1
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Torres-Rodriguez MD, Lee SG, Roy Choudhury S, Paul R, Selvam B, Shukla D, Jez JM, Pandey S. Structure-function analysis of plant G-protein regulatory mechanisms identifies key Gα-RGS protein interactions. J Biol Chem 2024; 300:107252. [PMID: 38569936 PMCID: PMC11061236 DOI: 10.1016/j.jbc.2024.107252] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Heterotrimeric GTP-binding protein alpha subunit (Gα) and its cognate regulator of G-protein signaling (RGS) protein transduce signals in eukaryotes spanning protists, amoeba, animals, fungi, and plants. The core catalytic mechanisms of the GTPase activity of Gα and the interaction interface with RGS for the acceleration of GTP hydrolysis seem to be conserved across these groups; however, the RGS gene is under low selective pressure in plants, resulting in its frequent loss. Our current understanding of the structural basis of Gα:RGS regulation in plants has been shaped by Arabidopsis Gα, (AtGPA1), which has a cognate RGS protein. To gain a comprehensive understanding of this regulation beyond Arabidopsis, we obtained the x-ray crystal structures of Oryza sativa Gα, which has no RGS, and Selaginella moellendorffi (a lycophyte) Gα that has low sequence similarity with AtGPA1 but has an RGS. We show that the three-dimensional structure, protein-protein interaction with RGS, and the dynamic features of these Gα are similar to AtGPA1 and metazoan Gα. Molecular dynamic simulation of the Gα-RGS interaction identifies the contacts established by specific residues of the switch regions of GTP-bound Gα, crucial for this interaction, but finds no significant difference due to specific amino acid substitutions. Together, our data provide valuable insights into the regulatory mechanisms of plant G-proteins but do not support the hypothesis of adaptive co-evolution of Gα:RGS proteins in plants.
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Affiliation(s)
| | - Soon Goo Lee
- Department of Molecular & Cellular Biology, Kennesaw State University, Kennesaw, Georgia, USA
| | - Swarup Roy Choudhury
- Donald Danforth Plant Science Center, St Louis, Missouri, USA; Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Rabindranath Paul
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Sona Pandey
- Donald Danforth Plant Science Center, St Louis, Missouri, USA.
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2
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Morris JS, Jez JM. A tale of two switches: Redox regulation of adenosine-5'-phosphosulfate kinase in humans and plants. Structure 2023; 31:757-759. [PMID: 37419098 DOI: 10.1016/j.str.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 07/09/2023]
Abstract
The sulfate donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) is a near-universal component of sulfur metabolism. In a report by Zhang et al. in this issue of Structure, X-ray crystal structures of the APS kinase domains from human PAPS synthase reveal dynamic substrate recognition and a regulatory "redox switch" analogous to that previously described only in plant APS kinases.
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Affiliation(s)
- Jeremy S Morris
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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3
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Kruse LH, Weigle AT, Irfan M, Martínez-Gómez J, Chobirko JD, Schaffer JE, Bennett AA, Specht CD, Jez JM, Shukla D, Moghe GD. Orthology-based analysis helps map evolutionary diversification and predict substrate class use of BAHD acyltransferases. Plant J 2022; 111:1453-1468. [PMID: 35816116 DOI: 10.1111/tpj.15902] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 03/02/2022] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Large enzyme families catalyze metabolic diversification by virtue of their ability to use diverse chemical scaffolds. How enzyme families attain such functional diversity is not clear. Furthermore, duplication and promiscuity in such enzyme families limits their functional prediction, which has produced a burgeoning set of incompletely annotated genes in plant genomes. Here, we address these challenges using BAHD acyltransferases as a model. This fast-evolving family expanded drastically in land plants, increasing from one to five copies in algae to approximately 100 copies in diploid angiosperm genomes. Compilation of >160 published activities helped visualize the chemical space occupied by this family and define eight different classes based on structural similarities between acceptor substrates. Using orthologous groups (OGs) across 52 sequenced plant genomes, we developed a method to predict BAHD acceptor substrate class utilization as well as origins of individual BAHD OGs in plant evolution. This method was validated using six novel and 28 previously characterized enzymes and helped improve putative substrate class predictions for BAHDs in the tomato genome. Our results also revealed that while cuticular wax and lignin biosynthetic activities were more ancient, anthocyanin acylation activity was fixed in BAHDs later near the origin of angiosperms. The OG-based analysis enabled identification of signature motifs in anthocyanin-acylating BAHDs, whose importance was validated via molecular dynamic simulations, site-directed mutagenesis and kinetic assays. Our results not only describe how BAHDs contributed to evolution of multiple chemical phenotypes in the plant world but also propose a biocuration-enabled approach for improved functional annotation of plant enzyme families.
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Affiliation(s)
- Lars H Kruse
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Jesús Martínez-Gómez
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, 14853, USA
- L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jason D Chobirko
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Jason E Schaffer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Chelsea D Specht
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, 14853, USA
- L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, 14853, USA
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4
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Glenn KC, Silvanovich A, Lee SG, Allen A, Park S, Dunn SE, Kessenich C, Meng C, Vicini JL, Jez JM. Biochemical and clinical studies of putative allergens to assess what distinguishes them from other non-allergenic proteins in the same family. Transgenic Res 2022; 31:507-524. [PMID: 35939227 PMCID: PMC9489553 DOI: 10.1007/s11248-022-00316-8] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 07/21/2022] [Indexed: 10/26/2022]
Abstract
Many protein families have numerous members listed in databases as allergens; however, some allergen database entries, herein called "orphan allergens", are members of large families of which all other members are not allergens. These orphan allergens provide an opportunity to assess whether specific structural features render a protein allergenic. Three orphan allergens [Cladosporium herbarum aldehyde dehydrogenase (ChALDH), Alternaria alternata ALDH (AaALDH), and C. herbarum mannitol dehydrogenase (ChMDH)] were recombinantly produced and purified for structure characterization and for clinical skin prick testing (SPT) in mold allergic participants. Examination of the X-ray crystal structures of ChALDH and ChMDH and a homology structure model of AaALDH did not identify any discernable epitopes that distinguish these putative orphan allergens from their non-allergenic protein relatives. SPT results were aligned with ChMDH being an allergen, 53% of the participants were SPT (+). AaALDH did not elicit SPT reactivity above control proteins not in allergen databases (i.e., Psedomonas syringae indole-3-acetaldehyde dehydrogenase and Zea mays ALDH). Although published results showed consequential human IgE reactivity with ChALDH, no SPT reactivity was observed in this study. With only one of these three orphan allergens, ChMDH, eliciting SPT(+) reactions consistent with the protein being included in allergen databases, this underscores the complicated nature of how bioinformatics is used to assess the potential allergenicity of food proteins that could be newly added to human diets and, when needed, the subsequent clinical testing of that bioinformatic assessment.Trial registration number and date of registration AAC-2017-0467, approved as WIRB protocol #20172536 on 07DEC2017 by WIRB-Copernicus (OHRP/FDA Registration #: IRB00000533, organization #: IORG0000432).
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Affiliation(s)
- Kevin C Glenn
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Andre Silvanovich
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Soon Goo Lee
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA.,Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | - Aron Allen
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Stephanie Park
- Allergy and Asthma Care of St. Louis, 8888 Ladue Road, Suite 105, St. Louis, MO, 63124, USA
| | - S Eliza Dunn
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Colton Kessenich
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Chen Meng
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - John L Vicini
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA.
| | - Joseph M Jez
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA
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5
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Mohanasundaram B, Dodds A, Kukshal V, Jez JM, Pandey S. Distribution and the evolutionary history of G-protein components in plant and algal lineages. Plant Physiol 2022; 189:1519-1535. [PMID: 35377452 PMCID: PMC9237705 DOI: 10.1093/plphys/kiac153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
Heterotrimeric G-protein complexes comprising Gα-, Gβ-, and Gγ-subunits and the regulator of G-protein signaling (RGS) are conserved across most eukaryotic lineages. Signaling pathways mediated by these proteins influence overall growth, development, and physiology. In plants, this protein complex has been characterized primarily from angiosperms with the exception of spreading-leaved earth moss (Physcomitrium patens) and Chara braunii (charophytic algae). Even within angiosperms, specific G-protein components are missing in certain species, whereas unique plant-specific variants-the extra-large Gα (XLGα) and the cysteine-rich Gγ proteins-also exist. The distribution and evolutionary history of G-proteins and their function in nonangiosperm lineages remain mostly unknown. We explored this using the wealth of available sequence data spanning algae to angiosperms representing extant species that diverged approximately 1,500 million years ago, using BLAST, synteny analysis, and custom-built Hidden Markov Model profile searches. We show that a minimal set of components forming the XLGαβγ trimer exists in the entire land plant lineage, but their presence is sporadic in algae. Additionally, individual components have distinct evolutionary histories. The XLGα exhibits many lineage-specific gene duplications, whereas Gα and RGS show several instances of gene loss. Similarly, Gβ remained constant in both number and structure, but Gγ diverged before the emergence of land plants and underwent changes in protein domains, which led to three distinct subtypes. These results highlight the evolutionary oddities and summarize the phyletic patterns of this conserved signaling pathway in plants. They also provide a framework to formulate pertinent questions on plant G-protein signaling within an evolutionary context.
