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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Marine Excitatory Amino Acids: Structure, Properties, Biosynthesis and Recent Approaches to Their Syntheses. Molecules 2020; 25:molecules25133049. [PMID: 32635311 PMCID: PMC7412112 DOI: 10.3390/molecules25133049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 11/26/2022] Open
Abstract
This review considers the results of recent studies on marine excitatory amino acids, including kainic acid, domoic acid, dysiherbaine, and neodysiherbaine A, known as potent agonists of one of subtypes of glutamate receptors, the so-called kainate receptors. Novel information, particularly concerning biosynthesis, environmental roles, biological action, and syntheses of these marine metabolites, obtained mainly in last 10–15 years, is summarized. The goal of the review was not only to discuss recently obtained data, but also to provide a brief introduction to the field of marine excitatory amino acid research.
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Harðardóttir S, Wohlrab S, Hjort DM, Krock B, Nielsen TG, John U, Lundholm N. Transcriptomic responses to grazing reveal the metabolic pathway leading to the biosynthesis of domoic acid and highlight different defense strategies in diatoms. BMC Mol Biol 2019; 20:7. [PMID: 30808304 PMCID: PMC6390554 DOI: 10.1186/s12867-019-0124-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND A major cause of phytoplankton mortality is predation by zooplankton. Strategies to avoid grazers have probably played a major role in the evolution of phytoplankton and impacted bloom dynamics and trophic energy transport. Certain species of the genus Pseudo-nitzschia produce the neurotoxin, domoic acid (DA), as a response to the presence of copepod grazers, suggesting that DA is a defense compound. The biosynthesis of DA comprises fusion of two precursors, a C10 isoprenoid geranyl pyrophosphate and L-glutamate. Geranyl pyrophosphate (GPP) may derive from the mevalonate isoprenoid (MEV) pathway in the cytosol or from the methyl-erythritol phosphate (MEP) pathway in the plastid. L-glutamate is suggested to derive from the citric acid cycle. Fragilariopsis, a phylogenetically related but nontoxic genus of diatoms, does not appear to possess a similar defense mechanism. We acquired information on genes involved in biosynthesis, precursor pathways and regulatory functions for DA production in the toxigenic Pseudo-nitzschia seriata, as well as genes involved in responses to grazers to resolve common responses for defense strategies in diatoms. RESULTS Several genes are expressed in cells of Pseudo-nitzschia when these are exposed to predator cues. No genes are expressed in Fragilariopsis when treated similarly, indicating that the two taxa have evolved different strategies to avoid predation. Genes involved in signal transduction indicate that Pseudo-nitzschia cells receive signals from copepods that transduce cascading molecular precursors leading to the formation of DA. Five out of seven genes in the MEP pathway for synthesis of GPP are upregulated, but none in the conventional MEV pathway. Five genes with known or suggested functions in later steps of DA formation are upregulated. We conclude that no gene regulation supports that L-glutamate derives from the citric acid cycle, and we suggest the proline metabolism to be a downstream precursor. CONCLUSIONS Pseudo-nitzschia cells, but not Fragilariopsis, receive and respond to copepod cues. The cellular route for the C10 isoprenoid product for biosynthesis of DA arises from the MEP metabolic pathway and we suggest proline metabolism to be a downstream precursor for L-glutamate. We suggest 13 genes with unknown function to be involved in diatom responses to grazers.
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Affiliation(s)
- Sara Harðardóttir
- Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Sylke Wohlrab
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Ammerländer Heestraße 231, Oldenburg, Germany
| | - Ditte Marie Hjort
- Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Bernd Krock
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Torkel Gissel Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Building 201, Kemitorvet, Lyngby Campus, 2800 Kgs. Lyngby, Denmark
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Ammerländer Heestraße 231, Oldenburg, Germany
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
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Brunson JK, McKinnie SMK, Chekan JR, McCrow JP, Miles ZD, Bertrand EM, Bielinski VA, Luhavaya H, Oborník M, Smith GJ, Hutchins DA, Allen AE, Moore BS. Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom. Science 2018; 361:1356-1358. [PMID: 30262498 PMCID: PMC6276376 DOI: 10.1126/science.aau0382] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/15/2018] [Indexed: 01/26/2023]
Abstract
Oceanic harmful algal blooms of Pseudo-nitzschia diatoms produce the potent mammalian neurotoxin domoic acid (DA). Despite decades of research, the molecular basis for its biosynthesis is not known. By using growth conditions known to induce DA production in Pseudo-nitzschia multiseries, we implemented transcriptome sequencing in order to identify DA biosynthesis genes that colocalize in a genomic four-gene cluster. We biochemically investigated the recombinant DA biosynthetic enzymes and linked their mechanisms to the construction of DA's diagnostic pyrrolidine skeleton, establishing a model for DA biosynthesis. Knowledge of the genetic basis for toxin production provides an orthogonal approach to bloom monitoring and enables study of environmental factors that drive oceanic DA production.
