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Li H, Chenglin G, Yae Z, Wanyu Z, Rong C. Identification and genetic characterisatin of cathepsin L in Demodex. Exp Appl Acarol 2023; 89:329-344. [PMID: 37058174 DOI: 10.1007/s10493-023-00789-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/23/2023] [Indexed: 05/09/2023]
Abstract
Owing to difficulties in obtaining functional gene sequences, molecular pathogenic mechanisms in Demodex have been understudied. In this study, overlap extension PCR was used to obtain the sequences of cathepsin L (CatL), a pathogenicity-related gene, to provide a foundation for subsequent functional research. Demodex folliculorum and Demodex brevis mites were obtained from the face skin of Chinese individuals, and Demodex canis mites were isolated from the skin lesions of a dog. RNA was extracted and used to synthesise double-stranded cDNA. PCR amplification, cloning, sequencing, and bioinformatics analysis of CatL were performed. CatL gene sequences of 1005, 1008, and 1008 bp were successfully amplified for D. brevis, D. folliculorum, and D. canis, respectively. These sequences showed 99.9 or 100% identity with templates previously obtained by RNA-seq. The Maximum Likelihood (ML) phylogenetic tree showed that D. folliculorum clustered with D. canis first, then with D. brevis, and finally with other Acariformes mite species. The three Demodex species had nine similar motifs to those of Sarcoptes scabies, Dermatophagoides pteronyssinus, and Dermatophagoides farinae, and motifs 10-13 were valuable for identification. CatL proteins of Demodex species were predicted to be approximately 38 kDa, be located in lysosomes, have a signal peptide but no transmembrane region, and have two functional domains, I29 and Pept_C1. However, interspecific differences were observed in secondary and tertiary protein structures. In conclusion, we successfully obtained CatL sequences of three Demodex species by overlap extension PCR, which creates conditions for further pathogenic mechanism studies.
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Affiliation(s)
- Hu Li
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Guan Chenglin
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Zhao Yae
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China.
| | - Zhang Wanyu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Chai Rong
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
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Hu Y, Xu F, Huang B, Chen X, Lin S. A Python script to design primers for overlap extension PCR to ligate two DNA fragments. PeerJ 2022; 10:e14283. [PMID: 36340189 PMCID: PMC9632469 DOI: 10.7717/peerj.14283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022] Open
Abstract
Ligating two or more DNA fragments is a regular operation for the subcloning and the engineering of vectors. The overlap extension PCR serves as a straightforward method to solve this issue. However, it takes a relatively long time to design the appropriate overlapping primers and the primers for the full-length sequence, and there has not been a professional offline software for such kind of primer design. Here, we propose a Python script to search, calculate and sort thousands of combinations of primers for users according to the predefined parameters. The results of script running and experimental validation show that this script is capable of generating the optimal pairs of primers based on the proper melting temperatures and lengths of the primers, which facilitates gene modification in research.
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Affiliation(s)
- Yunzhuo Hu
- Fujian Agriculture and Forestry University, Key Laboratory of Crop Biotechnology, Fuzhou, Fujian, China,Fujian Agriculture and Forestry University, College of Agronomy, Fuzhou, Fujian, China
| | - Fei Xu
- Fujian Agriculture and Forestry University, College of Life Science, Fuzhou, Fujian, China
| | - Bifang Huang
- Fujian Agriculture and Forestry University, College of Life Science, Fuzhou, Fujian, China
| | - Xuanyang Chen
- Fujian Agriculture and Forestry University, Key Laboratory of Crop Biotechnology, Fuzhou, Fujian, China,Fujian Agriculture and Forestry University, College of Agronomy, Fuzhou, Fujian, China
| | - Shiqiang Lin
- Fujian Agriculture and Forestry University, Key Laboratory of Crop Biotechnology, Fuzhou, Fujian, China,Fujian Agriculture and Forestry University, College of Life Science, Fuzhou, Fujian, China
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Mu M, Zhao H, Wang Y, Guo M, Nie X, Liu Y, Xing M. Interferon-beta, interferon-gamma and their fusion interferon of Siberian tigers (Panthera tigris altaica) in China are involved in positive-feedback regulation of interferon production. Dev Comp Immunol 2021; 125:104211. [PMID: 34329648 DOI: 10.1016/j.dci.2021.104211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