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Affiliation(s)
| | - Audrey Dodds
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Vandna Kukshal
- Department of Biology, Washington University, St Louis, Missouri 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University, St Louis, Missouri 63130, USA
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6
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Sawant M, Mahajan K, Renganathan A, Weimholt C, Luo J, Kukshal V, Jez JM, Jeon MS, Zhang B, Li T, Fang B, Luo Y, Lawrence NJ, Lawrence HR, Feng FY, Mahajan NP. Chronologically modified androgen receptor in recurrent castration-resistant prostate cancer and its therapeutic targeting. Sci Transl Med 2022; 14:eabg4132. [PMID: 35704598 PMCID: PMC10259236 DOI: 10.1126/scitranslmed.abg4132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Resistance to second-generation androgen receptor (AR) antagonists such as enzalutamide is an inevitable consequence in patients with castration-resistant prostate cancer (CRPC). There are no effective therapeutic options for this recurrent disease. The expression of truncated AR variant 7 (AR-V7) has been suggested to be one mechanism of resistance; however, its low frequency in patients with CRPC does not explain the almost universal acquisition of resistance. We noted that the ability of AR to translocate to nucleus in an enzalutamide-rich environment opens up the possibility of a posttranslational modification in AR that is refractory to enzalutamide binding. Chemical proteomics in enzalutamide-resistant CRPC cells revealed acetylation at Lys609 in the zinc finger DNA binding domain of AR (acK609-AR) that not only allowed AR translocation but also galvanized a distinct global transcription program, conferring enzalutamide insensitivity. Mechanistically, acK609-AR was recruited to the AR and ACK1/TNK2 enhancers, up-regulating their transcription. ACK1 kinase-mediated AR Y267 phosphorylation was a prerequisite for AR K609 acetylation, which spawned positive feedback loops at both the transcriptional and posttranslational level that regenerated and sustained high AR and ACK1 expression. Consistent with these findings, oral and subcutaneous treatment with ACK1 small-molecule inhibitor, (R)-9b, not only curbed AR Y267 phosphorylation and subsequent K609 acetylation but also compromised enzalutamide-resistant CRPC xenograft tumor growth in mice. Overall, these data uncover chronological modification events in AR that allows prostate cancer to evolve through progressive stages to reach the resilient recurrent CRPC stage, opening up a therapeutic vulnerability.
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Affiliation(s)
- Mithila Sawant
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
| | - Arun Renganathan
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Cody Weimholt
- Department of Anatomic and Clinical Pathology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jingqin Luo
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
| | - Vandna Kukshal
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63110, USA
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63110, USA
| | - Myung Sik Jeon
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
| | - Bo Zhang
- Bioinformatics Research Core, Center of Regenerative Medicine, Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Tiandao Li
- Bioinformatics Research Core, Center of Regenerative Medicine, Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Bin Fang
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Yunting Luo
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Nicholas J. Lawrence
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Harshani R. Lawrence
- Drug Discovery Department, Moffitt Cancer Center, Department of Oncologic Sciences, University of South Florida, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Felix Y. Feng
- Helen Diller Family Cancer Research Building, 1450 Third Street, Room 383, University of California, San Francisco, CA 94158, USA
| | - Nupam P. Mahajan
- Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO 63110, USA
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7
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Yokoyama R, de Oliveira MVV, Takeda-Kimura Y, Ishihara H, Alseekh S, Arrivault S, Kukshal V, Jez JM, Stitt M, Fernie AR, Maeda HA. Point mutations that boost aromatic amino acid production and CO 2 assimilation in plants. Sci Adv 2022; 8:eabo3416. [PMID: 35675400 PMCID: PMC9176744 DOI: 10.1126/sciadv.abo3416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Aromatic compounds having unusual stability provide high-value chemicals and considerable promise for carbon storage. Terrestrial plants can convert atmospheric CO2 into diverse and abundant aromatic compounds. However, it is unclear how plants control the shikimate pathway that connects the photosynthetic carbon fixation with the biosynthesis of aromatic amino acids, the major precursors of plant aromatic natural products. This study identified suppressor of tyra2 (sota) mutations that deregulate the first step in the plant shikimate pathway by alleviating multiple effector-mediated feedback regulation in Arabidopsis thaliana. The sota mutant plants showed hyperaccumulation of aromatic amino acids accompanied by up to a 30% increase in net CO2 assimilation. The identified mutations can be used to enhance plant-based, sustainable conversion of atmospheric CO2 to high-energy and high-value aromatic compounds.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Hirofumi Ishihara
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Vandna Kukshal
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Mark Stitt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Hiroshi A. Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
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Jez JM. Connecting primary and specialized metabolism: Amino acid conjugation of phytohormones by GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases. Curr Opin Plant Biol 2022; 66:102194. [PMID: 35219141 DOI: 10.1016/j.pbi.2022.102194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases catalyze the ATP-dependent conjugation of phytohormones with amino acids. Traditionally, GH3 proteins are associated with synthesis of the bioactive jasmonate hormone (+)-7- iso -jasmonoyl-l-isoleucine (JA-Ile) and conjugation of indole-3-acetic acid (IAA) with amino acids that tag the hormone for degradation and/or storage. Modifications of JA and IAA by GH3 acyl acid amido synthetases help maintain phytohormones homeostasis. Recent studies broaden the roles of GH3 proteins to include the regulation of JA biosynthesis; the modification of other auxins (i.e., phenylacetic acid and indole-3-butyric acid); the conjugation of auxinic herbicides, such as 4-dichlorophenoxyacetic acid, 4-(2,4-dichlorophenoxy)butyric acid, and dicamba; and the missing step in the isochorismate pathway for the biosynthesis of salicylic acid. The GH3 protein family joins the growing number of versatile enzyme families that blur the line between primary and specialized metabolism for an increasing range of biology functions.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130 USA.
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9
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Frasse PM, Miller JJ, Polino AJ, Soleimani E, Zhu JS, Jakeman DL, Jez JM, Goldberg DE, Odom John AR. Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria-causing parasites. J Biol Chem 2022; 298:101550. [PMID: 34973333 PMCID: PMC8808168 DOI: 10.1016/j.jbc.2021.101550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/21/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/05/2022] Open
Abstract
The malaria-causing parasite Plasmodium falciparum is responsible for over 200 million infections and 400,000 deaths per year. At multiple stages during its complex life cycle, P. falciparum expresses several essential proteins tethered to its surface by glycosylphosphatidylinositol (GPI) anchors, which are critical for biological processes such as parasite egress and reinvasion of host red blood cells. Targeting this pathway therapeutically has the potential to broadly impact parasite development across several life stages. Here, we characterize an upstream component of parasite GPI anchor biosynthesis, the putative phosphomannomutase (PMM) (EC 5.4.2.8), HAD5 (PF3D7_1017400). We confirmed the PMM and phosphoglucomutase activities of purified recombinant HAD5 by developing novel linked enzyme biochemical assays. By regulating the expression of HAD5 in transgenic parasites with a TetR-DOZI-inducible knockdown system, we demonstrated that HAD5 is required for malaria parasite egress and erythrocyte reinvasion, and we assessed the role of HAD5 in GPI anchor synthesis by autoradiography of radiolabeled glucosamine and thin layer chromatography. Finally, we determined the three-dimensional X-ray crystal structure of HAD5 and identified a substrate analog that specifically inhibits HAD5 compared to orthologous human PMMs in a time-dependent manner. These findings demonstrate that the GPI anchor biosynthesis pathway is exceptionally sensitive to inhibition in parasites and that HAD5 has potential as a specific, multistage antimalarial target.
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Affiliation(s)
- Philip M Frasse
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Justin J Miller
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alexander J Polino
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ebrahim Soleimani
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Chemistry, Razi University, Kermanshah, Iran
| | - Jian-She Zhu
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Daniel E Goldberg
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Lopez-Nieves S, El-Azaz J, Men Y, Holland CK, Feng T, Brockington SF, Jez JM, Maeda HA. Two independently evolved natural mutations additively deregulate TyrA enzymes and boost tyrosine production in planta. Plant J 2022; 109:844-855. [PMID: 34807484 DOI: 10.1111/tpj.15597] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/29/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
l-Tyrosine is an essential amino acid for protein synthesis and is also used in plants to synthesize diverse natural products. Plants primarily synthesize tyrosine via TyrA arogenate dehydrogenase (TyrAa or ADH), which are typically strongly feedback inhibited by tyrosine. However, two plant lineages, Fabaceae (legumes) and Caryophyllales, have TyrA enzymes that exhibit relaxed sensitivity to tyrosine inhibition and are associated with elevated production of tyrosine-derived compounds, such as betalain pigments uniquely produced in core Caryophyllales. Although we previously showed that a single D222N substitution is primarily responsible for the deregulation of legume TyrAs, it is unknown when and how the deregulated Caryophyllales TyrA emerged. Here, through phylogeny-guided TyrA structure-function analysis, we found that functionally deregulated TyrAs evolved early in the core Caryophyllales before the origin of betalains, where the E208D amino acid substitution in the active site, which is at a different and opposite location from D222N found in legume TyrAs, played a key role in the TyrA functionalization. Unlike legumes, however, additional substitutions on non-active site residues further contributed to the deregulation of TyrAs in Caryophyllales. The introduction of a mutation analogous to E208D partially deregulated tyrosine-sensitive TyrAs, such as Arabidopsis TyrA2 (AtTyrA2). Moreover, the combined introduction of D222N and E208D additively deregulated AtTyrA2, for which the expression in Nicotiana benthamiana led to highly elevated accumulation of tyrosine in planta. The present study demonstrates that phylogeny-guided characterization of key residues underlying primary metabolic innovations can provide powerful tools to boost the production of essential plant natural products.
