1
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Dodge GJ, Anderson AJ, He Y, Liu W, Viner R, Imperiali B. Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle. eLife 2024; 12:RP91125. [PMID: 38358918 PMCID: PMC10942596 DOI: 10.7554/elife.91125] [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] [Indexed: 02/17/2024] Open
Abstract
Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge detergent-free methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from the Salmonella enterica (LT2) O-antigen biosynthesis. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for dimerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying other classes of small membrane proteins embedded in liponanoparticles beyond PGTs.
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Affiliation(s)
- Greg J Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Alyssa J Anderson
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yi He
- Thermo Fisher ScientificSan JoseUnited States
| | - Weijing Liu
- Thermo Fisher ScientificSan JoseUnited States
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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2
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Seebald LM, Haratipour P, Jacobs MR, Bernstein HM, Kashemirov BA, McKenna CE, Imperiali B. Uridine Bisphosphonates Differentiate Phosphoglycosyl Transferase Superfamilies. J Am Chem Soc 2024; 146:3220-3229. [PMID: 38271668 PMCID: PMC10922802 DOI: 10.1021/jacs.3c11402] [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] [Indexed: 01/27/2024]
Abstract
Complex bacterial glycoconjugates drive interactions between pathogens, symbionts, and their human hosts. Glycoconjugate biosynthesis is initiated at the membrane interface by phosphoglycosyl transferases (PGTs), which catalyze the transfer of a phosphosugar from a soluble uridine diphosphosugar (UDP-sugar) substrate to a membrane-bound polyprenol-phosphate (Pren-P). The two distinct superfamilies of PGT enzymes (polytopic and monotopic) show striking differences in their structure and mechanism. We designed and synthesized a series of uridine bisphosphonates (UBPs), wherein the diphosphate of the UDP and UDP-sugar is replaced by a substituted methylene bisphosphonate (CXY-BPs; X/Y = F/F, Cl/Cl, (S)-H/F, (R)-H/F, H/H, CH3/CH3). UBPs and UBPs incorporating an N-acetylglucosamine (GlcNAc) substituent at the β-phosphonate were evaluated as inhibitors of a polytopic PGT (WecA from Thermotoga maritima) and a monotopic PGT (PglC from Campylobacter jejuni). Although CHF-BP most closely mimics diphosphate with respect to its acid/base properties, the less basic CF2-BP conjugate more strongly inhibited PglC, whereas the more basic CH2-BP analogue was the strongest inhibitor of WecA. These surprising differences indicate different modes of ligand binding for the different PGT superfamilies, implicating a modified P-O- interaction with the structural Mg2+. For the monoPGT enzyme, the two diastereomeric CHF-BP conjugates, which feature a chiral center at the Pα-CHF-Pβ carbon, also exhibited strikingly different binding affinities and the inclusion of GlcNAc with the native α-anomer configuration significantly improved binding affinity. UBP-sugars are thus revealed as informative new mechanistic probes of PGTs that may aid development of novel antibiotic agents for the exclusively prokaryotic monoPGT superfamily.
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Affiliation(s)
- Leah M. Seebald
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Pouya Haratipour
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Michaela R. Jacobs
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Hannah M. Bernstein
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Boris A. Kashemirov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Charles E. McKenna
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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3
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Majumder A, Vuksanovic N, Ray LC, Bernstein HM, Allen KN, Imperiali B, Straub JE. Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble. J Biol Chem 2023; 299:105194. [PMID: 37633332 PMCID: PMC10519829 DOI: 10.1016/j.jbc.2023.105194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/30/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 08/28/2023] Open
Abstract
Complex glycans serve essential functions in all living systems. Many of these intricate and byzantine biomolecules are assembled employing biosynthetic pathways wherein the constituent enzymes are membrane-associated. A signature feature of the stepwise assembly processes is the essentiality of unusual linear long-chain polyprenol phosphate-linked substrates of specific isoprene unit geometry, such as undecaprenol phosphate (UndP) in bacteria. How these enzymes and substrates interact within a lipid bilayer needs further investigation. Here, we focus on a small enzyme, PglC from Campylobacter, structurally characterized for the first time in 2018 as a detergent-solubilized construct. PglC is a monotopic phosphoglycosyl transferase that embodies the functional core structure of the entire enzyme superfamily and catalyzes the first membrane-committed step in a glycoprotein assembly pathway. The size of the enzyme is significant as it enables high-level computation and relatively facile, for a membrane protein, experimental analysis. Our ensemble computational and experimental results provided a high-level view of the membrane-embedded PglC/UndP complex. The findings suggested that it is advantageous for the polyprenol phosphate to adopt a conformation in the same leaflet where the monotopic membrane protein resides as opposed to additionally disrupting the opposing leaflet of the bilayer. Further, the analysis showed that electrostatic steering acts as a major driving force contributing to the recognition and binding of both UndP and the soluble nucleotide sugar substrate. Iterative computational and experimental mutagenesis support a specific interaction of UndP with phosphoglycosyl transferase cationic residues and suggest a role for critical conformational transitions in substrate binding and specificity.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | | | - Leah C Ray
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hannah M Bernstein
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, USA; Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA.
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA.
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4
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Hamid R, Adam S, Lacour A, Monjas L, Köhnke J, Hirsch AKH. 1-deoxy-D-xylulose-5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding. J Biol Chem 2023; 299:105152. [PMID: 37567475 PMCID: PMC10504544 DOI: 10.1016/j.jbc.2023.105152] [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: 06/11/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
The ESKAPE bacteria are the six highly virulent and antibiotic-resistant pathogens that require the most urgent attention for the development of novel antibiotics. Detailed knowledge of target proteins specific to bacteria is essential to develop novel treatment options. The methylerythritol-phosphate (MEP) pathway, which is absent in humans, represents a potentially valuable target for the development of novel antibiotics. Within the MEP pathway, the enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) catalyzes a crucial, rate-limiting first step and a branch point in the biosynthesis of the vitamins B1 and B6. We report the high-resolution crystal structures of DXPS from the important ESKAPE pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae in both the co-factor-bound and the apo forms. We demonstrate that the absence of the cofactor thiamine diphosphate results in conformational changes that lead to disordered loops close to the active site that might be important for the design of potent DXPS inhibitors. Collectively, our results provide important structural details that aid in the assessment of DXPS as a potential target in the ongoing efforts to combat antibiotic resistance.
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Affiliation(s)
- Rawia Hamid
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Sebastian Adam
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Antoine Lacour
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Leticia Monjas
- Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Jesko Köhnke
- Institute of Food Chemistry, Leibniz University Hannover, Hannover, Germany; School of Chemistry, University of Glasgow, Glasgow, UK
| | - Anna K H Hirsch
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany.
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5
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Anderson AJ, Dodge GJ, Allen KN, Imperiali B. Co-conserved sequence motifs are predictive of substrate specificity in a family of monotopic phosphoglycosyl transferases. Protein Sci 2023; 32:e4646. [PMID: 37096962 PMCID: PMC10186338 DOI: 10.1002/pro.4646] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/17/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Monotopic phosphoglycosyl transferases (monoPGTs) are an expansive superfamily of enzymes that catalyze the first membrane-committed step in the biosynthesis of bacterial glycoconjugates. MonoPGTs show a strong preference for their cognate nucleotide diphospho-sugar (NDP-sugar) substrates. However, despite extensive characterization of the monoPGT superfamily through previous development of a sequence similarity network comprising >38,000 nonredundant sequences, the connection between monoPGT sequence and NDP-sugar substrate specificity has remained elusive. In this work, we structurally characterize the C-terminus of a prototypic monoPGT for the first time and show that 19 C-terminal residues play a significant structural role in a subset of monoPGTs. This new structural information facilitated the identification of co-conserved sequence "fingerprints" that predict NDP-sugar substrate specificity for this subset of monoPGTs. A Hidden Markov model was generated that correctly assigned the substrate of previously unannotated monoPGTs. Together, these structural, sequence, and biochemical analyses have delivered new insight into the determinants guiding substrate specificity of monoPGTs and have provided a strategy for assigning the NDP-sugar substrate of a subset of enzymes in the superfamily that use UDP-di-N-acetyl bacillosamine. Moving forward, this approach may be applied to identify additional sequence motifs that serve as fingerprints for monoPGTs of differing UDP-sugar substrate specificity.
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Affiliation(s)
- Alyssa J. Anderson
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Greg J. Dodge
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
| | - Barbara Imperiali
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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6
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Zhang S, Wang Y, Cui Z, Li Q, Kong L, Luo J. Functional characterization of a Flavonol 3-O-rhamnosyltransferase and two UDP-rhamnose synthases from Hypericum monogynum. Plant Physiol Biochem 2023; 197:107643. [PMID: 36989989 DOI: 10.1016/j.plaphy.2023.107643] [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] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Rhamnosyltransferase (RT) and rhamnose synthase (Rhs) are the key enzymes that are responsible for the biosynthesis of rhamnosides and UDP-l-rhamnose (UDP-Rha) in plants, respectively. How to discover such enzymes efficiently for use is still a problem to be solved. Here, we identified HmF3RT, HmRhs1, and HmRhs2 from Hypericum monogynum, which is abundant in flavonol rhamnosides, with the help of a full-length and high throughput transcriptome sequencing platform. HmF3RT could regiospecifically transfer the rhamnose moiety of UDP-Rha onto the 3-OH position of flavonols and has weakly catalytic for UDP-xylose (UDP-Xyl) and UDP-glucose (UDP-Glc). HmF3RT showed well quercetin substrate affinity and high catalytic efficiency with Km of 5.14 μM and kcat/Km of 2.21 × 105 S-1 M-1, respectively. Docking, dynamic simulation, and mutagenesis studies revealed that V129, D372, and N373 are critical residues for the activity and sugar donor recognition of HmF3RT, mutant V129A, and V129T greatly enhance the conversion rate of catalytic flavonol glucosides. HmRhs1 and HmRhs2 convert UDP-Glc to UDP-Rha, which could be further used by HmF3RT. The HmF3RT and HmRhs1 co-expressed strain RTS1 could produce quercetin 3-O-rhamnoside (quercitrin), kaempferol 3-O-rhamnoside (afzelin), and myricetin 3-O-rhamnoside (myricitrin) at yields of 85.1, 110.7, and 77.6 mg L-1, respectively. It would provide a valuable reference for establishing a better and more efficient biocatalyst for preparing bioactive flavonol rhamnosides by identifying HmF3RT and HmRhs.
