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Wang H, Moghe GD, Kovaleski AP, Keller M, Martinson TE, Wright AH, Franklin JL, Hébert-Haché A, Provost C, Reinke M, Atucha A, North MG, Russo JP, Helwi P, Centinari M, Londo JP. NYUS.2: an automated machine learning prediction model for the large-scale real-time simulation of grapevine freezing tolerance in North America. Hortic Res 2024; 11:uhad286. [PMID: 38487294 PMCID: PMC10939402 DOI: 10.1093/hr/uhad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Accurate and real-time monitoring of grapevine freezing tolerance is crucial for the sustainability of the grape industry in cool climate viticultural regions. However, on-site data are limited due to the complexity of measurement. Current prediction models underperform under diverse climate conditions, which limits the large-scale deployment of these methods. We combined grapevine freezing tolerance data from multiple regions in North America and generated a predictive model based on hourly temperature-derived features and cultivar features using AutoGluon, an automated machine learning engine. Feature importance was quantified by AutoGluon and SHAP (SHapley Additive exPlanations) value. The final model was evaluated and compared with previous models for its performance under different climate conditions. The final model achieved an overall 1.36°C root-mean-square error during model testing and outperformed two previous models using three test cultivars at all testing regions. Two feature importance quantification methods identified five shared essential features. Detailed analysis of the features indicates that the model has adequately extracted some biological mechanisms during training. The final model, named NYUS.2, was deployed along with two previous models as an R shiny-based application in the 2022-23 dormancy season, enabling large-scale and real-time simulation of grapevine freezing tolerance in North America for the first time.
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Affiliation(s)
- Hongrui Wang
- School of Integrative Plant Science, Horticulture Section, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
| | - Gaurav D Moghe
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY 14850, USA
| | - Al P Kovaleski
- Plant and Agroecosystem Sciences Department, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Markus Keller
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
| | - Timothy E Martinson
- School of Integrative Plant Science, Horticulture Section, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
| | - A Harrison Wright
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Jeffrey L Franklin
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, Nova Scotia, B4N 1J5, Canada
| | | | - Caroline Provost
- Centre de Recherche Agroalimentaire de Mirabel, Mirabel, Québec, J7N 2X8, Canada
| | - Michael Reinke
- Southwest Michigan Research and Extension Center, Michigan State University, Benton Harbor, MI 49022, USA
| | - Amaya Atucha
- Plant and Agroecosystem Sciences Department, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Michael G North
- Plant and Agroecosystem Sciences Department, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Jennifer P Russo
- School of Integrative Plant Science, Horticulture Section, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
| | - Pierre Helwi
- Martell & Co., 7 place Edouard Martell, Cognac 16100, France
| | - Michela Centinari
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jason P Londo
- School of Integrative Plant Science, Horticulture Section, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
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2
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Mahood EH, Bennett AA, Komatsu K, Kruse LH, Lau V, Rahmati Ishka M, Jiang Y, Bravo A, Louie K, Bowen BP, Harrison MJ, Provart NJ, Vatamaniuk OK, Moghe GD. Information theory and machine learning illuminate large-scale metabolomic responses of Brachypodium distachyon to environmental change. Plant J 2023; 114:463-481. [PMID: 36880270 DOI: 10.1111/tpj.16160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 02/06/2023] [Accepted: 02/19/2023] [Indexed: 05/10/2023]
Abstract
Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)-based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML-based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co-accumulation analysis further identified condition-specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio-Analytic Resource for Plant Biology website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.
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Affiliation(s)
- Elizabeth H Mahood
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Karyn Komatsu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Vincent Lau
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Maryam Rahmati Ishka
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Yulin Jiang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Katherine Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Nicholas J Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Olena K Vatamaniuk
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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3
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Johnson AR, Yue Y, Carey SB, Park SJ, Kruse LH, Bao A, Pasha A, Harkess A, Provart NJ, Moghe GD, Frank MH. Chromosome-level Genome Assembly of Euphorbia peplus, a Model System for Plant Latex, Reveals that Relative Lack of Ty3 Transposons Contributed to Its Small Genome Size. Genome Biol Evol 2023; 15:7033215. [PMID: 36757383 PMCID: PMC10018070 DOI: 10.1093/gbe/evad018] [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: 10/17/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
Euphorbia peplus (petty spurge) is a small, fast-growing plant that is native to Eurasia and has become a naturalized weed in North America and Australia. Euphorbia peplus is not only medicinally valuable, serving as a source for the skin cancer drug ingenol mebutate, but also has great potential as a model for latex production owing to its small size, ease of manipulation in the laboratory, and rapid reproductive cycle. To help establish E. peplus as a new model, we generated a 267.2-Mb Hi-C-anchored PacBio HiFi nuclear genome assembly with a BUSCO score of 98.5%, a genome annotation based on RNA-seq data from six organs, and publicly accessible tools including a genome browser and an interactive organ-specific expression atlas. Chromosome number is highly variable across Euphorbia species. Using a comparative analysis of our newly sequenced E. peplus genome with other Euphorbiaceae genomes, we show that variation in Euphorbia chromosome number between E. peplus and Euphorbia lathyris is likely due to fragmentation and rearrangement rather than chromosomal duplication followed by diploidization of the duplicated sequence. Moreover, we found that the E. peplus genome is relatively compact compared with related members of the genus in part due to restricted expansion of the Ty3 transposon family. Finally, we identify a large gene cluster that contains many previously identified enzymes in the putative ingenol mebutate biosynthesis pathway, along with additional gene candidates for this biosynthetic pathway. The genomic resources we have created for E. peplus will help advance research on latex production and ingenol mebutate biosynthesis in the commercially important Euphorbiaceae family.
