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Ferro-Gallego P, Vila-Sanjurjo A, Valderrama Pereira AK, Porres Pérez G, Domínguez-Gerpe L. Circular PCR as an efficient and precise umbrella of methods for the generation of circular dsDNA with staggered nicks: Mechanism and types. Biol Methods Protoc 2024; 9:bpae051. [PMID: 39139995 PMCID: PMC11319657 DOI: 10.1093/biomethods/bpae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024] Open
Abstract
Here, we introduce the highly versatile circular polymerase chain reaction (CiPCR) technique, propose a mechanism of action, and describe a number of examples demonstrating the versatility of this technique. CiPCR takes place between two fragments of dsDNA with two homologous regions, as long as one of the fragments carries said regions at its 3'- and 5'-ends. Upon hybridization, elongation by a polymerase occurs from all 3'-ends continuously until a 5'-end is reached, leading to stable circular dsDNA with staggered nicks. When both dsDNA fragments carry the homology at their 3'- and 5'-ends (Type I CiPCR), all four 3'-ends effectively prime amplification of the intervening region and CiPCR products can function as template during the reaction. In contrast, when only one of the two dsDNA fragments carries the homologous regions at its 3'- and 5'-ends and the other carries such regions internally (Type II CiPCR), only two 3'-ends can be amplified and CiPCR products possess no template activity. We demonstrate the applicability of both CiPCR types via well-illustrated experimental examples. CiPCR is well adapted to the quick resolution of most of the molecular cloning challenges faced by the biology/biomedicine laboratory, including the generation of insertions, deletions, and mutations.
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Affiliation(s)
- Pedro Ferro-Gallego
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
- Present Address: IBIMA, Instituto de Investigación Biomédica y Plataforma en Nanomedicina, BIONAND, Málaga, 29590, Spain
| | - Antón Vila-Sanjurjo
- Grupo GIBE, Biology Department of the School of Sciences & Interdisciplinary Center for Chemistry and Biology (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Andrea Katherine Valderrama Pereira
- Chemistry Department of the School of Sciences & Interdisciplinary Center for Chemistry and Biology (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Gonzalo Porres Pérez
- Grupo GIBE, Biology Department of the School of Sciences & Interdisciplinary Center for Chemistry and Biology (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Lourdes Domínguez-Gerpe
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
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2
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Chen H, Wei C, Lin Z, Pei J, Pan H, Li H. Protocol to retrieve unknown flanking DNA sequences using semi-site-specific PCR-based genome walking. STAR Protoc 2024; 5:102864. [PMID: 38308839 PMCID: PMC10850853 DOI: 10.1016/j.xpro.2024.102864] [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: 09/01/2023] [Revised: 11/21/2023] [Accepted: 01/18/2024] [Indexed: 02/05/2024] Open
Abstract
Here, we describe a protocol based on semi-site-specific primer PCR (3SP-PCR) to access unknown flanking DNA sequences. We specify the guidelines for designing primers for 3SP-PCR. We also describe experimental procedures for the 3SP-PCR, along with PCR product purification and subsequent sequencing and analysis. For complete details on the use and execution of this protocol, please refer to Wei et al.1.
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Affiliation(s)
- Hong Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China
| | - Cheng Wei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China
| | - Zhiyu Lin
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China; School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, P.R. China
| | - Jinfen Pei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China
| | - Hao Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China; School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, P.R. China
| | - Haixing Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China.
