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Rittner A, Paithankar KS, Drexler DJ, Himmler A, Grininger M. Probing the modularity of megasynthases by rational engineering of a fatty acid synthase Type I. Protein Sci 2018; 28:414-428. [PMID: 30394635 DOI: 10.1002/pro.3550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022]
Abstract
Modularity is a fundamental property of megasynthases such as polyketide synthases (PKSs). In this study, we exploit the close resemblance between PKSs and animal fatty acid synthase (FAS) to re-engineer animal FAS to probe the modularity of the FAS/PKS family. Guided by sequence and structural information, we truncate and dissect animal FAS into its components, and reassemble them to generate new PKS-like modules as well as bimodular constructs. The novel re-engineered modules resemble all four common types of PKSs and demonstrate that this approach can be a powerful tool to deliver products with higher catalytic efficiency. Our data exemplify the inherent plasticity and robustness of the overall FAS/PKS fold, and open new avenues to explore FAS-based biosynthetic pathways for custom compound design.
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Affiliation(s)
- Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Karthik S Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - David Jan Drexler
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Aaron Himmler
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
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Affiliation(s)
- Arnold L. Demain
- Charles A. Dana Research Institute for Scientists Emeriti (RISE), Drew University, Madison, NJ
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Abstract
Here we review key applications of separation technology in applied biology. We first sketch out the field as a whole, but then narrow our scope to the processing of fermentation products, particularly to high-value biologicals such as proteins and nucleotides. We go on to provide a qualitative overview describing the importance and general nature of this large field, major trends, and the strategies that have proven most fruitful in evolving effective separation and purification processes. We then give a detailed description of individual separations equipment and the principles governing their operation. We concentrate throughout on making the available literature accessible to the reader; we provide what is hoped to be a representative set of basic references. However, these references, in turn, include some that suggest promising new developments as well as a number of more specialized reviews. We hope that our overall result provides the reader with access to the most relevant literature.
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Affiliation(s)
- E N Lightfoot
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, USA.
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Abstract
The versatility of microbial biosynthesis is enormous. The most industrially important primary metabolites are the amino acids, nucleotides, vitamins, solvents, and organic acids. Millions of tons of amino acids are produced each year with a total multibillion dollar market. Many synthetic vitamin production processes are being replaced by microbial fermentations. In addition to the multiple reaction sequences of fermentations, microorganisms are extremely useful in carrying out biotransformation processes. These are becoming essential to the fine chemical industry in the production of single-isomer intermediates. Microbially produced secondary metabolites are extremely important to our health and nutrition. As a group, they have tremendous economic importance. The antibiotic market amounts to almost 30 billion dollars and includes about 160 antibiotics and derivatives such as the beta-lactam peptide antibiotics, the macrolide polyketide erythromycin, tetracyclines, aminoglycosides and others. Other important pharmaceutical products produced by microrganisms are hypocholesterolemic agents, enzyme inhibitors, immunosuppressants and antitumor compounds, some having markets of over 1 billion dollars per year. Agriculturally important secondary metabolites include coccidiostats, animal growth promotants, antihelmintics and biopesticides. The modern biotechnology industry has made a major impact in the business world, biopharmaceuticals (recombinant protein drugs, vaccines and monoclonal antibodies) having a market of 15 billion dollars. Recombinant DNA technology has also produced a revolution in agriculture and has markedly increased markets for microbial enzymes. Molecular manipulations have been added to mutational techniques as means of increasing titers and yields of microbial procresses and in discovery of new drugs. Today, microbiology is a major participant in global industry. The best is yet to come as microbes move into the environmental and energy sectors.
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Affiliation(s)
- A L Demain
- Fermentation Microbiology Laboratory, Department of Biology 68-223, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Demain AL, Fang A. The natural functions of secondary metabolites. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2001; 69:1-39. [PMID: 11036689 DOI: 10.1007/3-540-44964-7_1] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Secondary metabolites, including antibiotics, are produced in nature and serve survival functions for the organisms producing them. The antibiotics are a heterogeneous group, the functions of some being related to and others being unrelated to their antimicrobial activities. Secondary metabolites serve: (i) as competitive weapons used against other bacteria, fungi, amoebae, plants, insects, and large animals; (ii) as metal transporting agents; (iii) as agents of symbiosis between microbes and plants, nematodes, insects, and higher animals; (iv) as sexual hormones; and (v) as differentiation effectors. Although antibiotics are not obligatory for sporulation, some secondary metabolites (including antibiotics) stimulate spore formation and inhibit or stimulate germination. Formation of secondary metabolites and spores are regulated by similar factors. This similarity could insure secondary metabolite production during sporulation. Thus the secondary metabolite can: (i) slow down germination of spores until a less competitive environment and more favorable conditions for growth exist; (ii) protect the dormant or initiated spore from consumption by amoebae; or (iii) cleanse the immediate environment of competing microorganisms during germination.
