1
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Fakhiri J, Schneider MA, Puschhof J, Stanifer M, Schildgen V, Holderbach S, Voss Y, El Andari J, Schildgen O, Boulant S, Meister M, Clevers H, Yan Z, Qiu J, Grimm D. Novel Chimeric Gene Therapy Vectors Based on Adeno-Associated Virus and Four Different Mammalian Bocaviruses. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 12:202-222. [PMID: 30766894 PMCID: PMC6360332 DOI: 10.1016/j.omtm.2019.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/11/2019] [Indexed: 02/06/2023]
Abstract
Parvoviruses are highly attractive templates for the engineering of safe, efficient, and specific gene therapy vectors, as best exemplified by adeno-associated virus (AAV). Another candidate that currently garners increasing attention is human bocavirus 1 (HBoV1). Notably, HBoV1 capsids can cross-package recombinant (r)AAV2 genomes, yielding rAAV2/HBoV1 chimeras that specifically transduce polarized human airway epithelia (pHAEs). Here, we largely expanded the repertoire of rAAV/BoV chimeras, by assembling packaging plasmids encoding the capsid genes of four additional primate bocaviruses, HBoV2–4 and GBoV (Gorilla BoV). Capsid protein expression and efficient rAAV cross-packaging were validated by immunoblotting and qPCR, respectively. Interestingly, not only HBoV1 but also HBoV4 and GBoV transduced pHAEs as well as primary human lung organoids. Flow cytometry analysis of pHAEs revealed distinct cellular specificities between the BoV isolates, with HBoV1 targeting ciliated, club, and KRT5+ basal cells, whereas HBoV4 showed a preference for KRT5+ basal cells. Surprisingly, primary human hepatocytes, skeletal muscle cells, and T cells were also highly amenable to rAAV/BoV transduction. Finally, we adapted our pipeline for AAV capsid gene shuffling to all five BoV isolates. Collectively, our chimeric rAAV/BoV vectors and bocaviral capsid library represent valuable new resources to dissect BoV biology and to breed unique gene therapy vectors.
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Affiliation(s)
- Julia Fakhiri
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,German Center for Lung Research (DZL), Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
| | - Jens Puschhof
- Hubrecht Institute and Oncode Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Megan Stanifer
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,Research Group "Cellular Polarity of Viral Infection", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Verena Schildgen
- Institute for Pathology, Kliniken der Stadt Köln gGmbH, Hospital of the Private University Witten/Herdecke, Cologne, Germany
| | - Stefan Holderbach
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Yannik Voss
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Jihad El Andari
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Oliver Schildgen
- Institute for Pathology, Kliniken der Stadt Köln gGmbH, Hospital of the Private University Witten/Herdecke, Cologne, Germany
| | - Steeve Boulant
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,Research Group "Cellular Polarity of Viral Infection", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,German Center for Lung Research (DZL), Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
| | - Hans Clevers
- Hubrecht Institute and Oncode Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.,University Medical Center (UMC) Utrecht, Utrecht, the Netherlands.,Princess Máxima Centre, Utrecht, the Netherlands
| | - Ziying Yan
- Department of Anatomy and Cell Biology, Center for Gene Therapy, The University of Iowa, Iowa City, IA, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
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2
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Chen Z, Wang X, Zhao N, Han L, Wang F, Li H, Cui Y, Zhao X. Improving the immunogenicity and protective efficacy of the EtMIC2 protein against Eimeria tenella infection through random mutagenesis. Vaccine 2018; 36:2435-2441. [DOI: 10.1016/j.vaccine.2018.03.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/27/2018] [Accepted: 03/15/2018] [Indexed: 01/07/2023]
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3
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Abstract
One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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Affiliation(s)
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CDMX, México
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4
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Pesce D, Lehman N, de Visser JAGM. Sex in a test tube: testing the benefits of in vitro recombination. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0529. [PMID: 27619693 DOI: 10.1098/rstb.2015.0529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2016] [Indexed: 01/06/2023] Open
Abstract
The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes. As this approach allows extreme control over evolutionary conditions and parameters, it also facilitates the detection of small or position-specific recombination benefits and benefits associated with recombination between highly divergent genotypes. Yet, in vitro approaches have been largely exploratory and motivated by obtaining improved end products rather than testing hypotheses of recombination benefits. Here, we review the various experimental systems and approaches used by in vitro studies of recombination, discuss what they say about the evolutionary role of recombination, and sketch their potential for addressing extant questions about the evolutionary role of sex and recombination, in particular on complex fitness landscapes. We also review recent insights into the role of 'extracellular recombination' during the origin of life.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Diego Pesce
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Niles Lehman
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
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5
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Hassanpour N, Ullah E, Yousofshahi M, Nair NU, Hassoun S. Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymes. Metab Eng Commun 2017; 4:37-47. [PMID: 29468131 PMCID: PMC5779715 DOI: 10.1016/j.meteno.2017.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/30/2016] [Accepted: 02/27/2017] [Indexed: 11/26/2022] Open
Abstract
Directed evolution of enzymes consists of an iterative process of creating mutant libraries and choosing desired phenotypes through screening or selection until the enzymatic activity reaches a desired goal. The biggest challenge in directed enzyme evolution is identifying high-throughput screens or selections to isolate the variant(s) with the desired property. We present in this paper a computational metabolic engineering framework, Selection Finder (SelFi), to construct a selection pathway from a desired enzymatic product to a cellular host and to couple the pathway with cell survival. We applied SelFi to construct selection pathways for four enzymes and their desired enzymatic products xylitol, D-ribulose-1,5-bisphosphate, methanol, and aniline. Two of the selection pathways identified by SelFi were previously experimentally validated for engineering Xylose Reductase and RuBisCO. Importantly, SelFi advances directed evolution of enzymes as there is currently no known generalized strategies or computational techniques for identifying high-throughput selections for engineering enzymes.
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Affiliation(s)
- Neda Hassanpour
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Ehsan Ullah
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Mona Yousofshahi
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, MA 02155, United States.,Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States
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6
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Lutz S, Williams E, Muthu P. Engineering Therapeutic Enzymes. DIRECTED ENZYME EVOLUTION: ADVANCES AND APPLICATIONS 2017:17-67. [DOI: 10.1007/978-3-319-50413-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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7
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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: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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8
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Yenenler A, Sezerman OU. Design and characterizations of two novel cellulases through single-gene shuffling of Cel12A (EG3) gene fromTrichoderma reseei. Protein Eng Des Sel 2016; 29:219-229. [DOI: 10.1093/protein/gzw011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/24/2016] [Indexed: 11/14/2022] Open
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9
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Adrio JL, Demain AL. Microbial enzymes: tools for biotechnological processes. Biomolecules 2014; 4:117-39. [PMID: 24970208 PMCID: PMC4030981 DOI: 10.3390/biom4010117] [Citation(s) in RCA: 313] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi.
