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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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2
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Schlüter U, Bouvier JW, Guerreiro R, Malisic M, Kontny C, Westhoff P, Stich B, Weber APM. Brassicaceae display variation in efficiency of photorespiratory carbon-recapturing mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6631-6649. [PMID: 37392176 PMCID: PMC10662225 DOI: 10.1093/jxb/erad250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/30/2023] [Indexed: 07/03/2023]
Abstract
Carbon-concentrating mechanisms enhance the carboxylase efficiency of Rubisco by providing supra-atmospheric concentrations of CO2 in its surroundings. Beside the C4 photosynthesis pathway, carbon concentration can also be achieved by the photorespiratory glycine shuttle which requires fewer and less complex modifications. Plants displaying CO2 compensation points between 10 ppm and 40 ppm are often considered to utilize such a photorespiratory shuttle and are termed 'C3-C4 intermediates'. In the present study, we perform a physiological, biochemical, and anatomical survey of a large number of Brassicaceae species to better understand the C3-C4 intermediate phenotype, including its basic components and its plasticity. Our phylogenetic analysis suggested that C3-C4 metabolism evolved up to five times independently in the Brassicaceae. The efficiency of the pathway showed considerable variation. Centripetal accumulation of organelles in the bundle sheath was consistently observed in all C3-C4-classified taxa, indicating a crucial role for anatomical features in CO2-concentrating pathways. Leaf metabolite patterns were strongly influenced by the individual species, but accumulation of photorespiratory shuttle metabolites glycine and serine was generally observed. Analysis of phosphoenolpyruvate carboxylase activities suggested that C4-like shuttles have not evolved in the investigated Brassicaceae. Convergent evolution of the photorespiratory shuttle indicates that it represents a distinct photosynthesis type that is beneficial in some environments.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Jacques W Bouvier
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Ricardo Guerreiro
- Institute for Quantitative Genetics and Genomics of Plants, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Milena Malisic
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Carina Kontny
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Philipp Westhoff
- Metabolomics and Metabolism Laboratory, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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3
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Abstract
C4 photosynthesis evolved multiple times independently from ancestral C3 photosynthesis in a broad range of flowering land plant families and in both monocots and dicots. The evolution of C4 photosynthesis entails the recruitment of enzyme activities that are not involved in photosynthetic carbon fixation in C3 plants to photosynthesis. This requires a different regulation of gene expression as well as a different regulation of enzyme activities in comparison to the C3 context. Further, C4 photosynthesis relies on a distinct leaf anatomy that differs from that of C3, requiring a differential regulation of leaf development in C4. We summarize recent progress in the understanding of C4-specific features in evolution and metabolic regulation in the context of C4 photosynthesis.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
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Yorimitsu Y, Kadosono A, Hatakeyama Y, Yabiku T, Ueno O. Transition from C 3 to proto-Kranz to C 3-C 4 intermediate type in the genus Chenopodium (Chenopodiaceae). JOURNAL OF PLANT RESEARCH 2019; 132:839-855. [PMID: 31473860 PMCID: PMC7205854 DOI: 10.1007/s10265-019-01135-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/26/2019] [Indexed: 05/28/2023]
Abstract
The Chenopodiaceae is one of the families including C4 species among eudicots. In this family, the genus Chenopodium is considered to include only C3 species. However, we report here a transition from C3 photosynthesis to proto-Kranz to C3-C4 intermediate type in Chenopodium. We investigated leaf anatomical and photosynthetic traits of 15 species, of which 8 species showed non-Kranz anatomy and a CO2 compensation point (Γ) typical of C3 plants. However, 5 species showed proto-Kranz anatomy and a C3-like Γ, whereas C. strictum showed leaf anatomy and a Γ typical of C3-C4 intermediates. Chenopodium album accessions examined included both proto-Kranz and C3-C4 intermediate types, depending on locality. Glycine decarboxylase, a key photorespiratory enzyme that is involved in the decarboxylation of glycine, was located predominantly in the mesophyll (M) cells of C3 species, in both M and bundle-sheath (BS) cells in proto-Kranz species, and exclusively in BS cells in C3-C4 intermediate species. The M/BS tissue area ratio, number of chloroplasts and mitochondria per BS cell, distribution of these organelles to the centripetal region of BS cells, the degree of inner positioning (vacuolar side of chloroplasts) of mitochondria in M cells, and the size of BS mitochondria also changed with the change in glycine decarboxylase localization. All Chenopodium species examined were C3-like regarding activities and amounts of C3 and C4 photosynthetic enzymes and δ13C values, suggesting that these species perform photosynthesis without contribution of the C4 cycle. This study demonstrates that Chenopodium is not a C3 genus and is valuable for studying evolution of C3-C4 intermediates.
