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Siddique S, Radakovic ZS, Hiltl C, Pellegrin C, Baum TJ, Beasley H, Bent AF, Chitambo O, Chopra D, Danchin EGJ, Grenier E, Habash SS, Hasan MS, Helder J, Hewezi T, Holbein J, Holterman M, Janakowski S, Koutsovoulos GD, Kranse OP, Lozano-Torres JL, Maier TR, Masonbrink RE, Mendy B, Riemer E, Sobczak M, Sonawala U, Sterken MG, Thorpe P, van Steenbrugge JJM, Zahid N, Grundler F, Eves-van den Akker S. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nat Commun 2022; 13:6190. [PMID: 36261416 PMCID: PMC9582021 DOI: 10.1038/s41467-022-33769-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.
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Affiliation(s)
- Shahid Siddique
- Department of Entomology and Nematology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Zoran S Radakovic
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
- P.H. Petersen Saatzucht Lundsgaard GmbH, D-24977, Grundhof, Germany
| | - Clarissa Hiltl
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Clement Pellegrin
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Helen Beasley
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Oliver Chitambo
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Divykriti Chopra
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Etienne G J Danchin
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Eric Grenier
- IGEPP, INRAE, Institut Agro, Université Rennes, 35650, Le Rheu, France
| | - Samer S Habash
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
- BASF Vegetable Seeds, Napoleonsweg 152, 6083, AB, Nunhem, The Netherlands
| | - M Shamim Hasan
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Johannes Helder
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Julia Holbein
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Martijn Holterman
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Solynta, Dreijenlaan 2, 6703, HA, Wageningen, The Netherlands
| | - Sławomir Janakowski
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | | | - Olaf P Kranse
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jose L Lozano-Torres
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Rick E Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA, 50010, USA
| | - Badou Mendy
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Esther Riemer
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Mirosław Sobczak
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Unnati Sonawala
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Peter Thorpe
- Mackenzie Institute for Early Diagnosis, School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - Joris J M van Steenbrugge
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Nageena Zahid
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-University of Bonn, Meckenheimer Allee 168, D-53115, Bonn, Germany
| | - Florian Grundler
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany.
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Biochemical characterization of pantoate kinase, a novel enzyme necessary for coenzyme A biosynthesis in the Archaea. J Bacteriol 2012; 194:5434-43. [PMID: 22865846 DOI: 10.1128/jb.06624-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although bacteria and eukaryotes share a pathway for coenzyme A (CoA) biosynthesis, we previously clarified that most archaea utilize a distinct pathway for the conversion of pantoate to 4'-phosphopantothenate. Whereas bacteria/eukaryotes use pantothenate synthetase and pantothenate kinase (PanK), the hyperthermophilic archaeon Thermococcus kodakarensis utilizes two novel enzymes: pantoate kinase (PoK) and phosphopantothenate synthetase (PPS). Here, we report a detailed biochemical examination of PoK from T. kodakarensis. Kinetic analyses revealed that the PoK reaction displayed Michaelis-Menten kinetics toward ATP, whereas substrate inhibition was observed with pantoate. PoK activity was not affected by the addition of CoA/acetyl-CoA. Interestingly, PoK displayed broad nucleotide specificity and utilized ATP, GTP, UTP, and CTP with comparable k(cat)/K(m) values. Sequence alignment of 27 PoK homologs revealed seven conserved residues with reactive side chains, and variant proteins were constructed for each residue. Activity was not detected when mutations were introduced to Ser104, Glu134, and Asp143, suggesting that these residues play vital roles in PoK catalysis. Kinetic analysis of the other variant proteins, with mutations S28A, H131A, R155A, and T186A, indicated that all four residues are involved in pantoate recognition and that Arg155 and Thr186 play important roles in PoK catalysis. Gel filtration analyses of the variant proteins indicated that Thr186 is also involved in dimer assembly. A sequence comparison between PoK and other members of the GHMP kinase family suggests that Ser104 and Glu134 are involved in binding with phosphate and Mg(2+), respectively, while Asp143 is the base responsible for proton abstraction from the pantoate hydroxy group.
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Satoh A, Konishi S, Tamura H, Stickland HG, Whitney HM, Smith AG, Matsumura H, Inoue T. Substrate-Induced Closing of the Active Site Revealed by the Crystal Structure of Pantothenate Synthetase from Staphylococcus aureus. Biochemistry 2010; 49:6400-10. [DOI: 10.1021/bi1004206] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Atsuko Satoh
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Saki Konishi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruka Tamura
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hannah G. Stickland
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Heather M. Whitney
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Hiroyoshi Matsumura
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- CREST, JST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- CREST, JST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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