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Affiliation(s)
- Samuel Lopez-Nieves
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jorge El-Azaz
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yusen Men
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cynthia K Holland
- Department of Biology, Williams College, Williamstown, MA, 01267, USA
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | | | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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11
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Jiang L, Wang Y, Xia A, Wang Q, Zhang X, Jez JM, Li Z, Tan W, He Y. A natural single-nucleotide polymorphism variant in sulfite reductase influences sulfur assimilation in maize. New Phytol 2021; 232:692-704. [PMID: 34254312 DOI: 10.1111/nph.17616] [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] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Plants absorb sulfur from the environment and assimilate it into suitable forms for the biosynthesis of a broad range of molecules. Although the biochemical pathway of sulfur assimilation is known, how genetic differences contribute to natural variation in sulfur assimilation remains poorly understood. Here, using a genome-wide association study, we uncovered a single-nucleotide polymorphism (SNP) variant in the sulfite reductase (SiR) gene that was significantly associated with SiR protein abundance in a maize natural association population. We also demonstrated that the synonymous C to G base change at SNP69 may repress translational activity by altering messenger RNA secondary structure, which leads to reduction in ZmSiR protein abundance and sulfur assimilation activity. Population genetic analyses showed that the SNP69C allele was likely a variant occurring after the initial maize domestication and accumulated with the spread of maize cultivation from tropical to temperate regions. This study provides the first evidence that genetic polymorphisms in the exon of ZmSiR could influence the protein abundance through a posttranscriptional mechanism and in part contribute to natural variation in sulfur assimilation. These findings provide a prospective target to improve maize varieties with proper sulfur nutrient levels assisted by molecular breeding and engineering.
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Affiliation(s)
- Luguang Jiang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Yan Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Aiai Xia
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Qi Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Xiaolei Zhang
- Safety and Quality Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Weiming Tan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Yan He
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
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12
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Kitainda V, Jez JM. Structural Studies of Aliphatic Glucosinolate Chain-Elongation Enzymes. Antioxidants (Basel) 2021; 10:antiox10091500. [PMID: 34573132 PMCID: PMC8468904 DOI: 10.3390/antiox10091500] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Plants evolved specialized metabolic pathways through gene duplication and functional divergence of enzymes involved in primary metabolism. The results of this process are varied pathways that produce an array of natural products useful to both plants and humans. In plants, glucosinolates are a diverse class of natural products. Glucosinolate function stems from their hydrolysis products, which are responsible for the strong flavors of Brassicales plants, such as mustard, and serve as plant defense molecules by repelling insects, fighting fungal infections, and discouraging herbivory. Additionally, certain hydrolysis products such as isothiocyanates can potentially serve as cancer prevention agents in humans. The breadth of glucosinolate function is a result of its great structural diversity, which comes from the use of aliphatic, aromatic and indole amino acids as precursors and elongation of some side chains by up to nine carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Aliphatic methionine-derived glucosinolates are the most abundant form of these compounds. Although both elongation and chemical modification of amino acid side chains are important for aliphatic glucosinolate diversity, its elongation process has not been well described at the molecular level. Here, we summarize new insights on the iterative chain-elongation enzymes methylthioalkylmalate synthase (MAMS) and isopropylmalate dehydrogenase (IPMDH).
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13
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Miller JJ, Shah IT, Hatten J, Barekatain Y, Mueller EA, Moustafa AM, Edwards RL, Dowd CS, Planet PJ, Muller FL, Jez JM, Odom John AR. Structure-guided microbial targeting of antistaphylococcal prodrugs. eLife 2021; 10:66657. [PMID: 34279224 PMCID: PMC8318587 DOI: 10.7554/elife.66657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/16/2021] [Indexed: 01/07/2023] Open
Abstract
Carboxy ester prodrugs are widely employed to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can mask problematic chemical features that prevent cellular uptake and may enable tissue-specific compound delivery. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, limiting their therapeutic potential. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes as microbial esterase-specific promoieties have not been described. Here we identify the bacterial esterases, GloB and FrmB, that activate carboxy ester prodrugs in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis of these preferences. Finally, we establish the carboxy ester substrate specificities of human and mouse sera, ultimately identifying several promoieties likely to be serum esterase-resistant and microbially labile. These studies will enable structure-guided design of antistaphylococcal promoieties and expand the range of molecules to target staphylococcal pathogens.
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Affiliation(s)
- Justin J Miller
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States.,Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Ishaan T Shah
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Jayda Hatten
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Yasaman Barekatain
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Elizabeth A Mueller
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Ahmed M Moustafa
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, United States
| | - Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Cynthia S Dowd
- Department of Chemistry, The George Washington University, Washington, United States
| | - Paul J Planet
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, United States
| | - Florian L Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
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14
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Abstract
The deep relationship between plants and humans predates civilization, and our reliance on plants as sources of food, feed, fiber, fuels, and pharmaceuticals continues to increase. Understanding how plants grow and overcome challenges to their survival is critical for using these organisms to meet current and future demands for food and other plant-derived materials. This thematic review series on "plants in the real world" presents a set of eight reviews that highlight advances in understanding plant health, including the role of thiamine (vitamin B1), iron, and the plant immune system; how plants use ethylene and ubiquitin systems to control growth and development; and how new gene-editing approaches, the redesign of plant cell walls, and deciphering herbicide resistance evolution can lead to the next generation of crops.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
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15
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Kim WS, Sun-Hyung J, Oehrle NW, Jez JM, Krishnan HB. Overexpression of ATP sulfurylase improves the sulfur amino acid content, enhances the accumulation of Bowman-Birk protease inhibitor and suppresses the accumulation of the β-subunit of β-conglycinin in soybean seeds. Sci Rep 2020; 10:14989. [PMID: 32929147 PMCID: PMC7490426 DOI: 10.1038/s41598-020-72134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/21/2020] [Accepted: 08/26/2020] [Indexed: 01/18/2023] Open
Abstract
ATP sulfurylase, an enzyme which catalyzes the conversion of sulfate to adenosine 5'-phosphosulfate (APS), plays a significant role in controlling sulfur metabolism in plants. In this study, we have expressed soybean plastid ATP sulfurylase isoform 1 in transgenic soybean without its transit peptide under the control of the 35S CaMV promoter. Subcellular fractionation and immunoblot analysis revealed that ATP sulfurylase isoform 1 was predominantly expressed in the cell cytoplasm. Compared with that of untransformed plants, the ATP sulfurylase activity was about 2.5-fold higher in developing seeds. High-resolution 2-D gel electrophoresis and immunoblot analyses revealed that transgenic soybean seeds overexpressing ATP sulfurylase accumulated very low levels of the β-subunit of β-conglycinin. In contrast, the accumulation of the cysteine-rich Bowman-Birk protease inhibitor was several fold higher in transgenic soybean plants when compared to the non-transgenic wild-type seeds. The overall protein content of the transgenic seeds was lowered by about 3% when compared to the wild-type seeds. Metabolite profiling by LC-MS and GC-MS quantified 124 seed metabolites out of which 84 were present in higher amounts and 40 were present in lower amounts in ATP sulfurylase overexpressing seeds compared to the wild-type seeds. Sulfate, cysteine, and some sulfur-containing secondary metabolites accumulated in higher amounts in ATP sulfurylase transgenic seeds. Additionally, ATP sulfurylase overexpressing seeds contained significantly higher amounts of phospholipids, lysophospholipids, diacylglycerols, sterols, and sulfolipids. Importantly, over expression of ATP sulfurylase resulted in 37-52% and 15-19% increases in the protein-bound cysteine and methionine content of transgenic seeds, respectively. Our results demonstrate that manipulating the expression levels of key sulfur assimilatory enzymes could be exploited to improve the nutritive value of soybean seeds.
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Affiliation(s)
- Won-Seok Kim
- Plant Science Division, University of Missouri, Columbia, MO, 65211, USA
| | - Jeong Sun-Hyung
- Plant Genetics Research, USDA-Agricultural Research Service, University of Missouri, 108 Curtis Hall, Columbia, MO, 65211, USA
| | - Nathan W Oehrle
- Plant Genetics Research, USDA-Agricultural Research Service, University of Missouri, 108 Curtis Hall, Columbia, MO, 65211, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, MO, 65211, USA.
- Plant Genetics Research, USDA-Agricultural Research Service, University of Missouri, 108 Curtis Hall, Columbia, MO, 65211, USA.