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Affiliation(s)
- Yuki Yorimitsu
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Aya Kadosono
- School of Agriculture, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuto Hatakeyama
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takayuki Yabiku
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Osamu Ueno
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
- School of Agriculture, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
- Faculty of Agriculture, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
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5
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Discriminating between C3, C4, and Mixed C3/C4 Pasture Grasses of a Grazed Landscape Using Multi-Temporal Sentinel-1a Data. REMOTE SENSING 2019. [DOI: 10.3390/rs11030253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In livestock grazing environments, the knowledge of C3/C4 species composition of a pasture field is invaluable, since such information assists graziers in making decisions around fertilizer application and stocking rates. The general aim of this research was to explore the potential of multi-temporal Sentinel-1 (S1) Synthetic Aperture Radar (SAR) to discriminate between C3, C4, and mixed-C3/C4 compositions. In this study, three Random Forest (RF) classification models were created using features derived from polarimetric SAR (polSAR) and grey-level co-occurrence textural metrics (glcmTEX). The first RF model involved only polSAR features and produced a prediction accuracy of 68% with a Kappa coefficient of 0.49. The second RF model used glcmTEX features and produced prediction accuracies of 76%, 62%, and 75% for C3, C4, and mixed C3/C4 grasses, respectively. The glcmTEX model achieved an overall prediction accuracy of 73% with a Kappa coefficient of 0.57. The polSAR and glcmTEX features were then combined (COMB model) to improve upon their individual classification performances. The COMB model produced prediction accuracies of 89%, 81%, and 84% for C3, C4, and mixed C3/C4 pasture grasses, and an overall prediction accuracy of 86% with a Kappa coefficient of 0.77. The contribution of the various model features could be attributed to the changes in dominant species between sampling sites through time, not only because of climatic variability but also because of preferential grazing.
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6
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Hatakeyama Y, Ueno O. Intracellular position of mitochondria in mesophyll cells differs between C 3 and C 4 grasses. JOURNAL OF PLANT RESEARCH 2017; 130:885-892. [PMID: 28434121 DOI: 10.1007/s10265-017-0947-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/06/2017] [Indexed: 06/07/2023]
Abstract
In C3 plants, part of the CO2 fixed during photosynthesis in chloroplasts is released from mitochondria during photorespiration by decarboxylation of glycine via glycine decarboxylase (GDC), thereby reducing photosynthetic efficiency. The apparent positioning of most mitochondria in the interior (vacuole side of chloroplasts) of mesophyll cells in C3 grasses would increase the efficiency of refixation of CO2 released from mitochondria by ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in chloroplasts. Therefore, in mesophyll cells of C4 grasses, which lack both GDC and Rubisco, the mitochondria ought not to be positioned the same way as in C3 mesophyll cells. To test this hypothesis, we investigated the intracellular position of mitochondria in mesophyll cells of 14 C4 grasses of different C4 subtypes and subfamilies (Chloridoideae, Micrairoideae, and Panicoideae) and a C3-C4 intermediate grass, Steinchisma hians, under an electron microscope. In C4 mesophyll cells, most mitochondria were positioned adjacent to the cell wall, which clearly differs from the positioning in C3 mesophyll cells. In S. hians mesophyll cells, the positioning was similar to that in C3 cells. These results suggest that the mitochondrial positioning in C4 mesophyll cells reflects the absence of both GDC and Rubisco in the mesophyll cells and the high activity of phosphoenolpyruvate carboxylase. In contrast, the relationship between the mitochondrial positioning and enzyme distribution in S. hians is complex, but the positioning may be related to the capture of respiratory CO2 by Rubisco. Our study provides new possible insight into the physiological role of mitochondrial positioning in photosynthetic cells.