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Affiliation(s)
- Shuai Zhang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Yingying Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Zhirong Cui
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Qianqian Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China.
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China.
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7
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Anderson AJ, Seebald LM, Arbour CA, Imperiali B. Probing Monotopic Phosphoglycosyl Transferases from Complex Cellular Milieu. ACS Chem Biol 2022; 17:3191-3197. [PMID: 36346917 PMCID: PMC9703085 DOI: 10.1021/acschembio.2c00648] [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: 11/09/2022]
Abstract
Monotopic phosphoglycosyl transferase enzymes (monoPGTs) initiate the assembly of prokaryotic glycoconjugates essential for bacterial survival and proliferation. MonoPGTs belong to an expansive superfamily with a diverse and richly annotated sequence space; however, the biochemical roles of most monoPGTs in glycoconjugate biosynthesis pathways remain elusive. To better understand these critical enzymes, we have implemented activity-based protein profiling (ABPP) probes as protein-centric, membrane protein compatible tools that lay the groundwork for understanding the activity and regulation of the monoPGT superfamily from a cellular proteome. With straightforward gel-based readouts, we demonstrate robust, covalent labeling at the active site of various representative monoPGTs from cell membrane fractions using 3-phenyl-2H-azirine probes.
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Affiliation(s)
- Alyssa J. Anderson
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leah M. Seebald
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christine A. Arbour
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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8
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Okada M, Unno H, Emi KI, Matsumoto M, Hemmi H. A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. J Biol Chem 2021; 296:100679. [PMID: 33872599 PMCID: PMC8131916 DOI: 10.1016/j.jbc.2021.100679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/11/2020] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022] Open
Abstract
Polyprenyl groups, products of isoprenoid metabolism, are utilized in peptidoglycan biosynthesis, protein N-glycosylation, and other processes. These groups are formed by cis-prenyltransferases, which use allylic prenyl pyrophosphates as prenyl-donors to catalyze the C-prenylation of the general acceptor substrate, isopentenyl pyrophosphate. Repetition of this reaction forms (Z,E-mixed)-polyprenyl pyrophosphates, which are converted later into glycosyl carrier lipids, such as undecaprenyl phosphate and dolichyl phosphate. MM_0014 from the methanogenic archaeon Methanosarcina mazei is known as a versatile cis-prenyltransferase that accepts both isopentenyl pyrophosphate and dimethylallyl pyrophosphate as acceptor substrates. To learn more about this enzyme’s catalytic activity, we determined the X-ray crystal structures of MM_0014 in the presence or absence of these substrates. Surprisingly, one structure revealed a complex with O-prenylglycerol, suggesting that the enzyme catalyzed the prenylation of glycerol contained in the crystallization buffer. Further analyses confirmed that the enzyme could catalyze the O-prenylation of small alcohols, such as 2-propanol, expanding our understanding of the catalytic ability of cis-prenyltransferases.
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Affiliation(s)
- Miyako Okada
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hideaki Unno
- Graduate School of Engineering, Nagasaki University, Nagasaki, Nagasaki, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Koh-Ichi Emi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Mayuko Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hisashi Hemmi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan.
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9
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Kurokawa H, Ambo T, Takahashi S, Koyama T. Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity. Biochem Biophys Res Commun 2020; 532:459-465. [PMID: 32892948 DOI: 10.1016/j.bbrc.2020.08.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 11/17/2022]
Abstract
cis-Prenyltransferases (cis-PTs) catalyze consecutive condensations of isopentenyl diphosphate to an allylic diphosphate acceptor to produce a linear polyprenyl diphosphate of designated length. Dimer formation is a prerequisite for cis-PTs to catalyze all cis-prenyl condensation reactions. The structure-function relationship of a conserved C-terminal RXG motif in cis-PTs that forms inter-subunit interactions and has a role in catalytic activity has attracted much attention. Here, we solved the crystal structure of a medium-chain cis-PT from Thermobifida fusca that produces dodecaprenyl diphosphate as a polyprenoid glycan carrier for cell wall synthesis. The structure revealed a characteristic dimeric architecture of cis-PTs in which a rigidified RXG motif of one monomer formed inter-subunit hydrogen bonds with the catalytic site of the other monomer, while the RXG motif of the latter remained flexible. Careful analyses suggested the existence of a possible long-range negative cooperativity between the two catalytic sites on the two monomeric subunits that allowed the binding of one subunit to stabilize the formation of the enzyme-substrate ternary complex and facilitated the release of Mg-PPi and subsequent intra-molecular translocation at the counter subunit so that the condensation reaction could occur in consecutive cycles. The current structure reveals the dynamic nature of the RXG motif and provides a rationale for pursuing further investigations to elucidate the inter-subunit cooperativity of cis-PTs.
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Affiliation(s)
- Hirofumi Kurokawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
| | - Takanori Ambo
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki Aza Aoba 6-6-11, Aoba-ku, Sendai, 980-8579, Japan
| | - Tanetoshi Koyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
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10
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Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A 2020; 117:20794-20802. [PMID: 32817466 PMCID: PMC7456142 DOI: 10.1073/pnas.2008381117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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] [Indexed: 01/07/2023] Open
Abstract
Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme's active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme's active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.
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Affiliation(s)
- Ban H Edani
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Kariona A Grabińska
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Rong Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Eon Joo Park
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin Siciliano
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Ya Ha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520;
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
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11
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Costa-Gutierrez SB, Lami MJ, Santo MCCD, Zenoff AM, Vincent PA, Molina-Henares MA, Espinosa-Urgel M, de Cristóbal RE. Plant growth promotion by Pseudomonas putida KT2440 under saline stress: role of eptA. Appl Microbiol Biotechnol 2020; 104:4577-4592. [PMID: 32221691 DOI: 10.1007/s00253-020-10516-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 12/05/2019] [Revised: 02/11/2020] [Accepted: 03/01/2020] [Indexed: 01/22/2023]
Abstract
New strategies to improve crop yield include the incorporation of plant growth-promoting bacteria in agricultural practices. The non-pathogenic bacterium Pseudomonas putida KT2440 is an excellent root colonizer of crops of agronomical importance and has been shown to activate the induced systemic resistance of plants in response to certain foliar pathogens. In this work, we have analyzed additional plant growth promotion features of this strain. We show it can tolerate high NaCl concentrations and determine how salinity influences traits such as the production of indole compounds, siderophore synthesis, and phosphate solubilization. Inoculation with P. putida KT2440 significantly improved seed germination and root and stem length of soybean and corn plants under saline conditions compared to uninoculated plants, whereas the effects were minor under non-saline conditions. Also, random transposon mutagenesis was used for preliminary identification of KT2440 genes involved in bacterial tolerance to saline stress. One of the obtained mutants was analyzed in detail. The disrupted gene encodes a predicted phosphoethanolamine-lipid A transferase (EptA), an enzyme described to be involved in the modification of lipid A during lipopolysaccharide (LPS) biosynthesis. This mutant showed changes in exopolysaccharide (EPS) production, low salinity tolerance, and reduced competitive fitness in the rhizosphere.
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Affiliation(s)
- Stefanie B Costa-Gutierrez
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI, San Miguel de Tucumán, Tucumán, Argentina
| | - María Jesús Lami
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI, San Miguel de Tucumán, Tucumán, Argentina
| | - María Carolina Caram-Di Santo
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI, San Miguel de Tucumán, Tucumán, Argentina
| | - Ana M Zenoff
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI, San Miguel de Tucumán, Tucumán, Argentina
| | - Paula A Vincent
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Ricardo E de Cristóbal
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT) and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Chacabuco 461, T4000ILI, San Miguel de Tucumán, Tucumán, Argentina.
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12
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Heib A, Niro G, Weck SC, Koppermann S, Ducho C. Muraymycin Nucleoside Antibiotics: Structure-Activity Relationship for Variations in the Nucleoside Unit. Molecules 2019; 25:molecules25010022. [PMID: 31861655 PMCID: PMC6983020 DOI: 10.3390/molecules25010022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 11/14/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/04/2022] Open
Abstract
Muraymycins are a subclass of naturally occurring nucleoside antibiotics with promising antibacterial activity. They inhibit the bacterial enzyme translocase I (MraY), a clinically yet unexploited target mediating an essential intracellular step of bacterial peptidoglycan biosynthesis. Several structurally simplified muraymycin analogues have already been synthesized for structure–activity relationship (SAR) studies. We now report on novel derivatives with unprecedented variations in the nucleoside unit. For the synthesis of these new muraymycin analogues, we employed a bipartite approach facilitating the introduction of different nucleosyl amino acid motifs. This also included thymidine- and 5-fluorouridine-derived nucleoside core structures. Using an in vitro assay for MraY activity, it was found that the introduction of substituents in the 5-position of the pyrimidine nucleobase led to a significant loss of inhibitory activity towards MraY. The loss of nucleobase aromaticity (by reduction of the uracil C5-C6 double bond) resulted in a ca. tenfold decrease in inhibitory potency. In contrast, removal of the 2′-hydroxy group furnished retained activity, thus demonstrating that modifications of the ribose moiety might be well-tolerated. Overall, these new SAR insights will guide the future design of novel muraymycin analogues for their potential development towards antibacterial drug candidates.
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13
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Alexander SPH, Fabbro D, Kelly E, Mathie A, Peters JA, Veale EL, Armstrong JF, Faccenda E, Harding SD, Pawson AJ, Sharman JL, Southan C, Davies JA. THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Enzymes. Br J Pharmacol 2019; 176 Suppl 1:S297-S396. [PMID: 31710714 PMCID: PMC6844577 DOI: 10.1111/bph.14752] [Citation(s) in RCA: 394] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide represents approximately 400 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.14752. Enzymes are one of the six major pharmacological targets into which the Guide is divided, with the others being: G protein-coupled receptors, ion channels, nuclear hormone receptors, catalytic receptors and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2019, and supersedes data presented in the 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
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Affiliation(s)
| | | | - Eamonn Kelly
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Alistair Mathie
- Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Emma L Veale
- Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Jane F Armstrong
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Elena Faccenda
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Simon D Harding
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Adam J Pawson
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Joanna L Sharman
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Christopher Southan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Jamie A Davies
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
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14
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Halder AK, Chatterjee P, Nasipuri M, Plewczynski D, Basu S. 3gClust: Human Protein Cluster Analysis. IEEE/ACM Trans Comput Biol Bioinform 2019; 16:1773-1784. [PMID: 29993556 DOI: 10.1109/tcbb.2018.2840996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a human protein cluster analysis by combining: 1) n-gram based amino acid frequency features, 2) optimal feature selection, 3) hierarchical clustering, and 4) advanced partitioning techniques. Our method qualitatively and quantitatively groups proteins with increasing sequence similarity into similar clusters by calculating the frequency model of amino acids using n-grams. We experiment with n = 1, i.e., unigrams, n = 2, i.e., bigrams, and finally n = 3, i.e., trigrams for optimal selection of features to design the 3gClust algorithm. The benchmarking results on 20,105 manually curated human proteins show that 3gClust ensures better cluster compactness in the case of proteins with similar functional groups, biological processes, structural alignment, and shared domains (e.g., aquaporins, keratins). Quantitative analysis of non singleton clusters shows significant improvement in their compactness in comparison to other state-of-the art methodologies. 3gClust is available at https://sites.google.com/site/bioinfoju/projects/3gclust for academic use along with supplementary materials, which can be found on the Computer Society Digital Library at http://doi.ieeecomputersociety.org/10.1109/TCBB.2018.2840996, and datasets.
