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Karlo J, Gupta A, Singh SP. In situ monitoring of the shikimate pathway: a combinatorial approach of Raman reverse stable isotope probing and hyperspectral imaging. Analyst 2024; 149:2833-2841. [PMID: 38587502 DOI: 10.1039/d4an00203b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Sensing and visualization of metabolites and metabolic pathways in situ are significant requirements for tracking their spatiotemporal dynamics in a non-destructive manner. The shikimate pathway is an important cellular mechanism that leads to the de novo synthesis of many compounds containing aromatic rings of high importance such as phenylalanine, tyrosine, and tryptophan. In this work, we present a cost-effective and extraction-free method based on the principles of stable isotope-coupled Raman spectroscopy and hyperspectral Raman imaging to monitor and visualize the activity of the shikimate pathway. We also demonstrated the applicability of this approach for nascent aromatic amino acid localization and tracking turnover dynamics in both prokaryotic and eukaryotic model systems. This method can emerge as a promising tool for both qualitative and semi-quantitative in situ metabolomics, contributing to a better understanding of aromatic ring-containing metabolite dynamics across various organisms.
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Affiliation(s)
- Jiro Karlo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, 580011, India.
| | - Aryan Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, 580011, India.
| | - Surya Pratap Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, 580011, India.
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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- 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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3
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Utomo JC, Barrell HB, Kumar R, Smith J, Brant MS, De la Hoz Siegler H, Ro DK. Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux. Metab Eng 2024; 82:286-296. [PMID: 38387678 DOI: 10.1016/j.ymben.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2-19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (∼4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.
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Affiliation(s)
- Joseph Christian Utomo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hailey Brynn Barrell
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Rahul Kumar
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Jessica Smith
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Maximilian Simon Brant
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hector De la Hoz Siegler
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
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Winters NP, Wafula EK, Knollenberg BJ, Hämälä T, Timilsena PR, Perryman M, Zhang D, Sheaffer LL, Praul CA, Ralph PE, Prewitt S, Leandro-Muñoz ME, Delgadillo-Duran DA, Altman NS, Tiffin P, Maximova SN, dePamphilis CW, Marden JH, Guiltinan MJ. A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora. BMC Biol 2024; 22:38. [PMID: 38360697 PMCID: PMC10870529 DOI: 10.1186/s12915-024-01831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora. RESULTS We began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp. CONCLUSIONS Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.
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Affiliation(s)
- Noah P Winters
- IGDP Ecology, The Pennsylvania State University, 422 Huck Life Sciences Building, University Park, PA, 16803, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Prakash R Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Perryman
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
| | - Lena L Sheaffer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Craig A Praul
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Siela N Maximova
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mark J Guiltinan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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5
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Usami Y, Mizobuchi Y, Ijuin M, Yamada T, Morita M, Mizuki K, Yoneyama H, Harusawa S. Synthesis of 6-Halo-Substituted Pericosine A and an Evaluation of Their Antitumor and Antiglycosidase Activities. Mar Drugs 2022; 20:md20070438. [PMID: 35877731 PMCID: PMC9323573 DOI: 10.3390/md20070438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
The enantiomers of 6-fluoro-, 6-bromo-, and 6-iodopericosine A were synthesized. An efficient synthesis of both enantiomers of pericoxide via 6-bromopericosine A was also developed. These 6-halo-substituted pericosine A derivatives were evaluated in terms of their antitumor activity against three types of tumor cells (p388, L1210, and HL-60) and glycosidase inhibitory activity. The bromo- and iodo-congeners exhibited moderate antitumor activity similar to pericosine A against the three types of tumor cell lines studied. The fluorinated compound was less active than the others, including pericosine A. In the antitumor assay, no significant difference in potency between the enantiomers was observed for any of the halogenated compounds. Meanwhile, the (−)-6-fluoro- and (−)-6-bromo-congeners inhibited α-glucosidase to a greater extent than those of their corresponding (+)-enantiomers, whereas (+)-iodopericosine A showed increased activity when compared to its (−)-enantiomer.
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Affiliation(s)
- Yoshihide Usami
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan; (Y.M.); (M.I.); (M.M.); (K.M.); (H.Y.); (S.H.)
- Correspondence: ; Tel.: +81-796-90-1087; Fax: +81-796-90-1005
| | - Yoshino Mizobuchi
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan; (Y.M.); (M.I.); (M.M.); (K.M.); (H.Y.); (S.H.)
| | - Mai Ijuin
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan; (Y.M.); (M.I.); (M.M.); (K.M.); (H.Y.); (S.H.)
| | - Takeshi Yamada
- Department of Medicinal Molecular Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan;
| | - Mizuki Morita
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan; (Y.M.); (M.I.); (M.M.); (K.M.); (H.Y.); (S.H.)
| | - Koji Mizuki
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan; (Y.M.); (M.I.); (M.M.); (K.M.); (H.Y.); (S.H.)
| | - Hiroki Yoneyama
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan; (Y.M.); (M.I.); (M.M.); (K.M.); (H.Y.); (S.H.)
| | - Shinya Harusawa
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki 569-1094, Osaka, Japan; (Y.M.); (M.I.); (M.M.); (K.M.); (H.Y.); (S.H.)
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Lim CA, Jha P, Kumar V, Dyer AT. Effect of EPSPS gene copy number and glyphosate selection on fitness of glyphosate-resistant Bassia scoparia in the field. Sci Rep 2021; 11:16083. [PMID: 34373526 PMCID: PMC8352990 DOI: 10.1038/s41598-021-95517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
The widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. With the continued use of glyphosate in GR sugar beet, the effect of increasing glyphosate rates (applied as single or sequential applications) on the fitness of GR B. scoparia individuals with variable EPSPS gene copies was tested under field conditions. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2214 g ae ha-1 or higher prevented seed production in B. scoparia plants with 2-4 (low levels of resistance) and 5-6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2-6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.
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Affiliation(s)
- Charlemagne Ajoc Lim
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Prashant Jha
- Department of Agronomy, Iowa State University, Ames, IA, USA.
| | - Vipan Kumar
- Agricultural Research Center, Kansas State University, Hays, KS, USA
| | - Alan T Dyer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
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Usami Y, Higuchi M, Mizuki K, Yamamoto M, Kanki M, Nakasone C, Sugimoto Y, Shibano M, Uesawa Y, Nagai J, Yoneyama H, Harusawa S. Syntheses and Glycosidase Inhibitory Activities, and in Silico Docking Studies of Pericosine E Analogs Methoxy-Substituted at C6. Mar Drugs 2020; 18:E221. [PMID: 32326065 PMCID: PMC7230162 DOI: 10.3390/md18040221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
Inspired by the significant -glucosidase inhibitory activities of (+)- and (-)-pericosine E, we herein designed and synthesized 16 analogs of these marine natural products bearing a methoxy group instead of a chlorine atom at C6. Four of these compounds exhibited moderate -glucosidase inhibitory activities, which were weaker than those of the corresponding chlorine-containing species. The four compounds could be prepared by coupling reactions utilizing the (-)-pericosine B moiety. An additional in silico docking simulation suggested that the reason of reduced activity of the C6-methoxylated analogs might be an absence of hydrogen bonding between a methoxy group with the surrounding amino acid residues in the active site in -glucosidase.
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Affiliation(s)
- Yoshihide Usami
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Megumi Higuchi
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Koji Mizuki
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Mizuki Yamamoto
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Mao Kanki
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Chika Nakasone
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Yuya Sugimoto
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Makio Shibano
- Department of Natural Products Research, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan;
| | - Yoshihiro Uesawa
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan; (Y.U.); (J.N.)
| | - Junko Nagai
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan; (Y.U.); (J.N.)
| | - Hiroki Yoneyama
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
| | - Shinya Harusawa
- Department of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara 4-20-1, Takatsuki, Osaka 569-1094, Japan; (M.H.); (K.M.); (M.Y.); (M.K.); (C.N.); (Y.S.); (H.Y.); (S.H.)
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8
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Qu C, Lin L, Yin X, Zhang X, Yang P, Zhang H, Kong H, Wu H, Ni J. Preformulation study and initial determination of biological Properties of isopropylidene shikimic acid. Pak J Pharm Sci 2018; 31:2329-2332. [PMID: 30473500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isopropylidene shikimic acid (ISA), a new drug derviatived from Shikimic Acid, had been proved to be effective in the cerebral protection after cerebral ischemia and reperfusion. But there was little research on the physical pharmacy and biopharmaceutical properties about the drug. In order to provide some useful data for the pharmaceutical development of ISA, the solubility, stability and Oil/Water partition coefficient (LogP) were determined by the classic preformulation study method, and the transmembrane performance of ISA was studied by Franz -diffusion cell method in vitro. The results showed that ISA was water-soluble with a solubility 32.52mg/ml, which could be improved to 44.32 mg/ml by 1% (w/v) sodium dodecylsulfate; the LogP was -0.63; ISA was less stable in water but it was stable when pH greater than 6.0 and unstable when pH less than 6.0; the accumulated permeation rates at 1h were about 50% and more than 80% at 6h. Data obtained by the study indicated that the medium selection and pH control were important for liquid preparation of ISA, and avoiding dissolution and absorption in stomach was critical for the oral solid dosage forms. Mucosal drug delivery systems would be considered, according to the certain hydrophilic-lipophilic characters and good transmembrane capability.