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16
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Lee SG, Harline K, Abar O, Akadri SO, Bastian AG, Chen HYS, Duan M, Focht CM, Groziak AR, Kao J, Kottapalli JS, Leong MC, Lin JJ, Liu R, Luo JE, Meyer CM, Mo AF, Pahng SH, Penna V, Raciti CD, Srinath A, Sudhakar S, Tang JD, Cox BR, Holland CK, Cascella B, Cruz W, McClerkin SA, Kunkel BN, Jez JM. The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase. J Biol Chem 2020; 295:13914-13926. [PMID: 32796031 DOI: 10.1074/jbc.ra120.014747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. Here we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD+ reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the "aromatic box" that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA
| | - Kate Harline
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Orchid Abar
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sakirat O Akadri
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alexander G Bastian
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hui-Yuan S Chen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Duan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Caroline M Focht
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Amanda R Groziak
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jesse Kao
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Matthew C Leong
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joy J Lin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Regina Liu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joanna E Luo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Christine M Meyer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Albert F Mo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Seong Ho Pahng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Vinay Penna
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chris D Raciti
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Abhinav Srinath
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shwetha Sudhakar
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph D Tang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brian R Cox
- Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Barrie Cascella
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wilhelm Cruz
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sheri A McClerkin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - Barbara N Kunkel
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
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17
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Lee SG, Chung MS, DeMarsilis AJ, Holland CK, Jaswaney RV, Jiang C, Kroboth JHP, Kulshrestha K, Marcelo RZW, Meyyappa VM, Nelson GB, Patel JK, Petronio AJ, Powers SK, Qin PR, Ramachandran M, Rayapati D, Rincon JA, Rocha A, Ferreira JGRN, Steinbrecher MK, Yao K, Zhang EJ, Zou AJ, Gang M, Sparks M, Cascella B, Cruz W, Jez JM. Structural and biochemical analysis of phosphoethanolamine methyltransferase from the pine wilt nematode Bursaphelenchus xylophilus. Mol Biochem Parasitol 2020; 238:111291. [PMID: 32479776 DOI: 10.1016/j.molbiopara.2020.111291] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 11/28/2022]
Abstract
In free-living and parasitic nematodes, the methylation of phosphoethanolamine to phosphocholine provides a key metabolite to sustain phospholipid biosynthesis for growth and development. Because the phosphoethanolamine methyltransferases (PMT) of nematodes are essential for normal growth and development, these enzymes are potential targets of inhibitor design. The pine wilt nematode (Bursaphelenchus xylophilus) causes extensive damage to trees used for lumber and paper in Asia. As a first step toward testing BxPMT1 as a potential nematicide target, we determined the 2.05 Å resolution x-ray crystal structure of the enzyme as a dead-end complex with phosphoethanolamine and S-adenosylhomocysteine. The three-dimensional structure of BxPMT1 served as a template for site-directed mutagenesis to probe the contribution of active site residues to catalysis and phosphoethanolamine binding using steady-state kinetic analysis. Biochemical analysis of the mutants identifies key residues on the β1d-α6 loop (W123F, M126I, and Y127F) and β1e-α7 loop (S155A, S160A, H170A, T178V, and Y180F) that form the phosphobase binding site and suggest that Tyr127 facilitates the methylation reaction in BxPMT1.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Michelle S Chung
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Antea J DeMarsilis
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Rohit V Jaswaney
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Cherry Jiang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Jakob H P Kroboth
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Kevin Kulshrestha
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Raymundo Z W Marcelo
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Vidhya M Meyyappa
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Grant B Nelson
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Janki K Patel
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Alex J Petronio
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Samantha K Powers
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Peter R Qin
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Mythili Ramachandran
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Divya Rayapati
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - John A Rincon
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Andreia Rocha
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | | | - Micah K Steinbrecher
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Kaisen Yao
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Eric J Zhang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Angela J Zou
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Margery Gang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Melanie Sparks
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Barrie Cascella
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Wilhelm Cruz
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States.
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18
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Edwards RL, Heueck I, Lee SG, Shah IT, Miller JJ, Jezewski AJ, Mikati MO, Wang X, Brothers RC, Heidel KM, Osbourn DM, Burnham CAD, Alvarez S, Fritz SA, Dowd CS, Jez JM, Odom John AR. Potent, specific MEPicides for treatment of zoonotic staphylococci. PLoS Pathog 2020; 16:e1007806. [PMID: 32497104 PMCID: PMC7297381 DOI: 10.1371/journal.ppat.1007806] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/16/2020] [Accepted: 04/11/2020] [Indexed: 12/20/2022] Open
Abstract
Coagulase-positive staphylococci, which frequently colonize the mucosal surfaces of animals, also cause a spectrum of opportunistic infections including skin and soft tissue infections, urinary tract infections, pneumonia, and bacteremia. However, recent advances in bacterial identification have revealed that these common veterinary pathogens are in fact zoonoses that cause serious infections in human patients. The global spread of multidrug-resistant zoonotic staphylococci, in particular the emergence of methicillin-resistant organisms, is now a serious threat to both animal and human welfare. Accordingly, new therapeutic targets that can be exploited to combat staphylococcal infections are urgently needed. Enzymes of the methylerythritol phosphate pathway (MEP) of isoprenoid biosynthesis represent potential targets for treating zoonotic staphylococci. Here we demonstrate that fosmidomycin (FSM) inhibits the first step of the isoprenoid biosynthetic pathway catalyzed by deoxyxylulose phosphate reductoisomerase (DXR) in staphylococci. In addition, we have both enzymatically and structurally determined the mechanism by which FSM elicits its effect. Using a forward genetic screen, the glycerol-3-phosphate transporter GlpT that facilitates FSM uptake was identified in two zoonotic staphylococci, Staphylococcus schleiferi and Staphylococcus pseudintermedius. A series of lipophilic ester prodrugs (termed MEPicides) structurally related to FSM were synthesized, and data indicate that the presence of the prodrug moiety not only substantially increased potency of the inhibitors against staphylococci but also bypassed the need for GlpT-mediated cellular transport. Collectively, our data indicate that the prodrug MEPicides selectively and robustly inhibit DXR in zoonotic staphylococci, and further, that DXR represents a promising, druggable target for future development.
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Affiliation(s)
- Rachel L. Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Isabel Heueck
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Soon Goo Lee
- University of North Carolina-Wilmington, Wilmington, North Carolina, United States of America
| | - Ishaan T. Shah
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Justin J. Miller
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew J. Jezewski
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Marwa O. Mikati
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xu Wang
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Robert C. Brothers
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Kenneth M. Heidel
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Damon M. Osbourn
- Department of Chemistry, Saint Louis University, St. Louis, Missouri, United States of America
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Stephanie A. Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Joseph M. Jez
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Audrey R. Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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19
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Abstract
The diversity of natural products not only fascinates us intellectually, but also provides an armamentarium against the microbes that threaten our health. The increased prevalence of pathogens that are resistant to one or more classes of available medicines continues to be a growing global threat. As drug-resistant pathogens erode the effectiveness of the current reserve of antibiotics and antifungals, methodological advances open additional avenues for discovery of new classes of drugs, as well as novel derivatives of existing (and proven) classes of compounds. In this Thematic Review Series, we aim to provide a snapshot of the current state of the art in natural product discovery. The reviews in this series encapsulate convergent approaches toward the identification of different classes of primary and specialized metabolites, including nonribosomal peptides, polyketides, and ribosomally synthesized and post-translationally modified peptides, from all kingdoms of life. Traction in unraveling new and diverse classes of molecules has come largely from the academic sector, which ensures availability of methods and data sets. Such knowledge is needed to thwart serious threats to human health and calls to mind the proverb praemonitus praemunitus (forewarned is forearmed).
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Affiliation(s)
- Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130.
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20
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Holland CK, Westfall CS, Schaffer JE, De Santiago A, Zubieta C, Alvarez S, Jez JM. Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid. J Biol Chem 2019; 294:16855-16864. [PMID: 31575658 DOI: 10.1074/jbc.ra119.009949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/29/2019] [Indexed: 11/06/2022] Open
Abstract
To modulate responses to developmental or environmental cues, plants use Gretchen Hagen 3 (GH3) acyl acid amido synthetases to conjugate an amino acid to a plant hormone, a reaction that regulates free hormone concentration and downstream responses. The model plant Arabidopsis thaliana has 19 GH3 proteins, of which 8 have confirmed biochemical functions. One Brassicaceae-specific clade of GH3 proteins was predicted to use benzoate as a substrate and includes AtGH3.7 and AtGH3.12/PBS3. Previously identified as a 4-hydroxybenzoic acid-glutamate synthetase, AtGH3.12/PBS3 influences pathogen defense responses through salicylic acid. Recent work has shown that AtGH3.12/PBS3 uses isochorismate as a substrate, forming an isochorismate-glutamate conjugate that converts into salicylic acid. Here, we show that AtGH3.7 and AtGH3.12/PBS3 can also conjugate chorismate to cysteine and glutamate, which act as precursors to aromatic amino acids and salicylic acid, respectively. The X-ray crystal structure of AtGH3.12/PBS3 in complex with AMP and chorismate at 1.94 Å resolution, along with site-directed mutagenesis, revealed how the active site potentially accommodates this substrate. Examination of Arabidopsis knockout lines indicated that the gh3.7 mutants do not alter growth and showed no increased susceptibility to the pathogen Pseudomonas syringae, unlike gh3.12 mutants, which were more susceptible than WT plants, as was the gh3.7/gh3.12 double mutant. The findings of our study suggest that GH3 proteins can use metabolic precursors of aromatic amino acids as substrates.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Corey S Westfall
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jason E Schaffer
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire & Végétale, University Grenoble Alpes, CNRS, CEA, INRA, IRIG, Grenoble, France
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
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21
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Abstract
Sulfur is an essential element for all organisms. Plants must assimilate this nutrient from the environment and convert it into metabolically useful forms for the biosynthesis of a wide range of compounds, including cysteine and glutathione. This review summarizes structural biology studies on the enzymes involved in plant sulfur assimilation [ATP sulfurylase, adenosine-5'-phosphate (APS) reductase, and sulfite reductase], cysteine biosynthesis (serine acetyltransferase and O-acetylserine sulfhydrylase), and glutathione biosynthesis (glutamate-cysteine ligase and glutathione synthetase) pathways. Overall, X-ray crystal structures of enzymes in these core pathways provide molecular-level information on the chemical events that allow plants to incorporate sulfur into essential metabolites and revealed new biochemical regulatory mechanisms, such as structural rearrangements, protein-protein interactions, and thiol-based redox switches, for controlling different steps in these pathways.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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22
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Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, Emenecker R, Han S, Tycksen E, Hwang I, Sozzani R, Jez JM, Pappu RV, Strader LC. Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. Mol Cell 2019; 76:177-190.e5. [PMID: 31421981 DOI: 10.1016/j.molcel.2019.06.044] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/06/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022]
Abstract
The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. The auxin response factor (ARF) transcription factor family regulates auxin-responsive gene expression and exhibits nuclear localization in regions of high auxin responsiveness. Here we show that the ARF7 and ARF19 proteins accumulate in micron-sized assemblies within the cytoplasm of tissues with attenuated auxin responsiveness. We found that the intrinsically disordered middle region and the folded PB1 interaction domain of ARFs drive protein assembly formation. Mutation of a single lysine within the PB1 domain abrogates cytoplasmic assemblies, promotes ARF nuclear localization, and results in an altered transcriptome and morphological defects. Our data suggest a model in which ARF nucleo-cytoplasmic partitioning regulates auxin responsiveness, providing a mechanism for cellular competence for auxin signaling.