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Affiliation(s)
- Yuto Hatakeyama
- Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Hakozaki 6-10-1, Fukuoka, 812-8581, Japan
- NARO Kyushu Okinawa Agricultural Research Center, Chikugoshi, Fukuoka, 833-0027, Japan
| | - Osamu Ueno
- Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Hakozaki 6-10-1, Fukuoka, 812-8581, Japan.
- Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka, 812-8581, Japan.
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7
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Kadereit G, Bohley K, Lauterbach M, Tefarikis DT, Kadereit JW. C 3 -C 4 intermediates may be of hybrid origin - a reminder. THE NEW PHYTOLOGIST 2017; 215:70-76. [PMID: 28397963 DOI: 10.1111/nph.14567] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/02/2017] [Indexed: 05/09/2023]
Abstract
The currently favoured model of the evolution of C4 photosynthesis relies heavily on the interpretation of the broad phenotypic range of naturally growing C3 -C4 intermediates as proxies for evolutionary intermediate steps. On the other hand, C3 -C4 intermediates had earlier been interpreted as hybrids or hybrid derivates. By first comparing experimentally generated with naturally growing C3 -C4 intermediates, and second summarising either direct or circumstantial evidence for hybridisation in lineages comprising C3 , C4 and C3 -C4 intermediates, we conclude that a possible hybrid origin of C3 -C4 intermediates deserves careful examination. While we acknowledge that the current model of C4 photosynthesis evolution is clearly the best available, C3 -C4 intermediates of hybrid origin, if existing, should not be used for further analysis of this model. However, experimental C3 × C4 hybrids potentially are excellent systems to analyse the genetic differences between C3 and C4 species and, also using segregating progeny, to study the relationship between individual photosynthetic traits and environmental factors.
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Affiliation(s)
- Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Katharina Bohley
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Maximilian Lauterbach
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Delphine T Tefarikis
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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8
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Schlüter U, Bräutigam A, Gowik U, Melzer M, Christin PA, Kurz S, Mettler-Altmann T, Weber AP. Photosynthesis in C3-C4 intermediate Moricandia species. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:191-206. [PMID: 28110276 PMCID: PMC5853546 DOI: 10.1093/jxb/erw391] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 09/29/2016] [Indexed: 05/09/2023]
Abstract
Evolution of C4 photosynthesis is not distributed evenly in the plant kingdom. Particularly interesting is the situation in the Brassicaceae, because the family contains no C4 species, but several C3-C4 intermediates, mainly in the genus Moricandia Investigation of leaf anatomy, gas exchange parameters, the metabolome, and the transcriptome of two C3-C4 intermediate Moricandia species, M. arvensis and M. suffruticosa, and their close C3 relative M. moricandioides enabled us to unravel the specific C3-C4 characteristics in these Moricandia lines. Reduced CO2 compensation points in these lines were accompanied by anatomical adjustments, such as centripetal concentration of organelles in the bundle sheath, and metabolic adjustments, such as the balancing of C and N metabolism between mesophyll and bundle sheath cells by multiple pathways. Evolution from C3 to C3-C4 intermediacy was probably facilitated first by loss of one copy of the glycine decarboxylase P-protein, followed by dominant activity of a bundle sheath-specific element in its promoter. In contrast to recent models, installation of the C3-C4 pathway was not accompanied by enhanced activity of the C4 cycle. Our results indicate that metabolic limitations connected to N metabolism or anatomical limitations connected to vein density could have constrained evolution of C4 in Moricandia.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
- Network Analysis and Modelling, Leibniz Institute of Plant Genetics and Crop Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Michael Melzer
