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Read CM, Plante K, Rafael G, Rossi SL, Braun W, Weaver SC, Schein CH. Designing multivalent immunogens for alphavirus vaccine optimization. Virology 2021; 561:117-124. [PMID: 33823988 DOI: 10.1016/j.virol.2020.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022]
Abstract
There is a pressing need for vaccines against mosquito-borne alphaviruses such as Venezualen and eastern equine encephalitis viruses (VEEV, EEEV). We demonstrate an approach to vaccine development based on physicochemical properties (PCP) of amino acids to design a PCP-consensus sequence of the epitope-rich B domain of the VEEV major antigenic E2 protein. The consensus "spike" domain was incorporated into a live-attenuated VEEV vaccine candidate (ZPC/IRESv1). Mice inoculated with either ZPC/IRESv1 or the same virus containing the consensus E2 protein fragment (VEEVconE2) were protected against lethal challenge with VEEV strains ZPC-738 and 3908, and Mucambo virus (MUCV, related to VEEV), and had comparable neutralizing antibody titers against each virus. Both vaccines induced partial protection against Madariaga virus (MADV), a close relative of EEEV, lowering mortality from 60% to 20%. Thus PCP-consensus sequences can be integrated into a replicating virus that could, with further optimization, provide a broad-spectrum vaccine against encephalitic alphaviruses.
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Affiliation(s)
- C M Read
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Kenneth Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Grace Rafael
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Shannan L Rossi
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Department of Pathology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Catherine H Schein
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA.
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Vu HLX, Pattnaik AK, Osorio FA. Strategies to broaden the cross-protective efficacy of vaccines against porcine reproductive and respiratory syndrome virus. Vet Microbiol 2016; 206:29-34. [PMID: 27692670 DOI: 10.1016/j.vetmic.2016.09.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important viral pathogens currently affecting swine production worldwide. Although PRRS vaccines have been commercially available for over 20 years, the available vaccines are considered inadequately effective for control and eradication of the virus. Major obstacles for the development of a highly effective PRRS vaccine include the highly variable nature of the viral genome, the viral ability to subvert the host immune system, and the incomplete understanding of the immune protection against PRRSV infection. This article summarizes the impediments for the development of a highly protective PRRS vaccine and reviews the vaccinology approaches that have been attempted to overcome one of the most formidable challenges, which is the substantial genetic variation among PRRSV isolates, to broaden the antigenic coverage of PRRS vaccines.
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Affiliation(s)
- Hiep L X Vu
- Nebraska Center for Virology, and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States.
| | - Asit K Pattnaik
- Nebraska Center for Virology, and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
| | - Fernando A Osorio
- Nebraska Center for Virology, and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
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Constructing Tumor Vaccines Targeting for Vascular Endothelial Growth Factor (VEGF) by DNA Shuffling. J Immunother 2016; 39:260-8. [DOI: 10.1097/cji.0000000000000129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Zhou L, Ni YY, Piñeyro P, Cossaboom CM, Subramaniam S, Sanford BJ, Dryman BA, Huang YW, Meng XJ. Broadening the heterologous cross-neutralizing antibody inducing ability of porcine reproductive and respiratory syndrome virus by breeding the GP4 or M genes. PLoS One 2013; 8:e66645. [PMID: 23826108 PMCID: PMC3691207 DOI: 10.1371/journal.pone.0066645] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/08/2013] [Indexed: 12/21/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important swine pathogens, which causes reproductive failure in sows and respiratory disease in piglets. A major hurdle to control PRRSV is the ineffectiveness of the current vaccines to confer protection against heterologous strains. Since both GP4 and M genes of PRRSV induce neutralizing antibodies, in this study we molecularly bred PRRSV through DNA shuffling of the GP4 and M genes, separately, from six genetically different strains of PRRSV in an attempt to identify chimeras with improved heterologous cross-neutralizing capability. The shuffled GP4 and M genes libraries were each cloned into the backbone of PRRSV strain VR2385 infectious clone pIR-VR2385-CA. Three GP4-shuffled chimeras and five M-shuffled chimeras, each representing sequences from all six parental strains, were selected and further characterized in vitro and in pigs. These eight chimeric viruses showed similar levels of replication with their backbone strain VR2385 both in vitro and in vivo, indicating that the DNA shuffling of GP4 and M genes did not significantly impair the replication ability of these chimeras. Cross-neutralization test revealed that the GP4-shuffled chimera GP4TS14 induced significantly higher cross-neutralizing antibodies against heterologous strains FL-12 and NADC20, and similarly that the M-shuffled chimera MTS57 also induced significantly higher levels of cross-neutralizing antibodies against heterologous strains MN184B and NADC20, when compared with their backbone parental strain VR2385 in infected pigs. The results suggest that DNA shuffling of the GP4 or M genes from different parental viruses can broaden the cross-neutralizing antibody-inducing ability of the chimeric viruses against heterologous PRRSV strains. The study has important implications for future development of a broadly protective vaccine against PRRSV.