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Affiliation(s)
- Changhai Qu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, PR China
| | - Longfei Lin
- Institute Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Xingbin Yin
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, PR China
| | - Xiaoyan Zhang
- Beijing Children's Hospital, Capital Medical University, Beijing, PR China
| | - Pei Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, PR China
| | - Hui Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, PR China
| | - Hui Kong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, PR China
| | - Huangyan Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, PR China
| | - Jian Ni
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, PR China
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9
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Abstract
Context 3,4-Oxo-isopropylidene-shikimic acid (ISA) is an analog of shikimic acid (SA). SA is extracted from the dry fruit of Illicium verum Hook. f. (Magnoliaceae), which has been used for treating stomachaches, skin inflammation and rheumatic pain. Objective To investigate the anti-inflammatory, analgesic and antioxidant activities of ISA. Materials and methods Analgesic and anti-inflammatory activities of ISA were evaluated using writhing, hot plate, xylene-induced ear oedema, carrageenan-induced paw oedema and cotton pellets-induced granuloma test, meanwhile the prostaglandin E2 (PGE2) and malondialdehyde (MDA) levels were assessed in the oedema paw tissue. ISA (60, 120 and 240 mg/kg in mice model and 50, 120 and 200 mg/kg in rat model) was administered orally, 30 min before induction of inflammation/pain. Additionally, ISA was administered for 12 d in rats from the day of cotton pellet implantation. The active oxygen species scavenging potencies of ISA (10(-3)-10(-5) M) were evaluated by the electron spin resonance spin-trapping technique. Results ISA caused a reduction of inflammation induced by xylene (18.1-31.4%), carrageenan (7.8-51.0%) and cotton pellets (11.4-24.0%). Furthermore, ISA decreased the production of PGE2 and MDA in the rat paw tissue by 1.0-15.6% and 6.3-27.6%, respectively. ISA also reduced pain induced by acetic acid (15.6-48.9%) and hot plate (10.5-28.5%). Finally, ISA exhibited moderate antioxidant activity by scavenging the superoxide radical and hydroxyl radical with IC50 values of 0.214 and 0.450 μg/mL, respectively. Discussion and conclusion Our findings confirmed the anti-inflammatory, analgesic and antioxidant activities of ISA.
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Affiliation(s)
- Jin-Yao Sun
- a School of Pharmacy , Xi'an Jiaotong University , Xi'an , China
- b Department of Pharmacy , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , China
| | - Cui-Yu You
- b Department of Pharmacy , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , China
| | - Kai Dong
- a School of Pharmacy , Xi'an Jiaotong University , Xi'an , China
| | - Hai-Sheng You
- b Department of Pharmacy , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , China
| | - Jian-Feng Xing
- a School of Pharmacy , Xi'an Jiaotong University , Xi'an , China
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10
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Sutton KA, Breen J, Russo TA, Schultz LW, Umland TC. Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2016; 72:179-87. [PMID: 26919521 PMCID: PMC4774876 DOI: 10.1107/s2053230x16001114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/19/2016] [Indexed: 01/01/2023] Open
Abstract
The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the sixth step of the seven-step shikimate pathway. Chorismate, the product of the pathway, is a precursor for the biosynthesis of aromatic amino acids, siderophores and metabolites such as folate, ubiquinone and vitamin K. The shikimate pathway is present in bacteria, fungi, algae, plants and apicomplexan parasites, but is absent in humans. The EPSP synthase enzyme produces 5-enolpyruvylshikimate 3-phosphate and phosphate from phosphoenolpyruvate and shikimate 3-phosphate via a transferase reaction, and is the target of the herbicide glyphosate. The Acinetobacter baumannii gene encoding EPSP synthase, aroA, has previously been demonstrated to be essential during host infection for the growth and survival of this clinically important drug-resistant ESKAPE pathogen. Prephenate dehydrogenase is also encoded by the bifunctional A. baumannii aroA gene, but its activity is dependent upon EPSP synthase since it operates downstream of the shikimate pathway. As part of an effort to evaluate new antimicrobial targets, recombinant A. baumannii EPSP (AbEPSP) synthase, comprising residues Ala301-Gln756 of the aroA gene product, was overexpressed in Escherichia coli, purified and crystallized. The crystal structure, determined to 2.37 Å resolution, is described in the context of a potential antimicrobial target and in comparison to EPSP synthases that are resistant or sensitive to the herbicide glyphosate.
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Affiliation(s)
- Kristin A. Sutton
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Jennifer Breen
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Thomas A. Russo
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
- Veterans Administration Western New York Healthcare System and Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - L. Wayne Schultz
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
- Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Timothy C. Umland
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
- Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
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11
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Peek J, Christendat D. The shikimate dehydrogenase family: functional diversity within a conserved structural and mechanistic framework. Arch Biochem Biophys 2014; 566:85-99. [PMID: 25524738 DOI: 10.1016/j.abb.2014.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/19/2014] [Accepted: 12/07/2014] [Indexed: 11/19/2022]
Abstract
Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-deydroshikimate to shikimate, an essential reaction in the biosynthesis of the aromatic amino acids and a large number of other secondary metabolites in plants and microbes. The indispensible nature of this enzyme makes it a potential target for herbicides and antimicrobials. SDH is the archetypal member of a large protein family, which contains at least four additional functional classes with diverse metabolic roles. The different members of the SDH family share a highly similar three-dimensional structure and utilize a conserved catalytic mechanism, but exhibit distinct substrate preferences, making the family a particularly interesting system for studying modes of substrate recognition used by enzymes. Here, we review our current understanding of the biochemical and structural properties of each of the five previously identified SDH family functional classes.
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Affiliation(s)
- James Peek
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
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12
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Yuan F, Chen W, Jia S, Wang Q. [Improving 3-dehydroshikimate production by metabolically engineered Escherichia coli]. Sheng Wu Gong Cheng Xue Bao 2014; 30:1549-1560. [PMID: 25726580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the aromatic amino acid biosynthetic pathway 3-dehydroshikimate (DHS) is a key intermediate. As a potent antioxidant and important feedstock for producing a variety of important industrial chemicals, such as adipate and vanillin, DHS is of great commercial value. Here, in this study, we investigated the effect of the co-expression of aroFFBR (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase mutant with tyrosine feedback-inhibition resistance) and tktA (Transketolase A) at different copy number on the production of DHS. The increased copy number of aroFFBR and tktA would enhance the production of DHS by the fold of 2.93. In order to further improve the production of DHS, we disrupted the key genes in by-product pathways of the parent strain Escherichia coli AB2834. The triple knockout strain of ldhA, ackA-pta and adhE would further increase the production of DHS. The titer of DHS in shake flask reached 1.83 g/L, 5.7-fold higher than that of the parent strain E. coli AB2834. In 5-L fed-batch fermentation, the metabolically engineered strain produced 25.48 g/L DHS after 62 h. Metabolically engineered E. coli has the potential to further improve the production of DHS.
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13
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Cao Y, Xu H, Xie L, Yi Y, Yu Y, Feng S, Qiao D, Cao Y. Fluorimetric analysis of the binding characteristics of 5-enolpyruvylshikimate-3-phosphate synthase with substrates in Dunaliella salina. J Basic Microbiol 2014; 54:937-44. [PMID: 24026867 DOI: 10.1002/jobm.201300324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/13/2013] [Indexed: 11/06/2022]
Abstract
A general model of the catalytic mechanism for 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) has already been proposed. But whether shikimate-3-phosphate (S3P) alone can cause EPSPs' conformation changes, and whether the binding site of phosphoenolpyruvate (PEP) and glyphosate is the same are still in debate. In this paper, DsaroA gene amplified and cloned from Dunaliella salina (our laboratory's early study) was used for DsEPSPs expression and purification. Then the DsEPSP conformation changes as it bind with different substrates were detected by fluorimetry. The results show that we obtained the DsEPSPs by prokaryotic expression and purification, and the S3P binding with DsEPSPs alone cannot cause DsEPSPs to form "close" conformation directly. However, when S3P exits, DsEPSPs did have a trend to change to the "close" conformation. Then the "close" conformation can be formed completely with the addition of phosphoenolpyruvate (PEP) or glyphosate. The inorganic phosphorus can help S3P to induce two domains of DsEPSPs to form "close" conformation. Besides, when DsEPSPs binds with S3P, in 295 nm, only the intensity of emission peak decreases, however, in 280 nm, not only the peak intensity reduces but also the blue-shift phenomenon takes place. The reason for blue-shift phenomenon was the distribution of aromatic amino acids in EPSPs. EPSPs is a good target for novel antibiotics and herbicides, because of shikimic acid pathway is only present in plants and microorganisms, completely absent in mammals, fish, birds, reptiles, and insects. The results demonstrate that the binding of substrates to EPSPs causes a conformational change from an open form to a closed form, that might be important for designing of novel antimicrobial and herbicidal agents that block closure of the enzyme.