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Affiliation(s)
- Jose L Adrio
- Neol Biosolutions SA, BIC Granada, Granada 18016, Spain.
| | - Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
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10
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Affinity improvement of a therapeutic antibody to methamphetamine and amphetamine through structure-based antibody engineering. Sci Rep 2014; 4:3673. [PMID: 24419156 PMCID: PMC4070344 DOI: 10.1038/srep03673] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/11/2013] [Indexed: 11/24/2022] Open
Abstract
Methamphetamine (METH) abuse is a worldwide threat, without any FDA approved medications.
Anti-METH IgGs and single chain fragments (scFvs) have shown efficacy in preclinical
studies. Here we report affinity enhancement of an anti-METH scFv for METH and its active
metabolite amphetamine (AMP), through the introduction of point mutations, rationally
designed to optimize the shape and hydrophobicity of the antibody binding pocket. The
binding affinity was measured using saturation binding technique. The mutant scFv-S93T
showed 3.1 fold enhancement in affinity for METH and 26 fold for AMP. The scFv-I37M and
scFv-Y34M mutants showed enhancement of 94, and 8 fold for AMP, respectively. Structural
analysis of scFv-S93T:METH revealed that the substitution of Ser residue by Thr caused the
expulsion of a water molecule from the cavity, creating a more hydrophobic environment for
the binding that dramatically increases the affinities for METH and AMP.
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11
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DNA shuffling of cytochromes P450 for indigoid pigment production. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 987:205-24. [PMID: 23475680 DOI: 10.1007/978-1-62703-321-3_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
DNA family shuffling is a powerful method of directed evolution applied for the generation of novel enzymes with the aim of improving their existing features or creating completely new enzyme properties. This method of evolution in vitro requires parental sequences containing a high level of sequence similarity, such as is found in family members of cytochrome P450 enzymes. Cytochromes P450 (P450s or CYPs) are capable of catalyzing a variety of chemical reactions and generating a wide range of products including dye production (e.g., pigments indigo and indirubin). Application of the method of DNA family shuffling described here has enabled us to create novel P450 enzymes and to further extend the capacity of P450 to oxidize indole, leading to pigment formation.
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12
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Prabhulkar S, Tian H, Wang X, Zhu JJ, Li CZ. Engineered proteins: redox properties and their applications. Antioxid Redox Signal 2012; 17:1796-822. [PMID: 22435347 PMCID: PMC3474195 DOI: 10.1089/ars.2011.4001] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices.
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Affiliation(s)
- Shradha Prabhulkar
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
| | - Hui Tian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Xiaotang Wang
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Jun-Jie Zhu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chen-Zhong Li
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
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13
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Xia X, Babcock JP, Blaber SI, Harper KM, Blaber M. Pharmacokinetic properties of 2nd-generation fibroblast growth factor-1 mutants for therapeutic application. PLoS One 2012; 7:e48210. [PMID: 23133616 PMCID: PMC3486806 DOI: 10.1371/journal.pone.0048210] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 09/24/2012] [Indexed: 01/18/2023] Open
Abstract
Fibroblast growth factor-1 (FGF-1) is an angiogenic factor with therapeutic potential for the treatment of ischemic disease. FGF-1 has low intrinsic thermostability and is characteristically formulated with heparin as a stabilizing agent. Heparin, however, adds a number of undesirable properties that negatively impact safety and cost. Mutations that increase the thermostability of FGF-1 may obviate the need for heparin in formulation and may prove to be useful “2nd-generation” forms for therapeutic use. We report a pharmacokinetic (PK) study in rabbits of human FGF-1 in the presence and absence of heparin, as well as three mutant forms having differential effects upon thermostability, buried reactive thiols, and heparin affinity. The results support the hypothesis that heparan sulfate proteoglycan (HSPG) in the vasculature of liver, kidney and spleen serves as the principle peripheral compartment in the distribution kinetics. The addition of heparin to FGF-1 is shown to increase endocrine-like properties of distribution. Mutant forms of FGF-1 that enhance thermostability or eliminate buried reactive thiols demonstrate a shorter distribution half-life, a longer elimination half-life, and a longer mean residence time (MRT) in comparison to wild-type FGF-1. The results show how such mutations can produce useful 2nd-generation forms with tailored PK profiles for specific therapeutic application.
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Affiliation(s)
- Xue Xia
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, United States of America
| | - Joseph P. Babcock
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, United States of America
| | - Sachiko I. Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, United States of America
| | - Kathleen M. Harper
- Biomedical Research Laboratory Animal Resources, Florida State University, Tallahassee, Florida, United States of America
| | - Michael Blaber
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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14
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Preparation of photoreactive azidophenyl hyaluronic acid derivative: Protein immobilization for medical applications. Macromol Res 2012. [DOI: 10.1007/s13233-013-1016-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Abstract
Microorganisms are one of the greatest sources of metabolic and enzymatic diversity. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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16
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Alsenaidy MA, Wang T, Kim JH, Joshi SB, Lee J, Blaber M, Volkin DB, Middaugh CR. An empirical phase diagram approach to investigate conformational stability of "second-generation" functional mutants of acidic fibroblast growth factor-1. Protein Sci 2012; 21:418-32. [PMID: 22113934 DOI: 10.1002/pro.2008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/17/2011] [Accepted: 11/18/2011] [Indexed: 11/06/2022]
Abstract
Acidic fibroblast growth factor-1 (FGF-1) is an angiogenic protein which requires binding to a polyanion such as heparin for its mitogenic activity and physicochemical stability. To evaluate the extent to which this heparin dependence on solution stability could be reduced or eliminated, the structural integrity and conformational stability of 10 selected FGF-1 mutants were examined as a function of solution pH and temperature by a series of spectroscopic methods including circular dichroism, intrinsic and extrinsic fluorescence spectroscopy and static light scattering. The biophysical data were summarized in the form of colored empirical phase diagrams (EPDs). FGF-1 mutants were identified with stability profiles in the absence of heparin comparable to that of wild-type FGF-1 in the presence of heparin while still retaining their biological activity. In addition, a revised version of the EPD methodology was found to provide an information rich, high throughput approach to compare the effects of mutations on the overall conformational stability of proteins in terms of their response to environmental stresses such as pH and temperature.