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15
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Mashalidis EH, Kaeser B, Terasawa Y, Katsuyama A, Kwon DY, Lee K, Hong J, Ichikawa S, Lee SY. Chemical logic of MraY inhibition by antibacterial nucleoside natural products. Nat Commun 2019; 10:2917. [PMID: 31266949 PMCID: PMC6606608 DOI: 10.1038/s41467-019-10957-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 03/20/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023] Open
Abstract
Novel antibacterial agents are needed to address the emergence of global antibiotic resistance. MraY is a promising candidate for antibiotic development because it is the target of five classes of naturally occurring nucleoside inhibitors with potent antibacterial activity. Although these natural products share a common uridine moiety, their core structures vary substantially and they exhibit different activity profiles. An incomplete understanding of the structural and mechanistic basis of MraY inhibition has hindered the translation of these compounds to the clinic. Here we present crystal structures of MraY in complex with representative members of the liposidomycin/caprazamycin, capuramycin, and mureidomycin classes of nucleoside inhibitors. Our structures reveal cryptic druggable hot spots in the shallow inhibitor binding site of MraY that were not previously appreciated. Structural analyses of nucleoside inhibitor binding provide insights into the chemical logic of MraY inhibition, which can guide novel approaches to MraY-targeted antibiotic design.
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Affiliation(s)
- Ellene H Mashalidis
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Benjamin Kaeser
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Yuma Terasawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Kiyoun Lee
- Department of Chemistry, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.
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16
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Ann Benore M. What is in a name? (or a number?): The updated enzyme classifications. Biochem Mol Biol Educ 2019; 47:481-483. [PMID: 31063221 DOI: 10.1002/bmb.21251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Marilee Ann Benore
- Department of Natural Sciences, University of Michigan Dearborn, College of Arts Sciences and Letters, Dearborn, Michigan
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17
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Liu Y, Moura ECCM, Dörr JM, Scheidelaar S, Heger M, Egmond MR, Killian JA, Mohammadi T, Breukink E. Bacillus subtilis MraY in detergent-free system of nanodiscs wrapped by styrene-maleic acid copolymers. PLoS One 2018; 13:e0206692. [PMID: 30395652 PMCID: PMC6218056 DOI: 10.1371/journal.pone.0206692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/17/2018] [Indexed: 12/25/2022] Open
Abstract
As an integral membrane protein, purification and characterization of phospho-N- acetylmuramyl- pentapeptide translocase MraY have proven difficult. Low yield and concerns of retaining stability and activity after detergent solubilization have hampered the structure-function analysis. The recently developed detergent-free styrene-maleic acid (SMA) co-polymer system offers an alternative approach that may overcome these disadvantages. In this study, we used the detergent free system to purify MraY from Bacillus subtilis. This allowed efficient extraction of MraY that was heterologously produced in Escherichia coli membranes into SMA-wrapped nanodiscs. The purified MraY embedded in these nanodiscs (SMA-MraY) was comparable to the micellar MraY extracted with a conventional detergent (DDM) with regard to the yield and the purity of the recombinant protein but required significantly less time. The predominantly alpha-helical secondary structure of the protein in SMA-wrapped nanodiscs was also more stable against heat denaturation compared to the micellar protein. Thus, this detergent-free system is amenable to extract MraY efficiently and effectively while maintaining the biophysical properties of the protein. However, the apparent activity of the SMA-MraY was reduced compared to that of the detergent-solubilized protein. The present data indicates that this is caused by a lower accessibility of the enzyme in SMA-wrapped nanodiscs towards its polyisoprenoid substrate.
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Affiliation(s)
- Yao Liu
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Elisabete C. C. M. Moura
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Jonas M. Dörr
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Stefan Scheidelaar
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Michal Heger
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Maarten R. Egmond
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - J. Antoinette Killian
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Tamimount Mohammadi
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
- * E-mail:
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18
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Li J, Schuman MC, Halitschke R, Li X, Guo H, Grabe V, Hammer A, Baldwin IT. The decoration of specialized metabolites influences stylar development. eLife 2018; 7:e38611. [PMID: 30289384 PMCID: PMC6192696 DOI: 10.7554/elife.38611] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 05/24/2018] [Accepted: 09/23/2018] [Indexed: 01/05/2023] Open
Abstract
Plants produce many different specialized (secondary) metabolites that function in solving ecological challenges; few are known to function in growth or other primary processes. 17-Hydroxygeranylinalool diterpene glycosides (DTGs) are abundant herbivory-induced, structurally diverse and commonly malonylated defense metabolites in Nicotiana attenuata plants. By identifying and silencing a malonyltransferase, NaMaT1, involved in DTG malonylation, we found that DTG malonylation percentages are normally remarkably uniform, but when disrupted, result in DTG-dependent reduced floral style lengths, which in turn result from reduced stylar cell sizes, IAA contents, and YUC activity; phenotypes that could be restored by IAA supplementation or by silencing the DTG pathway. Moreover, the Nicotiana genus-specific JA-deficient short-style phenotype also results from alterations in DTG malonylation patterns. Decorations of plant specialized metabolites can be tuned to remarkably uniform levels, and this regulation plays a central but poorly understood role in controlling the development of specific plant parts, such as floral styles.
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Affiliation(s)
- Jiancai Li
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Meredith C Schuman
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
- Department of GeographyUniversity of ZurichZurichSwitzerland
| | - Rayko Halitschke
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Xiang Li
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Han Guo
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Veit Grabe
- Department of Evolutionary NeuroethologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Austin Hammer
- Department of BiologyBrigham Young UniversityProvoUnited States
| | - Ian T Baldwin
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
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19
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Entova S, Billod JM, Swiecicki JM, Martín-Santamaría S, Imperiali B. Insights into the key determinants of membrane protein topology enable the identification of new monotopic folds. eLife 2018; 7:40889. [PMID: 30168796 PMCID: PMC6133551 DOI: 10.7554/elife.40889] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 08/08/2018] [Accepted: 08/27/2018] [Indexed: 01/31/2023] Open
Abstract
Monotopic membrane proteins integrate into the lipid bilayer via reentrant hydrophobic domains that enter and exit on a single face of the membrane. Whereas many membrane-spanning proteins have been structurally characterized and transmembrane topologies can be predicted computationally, relatively little is known about the determinants of membrane topology in monotopic proteins. Recently, we reported the X-ray structure determination of PglC, a full-length monotopic membrane protein with phosphoglycosyl transferase (PGT) activity. The definition of this unique structure has prompted in vivo, biochemical, and computational analyses to understand and define key motifs that contribute to the membrane topology and to provide insight into the dynamics of the enzyme in a lipid bilayer environment. Using the new information gained from studies on the PGT superfamily we demonstrate that two motifs exemplify principles of topology determination that can be applied to the identification of reentrant domains among diverse monotopic proteins of interest.
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Affiliation(s)
- Sonya Entova
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
| | - Jean-Marc Billod
- Department of Structural & Chemical BiologyCentro de Investigaciones BiológicasMadridSpain
| | - Jean-Marie Swiecicki
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
| | | | - Barbara Imperiali
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
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20
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Lewis RD, Garcia-Borràs M, Chalkley MJ, Buller AR, Houk KN, Kan SBJ, Arnold FH. Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase. Proc Natl Acad Sci U S A 2018; 115:7308-7313. [PMID: 29946033 PMCID: PMC6048479 DOI: 10.1073/pnas.1807027115] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [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] [Indexed: 11/18/2022] Open
Abstract
Recently, heme proteins have been discovered and engineered by directed evolution to catalyze chemical transformations that are biochemically unprecedented. Many of these nonnatural enzyme-catalyzed reactions are assumed to proceed through a catalytic iron porphyrin carbene (IPC) intermediate, although this intermediate has never been observed in a protein. Using crystallographic, spectroscopic, and computational methods, we have captured and studied a catalytic IPC intermediate in the active site of an enzyme derived from thermostable Rhodothermus marinus (Rma) cytochrome c High-resolution crystal structures and computational methods reveal how directed evolution created an active site for carbene transfer in an electron transfer protein and how the laboratory-evolved enzyme achieves perfect carbene transfer stereoselectivity by holding the catalytic IPC in a single orientation. We also discovered that the IPC in Rma cytochrome c has a singlet ground electronic state and that the protein environment uses geometrical constraints and noncovalent interactions to influence different IPC electronic states. This information helps us to understand the impressive reactivity and selectivity of carbene transfer enzymes and offers insights that will guide and inspire future engineering efforts.
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Affiliation(s)
- Russell D Lewis
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Matthew J Chalkley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Andrew R Buller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
| | - S B Jennifer Kan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Frances H Arnold
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125;
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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21
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Koppermann S, Cui Z, Fischer PD, Wang X, Ludwig J, Thorson JS, Van Lanen SG, Ducho C. Insights into the Target Interaction of Naturally Occurring Muraymycin Nucleoside Antibiotics. ChemMedChem 2018; 13:779-784. [PMID: 29438582 PMCID: PMC6019934 DOI: 10.1002/cmdc.201700793] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 12/15/2017] [Revised: 02/02/2018] [Indexed: 11/08/2022]
Abstract
Muraymycins are a subclass of antimicrobially active uridine-derived natural products. Biological data on several muraymycin analogues have been reported, including some inhibitory in vitro activities toward their target protein, the bacterial membrane enzyme MraY. However, a structure-activity relationship (SAR) study on naturally occurring muraymycins based on such in vitro data has been missing so far. In this work, we report a detailed SAR investigation on representatives of the four muraymycin subgroups A-D using a fluorescence-based in vitro MraY assay. For some muraymycins, inhibition of MraY with IC50 values in the low-picomolar range was observed. These inhibitory potencies were compared with antibacterial activities and were correlated to modelling data derived from a previously reported X-ray crystal structure of MraY in complex with a muraymycin inhibitor. Overall, these results will pave the way for the development of muraymycin analogues with optimized properties as antibacterial drug candidates.