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Affiliation(s)
- Samantha K Powers
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David A Korasick
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Katherine H Schreiber
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; Center for Engineering MechanoBiology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Hongwei Jing
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; Center for Engineering MechanoBiology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ryan Emenecker
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Soeun Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Eric Tycksen
- Genome Technology Access Center, Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lucia C Strader
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; Center for Engineering MechanoBiology, Washington University in St. Louis, St. Louis, MO 63130, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA.
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23
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Burke JR, La Clair JJ, Philippe RN, Pabis A, Corbella M, Jez JM, Cortina GA, Kaltenbach M, Bowman ME, Louie GV, Woods KB, Nelson AT, Tawfik DS, Kamerlin SC, Noel JP. Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jason R. Burke
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - James J. La Clair
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Ryan N. Philippe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Anna Pabis
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marina Corbella
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph M. Jez
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - George A. Cortina
- Department of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Miriam Kaltenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marianne E. Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Gordon V. Louie
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Katherine B. Woods
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Andrew T. Nelson
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shina C.L. Kamerlin
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
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24
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Kumar R, Lee SG, Augustine R, Reichelt M, Vassão DG, Palavalli MH, Allen A, Gershenzon J, Jez JM, Bisht NC. Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates. Plant Cell 2019; 31:1633-1647. [PMID: 31023839 PMCID: PMC6635866 DOI: 10.1105/tpc.19.00046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/29/2019] [Accepted: 04/19/2019] [Indexed: 05/23/2023]
Abstract
The globally cultivated Brassica species possess diverse aliphatic glucosinolates, which are important for plant defense and animal nutrition. The committed step in the side chain elongation of methionine-derived aliphatic glucosinolates is catalyzed by methylthioalkylmalate synthase, which likely evolved from the isopropylmalate synthases of leucine biosynthesis. However, the molecular basis for the evolution of methylthioalkylmalate synthase and its generation of natural product diversity in Brassica is poorly understood. Here, we show that Brassica genomes encode multiple methylthioalkylmalate synthases that have differences in expression profiles and 2-oxo substrate preferences, which account for the diversity of aliphatic glucosinolates across Brassica accessions. Analysis of the 2.1 Å resolution x-ray crystal structure of Brassica juncea methylthioalkylmalate synthase identified key active site residues responsible for controlling the specificity for different 2-oxo substrates and the determinants of side chain length in aliphatic glucosinolates. Overall, these results provide the evolutionary and biochemical foundation for the diversification of glucosinolate profiles across globally cultivated Brassica species, which could be used with ongoing breeding strategies toward the manipulation of beneficial glucosinolate compounds for animal health and plant protection.
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Affiliation(s)
- Roshan Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Rehna Augustine
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Micheal Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Daniel G Vassão
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Manoj H Palavalli
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Aron Allen
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Naveen C Bisht
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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25
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Sherp AM, Lee SG, Schraft E, Jez JM. Modification of auxinic phenoxyalkanoic acid herbicides by the acyl acid amido synthetase GH3.15 from Arabidopsis. J Biol Chem 2018; 293:17731-17738. [PMID: 30315112 DOI: 10.1074/jbc.ra118.004975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/06/2018] [Indexed: 11/06/2022] Open
Abstract
Herbicide-resistance traits are the most widely used agriculture biotechnology products. Yet, to maintain their effectiveness and to mitigate selection of herbicide-resistant weeds, the discovery of new resistance traits that use different chemical modes of action is essential. In plants, the Gretchen Hagen 3 (GH3) acyl acid amido synthetases catalyze the conjugation of amino acids to jasmonate and auxin phytohormones. This reaction chemistry has not been explored as a possible approach for herbicide modification and inactivation. Here, we examined a set of Arabidopsis GH3 proteins that use the auxins indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) as substrates along with the corresponding auxinic phenoxyalkanoic acid herbicides 2,4-dichlorophenoxylacetic acid (2,4-D) and 4-(2,4-dichlorophenoxy)butyric acid (2,4-DB). The IBA-specific AtGH3.15 protein displayed high catalytic activity with 2,4-DB, which was comparable to its activity with IBA. Screening of phenoxyalkanoic and phenylalkyl acids indicated that side-chain length of alkanoic and alkyl acids is a key feature of AtGH3.15's substrate preference. The X-ray crystal structure of the AtGH3.15·2,4-DB complex revealed how the herbicide binds in the active site. In root elongation assays, Arabidopsis AtGH3.15-knockout and -overexpression lines grown in the presence of 2,4-DB exhibited hypersensitivity and tolerance, respectively, indicating that the AtGH3.15-catalyzed modification inactivates 2,4-DB. These findings suggest a potential use for AtGH3.15, and perhaps other GH3 proteins, as herbicide-modifying enzymes that employ a mode of action different from those of currently available herbicide-resistance traits.
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Affiliation(s)
- Ashley M Sherp
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Evelyn Schraft
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130.
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26
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Fellows R, Russo CM, Silva CS, Lee SG, Jez JM, Chisholm JD, Zubieta C, Nanao MH. A multisubstrate reductase from Plantago major: structure-function in the short chain reductase superfamily. Sci Rep 2018; 8:14796. [PMID: 30287897 PMCID: PMC6172241 DOI: 10.1038/s41598-018-32967-1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/17/2018] [Indexed: 11/18/2022] Open
Abstract
The short chain dehydrogenase/reductase superfamily (SDR) is a large family of NAD(P)H-dependent enzymes found in all kingdoms of life. SDRs are particularly well-represented in plants, playing diverse roles in both primary and secondary metabolism. In addition, some plant SDRs are also able to catalyse a reductive cyclisation reaction critical for the biosynthesis of the iridoid backbone that contains a fused 5 and 6-membered ring scaffold. Mining the EST database of Plantago major, a medicinal plant that makes iridoids, we identified a putative 5β-progesterone reductase gene, PmMOR (P. major multisubstrate oxido-reductase), that is 60% identical to the iridoid synthase gene from Catharanthus roseus. The PmMOR protein was recombinantly expressed and its enzymatic activity assayed against three putative substrates, 8-oxogeranial, citral and progesterone. The enzyme demonstrated promiscuous enzymatic activity and was able to not only reduce progesterone and citral, but also to catalyse the reductive cyclisation of 8-oxogeranial. The crystal structures of PmMOR wild type and PmMOR mutants in complex with NADP+ or NAD+ and either 8-oxogeranial, citral or progesterone help to reveal the substrate specificity determinants and catalytic machinery of the protein. Site-directed mutagenesis studies were performed and provide a foundation for understanding the promiscuous activity of the enzyme.
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Affiliation(s)
- Rachel Fellows
- European Synchrotron Radiation Facility, Structural Biology Group, 71 Avenue des Martyrs, F-38000, Grenoble, France
| | | | - Catarina S Silva
- European Synchrotron Radiation Facility, Structural Biology Group, 71 Avenue des Martyrs, F-38000, Grenoble, France.,Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRA, BIG, Grenoble, USA
| | - Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA
| | - John D Chisholm
- Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRA, BIG, Grenoble, USA.
| | - Max H Nanao
- European Synchrotron Radiation Facility, Structural Biology Group, 71 Avenue des Martyrs, F-38000, Grenoble, France.
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27
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Abstract
Arabidopsis thaliana (thale cress) has a past, current, and future role in the era of synthetic biology. Arabidopsis is one of the most well-studied plants with a wealth of genomics, genetics, and biochemical resources available for the metabolic engineer and synthetic biologist. Here we discuss the tools and resources that enable the identification of target genes and pathways in Arabidopsis and heterologous expression in this model plant. While there are numerous examples of engineering Arabidopsis for decreased lignin, increased seed oil, increased vitamins, and environmental remediation, this plant has provided biochemical tools for introducing Arabidopsis genes, pathways, and/or regulatory elements into other plants and microorganisms. Arabidopsis is not a vegetative or oilseed crop, but it is as an excellent model chassis for proof-of-concept metabolic engineering and synthetic biology experiments in plants.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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28
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Stewart CN, Patron N, Hanson AD, Jez JM. Plant metabolic engineering in the synthetic biology era: plant chassis selection. Plant Cell Rep 2018; 37:1357-1358. [PMID: 30196331 DOI: 10.1007/s00299-018-2342-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Affiliation(s)
- C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA.
| | | | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
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29
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Joseph M Jez
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States.