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3
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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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Chen CC, Liao RY, Yeh FY, Lin YR, Wu TY, Pastor AE, Zul DD, Hsu YC, Wu KY, Liu KF, Kannagi R, Chen JY, Cai BH. A Simple and Affordable Method to Create Nonsense Mutation Clones of p53 for Studying the Premature Termination Codon Readthrough Activity of PTC124. Biomedicines 2023; 11:biomedicines11051310. [PMID: 37238980 DOI: 10.3390/biomedicines11051310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
(1) Background: A premature termination codon (PTC) can be induced by a type of point mutation known as a nonsense mutation, which occurs within the coding region. Approximately 3.8% of human cancer patients have nonsense mutations of p53. However, the non-aminoglycoside drug PTC124 has shown potential to promote PTC readthrough and rescue full-length proteins. The COSMIC database contains 201 types of p53 nonsense mutations in cancers. We built a simple and affordable method to create different nonsense mutation clones of p53 for the study of the PTC readthrough activity of PTC124. (2) Methods: A modified inverse PCR-based site-directed mutagenesis method was used to clone the four nonsense mutations of p53, including W91X, S94X, R306X, and R342X. Each clone was transfected into p53 null H1299 cells and then treated with 50 μM of PTC124. (3) Results: PTC124 induced p53 re-expression in H1299-R306X and H1299-R342X clones but not in H1299-W91X and H1299-S94X clones. (4) Conclusions: Our data showed that PTC124 more effectively rescued the C-terminal of p53 nonsense mutations than the N-terminal of p53 nonsense mutations. We introduced a fast and low-cost site-directed mutagenesis method to clone the different nonsense mutations of p53 for drug screening.
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Affiliation(s)
- Chia-Chi Chen
- School of Medicine, I-Shou University, Kaohsiung City 82445, Taiwan
- Department of Physical Therapy, I-Shou University, Kaohsiung City 82445, Taiwan
- School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung City 82445, Taiwan
- Department of Pathology, E-Da Hospital, Kaohsiung City 82445, Taiwan
| | - Ruo-Yu Liao
- Department of Medical Laboratory Science, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Fang-Yu Yeh
- School of Medicine, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Yu-Rou Lin
- School of Medicine, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Tze-You Wu
- Department of Biomedical Engineering, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Alexa Escobar Pastor
- School of Medicine for International Students, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Danny Danilo Zul
- School of Medicine for International Students, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Yun-Chien Hsu
- School of Medicine, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Kuan-Yo Wu
- Department of Biological Science and Technology, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Ke-Fang Liu
- Department of Medical Laboratory Science, I-Shou University, Kaohsiung City 82445, Taiwan
| | - Reiji Kannagi
- Institute of Biomedical Sciences, Academia Sinica, Taipei City 11529, Taiwan
| | - Jang-Yi Chen
- Institute of Biology and Anatomy, National Defense Medical Center, Taipei City 11529, Taiwan
| | - Bi-He Cai
- School of Medicine, I-Shou University, Kaohsiung City 82445, Taiwan
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5
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Evolution of plasmid-construction. Int J Biol Macromol 2022; 209:1319-1326. [PMID: 35452702 DOI: 10.1016/j.ijbiomac.2022.04.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/23/2022]
Abstract
Developing for almost half a century, plasmid-construction has explored more than 37 methods. Some methods have evolved into new versions. From a global and evolutionary viewpoint, a review will make a clear understand and an easy practice for plasmid-construction. The 37 methods employ three principles as creating single-strand overhang, recombining homology arms, or serving amplified insert as mega-primer, and are classified into three groups as single strand overhang cloning, homologous recombination cloning, and mega-primer cloning. The methods evolve along a route for easy, efficient, or/and seamless cloning. Mechanism of plasmid-construction is primer annealing or/and primer invasion. Scar junction is a must-be faced scientific problem in plasmid-construction.
