1
|
Bathe U, Leong BJ, Van Gelder K, Barbier GG, Henry CS, Amthor JS, Hanson AD. Respiratory energy demands and scope for demand expansion and destruction. Plant Physiol 2023; 191:2093-2103. [PMID: 36271857 PMCID: PMC10069906 DOI: 10.1093/plphys/kiac493] [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: 09/01/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Nonphotosynthetic plant metabolic processes are powered by respiratory energy, a limited resource that metabolic engineers—like plants themselves—must manage prudently.
Collapse
Affiliation(s)
| | | | | | | | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Jeffrey S Amthor
- Northern Arizona University Center for Ecosystem Science and Society, Flagstaff, Arizona 86011, USA
| | | |
Collapse
|
2
|
Leong BJ, Hanson AD. Continuous Directed Evolution of a Feedback-Resistant Arabidopsis Arogenate Dehydratase in Plantized Escherichia coli. ACS Synth Biol 2023; 12:43-50. [PMID: 36534785 PMCID: PMC9872817 DOI: 10.1021/acssynbio.2c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 12/24/2022]
Abstract
Continuous directed evolution (CDE) is a powerful tool for enzyme engineering due to the depth and scale of evolutionary search that it enables. If suitably controlled and calibrated, CDE could be widely applied in plant breeding and biotechnology to improve plant enzymes ex planta. We tested this concept by evolving Arabidopsis arogenate dehydratase (AtADT2) for resistance to feedback inhibition. We used an Escherichia coli platform with a phenylalanine biosynthesis pathway reconfigured ("plantized") to mimic the plant pathway, a T7RNA polymerase-base deaminase hypermutation system (eMutaT7), and 4-fluorophenylalanine as selective agent. Selection schemes were prevalidated using a known feedback-resistant AtADT2 variant. We obtained variants that had 4-fluorophenylalanine resistance at least matching the known variant and that carried mutations in the ACT domain responsible for feedback inhibition. We conclude that ex planta CDE of plant enzymes in a microbial platform is a viable way to tailor characteristics that involve interaction with small molecules.
Collapse
Affiliation(s)
- Bryan J. Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
3
|
Leong BJ, Folz JS, Bathe U, Clark DG, Fiehn O, Hanson AD. Fluoroacetate distribution, response to fluoridation, and synthesis in juvenile Gastrolobium bilobum plants. Phytochemistry 2022; 202:113356. [PMID: 35934105 DOI: 10.1016/j.phytochem.2022.113356] [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: 04/21/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Like angiosperms from several other families, the leguminous shrub Gastrolobium bilobum R.Br. produces and accumulates fluoroacetate, indicating that it performs the difficult chemistry needed to make a C-F bond. Bioinformatic analyses indicate that plants lack homologs of the only enzymes known to make a C-F bond, i.e., the Actinomycete flurorinases that form 5'-fluoro-5'-deoxyadenosine from S-adenosylmethionine and fluoride ion. To probe the origin of fluoroacetate in G. bilobum we first showed that fluoroacetate accumulates to millimolar levels in young leaves but not older leaves, stems or roots, that leaf fluoroacetate levels vary >20-fold between individual plants and are not markedly raised by sodium fluoride treatment. Young leaves were fed adenosine-13C-ribose, 13C-serine, or 13C-acetate to test plausible biosynthetic routes to fluoroacetate from S-adenosylmethionine, a C3-pyridoxal phosphate complex, or acetyl-CoA, respectively. Incorporation of 13C into expected metabolites confirmed that all three precursors were taken up and metabolized. Consistent with the bioinformatic evidence against an Actinomycete-type pathway, no adenosine-13C-ribose was converted to 13C-fluoroacetate; nor was the characteristic 4-fluorothreonine product of the Actinomycete pathway detected. Similarly, no 13C from acetate or serine was incorporated into fluoroacetate. While not fully excluding the hypothetical pathways that were tested, these negative labeling data imply that G. bilobum creates the C-F bond by an unprecedented biochemical reaction. Enzyme(s) that mediate such a reaction could be of great value in pharmaceutical and agrochemical manufacturing.
Collapse
Affiliation(s)
- Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Jacob S Folz
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, Gainesville, FL, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
4
|
Leong BJ, Hurney S, Fiesel P, Anthony TM, Moghe G, Jones AD, Last RL. Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla). Plant Direct 2022; 6:e415. [PMID: 35774622 PMCID: PMC9219006 DOI: 10.1002/pld3.415] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/26/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Plants make a variety of specialized metabolites that can mediate interactions with animals, microbes, and competitor plants. Understanding how plants synthesize these compounds enables studies of their biological roles by manipulating their synthesis in vivo as well as producing them in vitro. Acylsugars are a group of protective metabolites that accumulate in the trichomes of many Solanaceae family plants. Acylinositol biosynthesis is of interest because it appears to be restricted to a subgroup of species within the Solanum genus. Previous work characterized a triacylinositol acetyltransferase involved in acylinositol biosynthesis in the Andean fruit plant Solanum quitoense (lulo or naranjilla). We characterized three additional S. quitoense trichome expressed enzymes and found that virus-induced gene silencing of each caused changes in acylinositol accumulation. pH was shown to influence the stability and rearrangement of the product of ASAT1H and could potentially play a role in acylinositol biosynthesis. Surprisingly, the in vitro triacylinositol products of these enzymes are distinct from those that accumulate in planta. This suggests that additional enzymes are required in acylinositol biosynthesis. These characterized S. quitoense enzymes, nonetheless, provide opportunities to test the biological impact and properties of these triacylinositols in vitro.