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Affiliation(s)
- Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Patrick D Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, P.R. China
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Jannine Ludwig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
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22
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Guo D, Yang ZP, Li HL, Wang Y, Zhu JH, Peng SQ. The 14-3-3 protein HbGF14a interacts with a RING zinc finger protein to regulate expression of the rubber transferase gene in Hevea brasiliensis. J Exp Bot 2018; 69:1903-1912. [PMID: 29432591 DOI: 10.1093/jxb/ery049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hevea brasiliensis is a key commercial source of natural rubber (cis 1,4-polyisoprene). In H. brasiliensis, rubber transferase is responsible for cis-1,4-polymerization of isoprene units from isopentenyl diphosphate and thus affects the yield of rubber. Little is known about the regulatory mechanisms of the rubber transferase gene at a molecular level. In this study we show that the 5'UTR intron of the promoter of the rubber transferase gene (HRT2) suppresses the expression of HRT2. A H. brasiliensis RING zinc finger protein (designated as HbRZFP1) was able to interact specifically with the HRT2 promoter to down-regulate its transcription in vivo. A 14-3-3 protein (named as HbGF14a) was identified as interacting with HbRZFP1, both in yeast and in planta. Transient co-expression of HbGF14a and HbRZFP1-encoding cDNAs resulted in HbRZFP1-mediated HRT2 transcription inhibition being relieved. HbGF14a repressed the protein-DNA binding of HbRZFP1 with the HRT2 promoter in yeast. We propose a regulatory mechanism by which the binding of HbGF14a to HbRZFP1 interferes with the interaction of HbRZFP1 with the HRT2 promoter, thereby repressing the protein-DNA binding between them. This study provides new insights into the role of HbGF14a in mediating expression of the rubber transferase gene in Hevea brasiliensis.
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Affiliation(s)
- Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zi-Ping Yang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Tropical Crop Genetic Improvement Key Laboratory of Zhanjiang, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Hui-Liang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Ying Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jia-Hong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Shi-Qing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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23
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Gopalan AB, Vallurupalli P. Measuring the signs of the methyl 1H chemical shift differences between major and 'invisible' minor protein conformational states using methyl 1H multi-quantum spectroscopy. J Biomol NMR 2018; 70:187-202. [PMID: 29564579 DOI: 10.1007/s10858-018-0171-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the μs to millisecond (ms) timescale between a visible major state and 'invisible' minor states. The exchange rate(s) ([Formula: see text]), population(s) of the minor state(s) and the absolute value of the chemical shift difference [Formula: see text] (ppm) between different exchanging states can be extracted from the CPMG data. However the sign of [Formula: see text] that is required to reconstruct the spectrum of the 'invisible' minor state(s) cannot be obtained from CPMG data alone. Building upon the recently developed triple quantum (TQ) methyl [Formula: see text] CPMG experiment (Yuwen in Angew Chem 55:11490-11494, 2016) we have developed pulse sequences that use carbon detection to generate and evolve single quantum (SQ), double quantum (DQ) and TQ coherences from methyl protons in the indirect dimension to measure the chemical exchange-induced shifts of the SQ, DQ and TQ coherences from which the sign of [Formula: see text] is readily obtained for two state exchange. Further a combined analysis of the CPMG data and the difference in exchange induced shifts between the SQ and DQ resonances and between the SQ and TQ resonances improves the estimates of exchange parameters like the population of the minor state. We demonstrate the use of these experiments on two proteins undergoing exchange: (1) the ~ 18 kDa cavity mutant of T4 Lysozyme ([Formula: see text]) and (2) the [Formula: see text] kDa Peripheral Sub-unit Binding Domain (PSBD) from the acetyl transferase of Bacillus stearothermophilus ([Formula: see text]).
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Affiliation(s)
- Anusha B Gopalan
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal Ranga Reddy District, Hyderabad, Telangana, 500107, India
| | - Pramodh Vallurupalli
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal Ranga Reddy District, Hyderabad, Telangana, 500107, India.
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24
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de Lira NPV, Pauletti BA, Marques AC, Perez CA, Caserta R, de Souza AA, Vercesi AE, Paes Leme AF, Benedetti CE. BigR is a sulfide sensor that regulates a sulfur transferase/dioxygenase required for aerobic respiration of plant bacteria under sulfide stress. Sci Rep 2018; 8:3508. [PMID: 29472641 PMCID: PMC5823870 DOI: 10.1038/s41598-018-21974-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 12/11/2017] [Accepted: 02/13/2018] [Indexed: 12/24/2022] Open
Abstract
To cope with toxic levels of H2S, the plant pathogens Xylella fastidiosa and Agrobacterium tumefaciens employ the bigR operon to oxidize H2S into sulfite. The bigR operon is regulated by the transcriptional repressor BigR and it encodes a bifunctional sulfur transferase (ST) and sulfur dioxygenase (SDO) enzyme, Blh, required for H2S oxidation and bacterial growth under hypoxia. However, how Blh operates to enhance bacterial survival under hypoxia and how BigR is deactivated to derepress operon transcription is unknown. Here, we show that the ST and SDO activities of Blh are in vitro coupled and necessary to oxidize sulfide into sulfite, and that Blh is critical to maintain the oxygen flux during A. tumefaciens respiration when oxygen becomes limited to cells. We also show that H2S and polysulfides inactivate BigR leading to operon transcription. Moreover, we show that sulfite, which is produced by Blh in the ST and SDO reactions, is toxic to Citrus sinensis and that X. fastidiosa-infected plants accumulate sulfite and higher transcript levels of sulfite detoxification enzymes, suggesting that they are under sulfite stress. These results indicate that BigR acts as a sulfide sensor in the H2S oxidation mechanism that allows pathogens to colonize plant tissues where oxygen is a limiting factor.
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Affiliation(s)
- Nayara Patricia Vieira de Lira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP 13083-100, Campinas, SP, Brazil
| | - Bianca Alves Pauletti
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP 13083-100, Campinas, SP, Brazil
| | - Ana Carolina Marques
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, 13083-887, Campinas, SP, Brazil
| | - Carlos Alberto Perez
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), CEP 13083-100, Campinas, SP, Brazil
| | - Raquel Caserta
- Agronomic Institute of Campinas, Citriculture Research Center 'Sylvio Moreira', CEP 13490-970, Cordeirópolis, SP, Brazil
| | - Alessandra Alves de Souza
- Agronomic Institute of Campinas, Citriculture Research Center 'Sylvio Moreira', CEP 13490-970, Cordeirópolis, SP, Brazil
| | - Aníbal Eugênio Vercesi
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, 13083-887, Campinas, SP, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP 13083-100, Campinas, SP, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP 13083-100, Campinas, SP, Brazil.
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25
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Abstract
Recent innovations in peptide natural product biosynthesis reveal a surprising wealth of previously uncharacterized biochemical reactions that have potential applications in synthetic biology. Among these, the cyanobactins are noteworthy because these peptides are protected at their N- and C-termini by macrocyclization. Here, we use a novel bifunctional enzyme AgeMTPT to protect linear peptides by attaching prenyl and methyl groups at their free N- and C-termini. Using this peptide protectase in combination with other modular biosynthetic enzymes, we describe the total synthesis of the natural product aeruginosamide B and the biosynthesis of linear cyanobactin natural products. Our studies help to define the enzymatic mechanism of macrocyclization, providing evidence against the water exclusion hypothesis of transpeptidation and favoring the kinetic lability hypothesis.
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Affiliation(s)
- Debosmita Sardar
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah
| | - Yue Hao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah
| | - Maho Morita
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah
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26
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Abstract
Fresh frozen sections of rodent palate and gingiva were stained for phosphorylase and amylo-1,6-transglucosidase by the method of Takeuchi. Although phosphorylase has been reported to be lacking in rodent skin it appears to be present in rodent oral mucous membrane. The activity appears to be of a low intensity in this region since consistent staining was obtained only with thick sections (70 µ). Straight chain and branching enzymes were found to be more abundant in the palate than the gingiva, and the observed activity diminished with increasing age. Straight chain enzyme activity appeared abundant in the basal cells of the stratum Malpighii although stainable glycogen is usually lacking in these cells.
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27
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Nemeria NS, Shome B, DeColli AA, Heflin K, Begley TP, Meyers CF, Jordan F. Competence of Thiamin Diphosphate-Dependent Enzymes with 2'-Methoxythiamin Diphosphate Derived from Bacimethrin, a Naturally Occurring Thiamin Anti-vitamin. Biochemistry 2016; 55:1135-48. [PMID: 26813608 PMCID: PMC4852132 DOI: 10.1021/acs.biochem.5b01300] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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
Bacimethrin (4-amino-5-hydroxymethyl-2-methoxypyrimidine), a natural product isolated from some bacteria, has been implicated as an inhibitor of bacterial and yeast growth, as well as in inhibition of thiamin biosynthesis. Given that thiamin biosynthetic enzymes could convert bacimethrin to 2'-methoxythiamin diphosphate (MeOThDP), it is important to evaluate the effect of this coenzyme analogue on thiamin diphosphate (ThDP)-dependent enzymes. The potential functions of MeOThDP were explored on five ThDP-dependent enzymes: the human and Escherichia coli pyruvate dehydrogenase complexes (PDHc-h and PDHc-ec, respectively), the E. coli 1-deoxy-D-xylulose 5-phosphate synthase (DXPS), and the human and E. coli 2-oxoglutarate dehydrogenase complexes (OGDHc-h and OGDHc-ec, respectively). Using several mechanistic tools (fluorescence, circular dichroism, kinetics, and mass spectrometry), it was demonstrated that MeOThDP binds in the active centers of ThDP-dependent enzymes, however, with a binding mode different from that of ThDP. While modest activities resulted from addition of MeOThDP to E. coli PDHc (6-11%) and DXPS (9-14%), suggesting that MeOThDP-derived covalent intermediates are converted to the corresponding products (albeit with rates slower than that with ThDP), remarkably strong activity (up to 75%) resulted upon addition of the coenzyme analogue to PDHc-h. With PDHc-ec and PDHc-h, the coenzyme analogue could support all reactions, including communication between components in the complex. No functional substitution of MeOThDP for ThDP was in evidence with either OGDH-h or OGDH-ec, shown to be due to tight binding of ThDP.