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Hawley KL, Montezuma-Rusca JM, Delgado KN, Singh N, Uversky VN, Caimano MJ, Radolf JD, Luthra A. Structural Modeling of the Treponema pallidum Outer Membrane Protein Repertoire: a Road Map for Deconvolution of Syphilis Pathogenesis and Development of a Syphilis Vaccine. J Bacteriol 2021; 203:e0008221. [PMID: 33972353 PMCID: PMC8407342 DOI: 10.1128/jb.00082-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/27/2021] [Indexed: 01/11/2023] Open
Abstract
Treponema pallidum, an obligate human pathogen, has an outer membrane (OM) whose physical properties, ultrastructure, and composition differ markedly from those of phylogenetically distant Gram-negative bacteria. We developed structural models for the outer membrane protein (OMP) repertoire (OMPeome) of T. pallidum Nichols using solved Gram-negative structures, computational tools, and small-angle X-ray scattering (SAXS) of selected recombinant periplasmic domains. The T. pallidum "OMPeome" harbors two "stand-alone" proteins (BamA and LptD) involved in OM biogenesis and four paralogous families involved in the influx/efflux of small molecules: 8-stranded β-barrels, long-chain-fatty-acid transporters (FadLs), OM factors (OMFs) for efflux pumps, and T. pallidum repeat proteins (Tprs). BamA (TP0326), the central component of a β-barrel assembly machine (BAM)/translocation and assembly module (TAM) hybrid, possesses a highly flexible polypeptide-transport-associated (POTRA) 1-5 arm predicted to interact with TamB (TP0325). TP0515, an LptD ortholog, contains a novel, unstructured C-terminal domain that models inside the β-barrel. T. pallidum has four 8-stranded β-barrels, each containing positively charged extracellular loops that could contribute to pathogenesis. Three of five FadL-like orthologs have a novel α-helical, presumptively periplasmic C-terminal extension. SAXS and structural modeling further supported the bipartite membrane topology and tridomain architecture of full-length members of the Tpr family. T. pallidum's two efflux pumps presumably extrude noxious small molecules via four coexpressed OMFs with variably charged tunnels. For BamA, LptD, and OMFs, we modeled the molecular machines that deliver their substrates into the OM or external milieu. The spirochete's extended families of OM transporters collectively confer a broad capacity for nutrient uptake. The models also furnish a structural road map for vaccine development. IMPORTANCE The unusual outer membrane (OM) of T. pallidum, the syphilis spirochete, is the ultrastructural basis for its well-recognized capacity for invasiveness, immune evasion, and persistence. In recent years, we have made considerable progress in identifying T. pallidum's repertoire of OMPs. Here, we developed three-dimensional (3D) models for the T. pallidum Nichols OMPeome using structural modeling, bioinformatics, and solution scattering. The OM contains three families of OMP transporters, an OMP family involved in the extrusion of noxious molecules, and two "stand-alone" proteins involved in OM biogenesis. This work represents a major advance toward elucidating host-pathogen interactions during syphilis; understanding how T. pallidum, an extreme auxotroph, obtains a wide array of biomolecules from its obligate human host; and developing a vaccine with global efficacy.
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Affiliation(s)
- Kelly L. Hawley
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, Connecticut, USA
| | - Jairo M. Montezuma-Rusca
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases, UConn Health, Farmington, Connecticut, USA
| | | | - Navreeta Singh
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Melissa J. Caimano
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Justin D. Radolf
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Amit Luthra
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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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: 1] [Impact Index Per Article: 0.3] [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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Luthra A, Montezuma-Rusca JM, La Vake CJ, LeDoyt M, Delgado KN, Davenport TC, Fiel-Gan M, Caimano MJ, Radolf JD, Hawley KL. Evidence that immunization with TP0751, a bipartite Treponema pallidum lipoprotein with an intrinsically disordered region and lipocalin fold, fails to protect in the rabbit model of experimental syphilis. PLoS Pathog 2020; 16:e1008871. [PMID: 32936831 PMCID: PMC7521688 DOI: 10.1371/journal.ppat.1008871] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/28/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Deconvolution of syphilis pathogenesis and selection of candidate syphilis vaccinogens requires detailed knowledge of the molecular architecture of the Treponema pallidum outer membrane (OM). The T. pallidum OM contains a low density of integral OM proteins, while the spirochete's many lipoprotein immunogens are periplasmic. TP0751, a lipoprotein with a lipocalin fold, is reportedly a surface-exposed protease/adhesin and protective antigen. The rapid expansion of calycin/lipocalin structures in the RCSB PDB database prompted a comprehensive reassessment of TP0751. Small angle X-ray scattering analysis of full-length protein revealed a bipartite topology consisting of an N-terminal, intrinsically disordered region (IDR) and the previously characterized C-terminal lipocalin domain. A DALI server query using the lipocalin domain yielded 97 hits, 52 belonging to the calycin superfamily, including 15 bacterial lipocalins, but no Gram-negative surface proteins. Surprisingly, Tpp17 (TP0435) was identified as a structural ortholog of TP0751. In silico docking predicted that TP0751 can bind diverse ligands along the rim of its eight-stranded β-barrel; high affinity binding of one predicted ligand, heme, to the lipocalin domain was demonstrated. qRT-PCR and immunoblotting revealed very low expression of TP0751 compared to other T. pallidum lipoproteins. Immunoblot analysis of immune rabbit serum failed to detect TP0751 antibodies, while only one of five patients with secondary syphilis mounted a discernible TP0751-specific antibody response. In opsonophagocytosis assays, neither TP0751 nor Tpp17 antibodies promoted uptake of T. pallidum by rabbit peritoneal macrophages. Rabbits immunized with intact, full-length TP0751 showed no protection against local or disseminated infection following intradermal challenge with T. pallidum. Our data argue that, like other lipoprotein lipocalins in dual-membrane bacteria, TP0751 is periplasmic and binds small molecules, and we propose that its IDR facilitates ligand binding by and offloading from the lipocalin domain. The inability of TP0751 to elicit opsonic or protective antibodies is consistent with a subsurface location.