Collapse
Affiliation(s)
- Bryan J. Leong
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Present address:
Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Steven Hurney
- Department of ChemistryMichigan State UniversityEast LansingMichiganUSA
- Present address:
Michigan Department of Health and Human ServicesLansingMichiganUSA
| | - Paul Fiesel
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Thilani M. Anthony
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Gaurav Moghe
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
- Present address:
Plant Biology Section, School of Integrative Plant SciencesCornell UniversityIthacaNew YorkUSA
| | - Arthur Daniel Jones
- Department of ChemistryMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Robert L. Last
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| |
Collapse
|
5
|
García-García JD, Van Gelder K, Joshi J, Bathe U, Leong BJ, Bruner SD, Liu CC, Hanson AD. Using continuous directed evolution to improve enzymes for plant applications. Plant Physiol 2022; 188:971-983. [PMID: 34718794 PMCID: PMC8825276 DOI: 10.1093/plphys/kiab500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/29/2021] [Indexed: 05/12/2023]
Abstract
Continuous directed evolution of enzymes and other proteins in microbial hosts is capable of outperforming classical directed evolution by executing hypermutation and selection concurrently in vivo, at scale, with minimal manual input. Provided that a target enzyme's activity can be coupled to growth of the host cells, the activity can be improved simply by selecting for growth. Like all directed evolution, the continuous version requires no prior mechanistic knowledge of the target. Continuous directed evolution is thus a powerful way to modify plant or non-plant enzymes for use in plant metabolic research and engineering. Here, we first describe the basic features of the yeast (Saccharomyces cerevisiae) OrthoRep system for continuous directed evolution and compare it briefly with other systems. We then give a step-by-step account of three ways in which OrthoRep can be deployed to evolve primary metabolic enzymes, using a THI4 thiazole synthase as an example and illustrating the mutational outcomes obtained. We close by outlining applications of OrthoRep that serve growing demands (i) to change the characteristics of plant enzymes destined for return to plants, and (ii) to adapt ("plantize") enzymes from prokaryotes-especially exotic prokaryotes-to function well in mild, plant-like conditions.
Collapse
Affiliation(s)
- Jorge D García-García
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Zapopan, Mexico
| | - Kristen Van Gelder
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Steven D Bruner
- Chemistry Department, University of Florida, Gainesville, Florida 32611
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, California 92617
- Department of Chemistry, University of California, Irvine, California 92617
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
- Author for communication:
| |
Collapse
|
6
|
Bathe U, Leong BJ, McCarty DR, Henry CS, Abraham PE, Wilson MA, Hanson AD. The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair. Biochemistry 2021; 60:3555-3565. [PMID: 34729986 DOI: 10.1021/acs.biochem.1c00613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Enzymes have in vivo life spans. Analysis of life spans, i.e., lifetime totals of catalytic turnovers, suggests that nonsurvivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme life span might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements are lacking: there are too few measurements of in vivo life span, and existing information about the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach for identifying, predicting, and validating instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability and could change our thinking about which enzymes die young in vivo, and why.
Collapse
Affiliation(s)
- Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
7
|
Fan P, Wang P, Lou YR, Leong BJ, Moore BM, Schenck CA, Combs R, Cao P, Brandizzi F, Shiu SH, Last RL. Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity. eLife 2020; 9:e56717. [PMID: 32613943 PMCID: PMC7386920 DOI: 10.7554/elife.56717] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity and recruitment of primary metabolic enzymes and examples of genomic clustering of pathway genes. Solanaceae glandular trichomes produce defensive acylsugars, with sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity.