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Affiliation(s)
- Yu Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan, P. R. China
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14
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Zhang Y, Yi L, Lin Y, Zhang L, Shao Z, Liu Z. Characterization and site-directed mutagenesis of a novel class II 5-enopyruvylshikimate-3-phosphate (EPSP) synthase from the deep-sea bacterium Alcanivorax sp. L27. Enzyme Microb Technol 2014; 63:64-70. [PMID: 25039062 DOI: 10.1016/j.enzmictec.2014.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/10/2014] [Accepted: 02/18/2014] [Indexed: 11/21/2022]
Abstract
The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is a key enzyme in the aromatic amino acid biosynthetic pathway in microorganisms and plants, which catalyzes the formation of 5-enolpyruvylshikimate-3-phosphate (EPSP) from shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP). In this study, a novel AroA-encoding gene was identified from the deep sea bacterium Alcanivorax sp. L27 through screening the genomic library and termed as AroAA.sp. A phylogenetic analysis revealed that AroAA.sp (1317 bp and 438 amino acids) is a class II AroA. This enzyme exhibited considerable activity between pH 5.5 and pH 8.0 and notable activity at low temperatures. The KM for PEP and IC50 [glyphosate] values (the concentration of glyphosate that inhibited enzyme activity by 50%) of AroAA.sp were 78 μM and 1.5 mM, respectively. Furthermore, site-directed mutagenesis revealed that the G100A mutant had a 30-fold increase in the IC50 [glyphosate] value; while the L105P mutant showed only 20% catalytic activity compared to wild-type AroAA.sp. The specific activity of the wild-type AroAA.sp, the G100A mutant and the L105P mutant were 7.78 U/mg, 7.26 U/mg and 1.76 U/mg, respectively. This is the first report showing that the G100A mutant of AroA displays considerably improved glyphosate resistance and demonstrates that Leu105 is essential for the enzyme's activity.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Licong Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, College of Life Science, Tarim University, Alar, Xinjiang 843300, People's Republic of China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen 361005, People's Republic of China
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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15
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Adachi O, Ano Y, Toyama H, Matsushita K. High Shikimate Production from Quinate with Two Enzymatic Systems of Acetic Acid Bacteria. Biosci Biotechnol Biochem 2014; 70:2579-82. [PMID: 17031026 DOI: 10.1271/bbb.60259] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
3-Dehydroshikimate was formed with a yield of 57-77% from quinate via 3-dehydroquinate by two successive enzyme reactions, quinoprotein quinate dehydrogenase (QDH) and 3-dehydroquinate dehydratase, in the cytoplasmic membranes of acetic acid bacteria. 3-Dehydroshikimate was then reduced to shikimate (SKA) with NADP-dependent SKA dehydrogenase (SKDH) from the same organism. When SKDH was coupled with NADP-dependent D-glucose dehydrogenase (GDH) in the presence of excess D-glucose as an NADPH re-generating system, SKDH continued to produce SKA until 3-dehydroshikimate added initially in the reaction mixture was completely converted to SKA. Based on the data presented, a strategy for high SKA production was proposed.
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Affiliation(s)
- Osao Adachi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Japan.
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16
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Grunewald W, Bury J. Comment on 'A novel 5-enolpyruvoylshikimate-3-phosphate (EPSP) synthase transgene for glyphosate resistance stimulates growth and fecundity in weedy rice (Oryza sativa) without herbicide' by Wang et al. (2014). New Phytol 2014; 202:367-369. [PMID: 24645784 DOI: 10.1111/nph.12683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Wim Grunewald
- VIB, The Flanders Institute for Biotechnology, Rijvisschestraat 120, 9052, Gent, Belgium
| | - Jo Bury
- VIB, The Flanders Institute for Biotechnology, Rijvisschestraat 120, 9052, Gent, Belgium
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17
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Lu BR, Snow AA, Yang X, Wang W. Scientific data published by a peer-reviewed journal should be properly interpreted: a reply to the letter by Gressel et al. (2014). New Phytol 2014; 202:363-366. [PMID: 24645783 DOI: 10.1111/nph.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Bao-Rong Lu
- Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Handan Road 220, Shanghai, 200433, China
| | - Allison A Snow
- Department of Evolution, Ecology & Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Xiao Yang
- Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Handan Road 220, Shanghai, 200433, China
| | - Wei Wang
- Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Handan Road 220, Shanghai, 200433, China
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18
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Gressel J, Neal Stewart C, Giddings LV, Fischer AJ, Streibig JC, Burgos NR, Trewavas A, Merotto A, Leaver CJ, Ammann K, Moses V, Lawton-Rauh A. Overexpression of epsps transgene in weedy rice: insufficient evidence to support speculations about biosafety. New Phytol 2014; 202:360-362. [PMID: 24645782 DOI: 10.1111/nph.12615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Jonathan Gressel
- Plant Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - C Neal Stewart
- Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - L Val Giddings
- Information Technology & Innovation Foundation, 1101 K Street NW Suite 610, Washington, DC, 20005, USA
| | - Albert J Fischer
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jens Carl Streibig
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630, Taastrup, Denmark
| | - Nilda R Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 1366 W. Altheimer Drive, Fayetteville, AR, 72704, USA
| | - Anthony Trewavas
- Institute of Molecular Plant Science, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JH, UK
| | - Aldo Merotto
- Crop Science Department, Federal University of Rio Grande do Sul, 7712 Bento Goncalves Ave, Porto Alegre, RS 91501-970, Brazil
| | | | - Klaus Ammann
- University of Bern, Monruz 20, 2000, Neuchâtel, Switzerland
| | - Vivian Moses
- King's College, University of London, London, SE1 9NH, UK
| | - Amy Lawton-Rauh
- Department Genetics and Biochemistry, Clemson University, Clemson, SC, 29634-0318, USA
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Lu BR, Snow AA, Yang X, Wang W. Using a single transgenic event to infer fitness effects in crop-weed hybrids: a reply to the Letter by Grunewald & Bury (2014). New Phytol 2014; 202:370-372. [PMID: 24645785 DOI: 10.1111/nph.12748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Bao-Rong Lu
- Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Handan Road 220, Shanghai, 200433, China
| | - Allison A Snow
- Department of Evolution, Ecology & Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Xiao Yang
- Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Handan Road 220, Shanghai, 200433, China
| | - Wei Wang
- Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Handan Road 220, Shanghai, 200433, China
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20
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Wang W, Xia H, Yang X, Xu T, Si HJ, Cai XX, Wang F, Su J, Snow AA, Lu BR. A novel 5-enolpyruvoylshikimate-3-phosphate (EPSP) synthase transgene for glyphosate resistance stimulates growth and fecundity in weedy rice (Oryza sativa) without herbicide. New Phytol 2014; 202:679-688. [PMID: 23905647 PMCID: PMC4286024 DOI: 10.1111/nph.12428] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/27/2013] [Indexed: 05/27/2023]
Abstract
Understanding evolutionary interactions among crops and weeds can facilitate effective weed management. For example, gene flow from crops to their wild or weedy relatives can lead to rapid evolution in recipient populations. In rice (Oryza sativa), transgenic herbicide resistance is expected to spread to conspecific weedy rice (Oryza sativa f. spontanea) via hybridization. Here, we studied fitness effects of transgenic over-expression of a native 5-enolpyruvoylshikimate-3-phosphate synthase (epsps) gene developed to confer glyphosate resistance in rice. Controlling for genetic background, we examined physiological traits and field performance of crop-weed hybrid lineages that segregated for the presence or absence of this novel epsps transgene. Surprisingly, we found that transgenic F2 crop-weed hybrids produced 48-125% more seeds per plant than nontransgenic controls in monoculture- and mixed-planting designs without glyphosate application. Transgenic plants also had greater EPSPS protein levels, tryptophan concentrations, photosynthetic rates, and per cent seed germination compared with nontransgenic controls. Our findings suggest that over-expression of a native rice epsps gene can lead to fitness advantages, even without exposure to glyphosate. We hypothesize that over-expressed epsps may be useful to breeders and, if deployed, could result in fitness benefits in weedy relatives following transgene introgression.