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Affiliation(s)
- Amit Luthra
- Department of Medicine, UConn Health, Farmington, United States of America
| | - Jairo M. Montezuma-Rusca
- Department of Medicine, UConn Health, Farmington, United States of America
- Division of Infectious Diseases, UConn Health, Farmington, United States of America
- Department of Pediatrics, UConn Health, Farmington, United States of America
| | - Carson J. La Vake
- Department of Pediatrics, UConn Health, Farmington, United States of America
| | - Morgan LeDoyt
- Department of Medicine, UConn Health, Farmington, United States of America
| | | | | | - Mary Fiel-Gan
- Department of Pathology, Hartford Hospital, Hartford, United States of America
| | - Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, United States of America
- Department of Pediatrics, UConn Health, Farmington, United States of America
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, United States of America
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, United States of America
- Department of Pediatrics, UConn Health, Farmington, United States of America
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, United States of America
- Department of Genetics and Genome Sciences, UConn Health, Farmington, United States of America
- Department of Immunology, UConn Health, Farmington, United States of America
| | - Kelly L. Hawley
- Department of Pediatrics, UConn Health, Farmington, United States of America
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, United States of America
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Liang Y, Zhang Y, Liu L. Intra-Molecular Homologous Recombination of Scarless Plasmid. Int J Mol Sci 2020; 21:E1697. [PMID: 32131382 PMCID: PMC7084384 DOI: 10.3390/ijms21051697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/25/2020] [Accepted: 02/28/2020] [Indexed: 01/15/2023] Open
Abstract
Although many methods have been reported, plasmid construction compromises transformant efficiency (number of transformants per ng of DNAs) with plasmid accuracy (rate of scarless plasmids). An efficient method is two-step PCR serving DNA amplification. An accurate method is ExnaseII cloning serving homology recombination (HR). We combine DNA amplification and HR to develop an intra-molecular HR by amplifying plasmid DNAs to contain homology 5'- and 3'-terminus and recombining the plasmid DNAs in vitro. An example was to construct plasmid pET20b-AdD. The generality was checked by constructing plasmid pET21a-AdD and pET22b-AdD in parallel. The DNAs having 30-bp homology arms were optimal for intra-molecular HR, and transformation of which created 14.2 transformants/ng and 90% scarless plasmids, more than the two-step PCR and the ExnaseII cloning. Transformant efficiency correlated with the component of nicked circular plasmid DNAs of HR products, indicating nick modification in vivo leads to scar plasmids.
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Affiliation(s)
- Yaping Liang
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (Y.Z.)
| | - Yu Zhang
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (Y.Z.)
| | - Liangwei Liu
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (Y.Z.)
