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Phansopa C, Dunning LT, Reid JD, Christin PA. Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry. Mol Biol Evol 2021; 37:3094-3104. [PMID: 32521019 PMCID: PMC7751175 DOI: 10.1093/molbev/msaa143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.
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Affiliation(s)
- Chatchawal Phansopa
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - James D Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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Nguyen GTT, Erlenkamp G, Jäck O, Küberl A, Bott M, Fiorani F, Gohlke H, Groth G. Chalcone-based Selective Inhibitors of a C4 Plant Key Enzyme as Novel Potential Herbicides. Sci Rep 2016; 6:27333. [PMID: 27263468 PMCID: PMC4893628 DOI: 10.1038/srep27333] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
Weeds are a challenge for global food production due to their rapidly evolving resistance against herbicides. We have identified chalcones as selective inhibitors of phosphoenolpyruvate carboxylase (PEPC), a key enzyme for carbon fixation and biomass increase in the C4 photosynthetic pathway of many of the world's most damaging weeds. In contrast, many of the most important crop plants use C3 photosynthesis. Here, we show that 2',3',4',3,4-Pentahydroxychalcone (IC50 = 600 nM) and 2',3',4'-Trihydroxychalcone (IC50 = 4.2 μM) are potent inhibitors of C4 PEPC but do not affect C3 PEPC at a same concentration range (selectivity factor: 15-45). Binding and modeling studies indicate that the active compounds bind at the same site as malate/aspartate, the natural feedback inhibitors of the C4 pathway. At the whole plant level, both substances showed pronounced growth-inhibitory effects on the C4 weed Amaranthus retroflexus, while there were no measurable effects on oilseed rape, a C3 plant. Growth of selected soil bacteria was not affected by these substances. Our chalcone compounds are the most potent and selective C4 PEPC inhibitors known to date. They offer a novel approach to combat C4 weeds based on a hitherto unexplored mode of allosteric inhibition of a C4 plant key enzyme.
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Affiliation(s)
- G. T. T. Nguyen
- Biochemical Plant Physiology, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - G. Erlenkamp
- Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - O. Jäck
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - A. Küberl
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - M. Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - F. Fiorani
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - H. Gohlke
- Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - G. Groth
- Biochemical Plant Physiology, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
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Aldous SH, Weise SE, Sharkey TD, Waldera-Lupa DM, Stühler K, Mallmann J, Groth G, Gowik U, Westhoff P, Arsova B. Evolution of the Phosphoenolpyruvate Carboxylase Protein Kinase Family in C3 and C4 Flaveria spp. PLANT PHYSIOLOGY 2014; 165:1076-1091. [PMID: 24850859 PMCID: PMC4081323 DOI: 10.1104/pp.114.240283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/20/2014] [Indexed: 05/04/2023]
Abstract
The key enzyme for C4 photosynthesis, Phosphoenolpyruvate Carboxylase (PEPC), evolved from nonphotosynthetic PEPC found in C3 ancestors. In all plants, PEPC is phosphorylated by Phosphoenolpyruvate Carboxylase Protein Kinase (PPCK). However, differences in the phosphorylation pattern exist among plants with these photosynthetic types, and it is still not clear if they are due to interspecies differences or depend on photosynthetic type. The genus Flaveria contains closely related C3, C3-C4 intermediate, and C4 species, which are evolutionarily young and thus well suited for comparative analysis. To characterize the evolutionary differences in PPCK between plants with C3 and C4 photosynthesis, transcriptome libraries from nine Flaveria spp. were used, and a two-member PPCK family (PPCKA and PPCKB) was identified. Sequence analysis identified a number of C3- and C4-specific residues with various occurrences in the intermediates. Quantitative analysis of transcriptome data revealed that PPCKA and PPCKB exhibit inverse diel expression patterns and that C3 and C4 Flaveria spp. differ in the expression levels of these genes. PPCKA has maximal expression levels during the day, whereas PPCKB has maximal expression during the night. Phosphorylation patterns of PEPC varied among C3 and C4 Flaveria spp. too, with PEPC from the C4 species being predominantly phosphorylated throughout the day, while in the C3 species the phosphorylation level was maintained during the entire 24 h. Since C4 Flaveria spp. evolved from C3 ancestors, this work links the evolutionary changes in sequence, PPCK expression, and phosphorylation pattern to an evolutionary phase shift of kinase activity from a C3 to a C4 mode.
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Affiliation(s)
- Sophia H Aldous
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Sean E Weise
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Thomas D Sharkey
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Daniel M Waldera-Lupa
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Kai Stühler
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Julia Mallmann
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Georg Groth
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Udo Gowik
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Peter Westhoff
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Borjana Arsova
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
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