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Affiliation(s)
- Natalia S Nemeria
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
| | - Brateen Shome
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | - Alicia A DeColli
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland 21205, United States
| | - Kathryn Heflin
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland 21205, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | - Caren Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland 21205, United States
| | - Frank Jordan
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
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28
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Dulaney S, Xu Y, Wang P, Tiruchinapally G, Wang Z, Kathawa J, El-Dakdouki MH, Yang B, Liu J, Huang X. Divergent Synthesis of Heparan Sulfate Oligosaccharides. J Org Chem 2015; 80:12265-79. [PMID: 26574650 PMCID: PMC4685427 DOI: 10.1021/acs.joc.5b02172] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 12/01/2022]
Abstract
Heparan sulfates are implicated in a wide range of biological processes. A major challenge in deciphering their structure and activity relationship is the synthetic difficulties to access diverse heparan sulfate oligosaccharides with well-defined sulfation patterns. In order to expedite the synthesis, a divergent synthetic strategy was developed. By integrating chemical synthesis and two types of O-sulfo transferases, seven different hexasaccharides were obtained from a single hexasaccharide precursor. This approach combined the flexibility of chemical synthesis with the selectivity of enzyme-catalyzed sulfations, thus simplifying the overall synthetic operations. In an attempt to establish structure activity relationships of heparan sulfate binding with its receptor, the synthesized oligosaccharides were incorporated onto a glycan microarray, and their bindings with a growth factor FGF-2 were examined. The unique combination of chemical and enzymatic approaches expanded the capability of oligosaccharide synthesis. In addition, the well-defined heparan sulfate structures helped shine light on the fine substrate specificities of biosynthetic enzymes and confirm the potential sequence of enzymatic reactions in biosynthesis.
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Affiliation(s)
- Steven
B. Dulaney
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Yongmei Xu
- Division
of Medicinal Chemistry and Natural Products, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Peng Wang
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Gopinath Tiruchinapally
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhen Wang
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jolian Kathawa
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Mohammad H. El-Dakdouki
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
- Department
of Chemistry, Beirut Arab University, P.O. Box 11-5020, Riad El Solh 11072809, Beirut, Lebanon
| | - Bo Yang
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jian Liu
- Division
of Medicinal Chemistry and Natural Products, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Xuefei Huang
- Department
of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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29
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Tong Y, Su P, Zhao Y, Zhang M, Wang X, Liu Y, Zhang X, Gao W, Huang L. Molecular Cloning and Characterization of DXS and DXR Genes in the Terpenoid Biosynthetic Pathway of Tripterygium wilfordii. Int J Mol Sci 2015; 16:25516-35. [PMID: 26512659 PMCID: PMC4632813 DOI: 10.3390/ijms161025516] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 09/07/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
1-Deoxy-d-xylulose-5-phosphate synthase (DXS) and 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) genes are the key enzyme genes of terpenoid biosynthesis but still unknown in Tripterygium wilfordii Hook. f. Here, three full-length cDNA encoding DXS1, DXS2 and DXR were cloned from suspension cells of T. wilfordii with ORF sizes of 2154 bp (TwDXS1, GenBank accession no.KM879187), 2148 bp (TwDXS2, GenBank accession no.KM879186), 1410 bp (TwDXR, GenBank accession no.KM879185). And, the TwDXS1, TwDXS2 and TwDXR were characterized by color complementation in lycopene accumulating strains of Escherichia coli, which indicated that they encoded functional proteins and promoted lycopene pathway flux. TwDXS1 and TwDXS2 are constitutively expressed in the roots, stems and leaves and the expression level showed an order of roots > stems > leaves. After the suspension cells were induced by methyl jasmonate, the mRNA expression level of TwDXS1, TwDXS2, and TwDXR increased, and triptophenolide was rapidly accumulated to 149.52 µg·g−1, a 5.88-fold increase compared with the control. So the TwDXS1, TwDXS2, and TwDXR could be important genes involved in terpenoid biosynthesis in Tripterygium wilfordii Hook. f.
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Affiliation(s)
- Yuru Tong
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Ping Su
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujun Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Meng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xiujuan Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujia Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xianan Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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30
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Bartee D, Morris F, Al-Khouja A, Freel Meyers CL. Hydroxybenzaldoximes Are D-GAP-Competitive Inhibitors of E. coli 1-Deoxy-D-Xylulose-5-Phosphate Synthase. Chembiochem 2015; 16:1771-81. [PMID: 26174207 PMCID: PMC4609000 DOI: 10.1002/cbic.201500119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 03/09/2015] [Indexed: 11/05/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase is the first enzyme in the methylerythritol phosphate pathway to essential isoprenoids in pathogenic bacteria and apicomplexan parasites. In bacterial pathogens, DXP lies at a metabolic branch point, serving also as a precursor in the biosynthesis of vitamins B1 and B6, which are critical for central metabolism. In an effort to identify new bisubstrate analogue inhibitors that exploit the large active site and distinct mechanism of DXP synthase, a library of aryl mixed oximes was prepared and evaluated. Trihydroxybenzaldoximes emerged as reversible, low-micromolar inhibitors, competitive against D-glyceraldehyde 3-phosphate (D-GAP) and either uncompetitive or noncompetitive against pyruvate. Hydroxybenzaldoximes are the first class of D-GAP-competitive DXP synthase inhibitors, offering new tools for mechanistic studies of DXP synthase and a new direction for the development of antimicrobial agents targeting isoprenoid biosynthesis.
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Affiliation(s)
- David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
| | - Francine Morris
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
- Present address: Albert Einstein College of Medicine, Department of Biochemistry, 1301 Morris Park Avenue, Bronx, NY 10461 (USA)
| | - Amer Al-Khouja
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA).
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31
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Abstract
The diversity-oriented chemoenzymatic synthesis of α-dystroglycan (α-DG) core M1 O-mannose glycans has been achieved via a three-step sequential one-pot multienzyme (OPME) glycosylation of a chemically prepared disaccharyl serine intermediate. The high flexibility and efficiency of this chemoenzymatic strategy was demonstrated for the synthesis of three more complex core M1 O-mannose glycans for the first time along with three previously reported core M1 structures.
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Affiliation(s)
- Yan Zhang
- National Glycoengineering Research Center, School of Pharmaceutical Science, Shandong University, Jinan 250012, China
| | - Caicai Meng
- National Glycoengineering Research Center, School of Pharmaceutical Science, Shandong University, Jinan 250012, China
| | - Lan Jin
- National Glycoengineering Research Center, School of Pharmaceutical Science, Shandong University, Jinan 250012, China
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA
| | - Fengshan Wang
- National Glycoengineering Research Center, School of Pharmaceutical Science, Shandong University, Jinan 250012, China
- Key Laboratory of Chemical Biology(Ministry of Education), Shandong University, Jinan 250012, China
| | - Hongzhi Cao
- National Glycoengineering Research Center, School of Pharmaceutical Science, Shandong University, Jinan 250012, China
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32
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Gutkowska M, Wnuk M, Nowakowska J, Lichocka M, Stronkowski MM, Swiezewska E. Rab geranylgeranyl transferase β subunit is essential for male fertility and tip growth in Arabidopsis. J Exp Bot 2015; 66:213-24. [PMID: 25316062 PMCID: PMC4265159 DOI: 10.1093/jxb/eru412] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rab proteins, key players in vesicular transport in all eukaryotic cells, are post-translationally modified by lipid moieties. Two geranylgeranyl groups are attached to the Rab protein by the heterodimeric enzyme Rab geranylgeranyl transferase (RGT) αβ. Partial impairment in this enzyme activity in Arabidopsis, by disruption of the AtRGTB1 gene, is known to influence plant stature and disturb gravitropic and light responses. Here it is shown that mutations in each of the RGTB genes cause a tip growth defect, visible as root hair and pollen tube deformations. Moreover, FM 1-43 styryl dye endocytosis and recycling are affected in the mutant root hairs. Finally, it is demonstrated that the double mutant, with both AtRGTB genes disrupted, is non-viable due to absolute male sterility. Doubly mutated pollen is shrunken, has an abnormal exine structure, and shows strong disorganization of internal membranes, particularly of the endoplasmic reticulum system.
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Affiliation(s)
- Malgorzata Gutkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Marta Wnuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Julita Nowakowska
- Warsaw University, Faculty of Biology, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Michal M Stronkowski
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Koszykowa 75, 00-662 Warsaw, Poland
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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33
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Park EJ, Grabińska KA, Guan Z, Stránecký V, Hartmannová H, Hodaňová K, Barešová V, Sovová J, Jozsef L, Ondrušková N, Hansíková H, Honzík T, Zeman J, Hůlková H, Wen R, Kmoch S, Sessa WC. Mutation of Nogo-B receptor, a subunit of cis-prenyltransferase, causes a congenital disorder of glycosylation. Cell Metab 2014; 20:448-57. [PMID: 25066056 PMCID: PMC4161961 DOI: 10.1016/j.cmet.2014.06.016] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/28/2014] [Accepted: 06/14/2014] [Indexed: 11/20/2022]
Abstract
Dolichol is an obligate carrier of glycans for N-linked protein glycosylation, O-mannosylation, and GPI anchor biosynthesis. cis-prenyltransferase (cis-PTase) is the first enzyme committed to the synthesis of dolichol. However, the proteins responsible for mammalian cis-PTase activity have not been delineated. Here we show that Nogo-B receptor (NgBR) is a subunit required for dolichol synthesis in yeast, mice, and man. Moreover, we describe a family with a congenital disorder of glycosylation caused by a loss of function mutation in the conserved C terminus of NgBR-R290H and show that fibroblasts isolated from patients exhibit reduced dolichol profiles and enhanced accumulation of free cholesterol identically to fibroblasts from mice lacking NgBR. Mutation of NgBR-R290H in man and orthologs in yeast proves the importance of this evolutionarily conserved residue for mammalian cis-PTase activity and function. Thus, these data provide a genetic basis for the essential role of NgBR in dolichol synthesis and protein glycosylation.