- The Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Henan Agricultural University, Zhengzhou 450002, China
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10
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Ortega C, Abreu C, Oppezzo P, Correa A. Overview of High-Throughput Cloning Methods for the Post-genomic Era. Methods Mol Biol 2019; 2025:3-32. [PMID: 31267446 DOI: 10.1007/978-1-4939-9624-7_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The advent of new DNA sequencing technologies leads to a dramatic increase in the number of available genome sequences and therefore of target genes with potential for functional analysis. The insertion of these sequences into proper expression vectors requires a simple an efficient cloning method. In addition, when expressing a target protein, quite often it is necessary to evaluate different DNA constructs to achieve a soluble and homogeneous expression of the target with satisfactory yields. The development of new molecular methods made possible the cloning of a huge number of DNA sequences in a high-throughput manner, necessary for meeting the increasing demands for soluble protein expression and characterization. In this chapter several molecular methods suitable for high-throughput cloning are reviewed.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Cecilia Abreu
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Molecular, Cellular and Animal Technology Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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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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Toh YK, Balakrishna AM, Manimekalai MSS, Chionh BB, Seetharaman RRC, Eisenhaber F, Eisenhaber B, Grüber G. Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F. Biochim Biophys Acta Gen Subj 2017; 1861:3201-3214. [DOI: 10.1016/j.bbagen.2017.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
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13
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OEPR Cloning: an Efficient and Seamless Cloning Strategy for Large- and Multi-Fragments. Sci Rep 2017; 7:44648. [PMID: 28300166 PMCID: PMC5353728 DOI: 10.1038/srep44648] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/09/2017] [Indexed: 12/27/2022] Open
Abstract
Here, an efficient cloning strategy for large DNA fragments and for simultaneous assembly of multiple DNA fragments assembly is presented. This strategy is named OEPR (based on Overlap Extension PCR and Recombination in vivo). OEPR cloning is a seamless, restriction- and ligation-independent method. The method takes advantage of both homologous recombination enzymes in E. coli and overlap PCR. Using OEPR cloning, a long fragment (1–6 kb) or multiple fragments (2–4 fragments) can be easily constructed and simultaneously assembled into a target vector.
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14
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Mega primer-mediated molecular cloning strategy for chimaeragenesis and long DNA fragment insertion. Biosci Rep 2017; 37:BSR20160608. [PMID: 28183872 PMCID: PMC5333777 DOI: 10.1042/bsr20160608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 02/05/2017] [Accepted: 02/08/2017] [Indexed: 12/04/2022] Open
Abstract
Molecular cloning methods based on primer and overlap-extension PCR are widely used due to their simplicity, reliability, low cost and high efficiency. In this article, an efficient mega primer-mediated (MP) cloning strategy for chimaeragenesis and long DNA fragment insertion is presented. MP cloning is a seamless, restriction/ligation-independent method that requires only three steps: (i) the first PCR for mega primer generation; (ii) the second PCR for exponential amplification mediated by the mega primers and (iii) DpnI digestion and transformation. Most importantly, for chimaeragenesis, genes can be assembled and constructed into the plasmid vector in a single PCR step. By employing this strategy, we successfully inserted four DNA fragments (approximately 500 bp each) into the same vector simultaneously. In conclusion, the strategy proved to be a simple and efficient tool for seamless cloning.
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15
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Kato A. In vivo cloning of large chromosomal segments into a BAC derivative by generalized transduction and recombineering in Salmonella enterica. J GEN APPL MICROBIOL 2016; 62:225-232. [PMID: 27666751 DOI: 10.2323/jgam.2016.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recombineering has been used to facilitate the development of in vivo cloning methods. However, the method relies heavily on PCR, which still generates a much higher error rate than DNA replication in vivo, even when amplifying large DNA inserts. Here, a precise technique is reported in Salmonella enterica that enables the cloning of up to at least 19 kb target chromosomal DNA segments that had been marked by FRTs, which were derived from two consecutive lambda Red-mediated recombination events. P22 phage was utilized to transduce the target DNA segments from donor strains to recipient strains harboring a derivative of bacterial artificial chromosome (BAC) containing a FRT and a plasmid expressing Flp recombinase. This method was successful in cloning a gene cluster responsible for lipopolysaccharide (LPS) modifications that confer polymyxin B resistance and in complementing its mutant. Further optimized procedures should be widely applicable because large insert fragments are precise clones of the wild-type genome.