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Affiliation(s)
- Wei Wang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityHandan Road 220, Shanghai, 200433, China
| | - Hui Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityHandan Road 220, Shanghai, 200433, China
| | - Xiao Yang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityHandan Road 220, Shanghai, 200433, China
| | - Ting Xu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityHandan Road 220, Shanghai, 200433, China
| | - Hong Jiang Si
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityHandan Road 220, Shanghai, 200433, China
| | - Xing Xing Cai
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityHandan Road 220, Shanghai, 200433, China
| | - Feng Wang
- Fujian Province Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural SciencesFuzhou, 350003, China
| | - Jun Su
- Fujian Province Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural SciencesFuzhou, 350003, China
| | - Allison A Snow
- Department of Evolution, Ecology, & Organismal Biology, Ohio State UniversityColumbus, OH, 43210-1293, USA
| | - Bao-Rong Lu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityHandan Road 220, Shanghai, 200433, China
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Escamilla-Treviño LL, Shen H, Hernandez T, Yin Y, Xu Y, Dixon RA. Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.). Plant Mol Biol 2014; 84:565-576. [PMID: 24190737 DOI: 10.1007/s11103-013-1252-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/26/2013] [Indexed: 05/28/2023]
Abstract
Studying lignin biosynthesis in Panicum virgatum (switchgrass) has provided a basis for generating plants with reduced lignin content and increased saccharification efficiency. Chlorogenic acid (CGA, caffeoyl quinate) is the major soluble phenolic compound in switchgrass, and the lignin and CGA biosynthetic pathways potentially share intermediates and enzymes. The enzyme hydroxycinnamoyl-CoA: quinate hydroxycinnamoyltransferase (HQT) is responsible for CGA biosynthesis in tobacco, tomato and globe artichoke, but there are no close orthologs of HQT in switchgrass or in other monocotyledonous plants with complete genome sequences. We examined available transcriptomic databases for genes encoding enzymes potentially involved in CGA biosynthesis in switchgrass. The protein products of two hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) genes (PvHCT1a and PvHCT2a), closely related to lignin pathway HCTs from other species, were characterized biochemically and exhibited the expected HCT activity, preferring shikimic acid as acyl acceptor. We also characterized two switchgrass coumaroyl shikimate 3'-hydroxylase (C3'H) enzymes (PvC3'H1 and PvC3'H2); both of these cytochrome P450s had the capacity to hydroxylate 4-coumaroyl shikimate or 4-coumaroyl quinate to generate caffeoyl shikimate or CGA. Another switchgrass hydroxycinnamoyl transferase, PvHCT-Like1, is phylogenetically distant from HCTs or HQTs, but exhibits HQT activity, preferring quinic acid as acyl acceptor, and could therefore function in CGA biosynthesis. The biochemical features of the recombinant enzymes, the presence of the corresponding activities in plant protein extracts, and the expression patterns of the corresponding genes, suggest preferred routes to CGA in switchgrass.
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Escamilla-Treviño LL, Shen H, Hernandez T, Yin Y, Xu Y, Dixon RA. Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.). Plant Mol Biol 2014; 84:565-76. [PMID: 24190737 DOI: 10.1007/s11103-013-0152-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/26/2013] [Indexed: 05/07/2023]
Abstract
Studying lignin biosynthesis in Panicum virgatum (switchgrass) has provided a basis for generating plants with reduced lignin content and increased saccharification efficiency. Chlorogenic acid (CGA, caffeoyl quinate) is the major soluble phenolic compound in switchgrass, and the lignin and CGA biosynthetic pathways potentially share intermediates and enzymes. The enzyme hydroxycinnamoyl-CoA: quinate hydroxycinnamoyltransferase (HQT) is responsible for CGA biosynthesis in tobacco, tomato and globe artichoke, but there are no close orthologs of HQT in switchgrass or in other monocotyledonous plants with complete genome sequences. We examined available transcriptomic databases for genes encoding enzymes potentially involved in CGA biosynthesis in switchgrass. The protein products of two hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) genes (PvHCT1a and PvHCT2a), closely related to lignin pathway HCTs from other species, were characterized biochemically and exhibited the expected HCT activity, preferring shikimic acid as acyl acceptor. We also characterized two switchgrass coumaroyl shikimate 3'-hydroxylase (C3'H) enzymes (PvC3'H1 and PvC3'H2); both of these cytochrome P450s had the capacity to hydroxylate 4-coumaroyl shikimate or 4-coumaroyl quinate to generate caffeoyl shikimate or CGA. Another switchgrass hydroxycinnamoyl transferase, PvHCT-Like1, is phylogenetically distant from HCTs or HQTs, but exhibits HQT activity, preferring quinic acid as acyl acceptor, and could therefore function in CGA biosynthesis. The biochemical features of the recombinant enzymes, the presence of the corresponding activities in plant protein extracts, and the expression patterns of the corresponding genes, suggest preferred routes to CGA in switchgrass.
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Höppner A, Schomburg D, Niefind K. Enzyme-substrate complexes of the quinate/shikimate dehydrogenase from Corynebacterium glutamicum enable new insights in substrate and cofactor binding, specificity, and discrimination. Biol Chem 2014; 394:1505-16. [PMID: 23929881 DOI: 10.1515/hsz-2013-0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 08/05/2013] [Indexed: 11/15/2022]
Abstract
Quinate dehydrogenase (QDH) catalyzes the reversible oxidation of quinate to 3-dehydroquinate by nicotineamide adenine dinucleotide (NADH) and is involved in the catabolic quinate metabolism required for the degradation of lignin. The enzyme is a member of the family of shikimate/quinate dehydrogenases (SDH/QDH) occurring in bacteria and plants. We characterized the dual-substrate quinate/shikimate dehydrogenase (QSDH) from Corynebacterium glutamicum (CglQSDH) kinetically and revealed a clear substrate preference of CglQSDH for quinate compared with shikimate both at the pH optimum and in a physiological pH range, which is a remarkable contrast to closely related SDH/QDH enzymes. With respect to the cosubstrate, CglQSDH is strictly NAD(H) dependent. These substrate and cosubstrate profiles correlate well with the details of three atomic resolution crystal structures of CglQSDH in different functional states we report here: with bound NAD+ (binary complex) and as ternary complexes with NADH plus either shikimate or quinate. The CglQSDH-NADH-quinate structure is the first complex structure of any member of the SDH/QDH family with quinate. Based on this novel structural information and systematic sequence and structure comparisons with closely related enzymes, we can explain the strict NAD(H) dependency of CglQSDH as well as its discrimination between shikimate and quinate.
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Rosado LA, Vasconcelos IB, Palma MS, Frappier V, Najmanovich RJ, Santos DS, Basso LA. The mode of action of recombinant Mycobacterium tuberculosis shikimate kinase: kinetics and thermodynamics analyses. PLoS One 2013; 8:e61918. [PMID: 23671579 PMCID: PMC3646032 DOI: 10.1371/journal.pone.0061918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 03/14/2013] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis remains as one of the main cause of mortality worldwide due to a single infectious agent, Mycobacterium tuberculosis. The aroK-encoded M. tuberculosis Shikimate Kinase (MtSK), shown to be essential for survival of bacilli, catalyzes the phosphoryl transfer from ATP to the carbon-3 hydroxyl group of shikimate (SKH), yielding shikimate-3-phosphate and ADP. Here we present purification to homogeneity, and oligomeric state determination of recombinant MtSK. Biochemical and biophysical data suggest that the chemical reaction catalyzed by monomeric MtSK follows a rapid-equilibrium random order of substrate binding, and ordered product release. Isothermal titration calorimetry (ITC) for binding of ligands to MtSK provided thermodynamic signatures of non-covalent interactions to each process. A comparison of steady-state kinetics parameters and equilibrium dissociation constant value determined by ITC showed that ATP binding does not increase the affinity of MtSK for SKH. We suggest that MtSK would more appropriately be described as an aroL-encoded type II shikimate kinase. Our manuscript also gives thermodynamic description of SKH binding to MtSK and data for the number of protons exchanged during this bimolecular interaction. The negative value for the change in constant pressure heat capacity (ΔCp) and molecular homology model building suggest a pronounced contribution of desolvation of non-polar groups upon binary complex formation. Thermodynamic parameters were deconvoluted into hydrophobic and vibrational contributions upon MtSK:SKH binary complex formation. Data for the number of protons exchanged during this bimolecular interaction are interpreted in light of a structural model to try to propose the likely amino acid side chains that are the proton donors to bulk solvent following MtSK:SKH complex formation.