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Affiliation(s)
- Arielle R Johnson
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Yuanzheng Yue
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Se Jin Park
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Ashley Bao
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Nicholas J Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Margaret H Frank
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
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4
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Kruse LH, Fehr B, Chobirko JD, Moghe GD. Phylogenomic analyses across land plants reveals motifs and coexpression patterns useful for functional prediction in the BAHD acyltransferase family. Front Plant Sci 2023; 14:1067613. [PMID: 36844084 PMCID: PMC9950517 DOI: 10.3389/fpls.2023.1067613] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
The BAHD acyltransferase family is one of the largest enzyme families in flowering plants, containing dozens to hundreds of genes in individual genomes. Highly prevalent in angiosperm genomes, members of this family contribute to several pathways in primary and specialized metabolism. In this study, we performed a phylogenomic analysis of the family using 52 genomes across the plant kingdom to gain deeper insights into its functional evolution and enable function prediction. We found that BAHD expansion in land plants was associated with significant changes in various gene features. Using pre-defined BAHD clades, we identified clade expansions in different plant groups. In some groups, these expansions coincided with the prominence of metabolite classes such as anthocyanins (flowering plants) and hydroxycinnamic acid amides (monocots). Clade-wise motif-enrichment analysis revealed that some clades have novel motifs fixed on either the acceptor or the donor side, potentially reflecting historical routes of functional evolution. Co-expression analysis in rice and Arabidopsis further identified BAHDs with similar expression patterns, however, most co-expressed BAHDs belonged to different clades. Comparing BAHD paralogs, we found that gene expression diverges rapidly after duplication, suggesting that sub/neo-functionalization of duplicate genes occurs quickly via expression diversification. Analyzing co-expression patterns in Arabidopsis in conjunction with orthology-based substrate class predictions and metabolic pathway models led to the recovery of metabolic processes of most of the already-characterized BAHDs as well as definition of novel functional predictions for some uncharacterized BAHDs. Overall, this study provides new insights into the evolution of BAHD acyltransferases and sets up a foundation for their functional characterization.
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Affiliation(s)
- Lars H. Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Benjamin Fehr
- Computational Biology Department, Cornell University, Ithaca, NY, United States
| | - Jason D. Chobirko
- Molecular Biology and Genetics Department, Cornell University, Ithaca, NY, United States
| | - Gaurav D. Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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5
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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: 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: 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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6
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de Crécy-lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O’Donoghue S, Orengo C, O’Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford) 2022; 2022:6663924. [PMID: 35961013 PMCID: PMC9374478 DOI: 10.1093/database/baac062] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 06/07/2022] [Revised: 06/28/2022] [Accepted: 08/03/2022] [Indexed: 12/23/2022]
Abstract
Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.
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Affiliation(s)
- Valérie de Crécy-lagard
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | | | - Cecilia Arighi
- Department of Computer and Information Sciences, University of Delaware , Newark, DE 19713, USA
| | - Jill Babor
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton CB10 1SD, UK
| | - Ian Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Crysten Blaby-Haas
- Biology Department, Brookhaven National Laboratory , Upton, NY 11973, USA
| | - Alan J Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire , Geneva 4 CH-1211, Switzerland
| | - Stephen K Burley
- RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA
| | - Stacey Cleveland
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Lucy J Colwell
- Departmenf of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, UK
| | - Ana Conesa
- Spanish National Research Council, Institute for Integrative Systems Biology , Paterna, Valencia 46980, Spain
| | - Christian Dallago
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology , i12, Boltzmannstr. 3, Garching/Munich 85748, Germany
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, The University of Hong Kong , 21 Sassoon Road, Pokfulam, SAR Hong Kong 999077, China
| | - Anita de Waard
- Research Collaboration Unit, Elsevier , Jericho, VT 05465, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Raquel Dias
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida , Gainesville, FL 32610, USA
| | - Gang Fang
- NYU-Shanghai , Shanghai 200120, China
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University , Ames, IA 50011, USA
| | - John Gerlt
- Institute for Genomic Biology and Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign , Urbana, IL 61801, USA
| | - Joshua Goldford
- Physics of Living Systems, Massachusetts Institute of Technology , Cambridge, MA 02139, USA
| | - Mark Gorelik
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Benjamin M Gyori
- Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA
| | - Christopher Henry
- Mathematics and Computer Science Division, Argonne National Laboratory , Argonne, IL 60439, USA
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Peter D Karp
- Bioinformatics Research Group, SRI International , Menlo Park, CA 94025, USA
| | | | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , 8600 Rockville Pike, Bethesda, MD 20817, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , 8600 Rockville Pike, Bethesda, MD 20817, USA