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Affiliation(s)
- Akinori Kato
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University
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16
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García-Nafría J, Watson JF, Greger IH. IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly. Sci Rep 2016; 6:27459. [PMID: 27264908 PMCID: PMC4893743 DOI: 10.1038/srep27459] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022] Open
Abstract
In vivo homologous recombination holds the potential for optimal molecular cloning, however, current strategies require specialised bacterial strains or laborious protocols. Here, we exploit a recA-independent recombination pathway, present in widespread laboratory E.coli strains, to develop IVA (In Vivo Assembly) cloning. This system eliminates the need for enzymatic assembly and reduces all molecular cloning procedures to a single-tube, single-step PCR, performed in <2 hours from setup to transformation. Unlike other methods, IVA is a complete system, and offers significant advantages over alternative methods for all cloning procedures (insertions, deletions, site-directed mutagenesis and sub-cloning). Significantly, IVA allows unprecedented simplification of complex cloning procedures: five simultaneous modifications of any kind, multi-fragment assembly and library construction are performed in approximately half the time of current protocols, still in a single-step fashion. This system is efficient, seamless and sequence-independent, and requires no special kits, enzymes or proprietary bacteria, which will allow its immediate adoption by the academic and industrial molecular biology community.
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Affiliation(s)
- Javier García-Nafría
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Jake F. Watson
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ingo H. Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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17
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Jajesniak P, Wong TS. QuickStep-Cloning: a sequence-independent, ligation-free method for rapid construction of recombinant plasmids. J Biol Eng 2015; 9:15. [PMID: 26388935 PMCID: PMC4574722 DOI: 10.1186/s13036-015-0010-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 07/21/2015] [Indexed: 11/16/2022] Open
Abstract
Background Molecular cloning is an essential step in biological engineering. Methods involving megaprimer-based PCR of a whole plasmid are promising alternatives to the traditional restriction-ligation-based molecular cloning. Their widespread use, however, is hampered by some of their inherent characteristics, e.g., linear amplification, use of self-annealing megaprimers and difficulty with performing point insertion of DNA. These limitations result in low product yield and reduced flexibility in the design of a genetic construct. Result Here, we present a novel technique of directional cloning, which overcomes these problems yet retaining the simplicity of whole-plasmid amplification. QuickStep-Cloning utilizes asymmetric PCRs to create a megaprimer pair with 3′-overhangs, and hence, facilitates the subsequent exponential whole-plasmid amplification. QuickStep-Cloning generates nicked-circular plasmids, thereby permitting direct bacterial transformation without DNA ligation. It allows DNA fragment integration into any plasmid at any position, in an efficient, time- and cost-effective manner, without tedious intermediate DNA gel purification, modified oligonucleotides, specialty enzymes and ultra-competent cells. The method is compatible with competent E. coli cells prepared using the conventional calcium chloride method. Conclusion QuickStep-Cloning expands the versatility of megaprimer-based cloning. It is an excellent addition to the cloning toolbox, for the benefit of protein engineers, metabolic engineers and synthetic biologists. Electronic supplementary material The online version of this article (doi:10.1186/s13036-015-0010-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pawel Jajesniak
- ChELSI Institute and Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Tuck Seng Wong
- ChELSI Institute and Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
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18
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Gandasi NR, Vestö K, Helou M, Yin P, Saras J, Barg S. Survey of Red Fluorescence Proteins as Markers for Secretory Granule Exocytosis. PLoS One 2015; 10:e0127801. [PMID: 26091288 PMCID: PMC4474633 DOI: 10.1371/journal.pone.0127801] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/18/2015] [Indexed: 12/18/2022] Open
Abstract
Fluorescent proteins (FPs) have proven to be valuable tools for high-resolution imaging studies of vesicle transport processes, including exo- and endocytosis. Since the pH of the vesicle lumen changes between acidic and neutral during these events, pH-sensitive FPs with near neutral pKa, such as pHluorin, are particularly useful. FPs with pKa>6 are readily available in the green spectrum, while red-emitting pH-sensitive FPs are rare and often not well characterized as reporters of exo- or endocytosis. Here we tested a panel of ten orange/red and two green FPs in fusions with neuropeptide Y (NPY) for use as secreted vesicle marker and reporter of dense core granule exocytosis and release. We report relative brightness, bleaching rate, targeting accuracy, sensitivity to vesicle pH, and their performance in detecting exocytosis in live cells. Tandem dimer (td)-mOrange2 was identified as well-targeted, bright, slowly bleaching and pH-sensitive FP that performed similar to EGFP. Single exocytosis events were readily observed, which allowed measurements of fusion pore lifetime and the dynamics of the exocytosis protein syntaxin at the release site during membrane fusion and cargo release.