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Affiliation(s)
- Lei Zhou
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agribiotechnology, China Agricultural University, Beijing, People’s Republic of China
| | - Yan-Yan Ni
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Pablo Piñeyro
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Caitlin M. Cossaboom
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Sakthivel Subramaniam
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Brenton J. Sanford
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Barbara A. Dryman
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Yao-Wei Huang
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
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Ni YY, Opriessnig T, Zhou L, Cao D, Huang YW, Halbur PG, Meng XJ. Attenuation of porcine reproductive and respiratory syndrome virus by molecular breeding of virus envelope genes from genetically divergent strains. J Virol 2013; 87:304-13. [PMID: 23077307 PMCID: PMC3536372 DOI: 10.1128/jvi.01789-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/11/2012] [Indexed: 12/14/2022] Open
Abstract
Molecular breeding via DNA shuffling can direct the evolution of viruses with desired traits. By using a positive-strand RNA virus, porcine reproductive and respiratory syndrome virus (PRRSV), as a model, rapid attenuation of the virus was achieved in this study by DNA shuffling of the viral envelope genes from multiple strains. The GP5 envelope genes of 7 genetically divergent PRRSV strains and the GP5-M genes of 6 different PRRSV strains were molecularly bred by DNA shuffling and iteration of the process, and the shuffled genes were cloned into the backbone of a DNA-launched PRRSV infectious clone. Two representative chimeric viruses, DS722 with shuffled GP5 genes and DS5M3 with shuffled GP5-M genes, were rescued and shown to replicate at a lower level and to form smaller plaques in vitro than their parental virus. An in vivo pathogenicity study revealed that pigs infected with the two chimeric viruses had significant reductions in viral-RNA loads in sera and lungs and in gross and microscopic lung lesions, indicating attenuation of the chimeric viruses. Furthermore, pigs vaccinated with the chimeric virus DS722, but not pigs vaccinated with DS5M3, still acquired protection against PRRSV challenge at a level similar to that of the parental virus. Therefore, this study reveals a unique approach through DNA shuffling of viral envelope genes to attenuate a positive-strand RNA virus. The results have important implications for future vaccine development and will generate broad general interest in the scientific community in rapidly attenuating other important human and veterinary viruses.
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Affiliation(s)
- Yan-Yan Ni
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
| | - Lei Zhou
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Dianjun Cao
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Yao-Wei Huang
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Patrick G. Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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Zhou L, Ni YY, Piñeyro P, Sanford BJ, Cossaboom CM, Dryman BA, Huang YW, Cao DJ, Meng XJ. DNA shuffling of the GP3 genes of porcine reproductive and respiratory syndrome virus (PRRSV) produces a chimeric virus with an improved cross-neutralizing ability against a heterologous PRRSV strain. Virology 2012; 434:96-109. [PMID: 23051709 DOI: 10.1016/j.virol.2012.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/30/2012] [Accepted: 09/10/2012] [Indexed: 11/19/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is an important swine pathogen. Here we applied the DNA shuffling approaches to molecularly breed the PRRSV GP3 gene, a neutralizing antibodies inducer, in an attempt to improve its heterologous cross-neutralizing ability. The GP3 genes of six different PRRSV strains were bred by traditional DNA shuffling. Additionally, synthetic DNA shuffling of the GP3 gene was also performed using degenerate oligonucleotides. The shuffled-GP3-libraries were cloned into the backbone of a DNA-launched PRRSV infectious clone pIR-VR2385-CA. Four traditional-shuffled chimeras each representing all 6 parental strains and four other synthetic-shuffled chimeras were successfully rescued. These chimeras displayed similar levels of replication both in vitro and in vivo, compared to the backbone parental virus, indicating that the GP3 shuffling did not impair the replication capability of the chimeras. One chimera GP3TS22 induced significantly higher levels of cross-neutralizing antibodies in pigs against a heterologous PRRSV strain FL-12.