| | - Maria-Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton CB10 1SD, UK
| | - Claire McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University , Princeton, NJ 08540, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University , Ithaca, NY 14853, USA
| | - Paul Monaghan
- Department of Agricultural Education and Communication, University of Florida , Gainesville, FL 32611, USA
| | - Anne Morgat
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire , Geneva 4 CH-1211, Switzerland
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Darren A Natale
- Georgetown University Medical Center , Washington, DC 20007, USA
| | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratories , Richland, WA 99354, USA
| | - Seán O’Donoghue
- School of Biotechnology and Biomolecular Sciences, University of NSW , Sydney, NSW 2052, Australia
| | - Christine Orengo
- Department of Structural and Molecular Biology, University College London , London WC1E 6BT, UK
| | | | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115, USA
| | - Colbie Reed
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | | | - Dmitri Rodionov
- Sanford Burnham Prebys Medical Discovery Institute , La Jolla, CA 92037, USA
| | - Irina A Rodionova
- Department of Bioengineering, Division of Engineering, University of California at San Diego , La Jolla, CA 92093-0412, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida , Gainesville, FL 32611, USA
| | - Lana Saleh
- New England Biolabs , Ipswich, MA 01938, USA
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia , Charlottesville, VA, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , 8600 Rockville Pike, Bethesda, MD 20817, USA
| | - Paul D Thomas
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033, USA
| | - Peter Uetz
- Center for Biological Data Science, Virginia Commonwealth University , Richmond, VA 23284, USA
| | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS , Evry 91057, France
| | - Erica Watson Carter
- Department of Plant Pathology, University of Florida Citrus Research and Education Center , 700 Experiment Station Rd., Lake Alfred, FL 33850, USA
| | | | - Valerie Wood
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1GA, UK
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Jin Xu
- Department of Plant Pathology, University of Florida Citrus Research and Education Center , 700 Experiment Station Rd., Lake Alfred, FL 33850, USA
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7
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Feng H, Acosta-Gamboa L, Kruse LH, Tracy JD, Chung SH, Nava Fereira AR, Shakir S, Xu H, Sunter G, Gore MA, Casteel CL, Moghe GD, Jander G. Acylsugars protect Nicotiana benthamiana against insect herbivory and desiccation. Plant Mol Biol 2022; 109:505-522. [PMID: 34586580 DOI: 10.1007/s11103-021-01191-3] [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] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Nicotiana benthamiana acylsugar acyltransferase (ASAT) is required for protection against desiccation and insect herbivory. Knockout mutations provide a new resource for investigation of plant-aphid and plant-whitefly interactions. Nicotiana benthamiana is used extensively as a transient expression platform for functional analysis of genes from other species. Acylsugars, which are produced in the trichomes, are a hypothesized cause of the relatively high insect resistance that is observed in N. benthamiana. We characterized the N. benthamiana acylsugar profile, bioinformatically identified two acylsugar acyltransferase genes, ASAT1 and ASAT2, and used CRISPR/Cas9 mutagenesis to produce acylsugar-deficient plants for investigation of insect resistance and foliar water loss. Whereas asat1 mutations reduced accumulation, asat2 mutations caused almost complete depletion of foliar acylsucroses. Three hemipteran and three lepidopteran herbivores survived, gained weight, and/or reproduced significantly better on asat2 mutants than on wildtype N. benthamiana. Both asat1 and asat2 mutations reduced the water content and increased leaf temperature. Our results demonstrate the specific function of two ASAT proteins in N. benthamiana acylsugar biosynthesis, insect resistance, and desiccation tolerance. The improved growth of aphids and whiteflies on asat2 mutants will facilitate the use of N. benthamiana as a transient expression platform for the functional analysis of insect effectors and resistance genes from other plant species. Similarly, the absence of acylsugars in asat2 mutants will enable analysis of acylsugar biosynthesis genes from other Solanaceae by transient expression.
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Affiliation(s)
- Honglin Feng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Lucia Acosta-Gamboa
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jake D Tracy
- Plant-Microbe Biology and Plant Pathology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Alba Ruth Nava Fereira
- Department of Biology, University of Texas San Antonio, San Antonio, TX, 78249, USA
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Sara Shakir
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Gembloux Agro-Bio Tech Institute, The University of Liege, Gembloux, Belgium
| | - Hongxing Xu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- College of Life Science, The Shaanxi Normal University, Xi'an, China
| | - Garry Sunter
- Department of Biology, University of Texas San Antonio, San Antonio, TX, 78249, USA
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Clare L Casteel
- Plant-Microbe Biology and Plant Pathology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.
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8
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Kruse LH, Bennett AA, Mahood EH, Lazarus E, Park SJ, Schroeder F, Moghe GD. Illuminating the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family using computational metabolomics. Hortic Res 2022; 9:uhab079. [PMID: 35039851 PMCID: PMC8825387 DOI: 10.1093/hr/uhab079] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/24/2021] [Accepted: 11/12/2021] [Indexed: 05/13/2023]
Abstract
Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse sub-class of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC-MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using Nuclear Magnetic Resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus - the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.