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Affiliation(s)
- John K Brunson
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Shaun M K McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - John P McCrow
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Zachary D Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Erin M Bertrand
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Miroslav Oborník
- Institute of Parasitology, University of South Bohemia and Biology Center CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - G Jason Smith
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, CA 95039, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew E Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA.
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Maeno Y, Kotaki Y, Terada R, Cho Y, Konoki K, Yotsu-Yamashita M. Six domoic acid related compounds from the red alga, Chondria armata, and domoic acid biosynthesis by the diatom, Pseudo-nitzschia multiseries. Sci Rep 2018; 8:356. [PMID: 29321590 PMCID: PMC5762911 DOI: 10.1038/s41598-017-18651-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/15/2017] [Indexed: 01/05/2023] Open
Abstract
Domoic acid (DA, 1), a potent neurotoxin that causes amnesic shellfish poisoning, has been found in diatoms and red algae. While biosynthetic pathway towards DA from geranyl diphosphate and L-glutamate has been previously proposed, its late stage is still unclear. Here, six novel DA related compounds, 7'-methyl-isodomoic acid A (2) and B (3), N-geranyl-L-glutamic acid (4), 7'-hydroxymethyl-isodomoic acid A (5) and B (6), and N-geranyl-3(R)-hydroxy-L-glutamic acid (7), were isolated from the red alga, Chondria armata, and their structures were determined. The compounds 4 and 7, linear compounds, are predictable as the precursors to form the DA pyrrolidine ring. The compounds 2 and 3 are thought as the cyclized products of 7; therefore, dehydration and electron transfer from the internal olefin of 7 is a possible mechanism for the pyrrolidine ring formation. One terminal methyl group of the side chain of 2 and 3 is predicted to be oxidized to hydroxymethyl (5, 6), and then to carboxylic acids, forming isodomoic acids A and B. Finally, the terminal olefin of isodomoic acid A would be isomerized to form DA. In addition, [15N, D]-labeled 4 was incorporated into DA using the diatom, Pseudo-nitzschia multiseries, demonstrating that 4 is the genuine precursor of DA.
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Affiliation(s)
- Yukari Maeno
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-0845, Japan
| | - Yuichi Kotaki
- Fukushima College, 1-1 Chigoike Miyashiro, Fukushima, 960-0181, Japan
| | - Ryuta Terada
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Yuko Cho
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-0845, Japan
| | - Keiichi Konoki
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-0845, Japan
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-0845, Japan.
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Transcriptome sequencing of three Pseudo-nitzschia species reveals comparable gene sets and the presence of Nitric Oxide Synthase genes in diatoms. Sci Rep 2015; 5:12329. [PMID: 26189990 PMCID: PMC4648414 DOI: 10.1038/srep12329] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/25/2015] [Indexed: 01/12/2023] Open
Abstract
Diatoms are among the most diverse eukaryotic microorganisms on Earth, they are responsible for a large fraction of primary production in the oceans and can be found in different habitats. Pseudo-nitzschia are marine planktonic diatoms responsible for blooms in coastal and oceanic waters. We analyzed the transcriptome of three species, Pseudo-nitzschia arenysensis, Pseudo-nitzschia delicatissima and Pseudo-nitzschia multistriata, with different levels of genetic relatedness. These species have a worldwide distribution and the last one produces the neurotoxin domoic acid. We were able to annotate about 80% of the sequences in each transcriptome and the analysis of the relative functional annotations allowed comparison of the main metabolic pathways, pathways involved in the biosynthesis of isoprenoids (MAV and MEP pathways), and pathways putatively involved in domoic acid synthesis. The search for homologous transcripts among the target species and other congeneric species resulted in the discovery of a sequence annotated as Nitric Oxide Synthase (NOS), found uniquely in Pseudo-nitzschia multistriata. The predicted protein product contained all the domains of the canonical metazoan sequence. Putative NOS sequences were found in other available diatom datasets, supporting a role for nitric oxide as signaling molecule in this group of microalgae.