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Affiliation(s)
- Leonardo Astolfi Rosado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Igor Bordin Vasconcelos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Mário Sérgio Palma
- Laboratório de Biologia Estrutural e Zooquímica, Centro de Estudos de Insetos Sociais, Departamento de Biologia, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Vincent Frappier
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Rafael Josef Najmanovich
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Diógenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
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Vanholme B, Cesarino I, Goeminne G, Kim H, Marroni F, Van Acker R, Vanholme R, Morreel K, Ivens B, Pinosio S, Morgante M, Ralph J, Bastien C, Boerjan W. Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. New Phytol 2013; 198:765-776. [PMID: 23432219 DOI: 10.1111/nph.12179] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/02/2013] [Indexed: 05/18/2023]
Abstract
Next-generation (NG) sequencing in a natural population of Populus nigra revealed a mutant with a premature stop codon in the gene encoding hydroxycinnamoyl-CoA : shikimate hydroxycinnamoyl transferase1 (HCT1), an essential enzyme in lignin biosynthesis. The lignin composition of P. nigra trees homozygous for the defective allele was compared with that of heterozygous trees and trees without the defective allele. The lignin was characterized by phenolic profiling, lignin oligomer sequencing, thioacidolysis and NMR. In addition, HCT1 was heterologously expressed for activity assays and crosses were made to introduce the mutation in different genetic backgrounds. HCT1 converts p-coumaroyl-CoA into p-coumaroyl shikimate. The mutant allele, PnHCT1-Δ73, encodes a truncated protein, and trees homozygous for this recessive allele have a modified lignin composition characterized by a 17-fold increase in p-hydroxyphenyl units. Using the lignin pathway as proof of concept, we illustrated that the capture of rare defective alleles is a straightforward approach to initiate reverse genetics and accelerate tree breeding. The proposed breeding strategy, called 'breeding with rare defective alleles' (BRDA), should be widely applicable, independent of the target gene or the species.
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Affiliation(s)
- Bartel Vanholme
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Igor Cesarino
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Geert Goeminne
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Hoon Kim
- Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Rebecca Van Acker
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Ruben Vanholme
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Kris Morreel
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Bart Ivens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Sara Pinosio
- Istituto di Genomica Applicata, 33100, Udine, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, 33100, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100, Udine, Italy
| | - John Ralph
- Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA
| | - Catherine Bastien
- INRA - Unité Amélioration, Génétique et Physiologie forestières, Olivet, France
| | - Wout Boerjan
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
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Caetano MS, Freitas MP, da Cunha EFF, Ramalho TC. Construction and assessment of reaction models of Class I EPSP synthase. Part II: investigation of the EPSP ketal. J Biomol Struct Dyn 2013; 31:393-402. [PMID: 22877309 DOI: 10.1080/07391102.2012.703066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Although the proposed mechanisms are reasonable, there are still many questions about the 5-enolpyruvyl shikimate-3-phosphate (EPSP) synthase mechanism that are difficult to answer by experimental means alone. EPSP synthase is a key enzyme in the shikimic acid pathway, which is found only in plants and some micro-organisms and is also molecular target of glyphosate, active component of one of the top-selling herbicides. In the study of reaction mechanism of EPSP synthase, in addition to inorganic phosphate and EPSP products, after long time at equilibrium, it was shown that a side product is formed, the EPSP ketal. In this line, studies using density functional theory (DFT) techniques were performed to investigate the reaction mechanism of formation of EPSP and the corresponding ketal. Our findings indicate some key amino acid residues in the EPSP synthase mechanism and a possible route for the formation of the EPSP ketal.
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Abstract
Rhizoma Smilacis Glabrae (RSG) and Rhizoma Smilacis Chinae (RSC) are two herbal materials that belong to the same genera and are both listed in the Chinese Pharmacopoeia. Chemical constituents in the two species were compared by HPLC-DAD-MS/MS. Many common constituents were found in both species, including shikimic acid, 5-O-caffeoylshikimic acid, trans-resveratrol, taxifolin, astilbin and its three stereoisomers, engeletin and isoengeletin. However, syringic acid was found only in RSG, while chlorogenic acid was found only in RSC.
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Affiliation(s)
- Qing-Feng Zhang
- Jiangxi Key Laboratory of Natural Product and Functional Food, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
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Zhang QF, Cheung HY, Zeng LB. Development of HPLC fingerprint for species differentiation and quality assessment of Rhizoma Smilacis Glabrae. J Nat Med 2012; 67:207-11. [PMID: 22382863 DOI: 10.1007/s11418-012-0648-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 02/13/2012] [Indexed: 11/30/2022]
Abstract
Rhizoma Smilacis Glabrae (RSG) is a commonly used herbal material in functional food and Traditional Chinese Medicine. A HPLC chromatographic fingerprint was developed for its quality control and species differentiation. Nine peaks were found in the chromatogram of RSG and all these peaks were identified by diode array detection and electrospray ionization-MS/MS: 5-O-caffeoylshikimic acid, taxifolin, engeletin, isoengeletin, trans-resveratrol, astilbin and its three stereoisomers. Six of these constituents were consistently found in 18 batches of samples. The standard fingerprint of RSG was generated by mean simulation of all tested samples. Using the standard fingerprint, RSG could be easily differentiated from Rhizoma Smilacis Chinae and Rhizoma Heterosmilacis, the two species that can be confused with RSG.
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Affiliation(s)
- Qing-Feng Zhang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China.
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Usami Y, Mizuki K. Stereostructure reassignment and determination of the absolute configuration of pericosine D(o) by a synthetic approach. J Nat Prod 2011; 74:877-81. [PMID: 21391658 DOI: 10.1021/np100843j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A combination of chemical synthesis and NMR methods was used to reassign the structure of pericosine D(o) (8), a cytotoxic marine natural product produced by the fungus Periconia byssoides OUPS-N133 that was originally derived from the sea hare Aplysia kurodai. Chemical synthesis was used to prepare pericoisne D(o) (8) from a known chlorohydrin that was in turn derived from (-)-quinic acid. The absolute configuration of natural pericosine D(o) (8) was determined to be methyl (3R,4S,5S,6S)-6-chloro-3,4,5-trihydroxy-1-cyclohexene-1-carboxylate. HPLC analyses using a chiral-phase column indicated that pericosine D(o) (8) exists in an enantiomerically pure form in nature.
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Affiliation(s)
- Yoshihide Usami
- Laboratory of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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30
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Muir RM, Ibáñez AM, Uratsu SL, Ingham ES, Leslie CA, McGranahan GH, Batra N, Goyal S, Joseph J, Jemmis ED, Dandekar AM. Mechanism of gallic acid biosynthesis in bacteria (Escherichia coli) and walnut (Juglans regia). Plant Mol Biol 2011; 75:555-65. [PMID: 21279669 PMCID: PMC3057006 DOI: 10.1007/s11103-011-9739-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Accepted: 01/15/2011] [Indexed: 05/21/2023]
Abstract
Gallic acid (GA), a key intermediate in the synthesis of plant hydrolysable tannins, is also a primary anti-inflammatory, cardio-protective agent found in wine, tea, and cocoa. In this publication, we reveal the identity of a gene and encoded protein essential for GA synthesis. Although it has long been recognized that plants, bacteria, and fungi synthesize and accumulate GA, the pathway leading to its synthesis was largely unknown. Here we provide evidence that shikimate dehydrogenase (SDH), a shikimate pathway enzyme essential for aromatic amino acid synthesis, is also required for GA production. Escherichia coli (E. coli) aroE mutants lacking a functional SDH can be complemented with the plant enzyme such that they grew on media lacking aromatic amino acids and produced GA in vitro. Transgenic Nicotiana tabacum lines expressing a Juglans regia SDH exhibited a 500% increase in GA accumulation. The J. regia and E. coli SDH was purified via overexpression in E. coli and used to measure substrate and cofactor kinetics, following reduction of NADP(+) to NADPH. Reversed-phase liquid chromatography coupled to electrospray mass spectrometry (RP-LC/ESI-MS) was used to quantify and validate GA production through dehydrogenation of 3-dehydroshikimate (3-DHS) by purified E. coli and J. regia SDH when shikimic acid (SA) or 3-DHS were used as substrates and NADP(+) as cofactor. Finally, we show that purified E. coli and J. regia SDH produced GA in vitro.