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Affiliation(s)
- Mohammad A Alsenaidy
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
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17
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Bornscheuer U, Kazlauskas RJ. Survey of protein engineering strategies. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 26:26.7.1-26.7.14. [PMID: 22045562 DOI: 10.1002/0471140864.ps2607s66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein engineering is altering the structure of a protein to improve or change its properties. This unit summarizes concepts for protein engineering using rational design, directed evolution, and combinations of them. Different strategies are presented for identifying the best mutagenesis method, how to identify desired variants by screening or selection, and examples for successful applications are given. This should enable researchers to choose the most promising tools to solve their protein engineering challenges.
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Affiliation(s)
- Uwe Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics and the Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
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18
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Du SX, Xu L, Zhang W, Tang S, Boenig RI, Chen H, Mariano EB, Zwick MB, Parren PWHI, Burton DR, Wrin T, Petropoulos CJ, Ballantyne JA, Chambers M, Whalen RG. A directed molecular evolution approach to improved immunogenicity of the HIV-1 envelope glycoprotein. PLoS One 2011; 6:e20927. [PMID: 21738594 PMCID: PMC3126809 DOI: 10.1371/journal.pone.0020927] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 05/12/2011] [Indexed: 12/14/2022] Open
Abstract
A prophylactic vaccine is needed to slow the spread of HIV-1 infection. Optimization of the wild-type envelope glycoproteins to create immunogens that can elicit effective neutralizing antibodies is a high priority. Starting with ten genes encoding subtype B HIV-1 gp120 envelope glycoproteins and using in vitro homologous DNA recombination, we created chimeric gp120 variants that were screened for their ability to bind neutralizing monoclonal antibodies. Hundreds of variants were identified with novel antigenic phenotypes that exhibit considerable sequence diversity. Immunization of rabbits with these gp120 variants demonstrated that the majority can induce neutralizing antibodies to HIV-1. One novel variant, called ST-008, induced significantly improved neutralizing antibody responses when assayed against a large panel of primary HIV-1 isolates. Further study of various deletion constructs of ST-008 showed that the enhanced immunogenicity results from a combination of effective DNA priming, an enhanced V3-based response, and an improved response to the constant backbone sequences.
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Affiliation(s)
- Sean X. Du
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
| | - Li Xu
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
| | - Wenge Zhang
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
| | - Susan Tang
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
| | - Rebecca I. Boenig
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
| | - Helen Chen
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
| | - Ellaine B. Mariano
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
| | - Michael B. Zwick
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Paul W. H. I. Parren
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbial Science, and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, United States of America
| | - Terri Wrin
- Monogram Biosciences, San Francisco, California, United States of America
| | | | | | | | - Robert G. Whalen
- Department of Infectious Diseases, Maxygen, Inc., Redwood City, California, United States of America
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19
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Glasner ME, Gerlt JA, Babbitt PC. Mechanisms of protein evolution and their application to protein engineering. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2010; 75:193-239, xii-xiii. [PMID: 17124868 DOI: 10.1002/9780471224464.ch3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein engineering holds great promise for the development of new biosensors, diagnostics, therapeutics, and agents for bioremediation. Despite some remarkable successes in experimental and computational protein design, engineered proteins rarely achieve the efficiency or specificity of natural enzymes. Current protein design methods utilize evolutionary concepts, including mutation, recombination, and selection, but the inability to fully recapitulate the success of natural evolution suggests that some evolutionary principles have not been fully exploited. One aspect of protein engineering that has received little attention is how to select the most promising proteins to serve as templates, or scaffolds, for engineering. Two evolutionary concepts that could provide a rational basis for template selection are the conservation of catalytic mechanisms and functional promiscuity. Knowledge of the catalytic motifs responsible for conserved aspects of catalysis in mechanistically diverse superfamilies could be used to identify promising templates for protein engineering. Second, protein evolution often proceeds through promiscuous intermediates, suggesting that templates which are naturally promiscuous for a target reaction could enhance protein engineering strategies. This review explores these ideas and alternative hypotheses concerning protein evolution and engineering. Future research will determine if application of these principles will lead to a protein engineering methodology governed by predictable rules for designing efficient, novel catalysts.
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Affiliation(s)
- Margaret E Glasner
- Department of Biopharmaceutical Sciences, University of California-San Francisco, San Francisco, CA 94143, USA
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20
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Schmidt M, Böttcher D, Bornscheuer UT. Directed Evolution of Industrial Biocatalysts. Ind Biotechnol (New Rochelle N Y) 2010. [DOI: 10.1002/9783527630233.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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21
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Adrio JL, Demain AL. Recombinant organisms for production of industrial products. Bioeng Bugs 2009; 1:116-31. [PMID: 21326937 DOI: 10.4161/bbug.1.2.10484] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/19/2022] Open
Abstract
A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products.
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Affiliation(s)
- Jose-Luis Adrio
- NeuronBioPharma, S.A., Parque Tecnologico de Ciencias de la Salud, Edificio BIC, Armilla, Granada, Spain
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22
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The Interaction between Thermodynamic Stability and Buried Free Cysteines in Regulating the Functional Half-Life of Fibroblast Growth Factor-1. J Mol Biol 2009; 393:113-27. [DOI: 10.1016/j.jmb.2009.08.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/11/2009] [Accepted: 08/12/2009] [Indexed: 11/23/2022]
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23
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Chiu HP, Kokona B, Fairman R, Cheng RP. Effect of Highly Fluorinated Amino Acids on Protein Stability at a Solvent-Exposed Position on an Internal Strand of Protein G B1 Domain. J Am Chem Soc 2009; 131:13192-3. [DOI: 10.1021/ja903631h] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hsien-Po Chiu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
| | - Bashkim Kokona
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
| | - Robert Fairman
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
| | - Richard P. Cheng
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
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24
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Songsiriritthigul C, Pesatcha P, Eijsink VGH, Yamabhai M. Directed evolution of a Bacillus chitinase. Biotechnol J 2009; 4:501-9. [PMID: 19370717 DOI: 10.1002/biot.200800258] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Chitinases have potential in various industrial applications including bioconversion of chitin waste from crustacean shells into chito-oligosaccharide-based value-added products. For industrial applications, obtaining suitable chitinases for efficient bioconversion processes will be beneficial. In this study, we established a straightforward directed evolution method for creating chitinase variants with improved properties. A library of mutant chitinases was constructed by error-prone PCR and DNA shuffling of two highly similar (99% identical) chitinase genes from Bacillus licheniformis. Activity screening was done in two steps: first, activity towards colloidal chitin was screened for on culturing plates (halo formation). This was followed by screening activity towards the chitotriose analogue p-nitrophenyl-beta-1,4-N, N'-diacetyl-chitobiose at various pH in microtiter plates. From a medium-throughput screening (517 colonies), we were able to isolate one mutant that demonstrated improved catalytic activity. When using p-nitrophenyl-beta-1,4-N, N'-diacetyl-chitobiose as substrate, the overall catalytic efficiency, k(cat)/K(m) of the improved chitinase was 2.7- and 2.3-fold higher than the average k(cat)/K(m) of wild types at pH 3.0 and 6.0, respectively. The mutant contained four residues that did not occur in either of the wild types. The approach presented here can easily be adopted for directed evolution of suitable chitinases for various applications.