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Affiliation(s)
- Nikhil R. Gandasi
- Institute of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden
| | - Kim Vestö
- Institute of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden
| | - Maria Helou
- Institute of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden
| | - Peng Yin
- Institute of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden
| | - Jan Saras
- Institute of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden
| | - Sebastian Barg
- Institute of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden
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Generating in vivo cloning vectors for parallel cloning of large gene clusters by homologous recombination. PLoS One 2013; 8:e79979. [PMID: 24244585 PMCID: PMC3823602 DOI: 10.1371/journal.pone.0079979] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 10/07/2013] [Indexed: 11/30/2022] Open
Abstract
A robust method for the in vivo cloning of large gene clusters was developed based on homologous recombination (HR), requiring only the transformation of PCR products into Escherichia coli cells harboring a receiver plasmid. Positive clones were selected by an acquired antibiotic resistance, which was activated by the recruitment of a short ribosome-binding site plus start codon sequence from the PCR products to the upstream position of a silent antibiotic resistance gene in receiver plasmids. This selection was highly stringent and thus the cloning efficiency of the GFPuv gene (size: 0.7 kb) was comparable to that of the conventional restriction-ligation method, reaching up to 4.3 × 104 positive clones per μg of DNA. When we attempted parallel cloning of GFPuv fusion genes (size: 2.0 kb) and carotenoid biosynthesis pathway clusters (sizes: 4 kb, 6 kb, and 10 kb), the cloning efficiency was similarly high regardless of the DNA size, demonstrating that this would be useful for the cloning of large DNA sequences carrying multiple open reading frames. However, restriction analyses of the obtained plasmids showed that the selected cells may contain significant amounts of receiver plasmids without the inserts. To minimize the amount of empty plasmid in the positive selections, the sacB gene encoding a levansucrase was introduced as a counter selection marker in receiver plasmid as it converts sucrose to a toxic levan in the E. coli cells. Consequently, this method yielded completely homogeneous plasmids containing the inserts via the direct transformation of PCR products into E. coli cells.
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Baumann T, Arndt KM, Müller KM. Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V. BMC Biotechnol 2013; 13:81. [PMID: 24090222 PMCID: PMC3856533 DOI: 10.1186/1472-6750-13-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/25/2013] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. RESULTS A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. CONCLUSIONS The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.
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Affiliation(s)
- Tobias Baumann
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Room UHG E2-143 Universitätsstr, 25, Bielefeld 33615, Germany.
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Schoberle TJ, Nguyen-Coleman CK, May GS. Plasmids for increased efficiency of vector construction and genetic engineering in filamentous fungi. Fungal Genet Biol 2013; 58-59:1-9. [PMID: 23867711 PMCID: PMC3817716 DOI: 10.1016/j.fgb.2013.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/01/2013] [Accepted: 07/03/2013] [Indexed: 01/15/2023]
Abstract
Fungal species are continuously being studied to not only understand disease in humans and plants but also to identify novel antibiotics and other metabolites of industrial importance. Genetic manipulations, such as gene deletion, gene complementation, and gene over-expression, are common techniques to investigate fungal gene functions. Although advances in transformation efficiency and promoter usage have improved genetic studies, some basic steps in vector construction are still laborious and time-consuming. Gateway cloning technology solves this problem by increasing the efficiency of vector construction through the use of λ phage integrase proteins and att recombination sites. We developed a series of Gateway-compatible vectors for use in genetic studies in a range of fungal species. They contain nutritional and drug-resistance markers and can be utilized to manipulate different filamentous fungal genomes.