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Affiliation(s)
- Lei Zhou
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061-0913, USA
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Zeng J, Xiong Y, Zhang LB, Ruan JD, Wu W, Sun WJ. The antitumor activity of recombinant antitumor antiviral protein and the associated molecular mechanism in pancreatic tumor cells. Cancer Biother Radiopharm 2012; 27:426-33. [PMID: 22783925 DOI: 10.1089/cbr.2012.1166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Pancreatic cancer has poor prognosis and high mortality. Currently, the therapy of pancreatic cancer remains a challenge. In this study, we compared the antitumor activity of the recombinant antitumor antiviral protein (RAAP), an improved interferon, with gemcitabine, a classic chemotherapy agent used for pancreatic cancer treatment. METHODS The proliferation of Bx-PC3 pancreatic cancer cells was evaluated by an MTT assay. Cell cycle arrest and apoptosis were evaluated by flow cytometry and annexin V-FITC/propidium iodide double staining, respectively. The expressions of matrix metalloproteinase (MMP)-2, MMP-9, caspase-3, caspase-8, and caspase-9 genes were evaluated by reverse transcription-polymerase chain reaction and the Western blot analysis. A xenograft pancreatic cancer model was established by inoculating Bx-PC3 cells into athymic nude mice. The antitumor activity of RAAP and gemcitabine was tested in the xenograft tumor model. RESULTS RAAP significantly inhibited proliferation, induced cell cycle arrest, and induced apoptosis in Bx-PC3 cells in vitro and delayed tumor growth in vivo. The antitumor activity of 20 ng/mL of RAAP was a little more effective than 10 μM of gemcitabine. The antitumor activity of RAAP was associated with its role in inducing caspase-3 and caspase-8 expression as well as downregulating MMP-2 expression. CONCLUSIONS RAAP can effectively suppress human pancreatic cancer cell growth in vitro and in vivo. The antitumor efficacy of RAAP is similar to gemcitabine.
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Affiliation(s)
- Jie Zeng
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, P.R. China
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Xiong AS, Peng RH, Zhuang J, Chen JM, Zhang B, Zhang J, Yao QH. A thermostable β-glucuronidase obtained by directed evolution as a reporter gene in transgenic plants. PLoS One 2011; 6:e26773. [PMID: 22096498 PMCID: PMC3212524 DOI: 10.1371/journal.pone.0026773] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 10/03/2011] [Indexed: 11/18/2022] Open
Abstract
A β-glucuronidase variant, GUS-TR3337, that was obtained by directed evolution exhibited higher thermostability than the wild-type enzyme, GUS-WT. In this study, the utility of GUS-TR337 as an improved reporter was evaluated. The corresponding gus-tr3337 and gus-wt genes were independently cloned in a plant expression vector and introduced into Arabidopsis thaliana. With 4-MUG as a substrate, plants containing the gus-wt gene showed no detectable β-glucuronidase activity after exposure to 60°C for 10 min, while those hosting the gus-tr3337 gene retained 70% or 50% activity after exposure to 80°C for 10 min or 30 min, respectively. Similarly, in vivo β-glucuronidase activity could be demonstrated by using X-GLUC as a substrate in transgenic Arabidopsis plants hosting the gus-tr3337 gene that were exposed to 80°C for up to 30 min. Thus, the thermostability of GUS-TR3337 can be exploited to distinguish between endogenous and transgenic β-glucuronidase activity, which is a welcome improvement in its use as a reporter.