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Affiliation(s)
- Eon Joo Park
- Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, 10 Amistad Street, New Haven, CT 06520, USA
| | - Kariona A Grabińska
- Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, 10 Amistad Street, New Haven, CT 06520, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, DUMC 2927, Durham, NC 27710, USA
| | - Viktor Stránecký
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Hana Hartmannová
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Kateřina Hodaňová
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Veronika Barešová
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Jana Sovová
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Levente Jozsef
- Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, 10 Amistad Street, New Haven, CT 06520, USA
| | - Nina Ondrušková
- Department of Pediatrics, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Hana Hansíková
- Department of Pediatrics, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Tomáš Honzík
- Department of Pediatrics, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Jiří Zeman
- Department of Pediatrics, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Helena Hůlková
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic
| | - Rong Wen
- Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, 900 NW 17th Street, Miami, FL 33136, USA
| | - Stanislav Kmoch
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, Prague 2, 128 08 Czech Republic.
| | - William C Sessa
- Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, 10 Amistad Street, New Haven, CT 06520, USA.
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Perera VR, Newton GL, Parnell JM, Komives EA, Pogliano K. Purification and characterization of the Staphylococcus aureus bacillithiol transferase BstA. Biochim Biophys Acta 2014; 1840:2851-61. [PMID: 24821014 PMCID: PMC4802972 DOI: 10.1016/j.bbagen.2014.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/26/2022]
Abstract
BACKGROUND Gram-positive bacteria in the phylum Firmicutes synthesize the low molecular weight thiol bacillithiol rather than glutathione or mycothiol. The bacillithiol transferase YfiT from Bacillus subtilis was identified as a new member of the recently discovered DinB/YfiT-like Superfamily. Based on structural similarity using the Superfamily program, we have determined 30 of 31 Staphylococcus aureus strains encode a single bacillithiol transferase from the DinB/YfiT-like Superfamily, while the remaining strain encodes two proteins. METHODS We have cloned, purified, and confirmed the activity of a recombinant bacillithiol transferase (henceforth called BstA) encoded by the S. aureus Newman ORF NWMN_2591. Moreover, we have studied the saturation kinetics and substrate specificity of this enzyme using in vitro biochemical assays. RESULTS BstA was found to be active with the co-substrate bacillithiol, but not with other low molecular weight thiols tested. BstA catalyzed bacillithiol conjugation to the model substrates monochlorobimane, 1-chloro-2,4-dinitrobenzene, and the antibiotic cerulenin. Several other molecules, including the antibiotic rifamycin S, were found to react directly with bacillithiol, but the addition of BstA did not enhance the rate of reaction. Furthermore, cells growing in nutrient rich medium exhibited low BstA activity. CONCLUSIONS BstA is a bacillithiol transferase from S. aureus that catalyzes the detoxification of cerulenin. Additionally, we have determined that bacillithiol itself might be capable of directly detoxifying electrophilic molecules. GENERAL SIGNIFICANCE BstA is an active bacillithiol transferase from S. aureus Newman and is the first DinB/YfiT-like Superfamily member identified from this organism. Interestingly, BstA is highly divergent from B. subtilis YfiT.
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Affiliation(s)
- Varahenage R Perera
- Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377
| | - Gerald L Newton
- Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377
| | - Jonathan M Parnell
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378
| | - Kit Pogliano
- Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377.
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Basta LAB, Patel H, Kakalis L, Jordan F, Meyers CLF. Defining critical residues for substrate binding to 1-deoxy-D-xylulose 5-phosphate synthase--active site substitutions stabilize the predecarboxylation intermediate C2α-lactylthiamin diphosphate. FEBS J 2014; 281:2820-2837. [PMID: 24767541 PMCID: PMC4065394 DOI: 10.1111/febs.12823] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 12/13/2013] [Revised: 04/06/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase catalyzes the formation of DXP from pyruvate and D-glyceraldehyde 3-phosphate (GraP) in a thiamin diphosphate-dependent manner, and is the first step in the essential pathway to isoprenoids in human pathogens. Understanding the mechanism of this unique enzyme is critical for developing new anti-infective agents that selectively target isoprenoid biosynthesis. The present study used mutagenesis and a combination of protein fluorescence, CD and kinetics experiments to investigate the roles of Arg420, Arg478 and Tyr392 in substrate binding and catalysis. The results support a random sequential, preferred order mechanism, and predict that Arg420 and Arg478 are involved in binding of the acceptor substrate, GraP. D-Glyceraldehyde, an alternative acceptor substrate lacking the phosphoryl group predicted to interact with Arg420 and Arg478, also accelerates decarboxylation of the predecarboxylation intermediate C2α-lactylthiamin diphosphate (LThDP) on DXP synthase, indicating that this binding interaction is not absolutely required, and that the hydroxyaldehyde sufficiently triggers decarboxylation. Unexpectedly, Tyr392 contributes to GraP affinity, and is not required for LThDP formation or its GraP-promoted decarboxylation. Time-resolved CD spectroscopy and NMR experiments indicate that LThDP is significantly stabilized on R420A and Y392F variants as compared with wild-type DXP synthase in the absence of acceptor substrate, but these substitutions do not appear to affect the rate of GraP-promoted LThDP decarboxylation in the presence of high levels of GraP, and LThDP formation remains the rate-limiting step. These results suggest a role of these residues in promoting GraP binding, which in turn facilitates decarboxylation, and also highlight interesting differences between DXP synthase and other thiamin diphosphate-dependent enzymes.
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Affiliation(s)
- Leighanne A. Brammer Basta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hetalben Patel
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Lazaros Kakalis
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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Surmacz L, Plochocka D, Kania M, Danikiewicz W, Swiezewska E. cis-Prenyltransferase atCPT6 produces a family of very short-chain polyisoprenoids in planta. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:240-50. [PMID: 24291644 DOI: 10.1016/j.bbalip.2013.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/13/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022]
Abstract
cis-Prenyltransferases (CPTs) comprise numerous enzymes synthesizing isoprenoid hydrocarbon skeleton with isoprenoid units in the cis (Z) configuration. The chain-length specificity of a particular plant CPT is in most cases unknown despite thecomposition of the accumulated isoprenoids in the tissue of interest being well established. In this report AtCPT6, one of the nine Arabidopsis thaliana CPTs, is shown to catalyze the synthesis of a family of very short-chain polyisoprenoid alcohols of six, seven, and eight isoprenoid units, those of seven units dominating The product specificity of AtCPT6 was established in vivo following its expression in the heterologous system of the yeast Saccharomyces cerevisiae and was confirmed by the absence of specific products in AtCPT6 T-DNA insertion mutants and their overaccumulation in AtCPT6-overexpressing plants. These observations are additionally validated in silico using an AtCPT6 model obtained by homology modeling. AtCPT6 only partially complements the function of the yeast homologue of CPT-Rer2 since it restores the growth but not protein glycosylation in rer2delta yeast.This is the first in planta characterization of specific products of a plant CPT producing polyisoprenoids. Their distribution suggests that a joint activity of several CPTs is required to produce the complex mixture of polyisoprenoid alcohols found in Arabidopsis roots.
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Havarushka N, Fischer-Schrader K, Lamkemeyer T, Schwarz G. Structural basis of thermal stability of the tungsten cofactor synthesis protein MoaB from Pyrococcus furiosus. PLoS One 2014; 9:e86030. [PMID: 24465852 PMCID: PMC3896444 DOI: 10.1371/journal.pone.0086030] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/06/2013] [Indexed: 12/17/2022] Open
Abstract
Molybdenum and tungsten cofactors share a similar pterin-based scaffold, which hosts an ene-dithiolate function being essential for the coordination of either molybdenum or tungsten. The biosynthesis of both cofactors involves a multistep pathway, which ends with the activation of the metal binding pterin (MPT) by adenylylation before the respective metal is incorporated. In the hyperthermophilic organism Pyrococcus furiosus, the hexameric protein MoaB (PfuMoaB) has been shown to catalyse MPT-adenylylation. Here we determined the crystal structure of PfuMoaB at 2.5 Å resolution and identified key residues of α3-helix mediating hexamer formation. Given that PfuMoaB homologues from mesophilic organisms form trimers, we investigated the impact on PfuMoaB hexamerization on thermal stability and activity. Using structure-guided mutagenesis, we successfully disrupted the hexamer interface in PfuMoaB. The resulting PfuMoaB-H3 variant formed monomers, dimers and trimers as determined by size exclusion chromatography. Circular dichroism spectroscopy as well as chemical cross-linking coupled to mass spectrometry confirmed a wild-type-like fold of the protomers as well as inter-subunits contacts. The melting temperature of PfuMoaB-H3 was found to be reduced by more than 15°C as determined by differential scanning calorimetry, thus demonstrating hexamerization as key determinant for PfuMoaB thermal stability. Remarkably, while a loss of activity at temperatures higher than 50°C was observed in the PfuMoaB-H3 variant, at lower temperatures, we determined a significantly increased catalytic activity. The latter suggests a gain in conformational flexibility caused by the disruption of the hexamerization interface.
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Affiliation(s)
- Nastassia Havarushka
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Cologne, Germany
| | | | - Tobias Lamkemeyer
- Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Guenter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Cologne, Germany
- Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- * E-mail:
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Danilov LL, Balagurova NM, Vinnikova AN, Utkina NS, Torgov VI, Kalinchuk NA, Druzhinina TN, Veselovsky VV. [Synthesis of 11-[(2-pyridyl)amino]- and 11-[(9-anthracenylcarbonyl)amino]undecyl phosphate and investigation of their acceptor properties in the enzymic reaction catalyzed by galactosylphosphotransferases from Salmonella]. Bioorg Khim 2014; 40:99-107. [PMID: 25898728 DOI: 10.1134/s1068162014010038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
11-[(2-Pyridyl)amino]undecyl phosphate and 11-[(9-anthracenylcarbonyl)amino]undecyl phosphate were chemically synthesized. The abiliy of these new fluorescent derivatives of undecyl phosphate to serve as acceptor substrate of galactosyl phosphate residue in the enzymic reaction catalyzed by galactosylphosphotransferase from Salmonella anatum or Salmonella newport membrane preparation was demonstrated.