- Structural Cell Biology, Leibniz Institute of Plant Genetics and Crop Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Samantha Kurz
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Andreas Pm Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
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9
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Schlüter U, Weber APM. The Road to C4 Photosynthesis: Evolution of a Complex Trait via Intermediary States. PLANT & CELL PHYSIOLOGY 2016; 57:881-9. [PMID: 26893471 DOI: 10.1093/pcp/pcw009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/05/2016] [Indexed: 05/09/2023]
Abstract
C4 photosynthesis enables high photosynthetic energy conversion efficiency as well as high nitrogen and water use efficiencies. Given the multitude of biochemical, structural and molecular changes in comparison with C3 photosynthesis, it appears unlikely that such a complex trait would evolve in a single step. C4 photosynthesis is therefore believed to have evolved from the ancestral C3 state via intermediary stages. Consequently, the identification and detailed characterization of plant species representing transitory states between C3 and C4 is important for the reconstruction of the sequence of evolutionary events, especially since C4 evolution occurred in very different phylogenetic backgrounds. There is also significant interest in engineering of C4 or at least C4-like elements into C3 crop plants. A detailed and mechanistic understanding of C3-C4 intermediates is likely to provide guidance for the experimental design of such approaches. Here we provide an overview on the most relevant results obtained on C3-C4 intermediates to date. Recent knowledge gains in this field will be described in more detail. We thereby concentrate especially on biochemical and physiological work. Finally, we will provide a perspective and outlook on the continued importance of research on C3-C4 intermediates.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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10
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Souza GM, Lüttge U. Stability as a Phenomenon Emergent from Plasticity–Complexity–Diversity in Eco-physiology. PROGRESS IN BOTANY 2015. [DOI: 10.1007/978-3-319-08807-5_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Chi S, Wu S, Yu J, Wang X, Tang X, Liu T. Phylogeny of C4-photosynthesis enzymes based on algal transcriptomic and genomic data supports an archaeal/proteobacterial origin and multiple duplication for most C4-related genes. PLoS One 2014; 9:e110154. [PMID: 25313828 PMCID: PMC4196954 DOI: 10.1371/journal.pone.0110154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 09/15/2014] [Indexed: 12/02/2022] Open
Abstract
Both Calvin-Benson-Bassham (C3) and Hatch-Slack (C4) cycles are most important autotrophic CO2 fixation pathways on today’s Earth. C3 cycle is believed to be originated from cyanobacterial endosymbiosis. However, studies on evolution of different biochemical variants of C4 photosynthesis are limited to tracheophytes and origins of C4-cycle genes are not clear till now. Our comprehensive analyses on bioinformatics and phylogenetics of novel transcriptomic sequencing data of 21 rhodophytes and 19 Phaeophyceae marine species and public genomic data of more algae, tracheophytes, cyanobacteria, proteobacteria and archaea revealed the origin and evolution of C4 cycle-related genes. Almost all of C4-related genes were annotated in extensive algal lineages with proteobacterial or archaeal origins, except for phosphoenolpyruvate carboxykinase (PCK) and aspartate aminotransferase (AST) with both cyanobacterial and archaeal/proteobacterial origin. Notably, cyanobacteria may not possess complete C4 pathway because of the flawed annotation of pyruvate orthophosphate dikinase (PPDK) genes in public data. Most C4 cycle-related genes endured duplication and gave rise to functional differentiation and adaptation in different algal lineages. C4-related genes of NAD-ME (NAD-malic enzyme) and PCK subtypes exist in most algae and may be primitive ones, while NADP-ME (NADP-malic enzyme) subtype genes might evolve from NAD-ME subtype by gene duplication in chlorophytes and tracheophytes.