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Affiliation(s)
- Taylor J. Schoberle
- The University of Texas Graduate School of Biomedical
Sciences at Houston; The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
| | - C. Kim Nguyen-Coleman
- Microbiology and Molecular Genetics, Division of Pathology
and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
| | - Gregory S. May
- Program in Genes and Development, Division of Pathology and
Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
- Microbiology and Molecular Genetics, Division of Pathology
and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
- The University of Texas Graduate School of Biomedical
Sciences at Houston; The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
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22
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Müller J, Schildknecht P, Müller N. Metabolism of nitro drugs metronidazole and nitazoxanide in Giardia lamblia: characterization of a novel nitroreductase (GlNR2). J Antimicrob Chemother 2013; 68:1781-9. [PMID: 23580565 DOI: 10.1093/jac/dkt106] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The protozoan parasite Giardia lamblia causes giardiasis, a persistent diarrhoea. Nitro drugs such as the nitroimidazole metronidazole and the nitrothiazolide nitazoxanide are used for the treatment of giardiasis. Nitroreductases may play a role in activating these drugs. G. lamblia contains two nitroreductases, GlNR1 and GlNR2. The aim of this work was to elucidate the role of GlNR2. METHODS Expression of GlNR2 was analysed by reverse transcription PCR. Recombinant GlNR2 was overexpressed in G. lamblia and drug susceptibility was analysed. Recombinant GlNR2 was subjected to functional assays. Escherichia coli expressing full-length or truncated GlNR1 and GlNR2 were grown in the presence of nitro compounds. Using E. coli reporter strains for nitric oxide and DNA damage responses, we analysed whether GlNR1 and GlNR2 elicited the respective responses in the presence, or absence, of the drugs. RESULTS G. lamblia trophozoites overexpressing GlNR2 were less susceptible to both nitro drugs as compared with control trophozoites. GlNR2 was a functional nitroreductase when expressed in E. coli. E. coli expressing GlNR1 was more susceptible to metronidazole under aerobic and semi-aerobic and to nitazoxanide under semi-aerobic growth conditions. E. coli expressing GlNR2 was not susceptible to either drug. In reporter strains, GlNR1, but not GlNR2, elicited nitric oxide and DNA repair responses, even in the absence of nitro drugs. CONCLUSIONS These findings suggest that GlNR2 is an active nitroreductase with a mode of action different from that of GlNR1. Thus, susceptibility to nitro drugs may depend not only on activation, but also on inactivation of the drugs by specific nitroreductases.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland
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Abstract
Yeast-based in vivo cloning is useful for cloning DNA fragments into plasmid vectors and is based on the ability of yeast to recombine the DNA fragments by homologous recombination. Although this method is efficient, it produces some by-products. We have developed an “ultra-low background DNA cloning system” on the basis of yeast-based in vivo cloning, by almost completely eliminating the generation of by-products and applying the method to commonly used Escherichia coli vectors, particularly those lacking yeast replication origins and carrying an ampicillin resistance gene (Ampr). First, we constructed a conversion cassette containing the DNA sequences in the following order: an Ampr 5′ UTR (untranslated region) and coding region, an autonomous replication sequence and a centromere sequence from yeast, a TRP1 yeast selectable marker, and an Ampr 3′ UTR. This cassette allowed conversion of the Ampr-containing vector into the yeast/E. coli shuttle vector through use of the Ampr sequence by homologous recombination. Furthermore, simultaneous transformation of the desired DNA fragment into yeast allowed cloning of this DNA fragment into the same vector. We rescued the plasmid vectors from all yeast transformants, and by-products containing the E. coli replication origin disappeared. Next, the rescued vectors were transformed into E. coli and the by-products containing the yeast replication origin disappeared. Thus, our method used yeast- and E. coli-specific “origins of replication” to eliminate the generation of by-products. Finally, we successfully cloned the DNA fragment into the vector with almost 100% efficiency.
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Affiliation(s)
- Kenta Goto
- Analytical Research Center for Experimental Sciences, Saga University, Honjo, Saga, Japan.
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