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Affiliation(s)
- Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- * E-mail: ,cn (A-SX); (JZ); (Q-HY)
| | - Ri-He Peng
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jing Zhuang
- Alberta Innovates-Technology Futures, Vegreville, Alberta, Canada
| | - Jian-Min Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Bin Zhang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jian Zhang
- Alberta Innovates-Technology Futures, Vegreville, Alberta, Canada
- * E-mail: ,cn (A-SX); (JZ); (Q-HY)
| | - Quan-Hong Yao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- * E-mail: ,cn (A-SX); (JZ); (Q-HY)
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Xiong AS, Peng RH, Zhuang J, Davies J, Zhang J, Yao QH. Advances in directed molecular evolution of reporter genes. Crit Rev Biotechnol 2011; 32:133-42. [DOI: 10.3109/07388551.2011.593503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening. Methods Mol Biol 2010; 634:239-56. [PMID: 20676989 DOI: 10.1007/978-1-60761-652-8_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Marker genes, such as gusA, lacZ, and gfp, have been applied comprehensively in biological studies. Directed in vitro evolution provides a powerful tool for modifying genes and for studying gene structure, expression, and function. Here, we describe a strategy for directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening. The protocol involves two processes of DNA shuffling and screening. The first DNA shuffling and screening process involves eight steps: (1) amplifying the target gene by PCR, (2) cutting the product into random fragments with DNase I, (3) purification of 50-100 bp fragments, (4) reassembly of the fragments in a primerless PCR, (5) amplification of the reassembled product by primer PCR, (6) cloning into expression vector, (7) transformation of E. coli by electroporation, and (8) screening the target mutants using a nitrocellulose filter. The second DNA shuffling and screening process also involves the same eight steps, except that degenerate oligonucleotide primers are based on the sequence of the selected mutant.
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Abstract
Vaccine development, which began with Edward Jenner's observations in the late 18th century, has entered its 4th century. From its beginnings, with the use of whole organisms that had been weakened or inactivated, to the modern-day use of genetic engineering, it has taken advantage of the tools discovered in other branches of microbiology. Numerous successful vaccines are in use, but the list of diseases for which vaccines do not exist is long. However, the multiplicity of strategies now available, discussed in this article, portends even more successful development of vaccines.
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Dupuy LC, Locher CP, Paidhungat M, Richards MJ, Lind CM, Bakken R, Parker MD, Whalen RG, Schmaljohn CS. Directed molecular evolution improves the immunogenicity and protective efficacy of a Venezuelan equine encephalitis virus DNA vaccine. Vaccine 2009; 27:4152-60. [PMID: 19406186 DOI: 10.1016/j.vaccine.2009.04.049] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 04/02/2009] [Accepted: 04/21/2009] [Indexed: 11/18/2022]
Abstract
We employed directed molecular evolution to improve the cross-reactivity and immunogenicity of the Venezuelan equine encephalitis virus (VEEV) envelope glycoproteins. The DNA encoding the E1 and E2 proteins from VEEV subtypes IA/B and IE, Mucambo virus (MUCV), and eastern and western equine encephalitis viruses (EEEV and WEEV) were recombined in vitro to create libraries of chimeric genes expressing variant envelope proteins. ELISAs specific for all five parent viruses were used in high-throughput screening to identify those recombinant DNAs that demonstrated cross-reactivity to VEEV, MUCV, EEEV, and WEEV after administration as plasmid vaccines in mice. Selected variants were then used to vaccinate larger cohorts of mice and their sera were assayed by both ELISA and by plaque reduction neutralization test (PRNT). Representative variants from a library in which the E1 gene from VEEV IA/B was held constant and only the E2 genes of the five parent viruses were recombined elicited significantly increased neutralizing antibody titers to VEEV IA/B compared to the parent DNA vaccine and provided improved protection against aerosol VEEV IA/B challenge. Our results indicate that it is possible to improve the immunogenicity and protective efficacy of alphavirus DNA vaccines using directed molecular evolution.