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30
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Krishnan HB, Jez JM. Review: The promise and limits for enhancing sulfur-containing amino acid content of soybean seed. Plant Sci 2018; 272:14-21. [PMID: 29807584 DOI: 10.1016/j.plantsci.2018.03.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 01/04/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Abstract
Soybeans are an excellent source of protein in monogastric diets and rations with ∼75% of soybeans produced worldwide used primarily for animal feed. Even though soybeans are protein-rich and have a well-balanced amino acid profile, the nutritive quality of this important crop could be further improved by elevating the concentrations of certain amino acids. The levels of the sulfur-containing amino acids cysteine and methionine in soybean seed proteins are inadequate for optimal growth and development of monogastric animals, which necessitates dietary supplementation. Subsequently, concerted efforts have been made to increase the concentrations of cysteine and methionine in soybean seeds by both classical breeding and genetic engineering; however, these efforts have met with only limited success. In this review, we discuss the strengths and weakness of different approaches in elevating the sulfur amino acid content of soybeans. Manipulation of enzymes involved in the sulfur assimilatory pathway appears to be a viable avenue for improving sulfur amino acid content. This approach requires a through biochemical characterization of sulfur assimilatory enzymes in soybean seeds. We highlight recent studies targeting key sulfur assimilatory enzymes and the manipulation of sulfur metabolism in transgenic soybeans to improve the nutritive value of soybean proteins.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri, Columbia, MO 65211, USA.
| | - Joseph M Jez
- Department of Biology,Washington University in St. Louis, St. Louis, MO 63130, USA
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31
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Holland CK, Berkovich DA, Kohn ML, Maeda H, Jez JM. Structural basis for substrate recognition and inhibition of prephenate aminotransferase from Arabidopsis. Plant J 2018; 94:304-314. [PMID: 29405514 DOI: 10.1111/tpj.13856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 05/23/2023]
Abstract
Aromatic amino acids are protein building blocks and precursors to a number of plant natural products, such as the structural polymer lignin and a variety of medicinally relevant compounds. Plants make tyrosine and phenylalanine by a different pathway from many microbes; this pathway requires prephenate aminotransferase (PAT) as the key enzyme. Prephenate aminotransferase produces arogenate, the unique and immediate precursor for both tyrosine and phenylalanine in plants, and also has aspartate aminotransferase (AAT) activity. The molecular mechanisms governing the substrate specificity and activation or inhibition of PAT are currently unknown. Here we present the X-ray crystal structures of the wild-type and various mutants of PAT from Arabidopsis thaliana (AtPAT). Steady-state kinetic and ligand-binding analyses identified key residues, such as Glu108, that are involved in both keto acid and amino acid substrate specificities and probably contributed to the evolution of PAT activity among class Ib AAT enzymes. Structures of AtPAT mutants co-crystallized with either α-ketoglutarate or pyridoxamine 5'-phosphate and glutamate further define the molecular mechanisms underlying recognition of keto acid and amino acid substrates. Furthermore, cysteine was identified as an inhibitor of PAT from A. thaliana and Antirrhinum majus plants as well as the bacterium Chlorobium tepidum, uncovering a potential new effector of PAT.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Daniel A Berkovich
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Madeleine L Kohn
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Hiroshi Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
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32
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Jez JM. Introduction to the Thematic Minireview Series: Green biological chemistry. J Biol Chem 2018; 293:5016-5017. [DOI: 10.1074/jbc.tm118.002424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Holland CK, Jez JM. Reaction Mechanism of Prephenate Dehydrogenase from the Alternative Tyrosine Biosynthesis Pathway in Plants. Chembiochem 2018; 19:1132-1136. [PMID: 29601138 DOI: 10.1002/cbic.201800085] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Indexed: 01/27/2023]
Abstract
Unlike metazoans, plants, bacteria, and fungi retain the enzymatic machinery necessary to synthesize the three aromatic amino acids l-phenylalanine, l-tyrosine, and l-tryptophan de novo. In legumes, such as soybean, alfalfa, and common bean, prephenate dehydrogenase (PDH) catalyzes the tyrosine-insensitive biosynthesis of 4-hydroxyphenylpyruvate, a precursor to tyrosine. The three-dimensional structure of soybean PDH1 was recently solved in complex with the NADP+ cofactor. This structure allowed for the identification of both the cofactor- and ligand-binding sites. Here, we present steady-state kinetic analysis of twenty site-directed active-site mutants of soybean (Glycine max) PDH compared to wild-type. Molecular docking of the substrate, prephenate, into the active site of the enzyme revealed its potential interactions with the active site residues and made a case for the importance of each residue in substrate recognition and/or catalysis, most likely through transition state stabilization. Overall, these results suggested that the active site of the enzyme is highly sensitive to any changes, as even subtle alterations substantially reduced the catalytic efficiency of the enzyme.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University in St. Louis, Brookings Drive, St. Louis, MO, 63112, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, Brookings Drive, St. Louis, MO, 63112, USA
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Sherp AM, Westfall CS, Alvarez S, Jez JM. Arabidopsis thaliana GH3.15 acyl acid amido synthetase has a highly specific substrate preference for the auxin precursor indole-3-butyric acid. J Biol Chem 2018; 293:4277-4288. [PMID: 29462792 DOI: 10.1074/jbc.ra118.002006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
Various phytohormones control plant growth and development and mediate biotic and abiotic stress responses. Gretchen Hagen 3 (GH3) acyl acid amido synthetases are plant enzymes that typically conjugate amino acids to indole-3-acetic acid (IAA) or jasmonic acid (JA) to inactivate or activate these phytohormones, respectively; however, the physiological and biological roles of many of these enzymes remain unclear. Using a biochemical approach, we found that the Arabidopsis thaliana GH3.15 (AtGH3.15) preferentially uses indole-3-butyric acid (IBA) and glutamine as substrates. The X-ray crystal structure of the AtGH3.15·AMP complex, modeling of IBA in the active site, and biochemical analysis of site-directed mutants provide insight on active site features that lead to AtGH3.15's preference for IBA. Assay-based in planta analysis of AtGH3.15-overexpressing lines indicated that their root elongation and lateral root density were resistant to IBA treatment but not to treatment with either IAA or JA. These findings suggest that AtGH3.15 may play a role in auxin homeostasis by modulating the levels of IBA for peroxisomal conversion to IAA. Analysis of AtGH3.15 promoter-driven yellow fluorescent protein reporter lines revealed that AtGH3.15 is expressed at significant levels in seedlings, roots, and parts of the siliques. We conclude that AtGH3.15 is unique in the GH3 protein family for its role in modifying IBA in auxin homeostasis and that it is the first GH3 protein shown to primarily modify a plant growth regulator other than IAA and JA.
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Affiliation(s)
- Ashley M Sherp
- From the Department of Biology, Washington University, St. Louis, Missouri 63130 and
| | - Corey S Westfall
- From the Department of Biology, Washington University, St. Louis, Missouri 63130 and
| | - Sophie Alvarez
- the Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130 and
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Krishnan HB, Song B, Oehrle NW, Cameron JC, Jez JM. Impact of overexpression of cytosolic isoform of O-acetylserine sulfhydrylase on soybean nodulation and nodule metabolome. Sci Rep 2018; 8:2367. [PMID: 29402985 PMCID: PMC5799319 DOI: 10.1038/s41598-018-20919-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/25/2018] [Indexed: 01/05/2023] Open
Abstract
Nitrogen-fixing nodules, which are also major sites of sulfur assimilation, contribute significantly to the sulfur needs of whole soybean plants. Nodules are the predominant sites for cysteine accumulation and the activity of O-acetylserine(thiol)lyase (OASS) is central to the sulfur assimilation process in plants. Here, we examined the impact of overexpressing OASS on soybean nodulation and nodule metabolome. Overexpression of OASS did not affect the nodule number, but negatively impacted plant growth. HPLC measurement of antioxidant metabolites demonstrated that levels of cysteine, glutathione, and homoglutathione nearly doubled in OASS overexpressing nodules when compared to control nodules. Metabolite profiling by LC-MS and GC-MS demonstrated that several metabolites related to serine, aspartate, glutamate, and branched-chain amino acid pathways were significantly elevated in OASS overexpressing nodules. Striking differences were also observed in the flavonoid levels between the OASS overexpressing and control soybean nodules. Our results suggest that OASS overexpressing plants compensate for the increase in carbon requirement for sulfur assimilation by reducing the biosynthesis of some amino acids, and by replenishing the TCA cycle through fatty acid hydrolysis. These data may indicate that in OASS overexpressing soybean nodules there is a moderate decease in the supply of energy metabolites to the nodule, which is then compensated by the degradation of cellular components to meet the needs of the nodule energy metabolism.
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Affiliation(s)
- Hari B Krishnan
- USDA-ARS, Plant Genetics Research Unit, 105 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA.