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25
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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: 32] [Impact Index Per Article: 2.0] [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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26
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Peralta-Yahya P, Carter BT, Lin H, Tao H, Cornish VW. High-throughput selection for cellulase catalysts using chemical complementation. J Am Chem Soc 2008; 130:17446-52. [PMID: 19053460 PMCID: PMC2981063 DOI: 10.1021/ja8055744] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient enzymatic hydrolysis of lignocellulosic material remains one of the major bottlenecks to cost-effective conversion of biomass to ethanol. Improvement of glycosylhydrolases, however, is limited by existing medium-throughput screening technologies. Here, we report the first high-throughput selection for cellulase catalysts. This selection was developed by adapting chemical complementation to provide a growth assay for bond cleavage reactions. First, a URA3 counter selection was adapted to link chemical dimerizer activated gene transcription to cell death. Next, the URA3 counter selection was shown to detect cellulase activity based on cleavage of a tetrasaccharide chemical dimerizer substrate and decrease in expression of the toxic URA3 reporter. Finally, the utility of the cellulase selection was assessed by isolating cellulases with improved activity from a cellulase library created by family DNA shuffling. This application provides further evidence that chemical complementation can be readily adapted to detect different enzymatic activities for important chemical transformations for which no natural selection exists. Because of the large number of enzyme variants that selections can now test as compared to existing medium-throughput screens for cellulases, this assay has the potential to impact the discovery of improved cellulases and other glycosylhydrolases for biomass conversion from libraries of cellulases created by mutagenesis or obtained from natural biodiversity.
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Affiliation(s)
| | | | | | | | - Virginia W. Cornish
- Contribution from the Department of Chemistry, Columbia University, New York, New York, 10027
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27
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Rao AG. The outlook for protein engineering in crop improvement. PLANT PHYSIOLOGY 2008; 147:6-12. [PMID: 18443101 PMCID: PMC2330291 DOI: 10.1104/pp.108.117929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2008] [Accepted: 03/10/2008] [Indexed: 05/26/2023]
Affiliation(s)
- A Gururaj Rao
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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28
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Busso D, Stierlé M, Thierry JC, Moras D. A comparison of inoculation methods to simplify recombinant protein expression screening in Escherichia coli. Biotechniques 2008; 44:101-6. [PMID: 18254387 DOI: 10.2144/000112632] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the past five years, Structural Genomics (SG) initiatives have established an automated pipeline for protein production in Escherichia coli to rapidly screen various conditions, resulting in soluble expression of recombinant proteins to aid in carrying out structural studies. However, some steps of the procedure are still extensive and require manual handling. Here, we present a comparative study of one step of the process, E. coli cultivation, using a set of 12 expression vectors encoding for fusion proteins of seven independent target proteins. First, we show that performing E. coli growth in auto-inducible medium (ZYM-5052) results in a comparable protein expression/solubility profile to that obtained when growing cells in classical Luria-Bertani (LB) medium. Second, we show that the transformation mix can be used directly to inoculate a culture, saving time and circumventing the error-prone step of colony picking, without impairing cell growth and the protein expression/solubility profile. Thus, we show that a basic, but nevertheless essential, step of a protein production pipeline, E. coli cultivation, can be simplified to a single event that is fully compatible with complete automation.
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Affiliation(s)
- Didier Busso
- Institut de Génetique et de Biologie Moléculaire et Cellulaire/Centre National de Recherche Scientifique/Institut National de la Santé de la Recherche Médicale, Université Louis Pasteur, Illkirch, France.
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29
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Abstract
Life on earth is not possible without microorganisms. Microbes have contributed to industrial science for over 100 years. They have given us diversity in enzymatic content and metabolic pathways. The advent of recombinant DNA brought many changes to industrial microbiology. New expression systems have been developed, biosynthetic pathways have been modified by metabolic engineering to give new metabolites, and directed evolution has provided enzymes with modified selectability, improved catalytic activity and stability. More and more genomes of industrial microorganisms are being sequenced giving valuable information about the genetic and enzymatic makeup of these valuable forms of life. Major tools such as functional genomics, proteomics, and metabolomics are being exploited for the discovery of new valuable small molecules for medicine and enzymes for catalysis.
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Affiliation(s)
- Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
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30
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Graziano JJ, Liu W, Perera R, Geierstanger BH, Lesley SA, Schultz PG. Selecting folded proteins from a library of secondary structural elements. J Am Chem Soc 2008; 130:176-85. [PMID: 18067292 PMCID: PMC2714538 DOI: 10.1021/ja074405w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A protein evolution strategy is described by which double-stranded DNA fragments encoding defined Escherichia coli protein secondary structural elements (alpha-helices, beta-strands, and loops) are assembled semirandomly into sequences comprised of as many as 800 amino acid residues. A library of novel polypeptides generated from this system was inserted into an enhanced green fluorescent protein (EGFP) fusion vector. Library members were screened by fluorescence activated cell sorting (FACS) to identify those polypeptides that fold into soluble, stable structures in vivo that comprised a subset of shorter sequences ( approximately 60 to 100 residues) from the semirandom sequence library. Approximately 108 clones were screened by FACS, a set of 1149 high fluorescence colonies were characterized by dPCR, and four soluble clones with varying amounts of secondary structure were identified. One of these is highly homologous to a domain of aspartate racemase from a marine bacterium (Polaromonas sp.) but is not homologous to any E. coli protein sequence. Several other selected polypeptides have no global sequence homology to any known protein but show significant alpha-helical content, limited dispersion in 1D nuclear magnetic resonance spectra, pH sensitive ANS binding and reversible folding into soluble structures. These results demonstrate that this strategy can generate novel polypeptide sequences containing secondary structure.