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Jiang S, Kuwano K, Ishikawa N, Yano M, Takatani T, Arakawa O. Production of domoic acid by laboratory culture of the red alga Chondria armata. Toxicon 2014; 92:1-5. [PMID: 25240296 DOI: 10.1016/j.toxicon.2014.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/01/2014] [Accepted: 09/09/2014] [Indexed: 10/24/2022]
Abstract
To clarify the production mechanisms and biologic functions of domoic acid (DA) by the red alga Chondria armata, we established a laboratory culture of C. armata. The alga grew better in modified PES medium (mPES) without trace metals or manganese than in unmodified mPES (seawater + nitrate, phosphate, iron, trace metals, vitamins, and 2-[4-(2-hydroxyethyl)-1-piperazinyl]-ethanesulfonic acid), suggesting that C. armata is especially hypersensitive to the toxicity of excessive manganese. C. armata cultured in N·P·Fe medium (seawater + nitrate, phosphate, and iron) grew best (mean growth rate 828.4%) at a relative nutrient concentration of 50%. Liquid chromatography-mass spectrometry analysis of the algal extracts revealed that the DA content of the cultured explants (2273-3308 ppm) was 4-5 fold higher than that of wild specimens. The extract of pooled explants (60 g) was purified by activated charcoal treatment and several types of column chromatography to afford ca. 10 mg DA. The (1)H-nuclear magnetic resonance spectrum of the preparation was indistinguishable from the previously reported spectrum of DA, indicating that C. armata itself has an ability to produce DA.
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Affiliation(s)
- Shanshan Jiang
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, 1-14, Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kazuyoshi Kuwano
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, 1-14, Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Nozomi Ishikawa
- Faculty of Fisheries, Nagasaki University, 1-14, Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Michiko Yano
- Faculty of Fisheries, Nagasaki University, 1-14, Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Tomohiro Takatani
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, 1-14, Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Osamu Arakawa
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, 1-14, Bunkyo-machi, Nagasaki 852-8521, Japan.
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Boissonneault KR, Henningsen BM, Bates SS, Robertson DL, Milton S, Pelletier J, Hogan DA, Housman DE. Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries. BMC Mol Biol 2013; 14:25. [PMID: 24180290 PMCID: PMC3832940 DOI: 10.1186/1471-2199-14-25] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions. RESULTS Through microarray analysis of exponential- and stationary-phase cultures with low and high domoic acid production, respectively, we identified candidate reference genes whose transcripts did not vary across conditions. We tested eleven potential reference genes for stability using RT-qPCR and GeNorm analyses. Our results indicated that transcripts encoding JmjC, dynein, and histone H3 proteins were the most suitable for normalization of expression data under conditions of silicon-limitation, in late-exponential through stationary phase. The microarray studies identified a number of genes that were up- and down-regulated under toxin-producing conditions. RT-qPCR analysis, using the validated controls, confirmed the up-regulation of transcripts predicted to encode a cycloisomerase, an SLC6 transporter, phosphoenolpyruvate carboxykinase, glutamate dehydrogenase, a small heat shock protein, and an aldo-keto reductase, as well as the down-regulation of a transcript encoding a fucoxanthin-chlorophyll a-c binding protein, under these conditions. CONCLUSION Our results provide a strong basis for further studies of RNA expression levels in Ps-n, which will contribute to our understanding of genes involved in the production and release of domoic acid, an important neurotoxin that affects human health as well as ecosystem function.
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Affiliation(s)
- Katie Rose Boissonneault
- Department of Biological Sciences, Plymouth State University, MSC 64, 17 High St., Plymouth, NH 03264, USA
- Koch Institute, Massachusetts Institute of Technology, 76-553, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Brooks M Henningsen
- Department of Biological Sciences, Plymouth State University, MSC 64, 17 High St., Plymouth, NH 03264, USA
- Present address: Mascoma Corporation, 67 Etna Road Suite 300, Lebanon, NH 03766, USA
| | - Stephen S Bates
- Fisheries and Oceans Canada, Gulf Fisheries Centre, P.O. Box 5030, Moncton, New Brunswick E1C 9B6, Canada
| | - Deborah L Robertson
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Sean Milton
- Koch Institute, Massachusetts Institute of Technology, 76-553, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Present address: Vertex Pharmaceuticals, 130 Waverly Street, Cambridge, MA 02139, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Vail Building Room 208, Dartmouth Medical School, Hanover, NH 03755, USA
| | - David E Housman
- Koch Institute, Massachusetts Institute of Technology, 76-553, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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