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Affiliation(s)
- Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Present Address: Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Present Address: Institute of Analytical Chemistry, Universität für Bodenkultur Wien, Vienna, 1090, Austria
| | - Elizabeth H Mahood
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Elena Lazarus
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Present Address: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Se Jin Park
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Frank Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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9
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Johnson AR, Moghe GD, Frank MH. Growing a glue factory: Open questions in laticifer development. Curr Opin Plant Biol 2021; 64:102096. [PMID: 34461600 DOI: 10.1016/j.pbi.2021.102096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/25/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Latex-containing cells called laticifers are present in at least 41 flowering plant families and are thought to have convergently evolved at least 12 times. These cells are known to function in defense, but little is known about the molecular genetic mechanisms of their development. The expansion of laticifers into their distinctive tube shape can occur through two distinct mechanisms, cell fusion and intrusive growth. The mechanism and extent of intrusive laticifer growth are still being investigated. Hormonal regulation by jasmonic acid and ethylene is important for both laticifer differentiation and latex biosynthesis. Current evidence suggests that laticifers can be specified independently of latex production, but extensive latex production requires specified laticifers. Laticifers are an emerging system for studying the intersection of cell identity specification and specialized metabolism.
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Affiliation(s)
- Arielle R Johnson
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Margaret H Frank
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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10
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Landis JB, Miller CM, Broz AK, Bennett AA, Carrasquilla-Garcia N, Cook DR, Last RL, Bedinger PA, Moghe GD. Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species. Mol Biol Evol 2021; 38:3202-3219. [PMID: 33822137 PMCID: PMC8321546 DOI: 10.1093/molbev/msab092] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites—a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4–6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone—a geographical landmark in the Andes with high endemism and isolated microhabitats—was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | | | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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11
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Mahood EH, Kruse LH, Moghe GD. Machine learning: A powerful tool for gene function prediction in plants. Appl Plant Sci 2020; 8:e11376. [PMID: 32765975 PMCID: PMC7394712 DOI: 10.1002/aps3.11376] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/19/2020] [Indexed: 05/06/2023]
Abstract
Recent advances in sequencing and informatic technologies have led to a deluge of publicly available genomic data. While it is now relatively easy to sequence, assemble, and identify genic regions in diploid plant genomes, functional annotation of these genes is still a challenge. Over the past decade, there has been a steady increase in studies utilizing machine learning algorithms for various aspects of functional prediction, because these algorithms are able to integrate large amounts of heterogeneous data and detect patterns inconspicuous through rule-based approaches. The goal of this review is to introduce experimental plant biologists to machine learning, by describing how it is currently being used in gene function prediction to gain novel biological insights. In this review, we discuss specific applications of machine learning in identifying structural features in sequenced genomes, predicting interactions between different cellular components, and predicting gene function and organismal phenotypes. Finally, we also propose strategies for stimulating functional discovery using machine learning-based approaches in plants.
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Affiliation(s)
- Elizabeth H. Mahood
- Plant Biology SectionSchool of Integrative Plant SciencesCornell UniversityIthacaNew York14853USA
| | - Lars H. Kruse
- Plant Biology SectionSchool of Integrative Plant SciencesCornell UniversityIthacaNew York14853USA
| | - Gaurav D. Moghe
- Plant Biology SectionSchool of Integrative Plant SciencesCornell UniversityIthacaNew York14853USA
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12
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Leong BJ, Hurney SM, Fiesel PD, Moghe GD, Jones AD, Last RL. Specialized Metabolism in a Nonmodel Nightshade: Trichome Acylinositol Biosynthesis. Plant Physiol 2020; 183:915-924. [PMID: 32354879 PMCID: PMC7333698 DOI: 10.1104/pp.20.00276] [Citation(s) in RCA: 4] [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: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 05/13/2023]
Abstract
Plants make many biologically active, specialized metabolites, which vary in structure, biosynthesis, and the processes they influence. An increasing number of these compounds are documented to protect plants from insects, pathogens, or herbivores or to mediate interactions with beneficial organisms, including pollinators and nitrogen-fixing microbes. Acylsugars, one class of protective compounds, are made in glandular trichomes of plants across the Solanaceae family. While most described acylsugars are acylsucroses, published examples also include acylsugars with hexose cores. The South American fruit crop naranjilla (lulo; Solanum quitoense) produces acylsugars containing a myoinositol core. We identified an enzyme that acetylates triacylinositols, a function homologous to the last step in the acylsucrose biosynthetic pathway of tomato (Solanum lycopersicum). Our analysis reveals parallels between S. lycopersicum acylsucrose and S. quitoense acylinositol biosynthesis, suggesting a common evolutionary origin.