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Affiliation(s)
| | | | | | - Bernhard H. Geierstanger
- To whom correspondence should be addressed. Telephone: 858-784-9273 (P.G.S.), 858-812-1551 (S.A.L.), or 858-812-1633 (B.H.G.). Fax: 858-784-9440 (P.G.S.), 858-812-1920 (S.A.L.), or 858-812-1746 (B.H.G.). ; ;
| | - Scott A. Lesley
- To whom correspondence should be addressed. Telephone: 858-784-9273 (P.G.S.), 858-812-1551 (S.A.L.), or 858-812-1633 (B.H.G.). Fax: 858-784-9440 (P.G.S.), 858-812-1920 (S.A.L.), or 858-812-1746 (B.H.G.). ; ;
| | - Peter G. Schultz
- To whom correspondence should be addressed. Telephone: 858-784-9273 (P.G.S.), 858-812-1551 (S.A.L.), or 858-812-1633 (B.H.G.). Fax: 858-784-9440 (P.G.S.), 858-812-1920 (S.A.L.), or 858-812-1746 (B.H.G.). ; ;
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31
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Demain AL, Adrio JL. Strain improvement for production of pharmaceuticals and other microbial metabolites by fermentation. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2008; 65:251-289. [PMID: 18084918 DOI: 10.1007/978-3-7643-8117-2_7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microbes have been good to us. They have given us thousands of valuable products with novel structures and activities. In nature, they only produce tiny amounts of these secondary metabolic products as a matter of survival. Thus, these metabolites are not overproduced in nature, but they must be overproduced in the pharmaceutical industry. Genetic manipulations are used in industry to obtain strains that produce hundreds or thousands of times more than that produced by the originally isolated strain. These strain improvement programs traditionally employ mutagenesis followed by screening or selection; this is known as 'brute-force' technology. Today, they are supplemented by modern strategic technologies developed via advances in molecular biology, recombinant DNA technology, and genetics. The progress in strain improvement has increased fermentation productivity and decreased costs tremendously. These genetic programs also serve other goals such as the elimination of undesirable products or analogs, discovery of new antibiotics, and deciphering of biosynthetic pathways.
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Affiliation(s)
- Arnold L Demain
- Research Institute for Scientists Emeriti (RISE), HS-330, Drew University, Madison, NJ 07940 USA.
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32
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Bachl J, Caldwell RB, Buerstedde JM. Biotechnology and the chicken B cell line DT40. Cytogenet Genome Res 2007; 117:189-94. [PMID: 17675859 DOI: 10.1159/000103179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 12/07/2006] [Indexed: 12/22/2022] Open
Abstract
Protein optimization is a major focus of the biotech and pharmaceutical industry. Various in vitro technologies have been developed to accelerate protein evolution and to achieve protein optimization of functional characteristics such as substrate specificity, enzymatic activity and thermostability. The chicken B cell line DT40 diversifies its immunoglobulin (Ig) gene by gene conversion and somatic hypermutation. This machinery can be directed to almost any gene inserted into the Ig locus. Enormously diverse protein libraries of any gene of interest can be quickly generated in DT40 by utilizing random shuffling of complex genetic domains (gene conversion) and by the introduction of novel non-templated genetic information (random mutagenesis). The unique characteristics of the chicken cell line DT40 make it a powerful in-cell diversification system to improve proteins of interest within living cells. One essential advantage of the DT40 protein optimization approach is the fact that variants are generated within an in-cell system thus allowing the direct screening for desired features in the context of intracellular networks. Utilizing specially designed selection strategies, such as the powerful fluorescent protein technology, enables the reliable identification of protein variants exhibiting the most desirable traits. Thus, DT40 is well positioned as a biotechnological tool to generate optimized proteins by applying a powerful combination of gene specific hypermutation, gene conversion and mutant selection.
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Affiliation(s)
- J Bachl
- GSF-National Research Center for Environment and Health, Institute for Molecular Radiobiology, Neuherberg-Munich, Germany
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33
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Brideau-Andersen AD, Huang X, Sun SCC, Chen TT, Stark D, Sas IJ, Zadik L, Dawes GN, Guptill DR, McCord R, Govindarajan S, Roy A, Yang S, Gao J, Chen YH, Skartved NJØ, Pedersen AK, Lin D, Locher CP, Rebbapragada I, Jensen AD, Bass SH, Nissen TLS, Viswanathan S, Foster GR, Symons JA, Patten PA. Directed evolution of gene-shuffled IFN-alpha molecules with activity profiles tailored for treatment of chronic viral diseases. Proc Natl Acad Sci U S A 2007; 104:8269-74. [PMID: 17494769 PMCID: PMC1895939 DOI: 10.1073/pnas.0609001104] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Type I IFNs are unusually pleiotropic cytokines that bind to a single heterodimeric receptor and have potent antiviral, antiproliferative, and immune modulatory activities. The diverse effects of the type I IFNs are of differential therapeutic importance; in cancer therapy, an enhanced antiproliferative effect may be beneficial, whereas in the therapy of viral infections (such as hepatitis B and hepatitis C), the antiproliferative effects lead to dose limiting bone marrow suppression. Studies have shown that various members of the natural IFN-alpha family and engineered variants, such as IFN-con1, vary in the ratios between various IFN-mediated cellular activities. We used DNA shuffling to explore and confirm the hypothesis that one could simultaneously increase the antiviral and Th1-inducing activity and decrease the antiproliferative activity. We report IFN-alpha hybrids wherein the ratio of antiviral:antiproliferative and Th1-inducing: antiproliferative potencies are markedly increased with respsect to IFN-con1 (75- and 80-fold, respectively). A four-residue motif that overlaps with the IFNAR1 binding site and is derived by cross breeding with a pseudogene contributes significantly to this phenotype. These IFN-alphas have an activity profile that may result in an improved therapeutic index and, consequently, better clinical efficacy for the treatment of chronic viral diseases such as hepatitis B virus, human papilloma virus, HIV, or chronic hepatitis C.