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Kang JH, Gonzales-Vigil E, Matsuba Y, Pichersky E, Barry CS. Determination of residues responsible for substrate and product specificity of Solanum habrochaites short-chain cis-prenyltransferases. Plant Physiol 2014; 164:80-91. [PMID: 24254315 PMCID: PMC3875827 DOI: 10.1104/pp.113.230466] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Isoprenoids are diverse compounds that have their biosynthetic origin in the initial condensation of isopentenyl diphosphate and dimethylallyl diphosphate to form C10 prenyl diphosphates that can be elongated by the addition of subsequent isopentenyl diphosphate units. These reactions are catalyzed by either cis-prenyltransferases (CPTs) or trans-prenyltransferases. The synthesis of volatile terpenes in plants typically proceeds through either geranyl diphosphate (C10) or trans-farnesyl diphosphate (C15), to yield monoterpenes and sesquiterpenes, respectively. However, terpene biosynthesis in glandular trichomes of tomato (Solanum lycopersicum) and related wild relatives also occurs via the cis-substrates neryl diphosphate (NPP) and 2Z,6Z-farnesyl diphosphate (Z,Z-FPP). NPP and Z,Z-FPP are synthesized by neryl diphosphate synthase1 (NDPS1) and Z,Z-farnesyl diphosphate synthase (zFPS), which are encoded by the orthologous CPT1 locus in tomato and Solanum habrochaites, respectively. In this study, comparative sequence analysis of NDPS1 and zFPS enzymes from S. habrochaites accessions that synthesize either monoterpenes or sesquiterpenes was performed to identify amino acid residues that correlate with the ability to synthesize NPP or Z,Z-FPP. Subsequent structural modeling, coupled with site-directed mutagenesis, highlighted the importance of four amino acids located within conserved domain II of CPT enzymes that form part of the second α-helix, for determining substrate and product specificity of these enzymes. In particular, the relative positioning of aromatic amino acid residues at positions 100 and 107 determines the ability of these enzymes to synthesize NPP or Z,Z-FPP. This study provides insight into the biochemical evolution of terpene biosynthesis in the glandular trichomes of Solanum species.
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Singh VK, Ghosh I. Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum. FEBS Lett 2013; 587:2806-17. [PMID: 23816706 DOI: 10.1016/j.febslet.2013.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 05/27/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 11/19/2022]
Abstract
The methylerythritol phosphate (MEP) pathway of Plasmodium falciparum (P. falciparum) has become an attractive target for anti-malarial drug discovery. This study describes a kinetic model of this pathway, its use in validating 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) as drug target from the systemic perspective, and additional target identification, using metabolic control analysis and in silico inhibition studies. In addition to DXR, 1-deoxy-d-xylulose 5-phosphate synthase (DXS) can be targeted because it is the first enzyme of the pathway and has the highest flux control coefficient followed by that of DXR. In silico inhibition of both enzymes caused large decrement in the pathway flux. An added advantage of targeting DXS is its influence on vitamin B1 and B6 biosynthesis. Two more potential targets, 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, were also identified. Their inhibition caused large accumulation of their substrates causing instability of the system. This study demonstrates that both types of enzyme targets, one acting via flux reduction and the other by metabolite accumulation, exist in P. falciparum MEP pathway. These groups of targets can be exploited for independent anti-malarial drugs.
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Affiliation(s)
- Vivek Kumar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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Itoh Y, Sekine SI, Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of Aquifex aeolicus SelA, a bacterial selenocysteine synthase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1128-33. [PMID: 22949212 PMCID: PMC3433215 DOI: 10.1107/s1744309112033519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 03/07/2012] [Accepted: 07/25/2012] [Indexed: 06/01/2023]
Abstract
Selenocysteine (Sec), the 21st amino acid, is synthesized on its specific tRNA (tRNA(Sec)) via a multi-step process. In bacteria, tRNA(Sec) is ligated first with serine by seryl-tRNA synthetase, which is followed by Ser-to-Sec conversion by Sec synthase (SelA). To elucidate its structure and catalytic mechanism, Aquifex aeolicus SelA was crystallized. Although wild-type SelA crystals diffracted X-rays poorly (to up to 8 Å resolution), the resolution was improved by introducing a quadruple point mutation targeting the loop regions and by methylating the lysine residues, which yielded 3.9 Å resolution diffraction data from a full-length SelA crystal. Truncation of the N-terminal region (ΔN) also improved the resolution. A 3.3 Å resolution data set for phase determination was obtained from a crystal of selenomethionine-substituted Lys-methylated SelA-ΔN.
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Affiliation(s)
- Yuzuru Itoh
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Laboratory of Membrane and Cytoskeleton Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shun-ichi Sekine
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
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Post J, van Deenen N, Fricke J, Kowalski N, Wurbs D, Schaller H, Eisenreich W, Huber C, Twyman RM, Prüfer D, Gronover CS. Laticifer-specific cis-prenyltransferase silencing affects the rubber, triterpene, and inulin content of Taraxacum brevicorniculatum. Plant Physiol 2012; 158:1406-17. [PMID: 22238421 PMCID: PMC3291264 DOI: 10.1104/pp.111.187880] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [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
Certain Taraxacum species, such as Taraxacum koksaghyz and Taraxacum brevicorniculatum, produce large amounts of high-quality natural rubber in their latex, the milky cytoplasm of specialized cells known as laticifers. This high-molecular mass biopolymer consists mainly of poly(cis-1,4-isoprene) and is deposited in rubber particles by particle-bound enzymes that carry out the stereospecific condensation of isopentenyl diphosphate units. The polymer configuration suggests that the chain-elongating enzyme (rubber transferase; EC 2.5.1.20) is a cis-prenyltransferase (CPT). Here, we present a comprehensive analysis of transgenic T. brevicorniculatum plants in which the expression of three recently isolated CPTs known to be associated with rubber particles (TbCPT1 to -3) was heavily depleted by laticifer-specific RNA interference (RNAi). Analysis of the CPT-RNAi plants by nuclear magnetic resonance, size-exclusion chromatography, and gas chromatography-mass spectrometry indicated a significant reduction in rubber biosynthesis and a corresponding 50% increase in the levels of triterpenes and the main storage carbohydrate, inulin. Transmission electron microscopy revealed that the laticifers in CPT-RNAi plants contained fewer and smaller rubber particles than wild-type laticifers. We also observed lower activity of hydroxymethylglutaryl-coenzyme A reductase, the key enzyme in the mevalonate pathway, reflecting homeostatic control of the isopentenyl diphosphate pool. To our knowledge, this is the first in planta demonstration of latex-specific CPT activity in rubber biosynthesis.
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Mukherjee T, Hanes J, Tews I, Ealick SE, Begley TP. Pyridoxal phosphate: biosynthesis and catabolism. Biochim Biophys Acta 2011; 1814:1585-96. [PMID: 21767669 DOI: 10.1016/j.bbapap.2011.06.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 06/26/2011] [Accepted: 06/29/2011] [Indexed: 11/19/2022]
Abstract
Vitamin B(6) is an essential cofactor that participates in a large number of biochemical reactions. Pyridoxal phosphate is biosynthesized de novo by two different pathways (the DXP dependent pathway and the R5P pathway) and can also be salvaged from the environment. It is one of the few cofactors whose catabolic pathway has been comprehensively characterized. It is also known to function as a singlet oxygen scavenger and has protective effects against oxidative stress in fungi. Enzymes utilizing vitamin B(6) are important targets for therapeutic agents. This review provides a concise overview of the mechanistic enzymology of vitamin B(6) biosynthesis and catabolism. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Tathagata Mukherjee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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Stein DC, Miller CJ, Bhoopalan SV, Sommer DD. Sequence-based predictions of lipooligosaccharide diversity in the Neisseriaceae and their implication in pathogenicity. PLoS One 2011; 6:e18923. [PMID: 21533118 PMCID: PMC3078933 DOI: 10.1371/journal.pone.0018923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 03/11/2011] [Indexed: 12/31/2022] Open
Abstract
Endotoxin [Lipopolysaccharide (LPS)/Lipooligosaccharide (LOS)] is an important virulence determinant in gram negative bacteria. While the genetic basis of endotoxin production and its role in disease in the pathogenic Neisseria has been extensively studied, little research has focused on the genetic basis of LOS biosynthesis in commensal Neisseria. We determined the genomic sequences of a variety of commensal Neisseria strains, and compared these sequences, along with other genomic sequences available from various sequencing centers from commensal and pathogenic strains, to identify genes involved in LOS biosynthesis. This allowed us to make structural predictions as to differences in LOS seen between commensal and pathogenic strains. We determined that all neisserial strains possess a conserved set of genes needed to make a common 3-Deoxy-D-manno-octulosonic acid -heptose core structure. However, significant genomic differences in glycosyl transferase genes support the published literature indicating compositional differences in the terminal oligosaccharides. This was most pronounced in commensal strains that were distally related to the gonococcus and meningococcus. These strains possessed a homolog of heptosyltransferase III, suggesting that they differ from the pathogenic strains by the presence a third heptose. Furthermore, most commensal strains possess homologs of genes needed to synthesize lipopolysaccharide (LPS). N. cinerea, a commensal species that is highly related to the gonococcus has lost the ability to make sialyltransferase. Overall genomic comparisons of various neisserial strains indicate that significant recombination/genetic acquisition/loss has occurred within the genus, and this muddles proper speciation.
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Affiliation(s)
- Daniel C Stein
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America.
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Yin C, Jin K, Xia Y. [Cloning and expression of prenyl transferase gene of Metarhizium ansopliae]. Wei Sheng Wu Xue Bao 2010; 50:897-902. [PMID: 20815236] [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: 05/29/2023]
Abstract
OBJECTIVE To clone and identify prenyl transferase gene from Metarhizium anisopliae and to understand the gene structure and expression. METHODS Using Switching Mechanism At 5' end of RNA Transcript (SMART) method, we isolated the full length cDNA sequence and DNA sequence. Then we used quantitative RT-PCR analysis of the gene expression levels at different stages of colonization of host hemolymph by M. anisopliae. RESULTS The Mpt gene had two exons and one intron and the CDS was 1026 bp which encoded a protein with 341 amino acid residues; qRT-PCR analysis showed that the gene expression levels were significantly different, especially highly up-regulated at the late stages. CONCLUSION The Mpt gene was successfully cloned from M. anisopliae for the first time and the gene had the characteristic of high expression levels at the late stages.
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Affiliation(s)
- Congsong Yin
- College of Bioengineering of Chongqing University, Genetic Engineering Research Centre of Chongqing University, Key Laboratory of Gene Function and Regulation at Chongqing, Chongqing 400030, China.