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Affiliation(s)
- Bryan J Leong
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Steven M Hurney
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Paul D Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - A Daniel Jones
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Robert L Last
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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13
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Smith SD, Angelovici R, Heyduk K, Maeda HA, Moghe GD, Pires JC, Widhalm JR, Wisecaver JH. The renaissance of comparative biochemistry. Am J Bot 2019; 106:3-13. [PMID: 30629738 DOI: 10.1002/ajb2.1216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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14
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Moghe GD, Kruse LH. The study of plant specialized metabolism: Challenges and prospects in the genomics era. Am J Bot 2018; 105:959-962. [PMID: 29924385 DOI: 10.1002/ajb2.1101] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
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15
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Xu H, Moghe GD, Wiegert-Rininger K, Schilmiller AL, Barry CS, Last RL, Pichersky E. Coexpression Analysis Identifies Two Oxidoreductases Involved in the Biosynthesis of the Monoterpene Acid Moiety of Natural Pyrethrin Insecticides in Tanacetum cinerariifolium. Plant Physiol 2018; 176:524-537. [PMID: 29122986 PMCID: PMC5761793 DOI: 10.1104/pp.17.01330] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 05/18/2023]
Abstract
Flowers of Tanacetum cinerariifolium produce a set of compounds known collectively as pyrethrins, which are commercially important pesticides that are strongly toxic to flying insects but not to most vertebrates. A pyrethrin molecule is an ester consisting of either trans-chrysanthemic acid or its modified form, pyrethric acid, and one of three alcohols, jasmolone, pyrethrolone, and cinerolone, that appear to be derived from jasmonic acid. Chrysanthemyl diphosphate synthase (CDS), the first enzyme involved in the synthesis of trans-chrysanthemic acid, was characterized previously and its gene isolated. TcCDS produces free trans-chrysanthemol in addition to trans-chrysanthemyl diphosphate, but the enzymes responsible for the conversion of trans-chrysanthemol to the corresponding aldehyde and then to the acid have not been reported. We used an RNA sequencing-based approach and coexpression correlation analysis to identify several candidate genes encoding putative trans-chrysanthemol and trans-chrysanthemal dehydrogenases. We functionally characterized the proteins encoded by these genes using a combination of in vitro biochemical assays and heterologous expression in planta to demonstrate that TcADH2 encodes an enzyme that oxidizes trans-chrysanthemol to trans-chrysanthemal, while TcALDH1 encodes an enzyme that oxidizes trans-chrysanthemal into trans-chrysanthemic acid. Transient coexpression of TcADH2 and TcALDH1 together with TcCDS in Nicotiana benthamiana leaves results in the production of trans-chrysanthemic acid as well as several other side products. The majority (58%) of trans-chrysanthemic acid was glycosylated or otherwise modified. Overall, these data identify key steps in the biosynthesis of pyrethrins and demonstrate the feasibility of metabolic engineering to produce components of these defense compounds in a heterologous host.
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Affiliation(s)
- Haiyang Xu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Gaurav D Moghe
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824
| | | | - Anthony L Schilmiller
- Mass Spectrometry and Metabolomics Core Facility, Michigan State University, East Lansing, Michigan 48824
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Robert L Last
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
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16
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Affiliation(s)
- Gaurav D Moghe
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Stacey D Smith
- Integrative Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80305, USA
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17
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Moghe GD, Leong BJ, Hurney SM, Daniel Jones A, Last RL. Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway. eLife 2017; 6:28468. [PMID: 28853706 PMCID: PMC5595436 DOI: 10.7554/elife.28468] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [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: 05/08/2017] [Accepted: 07/25/2017] [Indexed: 12/22/2022] Open
Abstract
The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non-model plant species that remain underexplored. There are about 300,000 species of plant on Earth, which together produce over a million different small molecules called metabolites. Plants use many of these molecules to grow, to communicate with each other or to defend themselves against pests and disease. Humans have co-opted many of the same molecules as well; for example, some are important nutrients while others are active ingredients in medicines. Many plant metabolites are found in almost all plants, but hundreds of thousands of them are more specialized and only found in small groups of related plant species. These specialized metabolites have a wide variety of structures, and are made by different enzymes working together to carry out a series of biochemical reactions. Acylsugars are an example of a group of specialized metabolites with particularly diverse structures. These small molecules are restricted to plants in the Solanaceae family, which includes tomato and tobacco plants. Moghe et al. have now focused on acylsugars to better understand how plants produce the large diversity of chemical structures found in specialized metabolites, and how these processes have evolved over time. An analysis of over 35 plant species from across the Solanaceae family revealed hundreds of acylsugars, with some plants accumulating 300 or more different types of these specialized metabolites. Moghe et al. then looked at the enzymes that make acylsugars from a poorly studied flowering plant called Salpiglossis sinuata, partly because it produces a large diversity of these small molecules and partly because it sits in a unique position in the Solanaceae family tree. The activities of the enzymes were confirmed both in test tubes and in plants. This suggested that many of the enzymes were “promiscuous”, meaning that they could likely use a variety of molecules as starting points for their chemical reactions. This finding could help to explain how this plant species can make such a wide variety of acylsugars. Moghe et al. also discovered that many of the enzymes that make acylsugars are encoded by genes that were originally copies of other genes and that have subsequently evolved new activities. Plant scientists and plant breeders value tomato plants that produce acylsugars because these natural chemicals protect against pests like whiteflies and spider mites. A clearer understanding of the diversity of acylsugars in the Solanaceae family, as well as the enzymes that make these specialized metabolites, could help efforts to breed crops that are more resistant to pests. Some of the enzymes related to those involved in acylsugar production could also help to make chemicals with pharmaceutical value. These new findings might also eventually lead to innovative ways to produce these chemicals on a large scale.
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Affiliation(s)
- Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Bryan J Leong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| | - Steven M Hurney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
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18
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Abstract
There are estimated to be >300,000 plant species, producing >200,000 metabolites. Many of these metabolites are restricted to specific plant lineages and are referred to as "specialized" metabolites. These serve varied functions in plants including defense against biotic and abiotic stresses, plant-plant and plant-microbe communication, and pollinator attraction. These compounds also have important applications in agriculture, medicine, skin care, and in diverse aspects of human culture. The specialized metabolic repertoire of plants can vary even within and between closely related species, in terms of the number and classes of specialized metabolites as well as their structural variants. This phenotypic variation can be exploited to discover the underlying variation in the metabolic enzymes. We describe approaches for using the diversity of specialized metabolites and variation in enzyme structure and function to identify novel enzymatic activities and understand the structural basis for these differences. The knowledge obtained from these studies will provide new modules for the synthetic biology toolbox.