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Affiliation(s)
| | - Xiaojian Huang
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | | | - Teddy T. Chen
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | - Diane Stark
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | - Ian J. Sas
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | - Linda Zadik
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | - Glenn N. Dawes
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | | | - Robert McCord
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | | | - Ajoy Roy
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | - Shumin Yang
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | - Judy Gao
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | - Yong Hong Chen
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | | | | | - David Lin
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | | | | | - Anne Dam Jensen
- Maxygen, Anpartsselskab, Agern Alle 1, DK-2970 Hoersholm, Denmark
| | - Steven H. Bass
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
| | | | | | - Graham R. Foster
- Queen Mary's School of Medicine and Dentistry, Institute of Cell and Molecular Science, The Royal London Hospital, 4 Newark Street, London E1 2AT, England
| | - Julian A. Symons
- Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304; and
| | - Phillip A. Patten
- *Maxygen, Incorporated, 515 Galveston Drive, Redwood City, CA 94063
- To whom correspondence should be addressed. E-mail:
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34
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Floss DM, Falkenburg D, Conrad U. Production of vaccines and therapeutic antibodies for veterinary applications in transgenic plants: an overview. Transgenic Res 2007; 16:315-32. [PMID: 17436059 PMCID: PMC7089296 DOI: 10.1007/s11248-007-9095-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 03/19/2007] [Indexed: 11/29/2022]
Abstract
During the past two decades, antibodies, antibody derivatives and vaccines have been developed for therapeutic and diagnostic applications in human and veterinary medicine. Numerous species of dicot and monocot plants have been genetically modified to produce antibodies or vaccines, and a number of diverse transformation methods and strategies to enhance the accumulation of the pharmaceutical proteins are now available. Veterinary applications are the specific focus of this article, in particular for pathogenic viruses, bacteria and eukaryotic parasites. We focus on the advantages and remaining challenges of plant-based therapeutic proteins for veterinary applications with emphasis on expression platforms, technologies and economic considerations.
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Affiliation(s)
- Doreen Manuela Floss
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466 Germany
| | | | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466 Germany
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35
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Low D, O'Leary R, Pujar NS. Future of antibody purification. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 848:48-63. [PMID: 17134947 DOI: 10.1016/j.jchromb.2006.10.033] [Citation(s) in RCA: 303] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 09/25/2006] [Accepted: 10/09/2006] [Indexed: 12/29/2022]
Abstract
Antibody purification seems to be safely ensconced in a platform, now well-established by way of multiple commercialized antibody processes. However, natural evolution compels us to peer into the future. This is driven not only by a large, projected increase in the number of antibody therapies, but also by dramatic improvements in upstream productivity, and process economics. Although disruptive technologies have yet escaped downstream processes, evolution of the so-called platform is already evident in antibody processes in late-stage development. Here we perform a wide survey of technologies that are competing to be part of that platform, and provide our [inherently dangerous] assessment of those that have the most promise.
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36
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Zhang XHF, Chasin LA. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc Natl Acad Sci U S A 2006; 103:13427-32. [PMID: 16938881 PMCID: PMC1569180 DOI: 10.1073/pnas.0603042103] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Orthologous gene structures in eight vertebrate species were compared on a genomic scale to detect the birth and maturation of new internal exons during the course of evolution. We found that 40% of new human exons are alternatively spliced, and most of these are cassette exons (exons that are either included or skipped in their entirety) with low inclusion rates. This proportion decreases steadily as older and older exons are examined, even as splicing efficiency increases. Remarkably, the great majority of new cassette exons are composed of highly repeated sequences, especially Alu. Many new cassette exons are 5' untranslated exons; the proportion that code for protein increases steadily with age. New protein-coding exons evolve at a high rate, as evidenced by the initially high substitution rates (K(s) and K(a)), as well as the SNP density compared with older exons. This dynamic picture suggests that de novo recruitment rather than shuffling is the major route by which exons are added to genes, and that species-specific repeats could play a significant role in recent evolution.
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Affiliation(s)
- Xiang H.-F. Zhang
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Lawrence A. Chasin
- Department of Biological Sciences, Columbia University, New York, NY 10027
- To whom correspondence should be addressed. E-mail:
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37
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Busso D, Poussin-Courmontagne P, Rosé D, Ripp R, Litt A, Thierry JC, Moras D. Structural genomics of eukaryotic targets at a laboratory scale. ACTA ACUST UNITED AC 2006; 6:81-8. [PMID: 16211503 DOI: 10.1007/s10969-005-1909-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Accepted: 01/16/2005] [Indexed: 11/29/2022]
Abstract
Structural genomics programs are distributed worldwide and funded by large institutions such as the NIH in United-States, the RIKEN in Japan or the European Commission through the SPINE network in Europe. Such initiatives, essentially managed by large consortia, led to technology and method developments at the different steps required to produce biological samples compatible with structural studies. Besides specific applications, method developments resulted mainly upon miniaturization and parallelization. The challenge that academic laboratories faces to pursue structural genomics programs is to produce, at a higher rate, protein samples. The Structural Biology and Genomics Department (IGBMC - Illkirch - France) is implicated in a structural genomics program of high eukaryotes whose goal is solving crystal structures of proteins and their complexes (including large complexes) related to human health and biotechnology. To achieve such a challenging goal, the Department has established a medium-throughput pipeline for producing protein samples suitable for structural biology studies. Here, we describe the setting up of our initiative from cloning to crystallization and we demonstrate that structural genomics may be manageable by academic laboratories by strategic investments in robotic and by adapting classical bench protocols and new developments, in particular in the field of protein expression, to parallelization.
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Affiliation(s)
- Didier Busso
- Département de Biologie et de Génomique Structurales, IGBMC, CNRS/INSERM/Université Louis Pasteur, Parc d'Innovation, 1 rue Laurent Fries, BP10142, 67404, Illkirch, cedex, France.
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38
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Harmsen MM, van Solt CB, van Zijderveld-van Bemmel AM, Niewold TA, van Zijderveld FG. Selection and optimization of proteolytically stable llama single-domain antibody fragments for oral immunotherapy. Appl Microbiol Biotechnol 2006; 72:544-51. [PMID: 16450109 DOI: 10.1007/s00253-005-0300-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 11/09/2005] [Accepted: 12/13/2005] [Indexed: 11/30/2022]
Abstract
We previously demonstrated that oral application of the recombinant single-domain antibody fragment (VHH) clone K609, directed against Escherichia coli F4 fimbriae, reduced E. coli-induced diarrhoea in piglets, but only at high VHH doses. We have now shown that a large portion of the orally applied K609 VHH is proteolytically degraded in the stomach. Stringent selection for proteolytic stability identified seven VHHs with 7- to 138-fold increased stability after in vitro incubation in gastric fluid. By DNA shuffling we obtained four clones with a further 1.5- to 3-fold increased in vitro stability. These VHHs differed by at most ten amino acid residues from each other and K609 that were scattered over the VHH sequence and did not overlap with predicted protease cleavage sites. The most stable clone, K922, retained 41% activity after incubation in gastric fluid and 90% in jejunal fluid. Oral application of K922 to piglets confirmed its improved proteolytic stability. In addition, K922 bound to F4 fimbriae with higher affinity and inhibited fimbrial adhesion at lower VHH concentrations. K922 is thus a promising candidate for prevention of piglet diarrhoea. Furthermore, our findings could guide selection and improvement by genetic engineering of other recombinant antibody fragments for oral use.