Collapse
Affiliation(s)
- Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Peipei Wang
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Bryan J Leong
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| | - Bethany M Moore
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- University of WisconsinMadisonUnited States
| | - Craig A Schenck
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Rachel Combs
- Division of Biological Sciences, University of MissouriColumbusUnited States
| | - Pengfei Cao
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast LansingUnited States
| | - Federica Brandizzi
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast LansingUnited States
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- Department of Computational Mathematics, Science, and Engineering, Michigan State UniversityEast LansingUnited States
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Fan P, Leong BJ, Last RL. Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae. Curr Opin Plant Biol 2019; 49:8-16. [PMID: 31009840 PMCID: PMC6688940 DOI: 10.1016/j.pbi.2019.03.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 05/11/2023]
Abstract
Acylsugars are insecticidal plant specialized metabolites produced in the Solanaceae (nightshade family). Despite having simple constituents, these compounds are unusually structurally diverse. Their structural variations in phylogenetically closely related species enable comparative biochemical approaches to understand acylsugar biosynthesis and pathway diversification. Thus far, varied enzyme classes contributing to their synthesis were characterized in cultivated and wild tomatoes, including from core metabolism - isopropylmalate synthase (Leu) and invertase (carbon) - and a group of evolutionarily related BAHD acyltransferases known as acylsucrose acyltransferases. Gene duplication and neofunctionalization of these enzymes drove acylsugar diversification both within and beyond tomato. The broad set of evolutionary mechanisms underlying acylsugar diversity in Solanaceae make this metabolic network an exemplar for detailed understanding of the evolution of metabolic form and function.
Collapse
Affiliation(s)
- Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Bryan J Leong
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
10
|
Leong BJ, Lybrand DB, Lou YR, Fan P, Schilmiller AL, Last RL. Evolution of metabolic novelty: A trichome-expressed invertase creates specialized metabolic diversity in wild tomato. Sci Adv 2019; 5:eaaw3754. [PMID: 31032420 PMCID: PMC6482016 DOI: 10.1126/sciadv.aaw3754] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/06/2019] [Indexed: 05/19/2023]
Abstract
Plants produce a myriad of taxonomically restricted specialized metabolites. This diversity-and our ability to correlate genotype with phenotype-makes the evolution of these ecologically and medicinally important compounds interesting and experimentally tractable. Trichomes of tomato and other nightshade family plants produce structurally diverse protective compounds termed acylsugars. While cultivated tomato (Solanum lycopersicum) strictly accumulates acylsucroses, the South American wild relative Solanum pennellii produces copious amounts of acylglucoses. Genetic, transgenic, and biochemical dissection of the S. pennellii acylglucose biosynthetic pathway identified a trichome gland cell-expressed invertase-like enzyme that hydrolyzes acylsucroses (Sopen03g040490). This enzyme acts on the pyranose ring-acylated acylsucroses found in the wild tomato but not on the furanose ring-decorated acylsucroses of cultivated tomato. These results show that modification of the core acylsucrose biosynthetic pathway leading to loss of furanose ring acylation set the stage for co-option of a general metabolic enzyme to produce a new class of protective compounds.
Collapse
Affiliation(s)
- Bryan J. Leong
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Daniel B. Lybrand
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Anthony L. Schilmiller
- Mass Spectrometry and Metabolomics Core, Michigan State University, East Lansing, MI, USA
| | - Robert L. Last
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Corresponding author.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Zhou Y, Smith D, Leong BJ, Brännström K, Almqvist F, Chapman MR. Promiscuous cross-seeding between bacterial amyloids promotes interspecies biofilms. J Biol Chem 2012; 287:35092-35103. [PMID: 22891247 DOI: 10.1074/jbc.m112.383737] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amyloids are highly aggregated proteinaceous fibers historically associated with neurodegenerative conditions including Alzheimers, Parkinsons, and prion-based encephalopathies. Polymerization of amyloidogenic proteins into ordered fibers can be accelerated by preformed amyloid aggregates derived from the same protein in a process called seeding. Seeding of disease-associated amyloids and prions is highly specific and cross-seeding is usually limited or prevented. Here we describe the first study on the cross-seeding potential of bacterial functional amyloids. Curli are produced on the surface of many Gram-negative bacteria where they facilitate surface attachment and biofilm development. Curli fibers are composed of the major subunit CsgA and the nucleator CsgB, which templates CsgA into fibers. Our results showed that curli subunit homologs from Escherichia coli, Salmonella typhimurium LT2, and Citrobacter koseri were able to cross-seed in vitro. The polymerization of Escherichia coli CsgA was also accelerated by fibers derived from a distant homolog in Shewanella oneidensis that shares less than 30% identity in primary sequence. Cross-seeding of curli proteins was also observed in mixed colony biofilms with E. coli and S. typhimurium. CsgA was secreted from E. coli csgB- mutants assembled into fibers on adjacent S. typhimurium that presented CsgB on its surfaces. Similarly, CsgA was secreted by S. typhimurium csgB- mutants formed curli on CsgB-presenting E. coli. This interspecies curli assembly enhanced bacterial attachment to agar surfaces and supported pellicle biofilm formation. Collectively, this work suggests that the seeding specificity among curli homologs is relaxed and that heterogeneous curli fibers can facilitate multispecies biofilm development.
Collapse
Affiliation(s)
- Yizhou Zhou
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Daniel Smith
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Bryan J Leong
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048
| | | | - Fredrik Almqvist
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden; Umeå Center for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Matthew R Chapman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048; Umeå Center for Microbial Research, Umeå University, 901 87 Umeå, Sweden.
| |
Collapse
|