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Affiliation(s)
- Shan Chi
- Ocean University of China, Qingdao, Shandong Province, People’s Republic of China
| | - Shuangxiu Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (XW); (TL)
| | - Xuexi Tang
- Ocean University of China, Qingdao, Shandong Province, People’s Republic of China
| | - Tao Liu
- Ocean University of China, Qingdao, Shandong Province, People’s Republic of China
- * E-mail: (XW); (TL)
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12
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Sage TL, Busch FA, Johnson DC, Friesen PC, Stinson CR, Stata M, Sultmanis S, Rahman BA, Rawsthorne S, Sage RF. Initial events during the evolution of C4 photosynthesis in C3 species of Flaveria. PLANT PHYSIOLOGY 2013; 163:1266-76. [PMID: 24064930 PMCID: PMC3813649 DOI: 10.1104/pp.113.221119] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/13/2013] [Indexed: 05/22/2023]
Abstract
The evolution of C4 photosynthesis in many taxa involves the establishment of a two-celled photorespiratory CO2 pump, termed C2 photosynthesis. How C3 species evolved C2 metabolism is critical to understanding the initial phases of C4 plant evolution. To evaluate early events in C4 evolution, we compared leaf anatomy, ultrastructure, and gas-exchange responses of closely related C3 and C2 species of Flaveria, a model genus for C4 evolution. We hypothesized that Flaveria pringlei and Flaveria robusta, two C3 species that are most closely related to the C2 Flaveria species, would show rudimentary characteristics of C2 physiology. Compared with less-related C3 species, bundle sheath (BS) cells of F. pringlei and F. robusta had more mitochondria and chloroplasts, larger mitochondria, and proportionally more of these organelles located along the inner cell periphery. These patterns were similar, although generally less in magnitude, than those observed in the C2 species Flaveria angustifolia and Flaveria sonorensis. In F. pringlei and F. robusta, the CO2 compensation point of photosynthesis was slightly lower than in the less-related C3 species, indicating an increase in photosynthetic efficiency. This could occur because of enhanced refixation of photorespired CO2 by the centripetally positioned organelles in the BS cells. If the phylogenetic positions of F. pringlei and F. robusta reflect ancestral states, these results support a hypothesis that increased numbers of centripetally located organelles initiated a metabolic scavenging of photorespired CO2 within the BS. This could have facilitated the formation of a glycine shuttle between mesophyll and BS cells that characterizes C2 photosynthesis.
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Affiliation(s)
| | | | - Daniel C. Johnson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
| | - Patrick C. Friesen
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
| | - Corey R. Stinson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
| | - Stefanie Sultmanis
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
| | - Beshar A. Rahman
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
| | - Stephen Rawsthorne
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
| | - Rowan F. Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada (T.L.S., F.A.B., D.C.J., P.C.F., C.R.S., M.S., S.S., B.A.R., R.F.S.); and
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (S.R.)
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13
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Karki S, Rizal G, Quick WP. Improvement of photosynthesis in rice (Oryza sativa L.) by inserting the C4 pathway. RICE (NEW YORK, N.Y.) 2013; 6:28. [PMID: 24280149 PMCID: PMC4883725 DOI: 10.1186/1939-8433-6-28] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/12/2013] [Indexed: 05/08/2023]
Abstract
To boost food production for a rapidly growing global population, crop yields must significantly increase. One of the avenues being recently explored is the improvement of photosynthetic capacity by installing the C4 photosynthetic pathway into C3 crops like rice to drastically increase their yield. Crops with an enhanced photosynthetic mechanism would better utilize the solar radiation that can be translated into yield. This subsequently will help in producing more grain yield, reduce water loss and increase nitrogen use efficiency especially in hot and dry environments. This review provides a summary of the factors that need to be modified in rice so that the C4 pathway can be introduced successfully. It also discusses the differences between the C3 and C4 photosynthetic pathways in terms of anatomy, biochemistry and genetics.
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Affiliation(s)
- Shanta Karki
- />C4 Rice Center, International Rice Research Institute, Los Banos, Laguna Philippines
| | - Govinda Rizal
- />C4 Rice Center, International Rice Research Institute, Los Banos, Laguna Philippines
| | - William Paul Quick
- />C4 Rice Center, International Rice Research Institute, Los Banos, Laguna Philippines
- />Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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14
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Xu J, Zhang X, Ye N, Zheng Z, Mou S, Dong M, Xu D, Miao J. Activities of principal photosynthetic enzymes in green macroalga Ulva linza: functional implication of C₄ pathway in CO₂ assimilation. SCIENCE CHINA-LIFE SCIENCES 2013; 56:571-80. [PMID: 23737004 DOI: 10.1007/s11427-013-4489-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 04/19/2013] [Indexed: 11/25/2022]
Abstract
The green-tide-forming macroalga Ulva linza was profiled by transcriptome sequencing to ascertain whether the alga carries both C3 and C4 photosynthesis genes. The key enzymes involved in C4 metabolism including pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxylase (PEPC), and phosphoenolpyruvate carboxykinase (PCK) were found. When measured under normal and different stress conditions, expression of rbcL was higher under normal conditions and lower under the adverse conditions, whereas that of PPDK was higher under some adverse conditions, namely desiccation, high salinity, and low salinity. Both ribulose-1, 5-biphosphate carboxylase (RuBPCase) and PPDK were found to play a role in carbon fixation, with significantly higher PPDK activity across the stress conditions. These results suggest that elevated PPDK activity alters carbon metabolism in U. linza leading to partial operation of the C4 carbon metabolism, a pathway that, under stress conditions, probably contributes to the hardy character of U. linza and thus to its wide distribution.