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Bo Song
- USDA-ARS, Plant Genetics Research Unit, 105 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA
- Key Laboratory of Soybean Biology at the Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Nathan W Oehrle
- USDA-ARS, Plant Genetics Research Unit, 105 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA
| | - Jeffrey C Cameron
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
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McClerklin SA, Lee SG, Harper CP, Nwumeh R, Jez JM, Kunkel BN. Indole-3-acetaldehyde dehydrogenase-dependent auxin synthesis contributes to virulence of Pseudomonas syringae strain DC3000. PLoS Pathog 2018; 14:e1006811. [PMID: 29293681 PMCID: PMC5766252 DOI: 10.1371/journal.ppat.1006811] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [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: 08/23/2016] [Revised: 01/12/2018] [Accepted: 12/14/2017] [Indexed: 12/02/2022] Open
Abstract
The bacterial pathogen Pseudomonas syringae modulates plant hormone signaling to promote infection and disease development. P. syringae uses several strategies to manipulate auxin physiology in Arabidopsis thaliana to promote pathogenesis, including its synthesis of indole-3-acetic acid (IAA), the predominant form of auxin in plants, and production of virulence factors that alter auxin responses in the host; however, the role of pathogen-derived auxin in P. syringae pathogenesis is not well understood. Here we demonstrate that P. syringae strain DC3000 produces IAA via a previously uncharacterized pathway and identify a novel indole-3-acetaldehyde dehydrogenase, AldA, that functions in IAA biosynthesis by catalyzing the NAD-dependent formation of IAA from indole-3-acetaldehyde (IAAld). Biochemical analysis and solving of the 1.9 Å resolution x-ray crystal structure reveal key features of AldA for IAA synthesis, including the molecular basis of substrate specificity. Disruption of aldA and a close homolog, aldB, lead to reduced IAA production in culture and reduced virulence on A. thaliana. We use these mutants to explore the mechanism by which pathogen-derived auxin contributes to virulence and show that IAA produced by DC3000 suppresses salicylic acid-mediated defenses in A. thaliana. Thus, auxin is a DC3000 virulence factor that promotes pathogenicity by suppressing host defenses. Pathogens have evolved multiple strategies for suppressing host defenses and modulating host physiology to promote colonization and disease development. For example, the plant pathogen Pseudomonas syringae uses several strategies to the manipulate hormone signaling of its hosts, including production of virulence factors that alter hormone responses in and synthesis of plant hormones or hormone mimics. Synthesis of indole-3-acetic acid (IAA), a common form of the plant hormone auxin, by many plant pathogens has been implicated in virulence. However, the role of pathogen-derived IAA during pathogenesis by leaf spotting pathogens such as P. syringae strain DC3000 is not well understood. Here, we demonstrate that P. syringae strain DC3000 uses a previously uncharacterized biochemical pathway to synthesize IAA, catalyzed by a novel aldehyde dehydrogenase, AldA, and carry out biochemical and structural studies of the AldA protein to investigate AldA activity and substrate specificity. We also generate an aldA mutant disrupted in IAA synthesis to show that IAA is a DC3000 virulence factor that promotes pathogenesis by suppressing host defense responses.
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Affiliation(s)
- Sheri A. McClerklin
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Christopher P. Harper
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Ron Nwumeh
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Joseph M. Jez
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Barbara N. Kunkel
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
- * E-mail:
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Damodaran S, Westfall CS, Kisely BA, Jez JM, Subramanian S. Nodule-Enriched GRETCHEN HAGEN 3 Enzymes Have Distinct Substrate Specificities and Are Important for Proper Soybean Nodule Development. Int J Mol Sci 2017; 18:E2547. [PMID: 29182530 PMCID: PMC5751150 DOI: 10.3390/ijms18122547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 10/20/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 11/16/2022] Open
Abstract
Legume root nodules develop as a result of a symbiotic relationship between the plant and nitrogen-fixing rhizobia bacteria in soil. Auxin activity is detected in different cell types at different stages of nodule development; as well as an enhanced sensitivity to auxin inhibits, which could affect nodule development. While some transport and signaling mechanisms that achieve precise spatiotemporal auxin output are known, the role of auxin metabolism during nodule development is unclear. Using a soybean root lateral organ transcriptome data set, we identified distinct nodule enrichment of three genes encoding auxin-deactivating GRETCHEN HAGEN 3 (GH3) indole-3-acetic acid (IAA) amido transferase enzymes: GmGH3-11/12, GmGH3-14 and GmGH3-15. In vitro enzymatic assays showed that each of these GH3 proteins preferred IAA and aspartate as acyl and amino acid substrates, respectively. GmGH3-15 showed a broad substrate preference, especially with different forms of auxin. Promoter:GUS expression analysis indicated that GmGH3-14 acts primarily in the root epidermis and the nodule primordium where as GmGH3-15 might act in the vasculature. Silencing the expression of these GH3 genes in soybean composite plants led to altered nodule numbers, maturity, and size. Our results indicate that these GH3s are needed for proper nodule maturation in soybean, but the precise mechanism by which they regulate nodule development remains to be explained.
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Affiliation(s)
- Suresh Damodaran
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Corey S Westfall
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Brian A Kisely
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Senthil Subramanian
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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38
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Lee SG, Jez JM. Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation. J Biol Chem 2017; 292:21690-21702. [PMID: 29084845 DOI: 10.1074/jbc.ra117.000106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/20/2017] [Indexed: 01/05/2023] Open
Abstract
Phosphocholine (pCho) is a precursor for phosphatidylcholine and osmoprotectants in plants. In plants, de novo synthesis of pCho relies on the phosphobase methylation pathway. Phosphoethanolamine methyltransferase (PMT) catalyzes the triple methylation of phosphoethanolamine (pEA) to pCho. The plant PMTs are di-domain methyltransferases that divide the methylation of pEA in one domain from subsequent methylations in the second domain. To understand the molecular basis of this architecture, we examined the biochemical properties of three Arabidopsis thaliana PMTs (AtPMT1-3) and determined the X-ray crystal structures of AtPMT1 and AtPMT2. Although each isoform synthesizes pCho from pEA, their physiological roles differ with AtPMT1 essential for normal growth and salt tolerance, whereas AtPMT2 and AtPMT3 overlap functionally. The structures of AtPMT1 and AtPMT2 reveal unique features in each methyltransferase domain, including active sites that use different chemical mechanisms for phosphobase methylation. These structures also show how rearrangements in both the active sites and the di-domain linker form catalytically competent active sites and provide insight on the evolution of the PMTs in plants, nematodes, and apicomplexans. Connecting conformational changes with catalysis in modular enzymes, like the PMT, provides new insights on interdomain communication in biosynthetic systems.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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39
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Hackenberg D, McKain MR, Lee SG, Roy Choudhury S, McCann T, Schreier S, Harkess A, Pires JC, Wong GKS, Jez JM, Kellogg EA, Pandey S. Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. New Phytol 2017; 216:562-575. [PMID: 27634188 DOI: 10.1111/nph.14180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 06/10/2016] [Accepted: 08/03/2016] [Indexed: 05/05/2023]
Abstract
Signaling pathways regulated by heterotrimeric G-proteins exist in all eukaryotes. The regulator of G-protein signaling (RGS) proteins are key interactors and critical modulators of the Gα protein of the heterotrimer. However, while G-proteins are widespread in plants, RGS proteins have been reported to be missing from the entire monocot lineage, with two exceptions. A single amino acid substitution-based adaptive coevolution of the Gα:RGS proteins was proposed to enable the loss of RGS in monocots. We used a combination of evolutionary and biochemical analyses and homology modeling of the Gα and RGS proteins to address their expansion and its potential effects on the G-protein cycle in plants. Our results show that RGS proteins are widely distributed in the monocot lineage, despite their frequent loss. There is no support for the adaptive coevolution of the Gα:RGS protein pair based on single amino acid substitutions. RGS proteins interact with, and affect the activity of, Gα proteins from species with or without endogenous RGS. This cross-functional compatibility expands between the metazoan and plant kingdoms, illustrating striking conservation of their interaction interface. We propose that additional proteins or alternative mechanisms may exist which compensate for the loss of RGS in certain plant species.
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Affiliation(s)
- Dieter Hackenberg
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Michael R McKain
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Soon Goo Lee
- Department of Biology, Washington University, One Brookings Drive, Campus Box 1137, St Louis, MO, 63130, USA
| | - Swarup Roy Choudhury
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Tyler McCann
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Spencer Schreier
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - J Chris Pires
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Joseph M Jez
- Department of Biology, Washington University, One Brookings Drive, Campus Box 1137, St Louis, MO, 63130, USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Sona Pandey
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
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Schenck CA, Holland CK, Schneider MR, Men Y, Lee SG, Jez JM, Maeda HA. Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants. Nat Chem Biol 2017; 13:1029-1035. [PMID: 28671678 DOI: 10.1038/nchembio.2414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/11/2017] [Indexed: 11/09/2022]
Abstract
L-Tyrosine (Tyr) is essential for protein synthesis and is a precursor of numerous specialized metabolites crucial for plant and human health. Tyr can be synthesized via two alternative routes by different key regulatory TyrA family enzymes, prephenate dehydrogenase (PDH, also known as TyrAp) or arogenate dehydrogenase (ADH, also known as TyrAa), representing a unique divergence of primary metabolic pathways. The molecular foundation underlying the evolution of these alternative Tyr pathways is currently unknown. Here we characterized recently diverged plant PDH and ADH enzymes, obtained the X-ray crystal structure of soybean PDH, and identified a single amino acid residue that defines TyrA substrate specificity and regulation. Structures of mutated PDHs co-crystallized with Tyr indicate that substitutions of Asn222 confer ADH activity and Tyr sensitivity. Reciprocal mutagenesis of the corresponding residue in divergent plant ADHs further introduced PDH activity and relaxed Tyr sensitivity, highlighting the critical role of this residue in TyrA substrate specificity that underlies the evolution of alternative Tyr biosynthetic pathways in plants.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Matthew R Schneider
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yusen Men
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Soon Goo Lee
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Xu Q, Liu F, Chen P, Jez JM, Krishnan HB. β-N-Oxalyl-l-α,β-diaminopropionic Acid (β-ODAP) Content in Lathyrus sativus: The Integration of Nitrogen and Sulfur Metabolism through β-Cyanoalanine Synthase. Int J Mol Sci 2017; 18:ijms18030526. [PMID: 28264526 PMCID: PMC5372542 DOI: 10.3390/ijms18030526] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 01/03/2017] [Revised: 02/06/2017] [Accepted: 02/21/2017] [Indexed: 11/16/2022] Open
Abstract
Grass pea (Lathyrus sativus L.) is an important legume crop grown mainly in South Asia and Sub-Saharan Africa. This underutilized legume can withstand harsh environmental conditions including drought and flooding. During drought-induced famines, this protein-rich legume serves as a food source for poor farmers when other crops fail under harsh environmental conditions; however, its use is limited because of the presence of an endogenous neurotoxic nonprotein amino acid β-N-oxalyl-l-α,β-diaminopropionic acid (β-ODAP). Long-term consumption of Lathyrus and β-ODAP is linked to lathyrism, which is a degenerative motor neuron syndrome. Pharmacological studies indicate that nutritional deficiencies in methionine and cysteine may aggravate the neurotoxicity of β-ODAP. The biosynthetic pathway leading to the production of β-ODAP is poorly understood, but is linked to sulfur metabolism. To date, only a limited number of studies have been conducted in grass pea on the sulfur assimilatory enzymes and how these enzymes regulate the biosynthesis of β-ODAP. Here, we review the current knowledge on the role of sulfur metabolism in grass pea and its contribution to β-ODAP biosynthesis. Unraveling the fundamental steps and regulation of β-ODAP biosynthesis in grass pea will be vital for the development of improved varieties of this underutilized legume.