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Affiliation(s)
- A L Demain
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.
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Khumtaveeporn K, DeSantis G, Jones J. Expanded structural and stereospecificity in peptide synthesis with chemically modified mutants of subtilisin. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0957-4166(99)00255-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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DeSantis G, Berglund P, Stabile MR, Gold M, Jones JB. Site-directed mutagenesis combined with chemical modification as a strategy for altering the specificity of the S1 and S1' pockets of subtilisin Bacillus lentus. Biochemistry 1998; 37:5968-73. [PMID: 9558332 DOI: 10.1021/bi9727951] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
By combining site-directed mutagenesis with chemical modification, we have altered the S1 and S1' pocket specificity of subtilisin Bacillus lentus (SBL) through the incorporation of unnatural amino acid moieties, in the following manner: WT --> Cysmutant + H3CSO2SR --> Cys-SR, where R may be infinitely variable. A paradigm between extent of activity changes and surface exposure of the modified residue has emerged. Modification of M222C, a buried residue in the S1' pocket of SBL, caused dramatic changes in kcat/KM, of an up to 122-fold decrease, while modification of S166C, which is located at the bottom of the S1 pocket and is partially surface exposed, effected more modest activity changes. Introduction of a positive charge at S166C does not alter kcat/KM, whereas the introduction of a negative charge results in lowered activity, possibly due to electrostatic interference with oxyanion stabilization. Activity is virtually unaltered upon modification of S156C, which is located toward the bottom of the S1 pocket and surface exposed and whose side chain is solvated. An unexpected structure-activity relationship was revealed for S166C-SR enzymes in that the pattern of activity changes observed with increasing steric size of R was not monotonic. Molecular modeling analysis was used to analyze this unprecedented structure-activity relationship and revealed that the position of the beta-carbon of Cys166 modulates binding of the P1 residue of the AAPF product inhibitor.
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Affiliation(s)
- G DeSantis
- Department of Chemistry, University of Toronto, Ontario, Canada
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Benedetti F, Berti F, Flego M, Resmini M, Bastiani E. A competitive immunoassay for the detection of esterolytic activity of antibodies and enzymes. Anal Biochem 1998; 256:67-73. [PMID: 9466799 DOI: 10.1006/abio.1997.2482] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Screening of a large number of clones produced in a fusion is often the bottleneck in the isolation of catalytic antibodies. The usual approach requires two steps: clones are first selected for their high affinity to the antigen, and then the good binders are tested for their catalytic activity. To simplify this selection process, a competitive enzyme-linked immunosorbent assay (ELISA) has been developed that allows direct screening of the antibodies on the basis of their catalytic activity. In this assay, the product of the catalyzed reaction binds to an immobilized anti-product antibody in competition with a peroxidase-product conjugate. The screening assay has been developed for the antibody-catalyzed hydrolysis of esters of p-aminophenylacetic acid and has been tested on the porcine liver esterase (PLE)-catalyzed hydrolysis of the same substrates. This test allows the detection of product formation at the nanomolar level, while, in a typical assay, the catalytic activity of PLE can be traced down to 200 fmol of enzyme. Under standard conditions for the screening of hybridomas obtained from a fusion, the competitive ELISA allows detection of catalytic species with values of kcat > or = 5 x 10(-7) mol l-1 s-1 and kcat/kuncat > or = 50. While the assay has been designed for the selection of catalytic antibodies, other potential applications of this methodology are in the screening of libraries of engineered and designed enzymes and, in general, in the quantitative measurement of enzyme activity.
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Affiliation(s)
- F Benedetti
- Dipartimento di Scienze Chimiche, Università di Trieste, Italy.
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Zaks A, Dodds DR. Application of biocatalysis and biotransformations to the synthesis of pharmaceuticals. Drug Discov Today 1997. [DOI: 10.1016/s1359-6446(97)01078-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Berglund P, DeSantis G, Stabile MR, Shang X, Gold M, Bott RR, Graycar TP, Lau TH, Mitchinson C, Jones JB. Chemical Modification of Cysteine Mutants of Subtilisin Bacillus lentus Can Create Better Catalysts Than the Wild-Type Enzyme. J Am Chem Soc 1997. [DOI: 10.1021/ja970344y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Per Berglund
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Grace DeSantis
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Michele R. Stabile
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Xiao Shang
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Marvin Gold
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Richard R. Bott
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Thomas P. Graycar
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Tony Hing Lau
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - Colin Mitchinson
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
| | - J. Bryan Jones
- Departments of Chemistry and of Molecular and Medical Genetics University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada Genencor International, Inc., 925 Page Mill Road Palo Alto, California 94304-1013
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