7605993 DOI: 10.1111/1759-7714.13660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022] Open
Abstract
Background Plasmid construction of small fragments of interest (such as insertion of small fragment marker genes, expression of shRNA, siRNA, etc) is the basis of many biomolecular experiments. Here, we describe a method to clone short DNA into vectors by polymerase chain reaction (PCR), named one‐step PCR cloning. Our method uses PCR to amplify the entire circular plasmid. The PCR was performed by the primers containing the gene of short DNA with overlapping sequences between 10–15 bp. The PCR products were then transformed into E. coli and cyclized by homologous recombination in vivo. Methods The pEGFP‐N1‐HA plasmid was constructed by one‐step PCR and transformation. Cells were transfected with pEGFP‐N1‐HA and pEGFP‐N1 plasmid using TurboFect transfection reagent. Protein expression was detected by western blotting and the HA‐GFP fusion protein was detected by confocal microscopy. Results The pEGFP‐N1‐HA plasmid was successfully constructed and HA expression in cells. Conclusions Free from the limitations of restriction enzyme sites and omitting the ligation process, our method offers a flexible and economical option of plasmid construction. Key points
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Affiliation(s)
- Cheng-Cheng Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ying Yang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Fang Li
- Department of Medical Oncology, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ling Qiao
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yue Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiao-Dong Sun
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,School of Biological Sciences and Technology, Chengdu Medical College, Chengdu, China
| | - Chang-Long Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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Guarino F, Zinghirino F, Mela L, Pappalardo XG, Ichas F, De Pinto V, Messina A. NRF-1 and HIF-1α contribute to modulation of human VDAC1 gene promoter during starvation and hypoxia in HeLa cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148289. [PMID: 32810507 DOI: 10.1016/j.bbabio.2020.148289] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
VDAC (Voltage Dependent Anion Channel) is a family of pore forming protein located in the outer mitochondrial membrane. Its channel property ensures metabolites exchange between mitochondria and the rest of the cell resulting in metabolism and bioenergetics regulation, and in cell death and life switch. VDAC1 is the best characterized and most abundant isoform, and is involved in many pathologies, as cancer or neurodegenerative diseases. However, little information is available about its gene expression regulation in normal and/or pathological conditions. In this work, we explored VDAC1 gene expression regulation in normal conditions and in the contest of some metabolic and energetic mitochondrial dysfunction and cell stress as example. The core of the putative promoter region was characterized in terms of transcription factors responsive elements both by bioinformatic studies and promoter activity experiments. In particular, we found an abundant presence of NRF-1 sites, together with other transcription factors binding sites involved in cell growth, proliferation, development, and we studied their prevalence in gene activity. Furthermore, upon depletion of nutrients or controlled hypoxia, as detected in various pathologies, we found that VDAC1 transcripts levels were significantly increased in a time related manner. VDAC1 promoter activity was also validated by gene reporter assays. According to PCR real-time experiments, it was confirmed that VDAC1 promoter activity is further stimulated when cells are exposed to stress. A bioinformatic survey suggested HIF-1α, besides NRF-1, as a most active TFBS. Their validation was obtained by TFBS mutagenesis and TF overexpression experiments. In conclusion, we experimentally demonstrated the involvement of both NRF-1 and HIF-1α in the regulation of VDAC1 promoter activation at basal level and in some peculiar cell stress conditions.
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Affiliation(s)
- Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy.
| | - Federica Zinghirino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Lia Mela
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - François Ichas
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, Bordeaux, France; INSERM, Laboratoire de Neurosciences Expérimentales et Cliniques, U-1084, Université de Poitiers, Poitiers, France
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy; National Institute for Biostructures and Biosystems, Section of Catania, Rome, Italy.