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Affiliation(s)
- P Fan
- Michigan State University, East Lansing, MI, United States
| | - G D Moghe
- Michigan State University, East Lansing, MI, United States
| | - R L Last
- Michigan State University, East Lansing, MI, United States.
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19
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Ning J, Moghe GD, Leong B, Kim J, Ofner I, Wang Z, Adams C, Jones AD, Zamir D, Last RL. A Feedback-Insensitive Isopropylmalate Synthase Affects Acylsugar Composition in Cultivated and Wild Tomato. Plant Physiol 2015; 169:1821-35. [PMID: 25986128 PMCID: PMC4634047 DOI: 10.1104/pp.15.00474] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/15/2015] [Indexed: 05/05/2023]
Abstract
Acylsugars are insecticidal specialized metabolites produced in the glandular trichomes of plants in the Solanaceae family. In the tomato clade of the Solanum genus, acylsugars consist of aliphatic acids of different chain lengths esterified to sucrose, or less frequently to glucose. Through liquid chromatography-mass spectrometry screening of introgression lines, we previously identified a region of chromosome 8 in the Solanum pennellii LA0716 genome (IL8-1/8-1-1) that causes the cultivated tomato Solanum lycopersicum to shift from producing acylsucroses with abundant 3-methylbutanoic acid acyl chains derived from leucine metabolism to 2-methylpropanoic acid acyl chains derived from valine metabolism. We describe multiple lines of evidence implicating a trichome-expressed gene from this region as playing a role in this shift. S. lycopersicum M82 SlIPMS3 (Solyc08g014230) encodes a functional end product inhibition-insensitive version of the committing enzyme of leucine biosynthesis, isopropylmalate synthase, missing the carboxyl-terminal 160 amino acids. In contrast, the S. pennellii LA0716 IPMS3 allele found in IL8-1/8-1-1 encodes a nonfunctional truncated IPMS protein. M82 transformed with an SlIPMS3 RNA interference construct exhibited an acylsugar profile similar to that of IL8-1-1, whereas the expression of SlIPMS3 in IL8-1-1 partially restored the M82 acylsugar phenotype. These IPMS3 alleles are polymorphic in 14 S. pennellii accessions spread throughout the geographical range of occurrence for this species and are associated with acylsugars containing varying amounts of 2-methylpropanoic acid and 3-methylbutanoic acid acyl chains.
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Affiliation(s)
- Jing Ning
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Gaurav D Moghe
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Bryan Leong
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Jeongwoon Kim
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Itai Ofner
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Zhenzhen Wang
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Christopher Adams
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Dani Zamir
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Robert L Last
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
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20
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Moghe GD, Last RL. Something Old, Something New: Conserved Enzymes and the Evolution of Novelty in Plant Specialized Metabolism. Plant Physiol 2015; 169:1512-23. [PMID: 26276843 PMCID: PMC4634076 DOI: 10.1104/pp.15.00994] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/13/2015] [Indexed: 05/18/2023]
Abstract
Plants produce hundreds of thousands of small molecules known as specialized metabolites, many of which are of economic and ecological importance. This remarkable variety is a consequence of the diversity and rapid evolution of specialized metabolic pathways. These novel biosynthetic pathways originate via gene duplication or by functional divergence of existing genes, and they subsequently evolve through selection and/or drift. Studies over the past two decades revealed that diverse specialized metabolic pathways have resulted from the incorporation of primary metabolic enzymes. We discuss examples of enzyme recruitment from primary metabolism and the variety of paths taken by duplicated primary metabolic enzymes toward integration into specialized metabolism. These examples provide insight into processes by which plant specialized metabolic pathways evolve and suggest approaches to discover enzymes of previously uncharacterized metabolic networks.
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Affiliation(s)
- Gaurav D Moghe
- Department of Biochemistry and Molecular Biology (G.D.M., R.L.L.) and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Robert L Last
- Department of Biochemistry and Molecular Biology (G.D.M., R.L.L.) and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
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21
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Lehti-Shiu MD, Uygun S, Moghe GD, Panchy N, Fang L, Hufnagel DE, Jasicki HL, Feig M, Shiu SH. Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana. Plant Physiol 2015; 168:1717-34. [PMID: 26103993 PMCID: PMC4528766 DOI: 10.1104/pp.15.00689] [Citation(s) in RCA: 16] [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] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 06/03/2015] [Indexed: 05/23/2023]
Abstract
Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from changes in patterns of expression, binding site divergence, and/or interactions with other proteins. Although plant TFs tend to be retained post polyploidization, many are lost within tens to hundreds of million years. Thus, it can be hypothesized that some TFs in plant genomes are in the process of becoming pseudogenes. Here, we use a pair of salt tolerance-conferring transcription factors, DWARF AND DELAYED FLOWERING1 (DDF1) and DDF2, that duplicated through paleopolyploidy 50 to 65 million years ago, as examples to illustrate potential mechanisms leading to duplicate retention and loss. We found that the expression patterns of Arabidopsis thaliana (At)DDF1 and AtDDF2 have diverged in a highly asymmetric manner, and AtDDF2 has lost most inferred ancestral stress responses. Consistent with promoter disablement, the AtDDF2 promoter has fewer predicted cis-elements and a methylated repetitive element. Through comparisons of AtDDF1, AtDDF2, and their Arabidopsis lyrata orthologs, we identified significant differences in binding affinities and binding site preference. In particular, an AtDDF2-specific substitution within the DNA-binding domain significantly reduces binding affinity. Cross-species analyses indicate that both AtDDF1 and AtDDF2 are under selective constraint, but among A. thaliana accessions, AtDDF2 has a higher level of nonsynonymous nucleotide diversity compared with AtDDF1. This may be the result of selection in different environments or may point toward the possibility of ongoing functional decay despite retention for millions of years after gene duplication.