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Affiliation(s)
- Jianfang Xu
- Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China
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15
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Leegood RC. Strategies for engineering C(4) photosynthesis. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:378-388. [PMID: 23245935 DOI: 10.1016/j.jplph.2012.10.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/30/2012] [Accepted: 10/30/2012] [Indexed: 06/01/2023]
Abstract
C(3) photosynthesis is an inefficient process, because the enzyme that lies at the heart of the Benson-Calvin cycle, ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco) is itself a very inefficient enzyme. The oxygenase activity of Rubisco is an unavoidable side reaction that is a consequence of its reaction mechanism. The product of oxygenation, glycollate 2-P, has to be retrieved by photorespiration, a process which results in the loss of a quarter of the carbon that was originally present in glycollate 2-P. Photorespiration therefore reduces carbon gain. Purely in terms of carbon economy, there is, therefore, a strong selection pressure on plants to reduce the rate of photorespiration so as to increase carbon gain, but it also improves water- and nitrogen-use efficiency. Possibilities for the manipulation of plants to decrease the amount of photorespiration include the introduction of improved Rubisco from other species, reconfiguring photorespiration, or introducing carbon-concentrating mechanisms, such as inorganic carbon transporters, carboxysomes or pyrenoids, or engineering a full C(4) Kranz pathway using the existing evolutionary progression in C(3)-C(4) intermediates as a blueprint. Possible routes and progress to suppressing photorespiration by introducing C(4) photosynthesis in C(3) crop plants will be discussed, including whether single cell C(4) photosynthesis is feasible, how the evolution of C(3)-C(4) intermediates can be used as a blueprint for engineering C(4) photosynthesis, which pathway for the C(4) cycle might be introduced and the extent to which processes and structures in C(3) plant might require optimisation.
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Affiliation(s)
- Richard C Leegood
- Robert Hill Institute and Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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16
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Xu J, Fan X, Zhang X, Xu D, Mou S, Cao S, Zheng Z, Miao J, Ye N. Evidence of coexistence of C₃ and C₄ photosynthetic pathways in a green-tide-forming alga, Ulva prolifera. PLoS One 2012; 7:e37438. [PMID: 22616009 PMCID: PMC3353924 DOI: 10.1371/journal.pone.0037438] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/22/2012] [Indexed: 11/19/2022] Open
Abstract
Ulva prolifera, a typical green-tide-forming alga, can accumulate a large biomass in a relatively short time period, suggesting that photosynthesis in this organism, particularly its carbon fixation pathway, must be very efficient. Green algae are known to generally perform C₃ photosynthesis, but recent metabolic labeling and genome sequencing data suggest that they may also perform C₄ photosynthesis, so C₄ photosynthesis might be more wide-spread than previously anticipated. Both C₃ and C₄ photosynthesis genes were found in U. prolifera by transcriptome sequencing. We also discovered the key enzymes of C₄ metabolism based on functional analysis, such as pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxylase (PEPC), and phosphoenolpyruvate carboxykinase (PCK). To investigate whether the alga operates a C₄-like pathway, the expression of rbcL and PPDK and their enzyme activities were measured under various forms and intensities of stress (differing levels of salinity, light intensity, and temperature). The expression of rbcL and PPDK and their enzyme activities were higher under adverse circumstances. However, under conditions of desiccation, the expression of rbcL and ribulose-1, 5-biphosphate carboxylase (RuBPCase) activity was lower, whereas that of PPDK was higher. These results suggest that elevated PPDK activity may alter carbon metabolism and lead to a partial operation of C₄-type carbon metabolism in U. prolifera, probably contributing to its wide distribution and massive, repeated blooms in the Yellow Sea.
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Affiliation(s)
- Jianfang Xu
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Shanli Mou
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Shaona Cao
- Qingdao Agricultural University, Qingdao, China
| | - Zhou Zheng
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Jinlai Miao
- Key Laboratory of Marine Bioactive substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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