As a group of cytokines, interferons are the first line of defense in the antiviral immunity. In this study, Siberian tiger IFN-β (PtIFN-β) and IFN-γ (PtIFN-γ) were successfully amplified, and the two were fused (PtIFN-γ) by overlap extension polymerase chain reaction (SOE-PCR). Bioinformatics analysis disclosed that PtIFN-β and PtIFN-γ have species-specificity and conservation in the course of evolution. After being expressed in prokaryotes, the antiviral activities and physicochemical properties of PtIFN-β, PtIFN-γ and PtIFNβ-γ were analyzed. In Feline kidney cells (F81), PtIFNβ-γ showed more active antiviral activity than PtIFN-β and PtIFN-γ, which has more stable physicochemical properties (acid and alkali resistance, high temperature resistance). In addition, PtIFN-β, PtIFN-γ and PtIFN-γ activated the JAK-STAT pathway and induced the transcription and expression of interferon-stimulated genes (ISGs). Janus kinase (JAK) 1 inhibitor inhibited ISGs expression induced by PtIFN-β, PtIFN-γ and PtIFN-γ. Overall, this research clarified that PtIFN-β, PtIFN-γ and PtIFNβ-γ have the ability to inhibit viral replication and send signals through the JAK-STAT pathway. These findings may facilitate further study on the role of PtIFN in the antiviral immune response, and help to develop approaches for the prophylactic and therapeutic of viral diseases based on fusion interferon.
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Affiliation(s)
- Mengyao Mu
- College of wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Hongjing Zhao
- College of wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Yu Wang
- College of wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Menghao Guo
- College of wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Xiaopan Nie
- College of wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Yachen Liu
- College of wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Mingwei Xing
- College of wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China.
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Abstract
PCR is a powerful tool for generating specific fragments of DNA that can be used to create gene variations or tagged expression constructs. Overlap extension PCR is a valuable technique that is commonly used for cloning large complex fragments, making edits to cloned genes or fusing two gene elements together. After difficulties in utilizing this technique following existing methods, we developed an optimized protocol. To accomplish this, three significant changes were made; 1) touchdown PCR cycling parameters were used to eliminate the need for optimizing PCR cycling conditions, 2) the high-fidelity, high-processivity Q5 DNA polymerase was used to improve full-length amplification quality, and 3) a reduced amount of primer in the final PCR amplification step decreased non-specific amplimers. This modified protocol results in consistent generation of gene fusion products, with little to no background and enhanced efficiency of the transgene construction process.
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Affiliation(s)
- Roland S. Hilgarth
- Vector Core, Biomedical Research Core Facilities, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Thomas M. Lanigan
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, United States
- Vector Core, Biomedical Research Core Facilities, University of Michigan, Ann Arbor, MI, 48109, United States
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Hu Z, Wang L, Shi Z, Jiang J, Li X, Chen Y, Li K, Luo D. Customized one-step preparation of sgRNA transcription templates via overlapping PCR Using short primers and its application in vitro and in vivo gene editing. Cell Biosci 2019; 9:87. [PMID: 31673328 PMCID: PMC6814055 DOI: 10.1186/s13578-019-0350-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/04/2019] [Indexed: 11/10/2022] Open
Abstract
Overlap extension polymerase chain reaction (PCR) is a powerful technology for DNA assembly. Based on this technology, we synthesized DNA templates, which were transcribed into sgRNA in vitro, and further detected their efficiency of purified sgRNAs with Cas9 nuclease. The sgRNAs synthesized by this approach can effectively cleave the DNA fragments of interest in vitro and in vivo. Compared with the conventional method for generating sgRNA, it does not require construction of recombinant plasmids and design of primers to amplify sgRNA core fragment. Only several short primers with overlapped sequences are needed to assemble a DNA fragment as the template of sgRNA. This modified and simplified method is highly applicable and less time-consuming.