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Affiliation(s)
- Lesley C Dupuy
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
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Xiong AS, Peng RH, Zhuang J, Gao F, Li Y, Cheng ZM, Yao QH. Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol Rev 2008; 32:522-40. [DOI: 10.1111/j.1574-6976.2008.00109.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Xiong AS, Peng RH, Zhuang J, Liu JG, Gao F, Xu F, Cai B, Yao QH. A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences. Biol Chem 2008; 388:1291-300. [PMID: 18020945 DOI: 10.1515/bc.2007.153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Directed evolution in vitro is a powerful molecular tool for the creation of new biological phenotypes. It is unclear whether it is more efficient to mutate an enzyme randomly or to mutate just the active sites or key sites. In this study, the strategy of a semi-rational design of directed evolution combined with whole sequence and sites was developed. The 1553 bp gene encoding the thermostable beta-galactosidase of Pyrococcus woesei was chemically synthesized and optimized for G+C content and mRNA secondary structures. The synthesized gene product was used as a template or as a wild-type control. On the basis of the first round of DNA shuffling, library construction and screening, one mutant of YH6754 was isolated with higher activity. Eight potential key sites were deduced from the sequence of the shuffled gene, and 16 degenerate oligonucleotides were designed according to those eight amino acids. Two variants of YG6765 and YG8252 were screened in the second part of DNA shuffling, library construction and screening. For comparison, one mutant of YH8757 was screened through the same routine rounds of directed evolution with YH6754 as template. The purified beta-galactosidase from YH8757 exhibited a lower specific activity at 25 degrees C than those purified from mutated YG6755 and YG8252.
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Affiliation(s)
- Ai-Sheng Xiong
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
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Ellis RW. Technologies for making new vaccines. Vaccines (Basel) 2008. [DOI: 10.1016/b978-1-4160-3611-1.50064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Wong TS, Roccatano D, Schwaneberg U. Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries. Environ Microbiol 2007; 9:2645-59. [DOI: 10.1111/j.1462-2920.2007.01411.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xiong AS, Peng RH, Zhuang J, Li X, Xue Y, Liu JG, Gao F, Cai B, Chen JM, Yao QH. Directed evolution of a beta-galactosidase from Pyrococcus woesei resulting in increased thermostable beta-glucuronidase activity. Appl Microbiol Biotechnol 2007; 77:569-78. [PMID: 17876575 DOI: 10.1007/s00253-007-1182-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 08/10/2007] [Accepted: 08/23/2007] [Indexed: 11/29/2022]
Abstract
We performed directed evolution on a chemically synthesized 1,533-bp recombinant beta-galactosidase gene from Pyrococcus woesei. More than 200,000 variant colonies in each round of directed evolution were screened using the pYPX251 vector and host strain Rosetta-Blue (DE3). One shifted beta-galactosidase to beta-glucuronidase mutant, named YG6762, was obtained after four rounds of directed evolution and screening. This mutant had eight mutated amino acid residues. T29A, V213I, L217M, N277H, I387V, R491C, and N496D were key mutations for high beta-glucuronidase activity, while E414D was not essential because the mutation did not lead to a change in beta-glucuronidase activity. The amino acid site 277 was the most essential because mutating H back to N resulted in a 50% decrease in beta-glucuronidase activity at 37 degrees C. We also demonstrated that amino acid 277 was the most essential site, as the mutation from N to H resulted in a 1.5-fold increase in beta-glucuronidase activity at 37 degrees C. Although most single amino acid changes lead to less than a 20% increase in beta-glucuronidase activity, the YG6762 variant, which was mutated at all eight amino acid sites, had a beta-glucuronidase activity that was about five and seven times greater than the wild-type enzyme at 37 and 25 degrees C, respectively.
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Affiliation(s)
- Ai-Sheng Xiong
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, 201106, China
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Braddock M. 11th annual Inflammatory and Immune Diseases Drug Discovery and Development Summit 12-13 March 2007, San Francisco, USA. Expert Opin Investig Drugs 2007; 16:909-17. [PMID: 17501702 DOI: 10.1517/13543784.16.6.909] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Strategic Research Institute (SRi) hosted the 11th International Inflammation and Immune Diseases Drug Discovery and Development World Summit in San Francisco during 12-13 March 2007. The summit comprised keynote sessions and two parallel tracks and focussed on targeting mechanisms for drug discovery and development, which modulate the immune response and which have anti-inflammatory activity in a number of human diseases. Indications included psoriasis, hepatitis C, allergic dermatitis, systemic lupus erythematosus, rheumatoid arthritis and osteoarthritis, multiple sclnerosis, cardiovascular disease and asthma. Data were presented supporting all stages of drug discovery from target identification and validation through to lead identification and optimisation to both early- and late-stage clinical development.