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Affiliation(s)
- Melissa D Lehti-Shiu
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - Sahra Uygun
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - Gaurav D Moghe
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - Nicholas Panchy
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - Liang Fang
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - David E Hufnagel
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - Hannah L Jasicki
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - Michael Feig
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
| | - Shin-Han Shiu
- Department of Plant Biology (M.D.L.-S., D.E.H., S.-H.S.), Genetics Program (S.U., N.P., S.-H.S.), Department of Energy Plant Research Laboratory (S.U.), Department of Biochemistry and Molecular Biology (G.D.M., L.F., M.F.), and Department of Chemistry (M.F.), Michigan State University, East Lansing, Michigan 48824; andLaPorte High School, LaPorte, Indiana 46350 (H.L.J.)
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22
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Lloyd JP, Seddon AE, Moghe GD, Simenc MC, Shiu SH. Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes. Plant Cell 2015; 27:2133-47. [PMID: 26286535 PMCID: PMC4568498 DOI: 10.1105/tpc.15.00051] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 06/22/2015] [Accepted: 07/25/2015] [Indexed: 05/18/2023]
Abstract
Essential genes represent critical cellular components whose disruption results in lethality. Characteristics shared among essential genes have been uncovered in fungal and metazoan model systems. However, features associated with plant essential genes are largely unknown and the full set of essential genes remains to be discovered in any plant species. Here, we show that essential genes in Arabidopsis thaliana have distinct features useful for constructing within- and cross-species prediction models. Essential genes in A. thaliana are often single copy or derived from older duplications, highly and broadly expressed, slow evolving, and highly connected within molecular networks compared with genes with nonlethal mutant phenotypes. These gene features allowed the application of machine learning methods that predicted known lethal genes as well as an additional 1970 likely essential genes without documented phenotypes. Prediction models from A. thaliana could also be applied to predict Oryza sativa and Saccharomyces cerevisiae essential genes. Importantly, successful predictions drew upon many features, while any single feature was not sufficient. Our findings show that essential genes can be distinguished from genes with nonlethal phenotypes using features that are similar across kingdoms and indicate the possibility for translational application of our approach to species without extensive functional genomic and phenomic resources.
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Affiliation(s)
- John P Lloyd
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Alexander E Seddon
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
| | - Matthew C Simenc
- Department of Biological Sciences, Humboldt State University, Arcata, California 95521
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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23
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Schilmiller AL, Moghe GD, Fan P, Ghosh B, Ning J, Jones AD, Last RL. Functionally divergent alleles and duplicated Loci encoding an acyltransferase contribute to acylsugar metabolite diversity in Solanum trichomes. Plant Cell 2015; 27:1002-17. [PMID: 25862303 PMCID: PMC4558703 DOI: 10.1105/tpc.15.00087] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/05/2015] [Accepted: 03/17/2015] [Indexed: 05/18/2023]
Abstract
Glandular trichomes from tomato (Solanum lycopersicum) and other species in the Solanaceae produce and secrete a mixture of O-acylsugars (aliphatic esters of sucrose and glucose) that contribute to insect defense. Despite their phylogenetic distribution and diversity, relatively little is known about how these specialized metabolites are synthesized. Mass spectrometric profiling of acylsugars in the S. lycopersicum x Solanum pennellii introgression lines identified a chromosome 11 locus containing a cluster of BAHD acyltransferases with one gene (named Sl-ASAT3) expressed in tip cells of type I trichomes where acylsugars are made. Sl-ASAT3 was shown to encode an acyl-CoA-dependent acyltransferase that catalyzes the transfer of short (four to five carbons) branched acyl chains to the furanose ring of di-acylsucrose acceptors to produce tri-acylsucroses, which can be further acetylated by Sl-ASAT4 (previously Sl-AT2). Among the wild tomatoes, diversity in furanose ring acyl chains on acylsucroses was most striking in Solanum habrochaites. S. habrochaites accessions from Ecuador and northern Peru produced acylsucroses with short (≤C5) or no acyl chains on the furanose ring. Accessions from central and southern Peru had the ability to add short or long (up to C12) acyl chains to the furanose ring. Multiple ASAT3-like sequences were found in most accessions, and their in vitro activities correlated with observed geographical diversity in acylsugar profiles.