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Affiliation(s)
- M M Harmsen
- Institute for Animal Science and Health (ID-Lelystad) of Wageningen University and Research Centre, Edelhertweg 15, 8219 PH, Lelystad, The Netherlands.
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39
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Abstract
Therapeutic antibodies are well established as an important class of drugs in modern medicine. The exquisite specificity and affinity for a specific target offered by antibodies has also encouraged their development as delivery vehicles for agents such as radionuclides to target tissues, for radioimmunoimaging and radioimmunotherapy. Specifically, in nuclear medicine, radionuclide-conjugated antibody molecules make it possible to image diseased loci with greater sensitivity than other imaging modalities such as magnetic resonance imaging. Furthermore, two radionuclide-conjugated antibodies have recently been approved for the therapy of non-Hodgkin's lymphoma. However, optimal implementation of antibodies has been limited by the extended circulation persistence that is characteristic of native antibodies, which is responsible for increased background activity in radioimmunoimaging applications and dose-related normal organ toxicities in radioimmunotherapy. In this article the current status of radiolabelled intact antibodies is reviewed, focusing on strategies to improve their pharmacokinetic properties to suit a desired application. Examples from the literature that represent different approaches to accomplishing this task in terms of their successes as well as limitations, and perspectives for the future are discussed.
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Affiliation(s)
- Vania Kenanova
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California-Los Angeles, 700 Westwood Plaza, Los Angeles, CA 90095, USA
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40
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Bornscheuer UT. Trends and challenges in enzyme technology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 100:181-203. [PMID: 16270658 DOI: 10.1007/b136413] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Several major developments took place in the field of biocatalysis over the past few years. These include the invention of directed evolution as an extremely useful method for biocatalyst improvement on the molecular level in combination with high-throughput screening systems, methods for accessing "nonculturable" biodiversity using metagenome approaches and progress in sequence-based biocatalyst discovery. In addition, new carriers and tools for immobilization of enzymes have been developed. For the synthesis of optically active compounds impressive examples using new enzymes and major progress in dynamic kinetic resolutions of racemates took place. These achievements are summarized in this review.
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Affiliation(s)
- Uwe T Bornscheuer
- Department of Technical Chemistry and Biotechnology, Institute of Chemistry and Biochemistry, Greifswald University, Soldmannstr. 16, 17487 Greifswald, Germany.
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Tsuzuki K, Tricoire L, Courjean O, Gibelin N, Rossier J, Lambolez B. Thermostable Mutants of the Photoprotein Aequorin Obtained by in Vitro Evolution. J Biol Chem 2005; 280:34324-31. [PMID: 15972815 DOI: 10.1074/jbc.m505303200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aequorin is a photoprotein that emits light upon binding calcium. Aequorin mutants showing increased intensity or slow decay of bioluminescence were isolated by in vitro evolution combining DNA shuffling and functional screening in bacteria. Luminescence decay mutants were isolated at the first round of screening and carried mutations located in EF-hand calcium binding sites or their vicinity. During in vitro evolution, the luminescence intensity of the population of mutants increased with the frequency of effective mutations whereas the frequency of other amino acid substitutions remained roughly stable. Luminescence intensity mutations neighbored the His-16 or His-169 coelenterazine binding residues or were located in the first EF-hand. None of the selected mutants exhibited an increase in photon yield when examined in a cell-free assay. However, we observed that two mutants, Q168R and L170I, exhibited an increase of the photoprotein lifetime at 37 degrees C that may underlie their high luminescence intensity in bacteria. Further analysis of Q168R and L170I mutations showed that they increased aequorin thermostability. Conversely, examination of luminescence decay mutants revealed that the F149S substitution decreased aequorin thermostability. Finally, screening of a library of random Gln-168 and Leu-170 mutants confirmed the involvement of both positions in thermostability and indicated that optimal thermostability was conferred by Q168R and L170I mutations selected through in vitro evolution. Our results suggest that Phe-149 and Gln-168 residues participate in stabilization of the coelenterazine peroxide and the triggering of photon emission by linking the third EF-hand to Trp-129 and His-169 coelenterazine binding residues.
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Affiliation(s)
- Keisuke Tsuzuki
- Laboratoire de Neurobiologie et Diversité Cellulaire, CNRS UMR 7637, Ecole Supérieure de Physique et de Chimie Industrielles, 75005 Paris, France
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42
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Abstract
Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.
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Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
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43
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Bornscheuer UT, Buchholz K. Highlights in Biocatalysis - Historical Landmarks and Current Trends. Eng Life Sci 2005. [DOI: 10.1002/elsc.200520089] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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44
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Minshull J, Ness JE, Gustafsson C, Govindarajan S. Predicting enzyme function from protein sequence. Curr Opin Chem Biol 2005; 9:202-9. [PMID: 15811806 DOI: 10.1016/j.cbpa.2005.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There are two main reasons to try to predict an enzyme's function from its sequence. The first is to identify the components and thus the functional capabilities of an organism, the second is to create enzymes with specific properties. Genomics, expression analysis, proteomics and metabonomics are largely directed towards understanding how information flows from DNA sequence to protein functions within an organism. This review focuses on information flow in the opposite direction: the applicability of what is being learned from natural enzymes to improve methods for catalyst design.
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45
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Lehman N, Unrau PJ. Recombination during in vitro evolution. J Mol Evol 2005; 61:245-52. [PMID: 16007485 DOI: 10.1007/s00239-004-0373-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Accepted: 03/16/2005] [Indexed: 10/25/2022]
Abstract
Recombination, the swapping of large portions of genetic information between and among parental genotypes, can be applied to in vitro evolution experiments on functional nucleic acids. Both homologous and heterologous recombination can be achieved using standard laboratory techniques. In many cases, recombination can allow for the discovery of a ribozyme or DNAzyme phenotype that would not likely be encountered by reliance on point mutations alone. In addition, recombination can often aid in the discovery of global optima in sequence space and/or lessen the number of generations it would take to reach optima. Recombination is most efficiently used in combination with point mutations and applied after the first couple of rounds of selection but before high-fitness genotypes dominate the selection. The "recombination zone" describes that region of sequence space-defined by the residues that will ultimately participate in the function of the winning nucleic acid(s)-where recombination is expected to be the most beneficial in the search for high-fitness genotypes.