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Affiliation(s)
- Martin Braddock
- Discovery Bioscience, AstraZeneca R&D Charnwood, Loughborough, Leicestershire, England, UK.
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Xiong AS, Peng RH, Cheng ZM, Li Y, Liu JG, Zhuang J, Gao F, Xu F, Qiao YS, Zhang Z, Chen JM, Yao QH. Concurrent mutations in six amino acids in β-glucuronidase improve its thermostability. Protein Eng Des Sel 2007; 20:319-25. [PMID: 17557766 DOI: 10.1093/protein/gzm023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To achieve a thermostable beta-glucuronidase (GUS) and identify key mutation sites, we applied in vitro directed evolution strategy through DNA shuffling and obtained a highly thermostable mutant GUS gene, gus-tr, after four rounds of DNA shuffling and screening. This variant had mutations in 15 nucleic acid sites, resulting in changes in 12 amino acids (AAs). Using gus-tr as the template, we further performed site-directed mutagenesis to reverse the individual mutation to the wild-type protein. We found that six sites (Q493R, T509A, M532T, N550S, G559S and N566S) present in GUS-TR3337, were the key AAs needed to confer its high thermostability. Of these, Q493R and T509A were not reported previously as important residues for thermostability of GUS. Furthermore, all of these six mutations must be present concurrently to confer the high thermostability. We expressed the gus-tr3337 gene and purified the GUS-TR3337 protein that contained the six AA mutations. Compared with the wild-type protein which lost its activity completely after 10 min at 70 degrees C, the mutant GUS-TR3337 protein retained 75% of its activity when heated at 80 degrees C for 10 min. The GUS-TR3337 exhibited high activity even heated at 100 degrees C for 30 min on nitrocellulose filter. The comparison of molecular models of the mutated and wild-type enzyme revealed the relation of protein function and these structural modifications.
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Affiliation(s)
- Ai-Sheng Xiong
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Xiong AS, Peng RH, Liu JG, Zhuang J, Qiao YS, Xu F, Cai B, Zhang Z, Chen JM, Yao QH. High efficiency and throughput system in directed evolution in vitro of reporter gene. Appl Microbiol Biotechnol 2007; 74:160-8. [PMID: 17009011 DOI: 10.1007/s00253-006-0659-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/25/2006] [Accepted: 09/04/2006] [Indexed: 11/25/2022]
Abstract
In vitro directed evolution, especially with DNA shuffling, is a powerful means in biological studies of protein structure and function, and consequently for industrial applications. Escherichia coli beta-glucuronidase (gusA) gene, a versatile and efficient reporter gene, was the model for studying in vitro directed evolution because of its stability, easy analysis of the enzyme properties and conveniently visible phenotype. We developed a high efficiency, throughput system for in vitro directed evolution using gusA reporter gene as the model. The system consisted mainly of three aspects: a prokaryotic expression vector pYPX251, an easy method for obtaining the mutated gene from DNA shuffling and a suitable selected strategy. The vector pYPX251 carried the moderately strong aacC1 gene promoter and T1T2 transcription terminator that allowed expression in E. coli. Over 10,000 individuals could be selected individually in a 9 cm Petri dish after colonies were absorbed on a nitrocellulose filter. A library, which contained 100,000 individuals was screened by incubating ten filter papers with X-Glu. The polymerase chain reaction products of the gusA gene, the fragments of 50-100 bp, with high mutation rates were purified using a dialysis bag from 10% PAGE after electrophoresis. The possibility of obtaining desirable mutations was increased dramatically as the size of the library expanded. A GUS variant, named GUS-TR, was obtained through this system, which is significantly more resistant to high temperature than the wild type enzyme. GUS-TR maintained its high activity even when the nitrocellulose filter containing the variant colony was heated at 100 degrees C for 30 min.
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Affiliation(s)
- Ai-Sheng Xiong
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai 201106, China
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