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Affiliation(s)
- Zheng Hu
- The First People's Hospital of Chenzhou, Affiliated to University of Southern Medical University, Chenzhou, 423000 People's Republic of China.,2National & Local Joint Engineering Laboratory for High-throughput Molecular Diagnosis Technology, Affiliated to The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000 People's Republic of China.,3Translational Medicine Institute, University of South China, Chenzhou, 423000 People's Republic of China
| | - Li Wang
- The First People's Hospital of Chenzhou, Affiliated to University of Southern Medical University, Chenzhou, 423000 People's Republic of China.,2National & Local Joint Engineering Laboratory for High-throughput Molecular Diagnosis Technology, Affiliated to The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000 People's Republic of China.,3Translational Medicine Institute, University of South China, Chenzhou, 423000 People's Republic of China
| | - Zhaoying Shi
- 4Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Jing Jiang
- 2National & Local Joint Engineering Laboratory for High-throughput Molecular Diagnosis Technology, Affiliated to The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000 People's Republic of China.,3Translational Medicine Institute, University of South China, Chenzhou, 423000 People's Republic of China
| | - Xiangning Li
- 2National & Local Joint Engineering Laboratory for High-throughput Molecular Diagnosis Technology, Affiliated to The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000 People's Republic of China.,3Translational Medicine Institute, University of South China, Chenzhou, 423000 People's Republic of China
| | - Yonglong Chen
- 4Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Kai Li
- 2National & Local Joint Engineering Laboratory for High-throughput Molecular Diagnosis Technology, Affiliated to The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000 People's Republic of China.,3Translational Medicine Institute, University of South China, Chenzhou, 423000 People's Republic of China.,Genetalks Bio-tech (Changsha) Limited Liability Company, Changsha, 410013 Hunan China
| | - Dixian Luo
- The First People's Hospital of Chenzhou, Affiliated to University of Southern Medical University, Chenzhou, 423000 People's Republic of China.,2National & Local Joint Engineering Laboratory for High-throughput Molecular Diagnosis Technology, Affiliated to The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000 People's Republic of China.,3Translational Medicine Institute, University of South China, Chenzhou, 423000 People's Republic of China
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Xu T, Li X, Wu Y, Shahzad KA, Wang W, Zhang L, Shen C. A Combination Strategy for Construction of Peptide-β2m-H-2K b Single Chain with Overlap Extension PCR and One-Step Cloning. J Microbiol Biotechnol 2017; 26:2184-2191. [PMID: 27586530 DOI: 10.4014/jmb.1606.06038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The time-consuming and high-cost preparation of soluble peptide-major histocompatibility complexes (pMHC) currently limits their wide uses in monitoring antigen-specific T cells. The single-chain trimer (SCT) of peptide-β2m-MHC class I heavy chain was developed as an alternative strategy, but its gene fusion is hindered in many cases owing to the incompatibility between the multiple restriction enzymes and the restriction endonuclease sites of plasmid vectors. In this study, overlap extension PCR and one-step cloning were adopted to overcome this restriction. The SCT gene of the OVA₂₅₇₋₂₆₄ peptide-(GS₄)₃-β2m-(GS₄)₄-H-2Kb heavy chain was constructed and inserted into plasmid pET28a by overlap extension PCR and one-step cloning, without the requirement of restriction enzymes. The SCT protein was expressed in Escherichia coli, and then purified and refolded. The resulting H-2Kb/OVA₂₅₇₋₂₆₄ complex showed the correct structural conformation and capability to bind with OVA₂₅₇₋₂₆₄-specific T-cell receptor. The overlap extension PCR and one-step cloning ensure the construction of single-chain MHC class I molecules associated with random epitopes, and will facilitate the preparation of soluble pMHC multimers.
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Affiliation(s)
- Tao Xu
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing 210009, P.R. China
| | - Xiaoe Li
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing 210009, P.R. China
| | - You Wu
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing 210009, P.R. China
| | - Khawar Ali Shahzad
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing 210009, P.R. China
| | - Wei Wang
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing 210009, P.R. China
| | - Lei Zhang
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing 210009, P.R. China
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing 210009, P.R. China
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Carvalho SL, Nagata T, Junqueira BR, Zanardo LG, Paiva ACS, Carvalho CM. Construction of a full-length infectious cDNA clone of Cowpea mild mottle virus. Virus Genes 2017; 53:137-140. [PMID: 27730428 DOI: 10.1007/s11262-016-1395-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/22/2016] [Indexed: 11/30/2022]
Abstract
Infectious cDNA clones are an important tool to study the molecular and cellular process of RNA virus infection. In vitro and in vivo transcription systems are the two main strategies used in the generation of infectious cDNA clones for RNA viruses. This study describes the first generation of a full-length infectious cDNA clone of Cowpea mild mottle virus (CPMMV), a Carlavirus. The full-length genome was synthesized by Overlap Extension PCR of two overlapping fragments and cloned in a pUC-based vector under control of the SP6 RNA polymerase promoter. After in vitro run-off transcription, the produced RNA was mechanically inoculated into soybean plants cv. CD206. The systemic infection was confirmed by RT-PCR and further sequencing of amplified cDNA fragments. To simplify the transfection process, the complete genome was subcloned into a binary vector under control of the 35S promoter of cauliflower mosaic virus by the Gibson Assembly protocol. The resulting clones were inoculated by particle bombardment onto soybean seedlings and the recovery of the virus was confirmed 2 weeks later by RT-PCR. Our results indicate the constructs of the full-length cDNA of CPMMV are fully infectious in both in vitro and in vivo transcription strategies.