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Sitthithaworn W, Wungsintaweekul J, Sirisuntipong T, Charoonratana T, Ebizuka Y, De-Eknamkul W. Cloning and expression of 1-deoxy-d-xylulose 5-phosphate synthase cDNA from Croton stellatopilosus and expression of 2C-methyl-d-erythritol 4-phosphate synthase and geranylgeranyl diphosphate synthase, key enzymes of plaunotol biosynthesis. J Plant Physiol 2010; 167:292-300. [PMID: 19782428 DOI: 10.1016/j.jplph.2009.09.001] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 05/28/2023]
Abstract
1-Deoxy-d-xylulose 5-phosphate synthase (DXS, EC: 4.1.3.37), the first enzyme in the 2C-methyl-d-erythritol 4-phosphate (MEP) pathway, is known to be responsible for the rate-limiting step of isoprenoid biosynthesis in Escherichia coli and Arabidopsis thaliana. In this study, the dxs gene from Croton stellatopilosus, designated csdxs, was cloned from leaf tissue using the rapid amplification of cDNA ends (RACE) technique. Leaves of C. stellatopilosus contain plaunotol, an acyclic diterpene alcohol. The csdxs cDNA containing the open reading frame of 2163 base pairs appeared to encode a polypeptide of 720 amino acids. Analysis of the deduced amino acid sequence revealed that the NH(2)-terminus of CSDXS carried a chloroplast transit peptide, a thiamine diphosphate binding site, and a transketolase motif, which are the important characteristics of DXS enzymes in higher plants. Multiple alignments of CSDXS with other plant DXSs have indicated that CSDXS has identity ranging between 68% and 89%. Expression levels of csdxs and genes encoding key enzymes in the plaunotol biosynthetic pathway, namely 2C-methyl-d-erythritol 4-phosphate synthase (meps) and geranylgeranyl diphosphate synthase (ggpps), were analysed by measuring transcript levels in leaves of different developmental stages. The results showed that dxs, meps, and ggpps are all active in young leaves prior to full expansion when plaunotol is synthesised from the DXP precursor in chloroplasts. The dense presence of chloroplasts and oil globules in the palisade cells of these leaves support the view that these genes are involved in plaunotol biosynthesis in chloroplast-containing tissues.
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Affiliation(s)
- Worapan Sitthithaworn
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Srinakharinwirot University, Nakonnayok 26120, Thailand
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Abstract
Two cDNAs encoding two distinct classes of DXSs were cloned from leaves (HbDXS1) and latex (HbDXS2) of Hevea brasiliensis by RT-PCR based methods. HbDXS1 encodes a protein of 720 amino acids, with a high homology to the class I of plant DXS proteins, and HbDXS2 encodes a protein predicted to contain 711 amino acids and with a high homology to the plant DXS class II proteins. Several important motifs and amino acid positions characteristic of DXS proteins are strictly conserved in both new HbDXS proteins. The two HbDXS genes were differentially expressed in various tissues of H. brasiliensis. The transcriptional levels of HbDXS2 were similar in both a high-yielding rubber clone (RRIM 600) and the wild type. Ethephon increased the latex yield and caused a transient increase of expression of the HbDXS2 gene. The expression of HbDXS2 in latex indicates that it may have a primary function in carotenoid biosynthesis rather than for natural rubber.
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Affiliation(s)
- Yortyot Seetang-Nun
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
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48
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Zhang M, Li K, Zhang C, Gai J, Yu D. Identification and characterization of class 1 DXS gene encoding 1-deoxy-D-xylulose-5-phosphate synthase, the first committed enzyme of the MEP pathway from soybean. Mol Biol Rep 2009; 36:879-87. [PMID: 18437529 DOI: 10.1007/s11033-008-9258-8] [Citation(s) in RCA: 29] [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] [Received: 01/10/2008] [Accepted: 04/15/2008] [Indexed: 11/27/2022]
Abstract
1-Deoxy-D-xylulose-5-phosphate synthase (DXS) catalyses the first committed step of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway, which is an alternative isoprenoids biosynthetic route that has been recently discovered. In this work, a DXS1-like cDNA (GmDXS1) was isolated from soybean. The full-length cDNA of GmDXS1 encoded 708 amino acid residues with a predicted molecular mass of 76.4 KD. Sequence alignment showed that GmDXS1 had high homology to known DXS proteins from other plant species and contained the conserved N-terminal plastid transit peptide, the N-terminal thiamine binding domain and pyridine binding DRAG domain. Phylogenetic analysis indicated that GmDXS1 belonged to the plant DXS1 cluster. Southern blot analysis indicated that a single copy of GmDXS1 gene existed in soybean genome. Tissue expression analysis revealed that GmDXS1 expressed in all photosynthetic tissues except pod walls and roots. Green fluorescence analysis with the fusion protein 35S:GmDXS1:GFP suggested that GmDXS1 was localized in plastid. The relatively higher photosynthetic pigment content in transgenic tobacco leaves compared to the control implied that GmDXS1 catalyzed the first potential regulatory step in photosynthetic pigment biosynthesis via the MEP pathway.
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Affiliation(s)
- Man Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing, People's Republic of China
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49
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Kim YB, Kim SM, Kang MK, Kuzuyama T, Lee JK, Park SC, Shin SC, Kim SU. Regulation of resin acid synthesis in Pinus densiflora by differential transcription of genes encoding multiple 1-deoxy-D-xylulose 5-phosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase genes. Tree Physiol 2009; 29:737-749. [PMID: 19203978 DOI: 10.1093/treephys/tpp002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Pinus densiflora Siebold et Zucc. is the major green canopy species in the mountainous area of Korea. To assess the response of resin acid biosynthetic genes to mechanical and chemical stimuli, we cloned cDNAs of genes encoding enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway (1-deoxy-d-xylulose 5-phosphate synthase (PdDXS), 1-deoxy-d-xylulose 5-phosphate reductoisomerase (PdDXR) and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (PdHDR)) by the rapid amplification of cDNA ends (RACE) technique. In addition, we cloned the gene encoding abietadiene synthase (PdABS) as a marker for the site of pine resin biosynthesis. PdHDR and PdDXS occurred as two gene families. In the phylogenetic trees, PdDXSs, PdDXR and PdHDRs each formed a separate clade from their respective angiosperm homologs. PdDXS2, PdHDR2 and PdDXR were most actively transcribed in stem wood, whereas PdABS was specifically transcribed. The abundance of PdDXS2 transcripts in wood in the resting state was generally 50-fold higher than the abundance of PdDXS1 transcripts, and PdHDR2 transcripts were more abundant by an order of magnitude in wood than in other tissues, with the ratio of PdHDR2 to PdHDR1 transcripts in wood being about 1. Application of 1 mM methyl jasmonate (MeJA) selectively enhanced the transcript levels of PdDXS2 and PdHDR2 in wood. The ratios of PdDXS2 to PdDXS1 and PdHDR2 to PdHDR1 reached 900 and 20, respectively, on the second day after MeJA treatment, whereas the transcript level of PdABS increased twofold by 3 days after MeJA treatment. Wounding of the stem differentially enhanced the transcript ratios of PdDXS2 to PdDXS1 and PdHDR2 to PdHDR1 to 300 and 70, respectively. The increase in the transcript levels of the MEP pathway genes in response to wounding was accompanied by two orders of magnitude increase in PdABS transcripts. These observations indicated that resin acid biosynthesis activity, represented by PdABS transcription, was correlated with the selective transcriptions of PdDXS2 and PdHDR2. Introduction of PdDXS2, PdHDR1 and PdHDR2 rescued their respective knockout Escherichia coli mutants, confirming that at least these three genes were functionally active. Intracellular targeting of the green fluorescent protein fused to the N-terminal 100 amino acid residues of these genes in the Arabidopsis transient expression system showed that the proteins were all targeted to the chloroplasts. Our results suggest that the MEP pathway regulates resin biosynthesis in the wood of P. densiflora by differential transcription of the multiple PdDXS and PdHDR genes.
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Affiliation(s)
- Yeon-Bok Kim
- Program in Applied Life Chemistry, Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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50
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Long RM, Lagisetti C, Coates RM, Croteau RB. Specificity of the N-benzoyl transferase responsible for the last step of Taxol biosynthesis. Arch Biochem Biophys 2008; 477:384-9. [PMID: 18621016 PMCID: PMC2574419 DOI: 10.1016/j.abb.2008.06.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [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: 05/06/2008] [Revised: 06/20/2008] [Accepted: 06/25/2008] [Indexed: 11/16/2022]
Abstract
The last few steps in the biosynthesis of the anticancer drug Taxol in yew (Taxus) species are thought to involve the attachment of beta-phenylalanine to the C13-O-position of the advanced taxane diterpenoid intermediate baccatin III to yield N-debenzoyl-2'-deoxytaxol, followed by hydroxylation on the side chain at the C2'-position to afford N-debenzoyltaxol, and finally N-benzoylation to complete the pathway. A cDNA encoding the N-benzoyl transferase that catalyzes the terminal step of the reaction sequence was previously isolated from a family of transferase clones (derived from an induced Taxus cell cDNA library) by functional characterization of the corresponding recombinant enzyme using the available surrogate substrate N-debenzoyl-2'-deoxytaxol [K. Walker, R. Long, R. Croteau, Proc. Nat. Acad. Sci. USA 99 (2002) 9166-9171]. Semi-synthetic N-debenzoyltaxol was prepared by coupling of 7-triethylsilybaccatin III and (2R,3S)-beta-phenylisoserine protected as the N-Boc N,O-isopropylidene derivative by means of carbodiimide activation and formic acid deprotections. The selectivity of the recombinant N-transferase for N-debenzoyltaxol was evaluated, and the enzyme was shown to prefer, by a catalytic efficiency factor of two, N-debenzoyltaxol over N-debenzoyl-2'-deoxytaxol as the taxoid co-substrate in the benzoyl transfer reaction, consistent with the assembly sequence involving 2'-hydroxylation prior to N-benzoylation. Selectivity for the acyl/aroyl-CoA co-substrate was also examined, and the enzyme was shown to prefer benzoyl-CoA. Transfer from tigloyl-CoA to N-debenzoyltaxol to afford cephalomannine (Taxol B) was not observed, nor was transfer observed from hexanoyl-CoA or butanoyl-CoA to yield Taxol C or Taxol D, respectively. These results support the proposed sequence of reactions for C13-O-side chain assembly in Taxol biosynthesis, and suggest that other N-transferases are responsible for the formation of related, late pathway, N-acylated taxoids.
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Affiliation(s)
- Robert M. Long
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Chandraiah Lagisetti
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Robert M. Coates
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rodney B. Croteau
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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