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Affiliation(s)
- Niles Lehman
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA.
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46
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Holmberg RC, Henry AA, Romesberg FE. Directed evolution of novel polymerases. ACTA ACUST UNITED AC 2005; 22:39-49. [PMID: 15857782 DOI: 10.1016/j.bioeng.2004.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 12/09/2004] [Accepted: 12/09/2004] [Indexed: 10/25/2022]
Abstract
DNA and RNA polymerases evolved to function in specific environments with specific substrates to propagate genetic information in all living organisms. The commercial availability of these polymerases has revolutionized the biotechnology industry, but for many applications native polymerases are limited by their stability or substrate recognition. Thus, there is great interest in the directed evolution of DNA and RNA polymerases to generate enzymes with novel, desired properties, such as thermal stability, resistance to inhibitors, and altered substrate specificity. Several screening and selection approaches have been developed, both in vivo and in vitro, and have been used to evolve polymerases with a variety of important activities. Both the techniques and the evolved polymerases are reviewed here, along with a comparison of the in vivo and in vitro approaches.
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Affiliation(s)
- Rebecca C Holmberg
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037-1000, USA
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47
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Schmidt M, Bornscheuer UT. High-throughput assays for lipases and esterases. ACTA ACUST UNITED AC 2005; 22:51-6. [PMID: 15857783 DOI: 10.1016/j.bioeng.2004.09.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Revised: 09/23/2004] [Accepted: 09/24/2004] [Indexed: 11/21/2022]
Abstract
In the past few years a considerable number of high-throughput screening (HTS) systems have been developed, especially for lipases and esterases. In this review, a range of HTS methods for the directed evolution of these hydrolases are covered. This includes spectrophotometric and fluorimetric formats as well as other approaches to allow for fast, efficient and reliable identification of desired enzyme variants within large mutant libraries. In addition, methods for library creation and application of lipases and esterases are briefly covered.
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Affiliation(s)
- Marlen Schmidt
- Institute of Chemistry and Biochemistry, Department of Technical Chemistry and Biotechnology, Greifswald University, Soldmannstr. 16, D-17487 Greifswald, Germany
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48
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Locher CP, Paidhungat M, Whalen RG, Punnonen J. DNA shuffling and screening strategies for improving vaccine efficacy. DNA Cell Biol 2005; 24:256-63. [PMID: 15812242 DOI: 10.1089/dna.2005.24.256] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The efficacy of vaccines can be improved by increasing their immunogenicity, broadening their crossprotective range, as well as by developing immunomodulators that can be coadministered with the vaccine antigen. One technology that can be applied to each of these aspects of vaccine development is MolecularBreeding directed molecular evolution. Essentially, this technology is used to evolve genes in vitro through an iterative process consisting of recombinant generation followed by selection of the desired recombinants. We have used DNA shuffling and screening strategies to develop and improve vaccine candidates against several infectious pathogens including Plasmodium falciparum (a common cause of severe and fatal human malaria), dengue virus, encephalitic alphaviruses such as Venezuelan, western and eastern equine encephalitis viruses (VEEV, WEEV, and EEEV, respectively), human immunodeficiency virus-1 (HIV-1), and hepatitis B virus (HBV). By recombining antigen-encoding genes from different serovar isolates, new chimeras are selected for crossreactivity; these vaccine candidates are expected to provide broader crossprotection than vaccines based on a single serovar. Furthermore, the vaccine candidates can be selected for improved immunogenicity, which would also improve their efficacy. In addition to vaccine candidates, we have applied the technology to evolve several immunomodulators that when coadministered with vaccines can improve vaccine efficacy by fine-tuning the T cell response. Thus, DNA shuffling and screening technology is a promising strategy to facilitate vaccine efficacy.
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Affiliation(s)
- Christopher P Locher
- Division of Infectious Diseases, Maxygen, Inc., Redwood City, California 94063, USA.
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49
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Fox R. Directed molecular evolution by machine learning and the influence of nonlinear interactions. J Theor Biol 2005; 234:187-99. [PMID: 15757678 DOI: 10.1016/j.jtbi.2004.11.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 11/03/2004] [Accepted: 11/22/2004] [Indexed: 10/25/2022]
Abstract
Alternative search strategies for the directed evolution of proteins are presented and compared with each other. In particular, two different machine learning strategies based on partial least-squares regression are developed: the first contains only linear terms that represent a given residue's independent contribution to fitness, the second contains additional nonlinear terms to account for potential epistatic coupling between residues. The nonlinear modeling strategy is further divided into two types, one that contains all possible nonlinear terms and another that makes use of a genetic algorithm to select a subset of important interaction terms. The performance of each modeling type as a function of training set size is analysed. Simulated molecular evolution on a synthetic protein landscape shows the use of machine learning techniques to guide library design can be a powerful addition to library generation methods such as DNA shuffling.
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Affiliation(s)
- Richard Fox
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA.
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50
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Locher CP, Heinrichs V, Apt D, Whalen RG. Overcoming antigenic diversity and improving vaccines using DNA shuffling and screening technologies. Expert Opin Biol Ther 2005; 4:589-97. [PMID: 15102607 DOI: 10.1517/14712598.4.4.589] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viral, bacterial and parasitic pathogens have evolved multiple strategies to evade the immune response, facilitate transmission and establish chronic infections. One of the underlying strategies that pathogens have evolved is antigenic variation of immune response targets that reduce the affinity of antigen binding to antibodies and major histocompatability complex class I and II receptors. Vaccine candidates generally target a limited number of these antigen variants or combine antigens from several variants to include in multivalent vaccine formulations. DNA shuffling and screening technologies, also known as MolecularBreeding (Maxygen, Inc.) directed molecular evolution, have been successfully used to identify and develop novel and chimaeric vaccine candidates capable of inducing immune responses that recognise and control multiple antigenic variants. DNA shuffling and screening strategies also select vaccine candidates with improved immunogenicity, increased expression as recombinant polypeptides and improved growth of whole viruses in cell culture. As DNA shuffling and screening strategies can be applied to many pathogens, there remain numerous applications of DNA shuffling to solve challenging problems in vaccine process development and manufacture.
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