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Affiliation(s)
- Ryann M. Muir
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Ana M. Ibáñez
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Sandra L. Uratsu
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Elizabeth S. Ingham
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Charles A. Leslie
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Gale H. McGranahan
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Neelu Batra
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Sham Goyal
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
| | - Jorly Joseph
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560 012 India
| | - Eluvathingal D. Jemmis
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560 012 India
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, 1 Shields Ave, Mail Stop 2, Davis, CA 95616-8683 USA
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Affiliation(s)
- Subhankar Tripathi
- Department of Chemistry, National Dong Hwa University, Hualien, 97401, Taiwan, ROC
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32
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Sullivan ML, Zarnowski R. Red clover coumarate 3'-hydroxylase (CYP98A44) is capable of hydroxylating p-coumaroyl-shikimate but not p-coumaroyl-malate: implications for the biosynthesis of phaselic acid. Planta 2010; 231:319-28. [PMID: 19921248 DOI: 10.1007/s00425-009-1054-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 10/28/2009] [Indexed: 05/21/2023]
Abstract
Red clover (Trifolium pratense) leaves accumulate several mumol of phaselic acid [2-O-caffeoyl-L-malate] per gram fresh weight. Post-harvest oxidation of such o-diphenols to o-quinones by endogenous polyphenol oxidases (PPO) prevents breakdown of forage protein during storage. Forages like alfalfa (Medicago sativa) lack both foliar PPO activity and o-diphenols. Consequently, breakdown of their protein upon harvest and storage results in economic losses and release of excess nitrogen into the environment. Understanding how red clover synthesizes o-diphenols such as phaselic acid will help in the development of forages utilizing this natural system of protein protection. We have proposed biosynthetic pathways in red clover for phaselic acid that involve a specific hydroxycinnamoyl-CoA:malate hydroxycinnamoyl transferase. It is unclear whether the transfer reaction to malate to form phaselic acid involves caffeic acid or p-coumaric acid and subsequent hydroxylation of the resulting p-coumaroyl-malate. The latter would require a coumarate 3'-hydroxylase (C3'H) capable of hydroxylating p-coumaroyl-malate, an activity not previously described. Here, a cytochrome P450 C3'H (CYP98A44) was identified and its gene cloned from red clover. CYP98A44 shares 96 and 79% amino acid identity with Medicago truncatula and Arabidopsis thaliana C3'H proteins that are capable of hydroxylating p-coumaroyl-shikimate and have been implicated in monolignol biosynthesis. CYP98A44 mRNA is expressed in stems and flowers and to a lesser extent in leaves. Immune serum raised against CYP98A44 recognizes a membrane-associated protein in red clover stems and leaves and cross-reacts with C3'H proteins from other species. CYP98A44 expressed in Saccharomyces cerevisiae is capable of hydroxylating p-coumaroyl-shikimate, but not p-coumaroyl-malate. This finding indicates that in red clover, phaselic acid is likely formed by transfer of a caffeoyl moiety to malic acid, although the existence of a second C3'H capable of hydroxylating p-coumaroyl-malate cannot be definitively ruled out.
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Affiliation(s)
- Michael L Sullivan
- US Dairy Forage Research Center, Agricultural Research Service, US Department of Agriculture, 1925 Linden Drive, Madison, WI 53706, USA.
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Li L, Lu W, Han Y, Ping S, Zhang W, Chen M, Zhao Z, Yan Y, Jiang Y, Lin M. A novel RPMXR motif among class II 5-enolpyruvylshikimate-3-phosphate synthases is required for enzymatic activity and glyphosate resistance. J Biotechnol 2009; 144:330-6. [PMID: 19799945 DOI: 10.1016/j.jbiotec.2009.09.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 09/10/2009] [Accepted: 09/14/2009] [Indexed: 11/21/2022]
Abstract
The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is an attractive target for drugs and herbicides. Here we identified a novel RPMXR motif that is strictly conserved among class II EPSP synthases. Site-directed mutational analysis of this motif showed that substitutions of the four strictly conserved amino acid residues, Arg127, Pro128, Met129, and Arg131, resulted in complete loss of enzymatic activity, whereas changes in the non-conserved Asn130 residue strongly influenced glyphosate resistance (all numbering according to Pseudomonas stutzeri A1501 EPSP synthase). These experimental results, combined with 3D structure modeling of the location and interaction of the RPMXR motif with phosphoenolpyruvate (PEP) and shikimate-3-phosphate (S3P), demonstrate that the novel motif is required for enzymatic activity and glyphosate resistance of class II EPSP synthases.
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Affiliation(s)
- Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Biotechnology, Ministry of Agriculture, Beijing 100081, China
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Abstract
Two new prenylated C(6)-C(3) compounds, 4-epi-illicinone E-12-shikimate (1) and 3-hydroxyillifunone B (2), together with five known prenylated C(6)-C(3) compounds (3-7), were isolated from the fruits of Illicium simonsii. Their structures were elucidated on the basis of extensive spectroscopic methods, including 1D and 2D NMR, CD spectra, and ESI-MS analysis.
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Affiliation(s)
- Xian-Fu Wu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
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35
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Petersen M, Abdullah Y, Benner J, Eberle D, Gehlen K, Hücherig S, Janiak V, Kim KH, Sander M, Weitzel C, Wolters S. Evolution of rosmarinic acid biosynthesis. Phytochemistry 2009; 70:1663-79. [PMID: 19560175 DOI: 10.1016/j.phytochem.2009.05.010] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 05/19/2009] [Accepted: 05/19/2009] [Indexed: 05/19/2023]
Abstract
Rosmarinic acid and chlorogenic acid are caffeic acid esters widely found in the plant kingdom and presumably accumulated as defense compounds. In a survey, more than 240 plant species have been screened for the presence of rosmarinic and chlorogenic acids. Several rosmarinic acid-containing species have been detected. The rosmarinic acid accumulation in species of the Marantaceae has not been known before. Rosmarinic acid is found in hornworts, in the fern family Blechnaceae and in species of several orders of mono- and dicotyledonous angiosperms. The biosyntheses of caffeoylshikimate, chlorogenic acid and rosmarinic acid use 4-coumaroyl-CoA from the general phenylpropanoid pathway as hydroxycinnamoyl donor. The hydroxycinnamoyl acceptor substrate comes from the shikimate pathway: shikimic acid, quinic acid and hydroxyphenyllactic acid derived from l-tyrosine. Similar steps are involved in the biosyntheses of rosmarinic, chlorogenic and caffeoylshikimic acids: the transfer of the 4-coumaroyl moiety to an acceptor molecule by a hydroxycinnamoyltransferase from the BAHD acyltransferase family and the meta-hydroxylation of the 4-coumaroyl moiety in the ester by a cytochrome P450 monooxygenase from the CYP98A family. The hydroxycinnamoyltransferases as well as the meta-hydroxylases show high sequence similarities and thus seem to be closely related. The hydroxycinnamoyltransferase and CYP98A14 from Coleus blumei (Lamiaceae) are nevertheless specific for substrates involved in RA biosynthesis showing an evolutionary diversification in phenolic ester metabolism. Our current view is that only a few enzymes had to be "invented" for rosmarinic acid biosynthesis probably on the basis of genes needed for the formation of chlorogenic and caffeoylshikimic acid while further biosynthetic steps might have been recruited from phenylpropanoid metabolism, tocopherol/plastoquinone biosynthesis and photorespiration.
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Affiliation(s)
- Maike Petersen
- Institut für Pharmazeutische Biologie, Philipps-Universität Marburg, Marburg, Germany.
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Kim HJ, Kim HW, Kang SH. Engineering and characterization of the isolated C-terminal domain of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase. J Microbiol Biotechnol 2007; 17:1385-1389. [PMID: 18051609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
5-Enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the formation of EPSP and inorganic phosphate from shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) in the biosynthesis of aromatic amino acids. To delineate the domain-specific function, we successfully isolated the discontinuous C-terminal domain (residues 1-21, linkers, 240-427) of EPSP synthase (427 residues) by site-directed mutagenesis. The engineered C-terminal domains containing no linker (CTD), or with gly-gly (CTD(GG)) and gly-ser-ser-gly (CTD(GSSG)) linkers were purified and characterized as having distinct native-like secondary and tertiary structures. However, isothermal titration calorimetry (ITC), 15N-HSQC, and 31P-NMR revealed that neither its substrate nor inhibitor binds the isolated domain. The isolated domain maintained structural integrity, but did not function as the half of the full-length protein.
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Affiliation(s)
- Hak Jun Kim
- Department of Applied Polar Science, Korea Polar Research Institute, Incheon 406-840, Korea
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37
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Usami Y, Takaoka I, Ichikawa H, Horibe Y, Tomiyama S, Ohtsuka M, Imanishi Y, Arimoto M. First Total Synthesis of Antitumor Natural Product (+)- and (−)-Pericosine A: Determination of Absolute Stereo Structure†. J Org Chem 2007; 72:6127-34. [PMID: 17628106 DOI: 10.1021/jo070715l] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first total synthesis of (+)- and (-)-pericosine A has been achieved, enabling the revision and determination of the absolute configuration of this antitumor natural product as methyl (3S,4S,5S,6S)-6-chloro-3,4,5-trihydroxy-1-cyclohexene-1-carboxylate. Every step of this total synthesis proceeded well with excellent stereoselectivity. Structures of the intermediates in crucial steps were confirmed by detailed 2D NMR analysis.