| | - Angela Messina
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; National Institute for Biostructures and Biosystems, Section of Catania, Rome, Italy
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10
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Quorum-sensing based small RNA regulation for dynamic and tuneable gene expression. Biotechnol Lett 2019; 41:1147-1154. [DOI: 10.1007/s10529-019-02719-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/05/2019] [Indexed: 01/18/2023]
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11
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Li WY, Liu CJ, Wu L, Wu JF, Yin XN, Deng KH, Zhang DY, Meng E. MCT cloning: a seamless cloning strategy for inserting DNA fragments. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1507756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Wen-Ying Li
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Chang-Jun Liu
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Lei Wu
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Jin-Feng Wu
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Xi-Nong Yin
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Kai-Hang Deng
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Dong-Yi Zhang
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Er Meng
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
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Royle KE, Polizzi K. A streamlined cloning workflow minimising the time-to-strain pipeline for Pichia pastoris. Sci Rep 2017; 7:15817. [PMID: 29150665 PMCID: PMC5693959 DOI: 10.1038/s41598-017-16172-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
Although recent advances in E. coli self-assembly have greatly simplified cloning, these have not yet been harnessed for the high-throughput generation of expression strains in the early research and discovery phases of biopharmaceutical production. Here, we have refined the technique and incorporated it into a streamlined workflow for the generation of Pichia pastoris expression strains, reducing the timeline by a third and removing the reliance on DNA editing enzymes, which often require troubleshooting and increase costs. We have validated the workflow by cloning 24 human proteins of biopharmaceutical value, either as direct therapeutics or as research targets, which span a continuous range in size and GC content. This includes demonstrating the applicability of the workflow to three-part assemblies for a monoclonal antibody and its single-chain antibody fragments derivatives. This workflow should enable future research into recombinant protein production by P. pastoris and a synthetic biology approach to this industrial host.
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Affiliation(s)
- Kate E Royle
- Department of Life Sciences, Imperial College London, London, UK.,Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
| | - Karen Polizzi
- Department of Life Sciences, Imperial College London, London, UK. .,Centre for Synthetic Biology and Innovation, Imperial College London, London, UK.
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Zeng F, Zang J, Zhang S, Hao Z, Dong J, Lin Y. AFEAP cloning: a precise and efficient method for large DNA sequence assembly. BMC Biotechnol 2017; 17:81. [PMID: 29137618 PMCID: PMC5686892 DOI: 10.1186/s12896-017-0394-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Background Recent development of DNA assembly technologies has spurred myriad advances in synthetic biology, but new tools are always required for complicated scenarios. Here, we have developed an alternative DNA assembly method named AFEAP cloning (Assembly of Fragment Ends After PCR), which allows scarless, modular, and reliable construction of biological pathways and circuits from basic genetic parts. Methods The AFEAP method requires two-round of PCRs followed by ligation of the sticky ends of DNA fragments. The first PCR yields linear DNA fragments and is followed by a second asymmetric (one primer) PCR and subsequent annealing that inserts overlapping overhangs at both sides of each DNA fragment. The overlapping overhangs of the neighboring DNA fragments annealed and the nick was sealed by T4 DNA ligase, followed by bacterial transformation to yield the desired plasmids. Results We characterized the capability and limitations of new developed AFEAP cloning and demonstrated its application to assemble DNA with varying scenarios. Under the optimized conditions, AFEAP cloning allows assembly of an 8 kb plasmid from 1-13 fragments with high accuracy (between 80 and 100%), and 8.0, 11.6, 19.6, 28, and 35.6 kb plasmids from five fragments at 91.67, 91.67, 88.33, 86.33, and 81.67% fidelity, respectively. AFEAP cloning also is capable to construct bacterial artificial chromosome (BAC, 200 kb) with a fidelity of 46.7%. Conclusions AFEAP cloning provides a powerful, efficient, seamless, and sequence-independent DNA assembly tool for multiple fragments up to 13 and large DNA up to 200 kb that expands synthetic biologist’s toolbox. Electronic supplementary material The online version of this article (doi: 10.1186/s12896-017-0394-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Jinping Zang
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Suhua Zhang
- Institute of Biophysics, Hebei University of Technology, Tianjin, 300401, People's Republic of China
| | - Zhimin Hao
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Jingao Dong
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China.
| | - Yibin Lin
- McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, 77030, USA.
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