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Affiliation(s)
- Quanle Xu
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
- Plant Genetics Research Unit, USDA-Agricultural Research Service, 108 Curtis Hall, University of Missouri, Columbia, MO 65211, USA.
| | - Fengjuan Liu
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Peng Chen
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA-Agricultural Research Service, 108 Curtis Hall, University of Missouri, Columbia, MO 65211, USA.
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Cascella B, Lee SG, Singh S, Jez JM, Mirica LM. The small molecule JIB-04 disrupts O 2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A. Chem Commun (Camb) 2017; 53:2174-2177. [PMID: 28144654 PMCID: PMC5511625 DOI: 10.1039/c6cc09882g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
JIB-04, a specific inhibitor of the O2-activating, Fe-dependent histone lysine demethylases, is revealed to disrupt the binding of O2 in KDM4A/JMJD2A through a continuous O2-consumption assay, X-ray crystal structure data, and molecular docking.
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Affiliation(s)
- Barbara Cascella
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA. and Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| | - Sukrit Singh
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA.
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| | - Liviu M Mirica
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA.
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43
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Jez JM. Revisiting protein structure, function, and evolution in the genomic era. J Invertebr Pathol 2017; 142:11-15. [DOI: 10.1016/j.jip.2016.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/04/2016] [Accepted: 07/28/2016] [Indexed: 02/05/2023]
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Holland CK, Cascella B, Jez JM. Dissonance Strikes a Chord in Stilbene Synthesizers. Cell Chem Biol 2016; 23:1440-1441. [PMID: 28009974 DOI: 10.1016/j.chembiol.2016.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this issue of Cell Chemical Biology, Mori et al. (2016) combine X-ray crystallography and biochemistry to discover a new mechanism for stilbene synthesis in bacteria. The dialkyl-condensing enzyme StlD catalyzes formation of cyclohexanediones using a non-canonical β-ketosynthase active site. Aromatization by StlC completes production of the stilbene product.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University in St. Louis, One Brookings Drive, CB1137, St. Louis, MO 63130, USA
| | - Barbara Cascella
- Department of Biology, Washington University in St. Louis, One Brookings Drive, CB1137, St. Louis, MO 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, CB1137, St. Louis, MO 63130, USA.
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45
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Jez JM, Ravilious GE, Herrmann J. Structural biology and regulation of the plant sulfation pathway. Chem Biol Interact 2016; 259:31-38. [DOI: 10.1016/j.cbi.2016.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 11/26/2022]
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46
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Machingura M, Salomon E, Jez JM, Ebbs SD. The β-cyanoalanine synthase pathway: beyond cyanide detoxification. Plant Cell Environ 2016; 39:2329-41. [PMID: 27116378 DOI: 10.1111/pce.12755] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 08/12/2015] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 05/21/2023]
Abstract
Production of cyanide through biological and environmental processes requires the detoxification of this metabolic poison. In the 1960s, discovery of the β-cyanoalanine synthase (β-CAS) pathway in cyanogenic plants provided the first insight on cyanide detoxification in nature. Fifty years of investigations firmly established the protective role of the β-CAS pathway in cyanogenic plants and its role in the removal of cyanide produced from ethylene synthesis in plants, but also revealed the importance of this pathway for plant growth and development and the integration of nitrogen and sulfur metabolism. This review describes the β-CAS pathway, its distribution across and within higher plants, and the diverse biological functions of the pathway in cyanide assimilation, plant growth and development, stress tolerance, regulation of cyanide and sulfide signalling, and nitrogen and sulfur metabolism. The collective roles of the β-CAS pathway highlight its potential evolutionary and ecological importance in plants.
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Affiliation(s)
- Marylou Machingura
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Eitan Salomon
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Stephen D Ebbs
- Department of Plant Biology and Center for Ecology, Southern Illinois University, Carbondale, IL, 62901, USA.
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47
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Kilgore MB, Holland CK, Jez JM, Kutchan TM. Identification of a Noroxomaritidine Reductase with Amaryllidaceae Alkaloid Biosynthesis Related Activities. J Biol Chem 2016; 291:16740-52. [PMID: 27252378 DOI: 10.1074/jbc.m116.717827] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 01/08/2023] Open
Abstract
Amaryllidaceae alkaloids are a large group of plant natural products with over 300 documented structures and diverse biological activities. Several groups of Amaryllidaceae alkaloids including the hemanthamine- and crinine-type alkaloids show promise as anticancer agents. Two reduction reactions are required for the production of these compounds: the reduction of norcraugsodine to norbelladine and the reduction of noroxomaritidine to normaritidine, with the enantiomer of noroxomaritidine dictating whether the derivatives will be the crinine-type or hemanthamine-type. It is also possible for the carbon-carbon double bond of noroxomaritidine to be reduced, forming the precursor for maritinamine or elwesine depending on the enantiomer reduced to an oxomaritinamine product. In this study, a short chain alcohol dehydrogenase/reductase that co-expresses with the previously discovered norbelladine 4'-O-methyltransferase from Narcissus sp. and Galanthus spp. was cloned and expressed in Escherichia coli Biochemical analyses and x-ray crystallography indicates that this protein functions as a noroxomaritidine reductase that forms oxomaritinamine from noroxomaritidine through a carbon-carbon double bond reduction. The enzyme also reduces norcraugsodine to norbelladine with a 400-fold lower specific activity. These studies identify a missing step in the biosynthesis of this pharmacologically important class of plant natural products.
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Affiliation(s)
- Matthew B Kilgore
- From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132 and the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Cynthia K Holland
- the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Joseph M Jez
- the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Toni M Kutchan
- From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132 and
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48
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Lee SG, Nwumeh R, Jez JM. Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS. J Biol Chem 2016; 291:13421-30. [PMID: 27137927 DOI: 10.1074/jbc.m116.730358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
Isopropylmalate dehydrogenase (IPMDH) and 3-(2'-methylthio)ethylmalate dehydrogenase catalyze the oxidative decarboxylation of different β-hydroxyacids in the leucine- and methionine-derived glucosinolate biosynthesis pathways, respectively, in plants. Evolution of the glucosinolate biosynthetic enzyme from IPMDH results from a single amino acid substitution that alters substrate specificity. Here, we present the x-ray crystal structures of Arabidopsis thaliana IPMDH2 (AtIPMDH2) in complex with either isopropylmalate and Mg(2+) or NAD(+) These structures reveal conformational changes that occur upon ligand binding and provide insight on the active site of the enzyme. The x-ray structures and kinetic analysis of site-directed mutants are consistent with a chemical mechanism in which Lys-232 activates a water molecule for catalysis. Structural analysis of the AtIPMDH2 K232M mutant and isothermal titration calorimetry supports a key role of Lys-232 in the reaction mechanism. This study suggests that IPMDH-like enzymes in both leucine and glucosinolate biosynthesis pathways use a common mechanism and that members of the β-hydroxyacid reductive decarboxylase family employ different active site features for similar reactions.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Ronald Nwumeh
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
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Holland CK, Jez JM. Structural Biology of Aromatic Amino Acid Biosynthesis in Plants: The Prephenate Branch Point. FASEB J 2016. [DOI: 10.1096/fasebj.30.1_supplement.1137.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Joseph M Jez
- BiologyWashington University in St. LouisSt. LouisMO
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50
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Korasick DA, Jez JM, Strader LC. Refining the nuclear auxin response pathway through structural biology. Curr Opin Plant Biol 2015; 27:22-8. [PMID: 26048079 PMCID: PMC4618177 DOI: 10.1016/j.pbi.2015.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/12/2015] [Indexed: 05/03/2023]
Abstract
Auxin is a key regulator of plant growth and development. Classical molecular and genetic techniques employed over the past 20 years identified the major players in auxin-mediated gene expression and suggest a canonical auxin response pathway. In recent years, structural and biophysical studies clarified the molecular details of auxin perception, the recognition of DNA by auxin transcription factors, and the interaction of auxin transcription factors with repressor proteins. These studies refine the auxin signal transduction model and raise new questions that increase the complexity of auxin signaling.
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Affiliation(s)
- David A Korasick
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
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