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Affiliation(s)
- Yoshihide Usami
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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Ran N, Frost JW. Directed Evolution of 2-Keto-3-deoxy-6-phosphogalactonate Aldolase To Replace 3-Deoxy-d-arabino-heptulosonic Acid 7-Phosphate Synthase. J Am Chem Soc 2007; 129:6130-9. [PMID: 17451239 DOI: 10.1021/ja067330p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Directed evolution of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase for microbial synthesis of shikimate pathway products provides an alternate strategy to circumvent the competition for phosphoenolpyruvate between 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) synthase and the phosphoenolpyruvate:carbohydrate phosphotransferase system in Escherichia coli. E. coli KDPGal aldolase was evolved using a combination of error-prone polymerase chain reaction, DNA shuffling, and multiple-site-directed mutagenesis to afford KDPGal aldolase variant NR8.276-2, which exhibits a 60-fold improvement in the ratio kcat/KM relative to that of wild-type E. coli KDPGal aldolase in catalyzing the addition of pyruvate to d-erythrose 4-phosphate to form DAHP. On the basis of its nucleotide sequence, NR8.276-2 contains seven amino acid changes from the wild-type E. coli KDPGal aldolase. Amplified expression of NR8.276-2 in the DAHP synthase and shikimate dehydrogenase-deficient E. coli strain NR7 under fed-batch fermentor-controlled cultivation conditions resulted in synthesis of 13 g/L 3-dehydroshikimic acid in 6.5% molar yield from glucose. Increased coexpression of the irreversible downstream enzyme 3-dehydroquinate synthase increased production of 3-dehydroshikimic acid to 19 g/L in 9.7% molar yield from glucose. Coamplification with transketolase, which increases d-erythrose 4-phosphate availability, afforded 16 g/L 3-dehydroshikimic acid in 8.5% molar yield.
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Affiliation(s)
- Ningqing Ran
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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39
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Prazeres VFV, Sánchez-Sixto C, Castedo L, Lamb H, Hawkins AR, Riboldi-Tunnicliffe A, Coggins JR, Lapthorn AJ, González-Bello C. Nanomolar Competitive Inhibitors ofMycobacterium tuberculosis andStreptomyces coelicolor Type II Dehydroquinase. ChemMedChem 2007; 2:194-207. [PMID: 17245805 DOI: 10.1002/cmdc.200600208] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Isomeric nitrophenyl and heterocyclic analogues of the known inhibitor (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid have been synthesized and tested as inhibitors of M. tuberculosis and S. coelicolor type II dehydroquinase, the third enzyme of the shikimic acid pathway. The target compounds were synthesized by a combination of Suzuki and Sonogashira cross-coupling and copper(I)-catalyzed 2,3-dipolar cycloaddition reactions from a common vinyl triflate intermediate. These studies showed that a para-nitrophenyl derivative is almost 20-fold more potent as a competitive inhibitor against the S. coelicolor enzyme than that of M. tuberculosis. The opposite results were obtained with the meta isomer. Five of the bicyclic analogues reported herein proved to be potent competitive inhibitors of S. coelicolor dehydroquinase, with inhibition constants in the low nanomolar range (4-30 nM). These derivatives are also competitive inhibitors of the M. tuberculosis enzyme, but with lower affinities. The most potent inhibitor against the S. coelicolor enzyme, a 6-benzothiophenyl derivative, has a K(i) value of 4 nM-over 2000-fold more potent than the best previously known inhibitor, (1R,4R,5R)-1,5-dihydroxy-4-(2-nitrophenyl)cyclohex-2-en-1-carboxylic acid (8 microM), making it the most potent known inhibitor against any dehydroquinase. The binding modes of the analogues in the active site of the S. coelicolor enzyme (GOLD 3.0.1), suggest a key pi-stacking interaction between the aromatic rings and Tyr 28, a residue that has been identified as essential for enzyme activity.
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Affiliation(s)
- Verónica F V Prazeres
- Laboratorio de Química Orgánica, CSIC and Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, Avenida de las Ciencias s/n, 15782 Santiago de Compostela, Spain
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40
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Abstract
Enolpyruvylshikimate-3-phosphate synthase (AroA, also called EPSP synthase) is a carboxyvinyl transferase involved in aromatic amino acid biosynthesis, forming EPSP from shikimate 3-phosphate and phosphoenolpyruvate. Upon extended incubation, EPSP ketal, a side product, forms by intramolecular nucleophilic addition of O4 to C2' of the enolpyruvyl group. The catalytic significance of this reaction was unclear, as it was initially proposed to arise from nonenzymatic breakdown of tetrahedral intermediate that had dissociated from AroA. This study shows that EPSP ketal formed in AroA's active site, not nonenzymatically, by demonstrating its formation in the presence of excess AroA. It formed both in the normal reaction and during AroA-catalyzed EPSP hydrolysis. In addition, nonenzymatic EPSP hydrolysis was studied to elucidate the catalytic imperative for enolpyruvyl reactions. Hydrolysis was acid-catalyzed, with a rate enhancement of >5 x 10(8)-fold. There was no detectable EPSP breakdown after 16 days at 90 degrees C in 1 M KOH, a solution that is 1000-fold more nucleophilic than neutral aqueous solutions. Thus, an unactivated enolpyruvyl group is not susceptible to nucleophilic attack. Enzymatic EPSP ketal formation therefore requires enolpyruvyl activation through protonation of C3' to form either a cationic intermediate or a highly cation-like transition state. Forming an EPSP cation requires the investment of considerable catalytic power by AroA. Such an intermediate is a potential target motif for inhibitor design.
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Affiliation(s)
- Meghann E Clark
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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41
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Adachi O, Ano Y, Toyama H, Matsushita K. Enzymatic preparation of metabolic intermediates, 3-dehydroquinate and 3-dehydroshikimate, in the shikimate pathway. Biosci Biotechnol Biochem 2006; 70:3081-3. [PMID: 17151445 DOI: 10.1271/bbb.60414] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A method for enzymatic preparation of 3-dehydroquinate and 3-dehydroshikimate in the shikimate pathway was established by controlling the enzyme activity of 3-dehydroquinate dehydratase. When quinate was incubated with the membrane fraction of acetic acid bacteria at pH 5.0, 3-dehydroquinate was formed as the predominant product. 3-Dehydroshikimate was the sole product when incubated at pH 8.0. Mutual separation of the metabolic intermediates was also exemplified.
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Affiliation(s)
- Osao Adachi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University.
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42
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Adachi O, Ano Y, Toyama H, Matsushita K. Purification and properties of NADP-dependent shikimate dehydrogenase from Gluconobacter oxydans IFO 3244 and its application to enzymatic shikimate production. Biosci Biotechnol Biochem 2006; 70:2786-9. [PMID: 17090918 DOI: 10.1271/bbb.60305] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
NADP-Dependent shikimate dehydrogenae (SKDH, EC 1.1.1.25) was purified from Gluconobacter oxydans IFO 3244. SKDH showed a single protein band on native-PAGE accompanying enzyme activity. It required NADP exclusively and catalyzed only the shuttle reaction between shikimate and 3-dehydroshikimate. The optimum pH for shikimate oxidation and 3-dehydroshikimate reduction was found at pH 10 and 7 respectively. SKDH proved to be a useful catalyst for shikimate production from 3-dehydroshikimate.
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Affiliation(s)
- Osao Adachi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.
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43
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Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD. Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis. J Mol Biol 2006; 364:411-23. [PMID: 17020768 DOI: 10.1016/j.jmb.2006.09.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2006] [Revised: 08/31/2006] [Accepted: 09/01/2006] [Indexed: 10/24/2022]
Abstract
The structural mechanism of the catalytic functioning of shikimate kinase from Mycobacterium tuberculosis was investigated on the basis of a series of high-resolution crystal structures corresponding to individual steps in the enzymatic reaction. The catalytic turnover of shikimate and ATP into the products shikimate-3-phosphate and ADP, followed by release of ADP, was studied in the crystalline environment. Based on a comparison of the structural states before initiation of the reaction and immediately after the catalytic step, we derived a structural model of the transition state that suggests that phosphoryl transfer proceeds with inversion by an in-line associative mechanism. The random sequential binding of shikimate and nucleotides is associated with domain movements. We identified a synergic mechanism by which binding of the first substrate may enhance the affinity for the second substrate.