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Affiliation(s)
- Silvia L Carvalho
- Department of Phytopathology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Tatsuya Nagata
- Department of Cell Biology, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Bruna R Junqueira
- Department of Cell Biology, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Larissa G Zanardo
- Department of Phytopathology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Ana C S Paiva
- Department of Phytopathology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Claudine M Carvalho
- Department of Phytopathology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n Campus Universitário, Viçosa, MG, 36570-900, Brazil.
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Eleniste PP, Hofstetter H, Hofstetter O. Expression and characterization of an enantioselective antigen-binding fragment directed against α-amino acids. Protein Expr Purif 2013; 91:20-9. [PMID: 23827208 PMCID: PMC3816624 DOI: 10.1016/j.pep.2013.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022]
Abstract
This work describes the design and expression of a stereoselective Fab that possesses binding properties comparable to those displayed by the parent monoclonal antibody. Utilizing mRNA from hybridoma clones that secrete a stereoselective anti-l-amino acid antibody, a corresponding biotechnologically produced Fab was generated. For that, appropriate primers were designed based on extensive literature and databank searches. Using these primers in PCR resulted in successful amplification of the VH, VL, CL and CH1 gene fragments. Overlap PCR was utilized to combine the VH and CH1 sequences and the VL and CL sequences, respectively, to obtain the genes encoding the HC and LC fragments. These sequences were separately cloned into the pEXP5-CT/TOPO expression vector and used for transfection of BL21(DE3) cells. Separate expression of the two chains, followed by assembly in a refolding buffer, yielded an Fab that was demonstrated to bind to l-amino acids but not to recognize the corresponding d-enantiomers.
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Affiliation(s)
| | - Heike Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University,
DeKalb, Illinois 60115, USA
| | - Oliver Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University,
DeKalb, Illinois 60115, USA
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Xie Z, Qi F, Merritt J. Cloning-independent plasmid construction for genetic studies in streptococci. J Microbiol Methods 2013; 94:77-82. [PMID: 23673081 DOI: 10.1016/j.mimet.2013.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/05/2013] [Accepted: 05/06/2013] [Indexed: 11/29/2022]
Abstract
Shuttle plasmids are among the few routinely utilized tools in the Streptococcus mutans genetic system that still require the use of classical cloning methodologies and intermediate hosts for genetic manipulation. Accordingly, it typically requires considerably less time and effort to introduce mutations onto the S. mutans chromosome than it does to construct shuttle vectors for expressing genes in trans. Occasionally, shuttle vector constructs also exhibit toxicity in Escherichia coli, which prevents their proper assembly. To circumvent these limitations, we modified a prolonged overlap extension PCR (POE-PCR) protocol to facilitate direct plasmid assembly in S. mutans. Using solely PCR, we created the reporter vector pZX7, which contains a single minimal streptococcal replication origin and harbors a spectinomycin resistance cassette and the gusA gene encoding β-glucuronidase. We compared the efficiency of pZX7 assembly using multiple strains of S. mutans and were able to obtain from 5 × 10³ to 2 × 10⁵ CFU/μg PCR product. Likewise, we used pZX7 to further demonstrate that Streptococcus sanguinis and Streptococcus gordonii are also excellent hosts for cloning-independent plasmid assembly, which suggests that this system is likely to function in numerous other streptococci. Consequently, it should be possible to completely forgo the use of E. coli-Streptococcus shuttle vectors in many streptococcal species, thereby decreasing the time and effort required to assemble constructs and eliminating any toxicity issues associated with intermediate hosts.
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Affiliation(s)
- Zhoujie Xie
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States
| | - Fengxia Qi
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States
| | - Justin Merritt
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States.
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