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Affiliation(s)
- Anthony L Schilmiller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Banibrata Ghosh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Jing Ning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319 Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1319
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319 Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824-1319
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24
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Abstract
Polyploidy is an important force shaping plant genomes. All flowering plants are descendants of an ancestral polyploid species, and up to 70% of extant vascular plant species are believed to be recent polyploids. Over the past century, a significant body of knowledge has accumulated regarding the prevalence and ecology of polyploid plants. In this review, we summarize our current understanding of the causes and molecular consequences of polyploidization in angiosperms. We also provide a discussion on the relationships between polyploidy and adaptation and suggest areas where further research may provide a better understanding of polyploidy.
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25
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Moghe GD, Hufnagel DE, Tang H, Xiao Y, Dworkin I, Town CD, Conner JK, Shiu SH. Consequences of Whole-Genome Triplication as Revealed by Comparative Genomic Analyses of the Wild Radish Raphanus raphanistrum and Three Other Brassicaceae Species. Plant Cell 2014; 26:1925-1937. [PMID: 24876251 PMCID: PMC4079359 DOI: 10.1105/tpc.114.124297] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/30/2014] [Accepted: 04/30/2014] [Indexed: 05/18/2023]
Abstract
Polyploidization events are frequent among flowering plants, and the duplicate genes produced via such events contribute significantly to plant evolution. We sequenced the genome of wild radish (Raphanus raphanistrum), a Brassicaceae species that experienced a whole-genome triplication event prior to diverging from Brassica rapa. Despite substantial gene gains in these two species compared with Arabidopsis thaliana and Arabidopsis lyrata, ∼70% of the orthologous groups experienced gene losses in R. raphanistrum and B. rapa, with most of the losses occurring prior to their divergence. The retained duplicates show substantial divergence in sequence and expression. Based on comparison of A. thaliana and R. raphanistrum ortholog floral expression levels, retained radish duplicates diverged primarily via maintenance of ancestral expression level in one copy and reduction of expression level in others. In addition, retained duplicates differed significantly from genes that reverted to singleton state in function, sequence composition, expression patterns, network connectivity, and rates of evolution. Using these properties, we established a statistical learning model for predicting whether a duplicate would be retained postpolyploidization. Overall, our study provides new insights into the processes of plant duplicate loss, retention, and functional divergence and highlights the need for further understanding factors controlling duplicate gene fate.
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Affiliation(s)
- Gaurav D Moghe
- Programs in Genetics and Quantitative Biology, Michigan State University, East Lansing, Michigan 48824
| | - David E Hufnagel
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, Maryland 20850
| | - Yongli Xiao
- National Institute of Allergy and Infectious Disease, National Institute of Health, Bethesda, Maryland 20892
| | - Ian Dworkin
- Department of Zoology, Michigan State University, East Lansing, Michigan 48824
| | | | - Jeffrey K Conner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 Kellogg Biological Station, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Programs in Genetics and Quantitative Biology, Michigan State University, East Lansing, Michigan 48824 Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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26
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Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol 2014; 164:513-24. [PMID: 24306534 PMCID: PMC3912085 DOI: 10.1104/pp.113.230144] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/26/2013] [Indexed: 05/18/2023]
Abstract
We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.
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27
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Moghe GD, Lehti-Shiu MD, Seddon AE, Yin S, Chen Y, Juntawong P, Brandizzi F, Bailey-Serres J, Shiu SH. Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis. Plant Physiol 2013; 161:210-24. [PMID: 23132786 PMCID: PMC3532253 DOI: 10.1104/pp.112.205245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/21/2012] [Indexed: 05/23/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) genome is the most well-annotated plant genome. However, transcriptome sequencing in Arabidopsis continues to suggest the presence of polyadenylated (polyA) transcripts originating from presumed intergenic regions. It is not clear whether these transcripts represent novel noncoding or protein-coding genes. To understand the nature of intergenic polyA transcription, we first assessed its abundance using multiple messenger RNA sequencing data sets. We found 6,545 intergenic transcribed fragments (ITFs) occupying 3.6% of Arabidopsis intergenic space. In contrast to transcribed fragments that map to protein-coding and RNA genes, most ITFs are significantly shorter, are expressed at significantly lower levels, and tend to be more data set specific. A surprisingly large number of ITFs (32.1%) may be protein coding based on evidence of translation. However, our results indicate that these "translated" ITFs tend to be close to and are likely associated with known genes. To investigate if ITFs are under selection and are functional, we assessed ITF conservation through cross-species as well as within-species comparisons. Our analysis reveals that 237 ITFs, including 49 with translation evidence, are under strong selective constraint and relatively distant from annotated features. These ITFs are likely parts of novel genes. However, the selective pressure imposed on most ITFs is similar to that of randomly selected, untranscribed intergenic sequences. Our findings indicate that despite the prevalence of ITFs, apart from the possibility of genomic contamination, many may be background or noisy transcripts derived from "junk" DNA, whose production may be inherent to the process of transcription and which, on rare occasions, may act as catalysts for the creation of novel genes.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Base Sequence
- Conserved Sequence
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Molecular Sequence Annotation
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Protein Biosynthesis
- Pseudogenes
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Selection, Genetic
- Sequence Analysis, RNA
- Transcription, Genetic
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Affiliation(s)
- Gaurav D. Moghe
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Melissa D. Lehti-Shiu
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Alex E. Seddon
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Shan Yin
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Yani Chen
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Piyada Juntawong
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Federica Brandizzi
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Julia Bailey-Serres
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Shin-Han Shiu
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
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