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Affiliation(s)
- Marcus D Hartmann
- Max Planck Unit for Structural Molecular Biology, MPG-ASMB c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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44
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Sánchez-Abella L, Fernández S, Armesto N, Ferrero M, Gotor V. Novel and Efficient Syntheses of (−)-Methyl 4-epi-Shikimate and 4,5-Epoxy-Quinic and -Shikimic Acid Derivatives as Key Precursors to Prepare New Analogues. J Org Chem 2006; 71:5396-9. [PMID: 16808536 DOI: 10.1021/jo0606249] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed simple methods that provide a rapid entry into the synthesis of a series of quinate and shikimate analogues, including (-)-methyl 4-epi-shikimate and the 4,5-epoxy analogues of the parent acids. Epoxy derivatives of quinic and shikimic acids were converted into methyl scyllo-quinate and (+)-methyl 3-epi-shikimate, respectively, by processes involving a regio- and stereoselective epoxide ring opening. The strategies described take place through short, high-yield reaction sequences.
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Affiliation(s)
- Laura Sánchez-Abella
- Departamento de Química Organica e Inorganica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
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Ndom JC, Mbafor JT, Azebaze AGB, Vardamides JC, Kakam Z, Kamdem AFW, Deville A, Ngando TM, Fomum ZT. Secondary metabolites from Senecio burtonii (Compositae). Phytochemistry 2006; 67:838-42. [PMID: 16580035 DOI: 10.1016/j.phytochem.2006.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Revised: 01/26/2006] [Accepted: 02/07/2006] [Indexed: 05/08/2023]
Abstract
A cacalolide derivative named 4alpha-[2'-hydroxymethylacryloxy]-1beta-hydroxy-14-(5-->6) abeo eremophilan-12,8-olide and a shikimic acid derivative named (3'E)-(1alpha)-3-hydroxymethyl-4beta,5alpha-dimethoxycyclohex-2-enyloctadec-3'-enoate along with three known compounds, octacosan-1-ol, 3beta-hydroxyolean-12-en-28-oic acid and 3beta-acetoxyolean-12-en-28-oic acid were isolated from Senecio burtonii. Their structures and relative configurations were established on the basis of spectroscopic analysis.
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Affiliation(s)
- J C Ndom
- Department of Chemistry, Faculty of Science, University of Douala, Cameroon.
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46
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McRobert L, Jiang S, Stead A, McConkey GA. Plasmodium falciparum: interaction of shikimate analogues with antimalarial drugs. Exp Parasitol 2005; 111:178-81. [PMID: 16140296 DOI: 10.1016/j.exppara.2005.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Revised: 07/19/2005] [Accepted: 07/20/2005] [Indexed: 10/25/2022]
Abstract
The shikimate pathway for aromatic biosynthesis presents a target for antimalarial drug development as this pathway is absent from animals. This study extends previous work on inhibitors of the shikimate pathway, by examining their interaction with the antimalarial drugs pyrimethamine and atovaquone. Combinations of atovaquone with several shikimate analogues exhibited synergistic effects. These findings highlight potential use of shikimate pathway inhibitors in combination therapy.
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47
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Abstract
The toxicity of aromatics frequently limits the yields of their microbial synthesis. For example, the 5% yield of catechol synthesized from glucose by Escherichia coli WN1/pWL1.290A under fermentor-controlled conditions reflects catechol's microbial toxicity. Use of in situ resin-based extraction to reduce catechol's concentration in culture medium and thereby its microbial toxicity during its synthesis from glucose by E. coli WN1/pWL1.290A led to a 7% yield of catechol. Interfacing microbial with chemical synthesis was then explored where glucose was microbially converted into a nontoxic intermediate followed by chemical conversion of this intermediate into catechol. Intermediates examined include 3-dehydroquinate, 3-dehydroshikimate, and protocatechuate. 3-Dehydroquinate and 3-dehydroshikimate synthesized, respectively, by E. coli QP1.1/pJY1.216A and E. coli KL3/pJY1.216A from glucose were extracted and then reacted in water heated at 290 degrees C to afford catechol in overall yields from glucose of 10% and 26%, respectively. The problematic extraction of these catechol precursors from culture medium was subsequently circumvented by high-yielding chemical dehydration of 3-dehydroquinate and 3-dehydroshikimate in culture medium followed by extraction of the resulting protocatechuate. After reaction of protocatechuate in water heated at 290 degrees C, the overall yields of catechol synthesized from glucose via chemical dehydration of 3-dehydroquinate and chemical dehydration of 3-dehydroshikimate were, respectively, 25% and 30%. Direct synthesis of protocatechuate from glucose using E. coli KL3/pWL2.46B followed by its extraction and chemical decarboxylation in water gave a 24% overall yield of catechol from glucose. In situ resin-based extraction of protocatechaute synthesized by E. coli KL3/pWL2.46B followed by chemical decarboxylation of this catechol percursor was then examined. This employment of both strategies for dealing with the microbial toxicity of aromatic products led to the highest overall yield with catechol synthesized in 43% overall yield from glucose.
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Affiliation(s)
- Wensheng Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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48
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Lim S, Schröder I, Monbouquette HG. A thermostable shikimate 5-dehydrogenase from the archaeon Archaeoglobus fulgidus. FEMS Microbiol Lett 2005; 238:101-6. [PMID: 15336409 DOI: 10.1016/j.femsle.2004.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Accepted: 07/13/2004] [Indexed: 11/17/2022] Open
Abstract
Shikimate 5-dehydrogenase (SKDH; EC 1.1.1.25) catalyzes the reversible reduction of 3-dehydroshikimate to shikimate and is a key enzyme in the aromatic amino acid biosynthesis pathway. The shikimate 5-dehydrogenase gene, aroE, from Archaeoglobus fulgidus was cloned and overexpressed in Escherichia coli. The recombinant enzyme purified as a homodimer and yielded a maximum specific activity of 732 U/mg at 87 degrees C (with NADP+ as coenzyme). Apparent Km values for shikimate, NADP+, and NAD+ were estimated at 0.17+/-0.03 mM, 0.19+/-0.01 mM, and 11.4+/-0.4 mM, respectively. The half-life of the A. fulgidus SKDH is 2 h at the assay temperature (87 degrees C) and 17 days at 60 degrees C. Addition of 1 M NaCl or KCl stabilized the enzyme's half-life to approximately 70 h at 87 degrees C and approximately 50 days at 60 degrees C. This work presents the first kinetic analysis of an archaeal SKDH.
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Affiliation(s)
- Sierin Lim
- Biomedical Engineering Interdepartmental Program, 7523 Boelter Hall, University of California, 1602 Molecular Sciences Bldg., Los Angeles, CA 90095-1489, USA
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Bulloch EMM, Jones MA, Parker EJ, Osborne AP, Stephens E, Davies GM, Coggins JR, Abell C. Identification of 4-amino-4-deoxychorismate synthase as the molecular target for the antimicrobial action of (6s)-6-fluoroshikimate. J Am Chem Soc 2004; 126:9912-3. [PMID: 15303852 DOI: 10.1021/ja048312f] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(6S)-6-Fluoroshikimate has antimicrobial activity. The molecular basis of this effect had not been identified, but there was speculation that (6S)-6-fluoroshikimate is first converted in vivo into 2-fluorochorismate, which then could inhibit 4-amino-4-deoxychorismate synthase (ADCS). 2-Fluorochorismate was prepared from E-fluorophosphoenolpyruvate and erythose-4-phosphate by the sequential reactions of DAHP synthase, dehydroquinate synthase, dehydroquinase, shikimate dehydrogenase, EPSP synthase, and chorismate synthase. Inhibition studies on ADCS showed that it was inhibited rapidly and irreversibly by 2-fluorochorismate. Electrospray mass spectrometry of the inactivated enzyme showed an additional mass of 198 +/- 10 Da. A novel peptide of 1087.6 Da was identified in the HPLC trace for the tryptic digest of 2-fluorochorismate-inactivated ADCS. Sequencing of this peptide by MS/MS showed that the peptide corresponded to residues 272-279 with a modification of 206.1 Da on Lys-274. This observation is particularly exciting in the context of a recent proposal for the catalytic mechanism of ADCS.
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Affiliation(s)
- Esther M M Bulloch
- Department of Chemistry, University of Cambridge, University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK
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50
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Abstract
[reaction: see text] Three ring-contracted mimics of shikimate-3-phosphate, formed from the triols by shikimate kinase, were evaluated as substrates of the next enzyme in the pathway, EPSP synthase. The cyclopentylidene analogue (+)-2P was converted enzymatically to the enolpyruvyl derivative, thus demonstrating the second step of an artificial biosynthetic sequence.
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Affiliation(s)
- Ming An
- Center for New Directions in Organic Synthesis, Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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