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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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2
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Tang Q, Huang Y, Ni X, Lyu MJA, Chen G, Sage R, Zhu XG. Increased α-ketoglutarate links the C3-C4 intermediate state to C4 photosynthesis in the genus Flaveria. PLANT PHYSIOLOGY 2024; 195:291-305. [PMID: 38377473 DOI: 10.1093/plphys/kiae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 02/22/2024]
Abstract
As a complex trait, C4 photosynthesis has multiple independent origins in evolution. Phylogenetic evidence and theoretical analysis suggest that C2 photosynthesis, which is driven by glycine decarboxylation in the bundle sheath cell, may function as a bridge from C3 to C4 photosynthesis. However, the exact molecular mechanism underlying the transition between C2 photosynthesis to C4 photosynthesis remains elusive. Here, we provide evidence suggesting a role of higher α-ketoglutarate (AKG) concentration during this transition. Metabolomic data of 12 Flaveria species, including multiple photosynthetic types, show that AKG concentration initially increased in the C3-C4 intermediate with a further increase in C4 species. Petiole feeding of AKG increases the concentrations of C4-related metabolites in C3-C4 and C4 species but not the activity of C4-related enzymes. Sequence analysis shows that glutamate synthase (Fd-GOGAT), which catalyzes the generation of glutamate using AKG, was under strong positive selection during the evolution of C4 photosynthesis. Simulations with a constraint-based model for C3-C4 intermediate further show that decreasing the activity of Fd-GOGAT facilitated the transition from a C2-dominant to a C4-dominant CO2 concentrating mechanism. All these results provide insight into the mechanistic switch from C3-C4 intermediate to C4 photosynthesis.
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Affiliation(s)
- Qiming Tang
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Yuhui Huang
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Xiaoxiang Ni
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Ming-Ju Amy Lyu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Genyun Chen
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Rowan Sage
- Department of Ecology and Evolution, The University of Toronto, Toronto, Ontario M5S3B2, Canada
| | - Xin-Guang Zhu
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
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Carpenter AC, Feist AM, Harrison FS, Paulsen IT, Williams TC. Have you tried turning it off and on again? Oscillating selection to enhance fitness-landscape traversal in adaptive laboratory evolution experiments. Metab Eng Commun 2023; 17:e00227. [PMID: 37538933 PMCID: PMC10393799 DOI: 10.1016/j.mec.2023.e00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/05/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023] Open
Abstract
Adaptive Laboratory Evolution (ALE) is a powerful tool for engineering and understanding microbial physiology. ALE relies on the selection and enrichment of mutations that enable survival or faster growth under a selective condition imposed by the experimental setup. Phenotypic fitness landscapes are often underpinned by complex genotypes involving multiple genes, with combinatorial positive and negative effects on fitness. Such genotype relationships result in mutational fitness landscapes with multiple local fitness maxima and valleys. Traversing local maxima to find a global maximum often requires an individual or sub-population of cells to traverse fitness valleys. Traversing involves gaining mutations that are not adaptive for a given local maximum but are necessary to 'peak shift' to another local maximum, or eventually a global maximum. Despite these relatively well understood evolutionary principles, and the combinatorial genotypes that underlie most metabolic phenotypes, the majority of applied ALE experiments are conducted using constant selection pressures. The use of constant pressure can result in populations becoming trapped within local maxima, and often precludes the attainment of optimum phenotypes associated with global maxima. Here, we argue that oscillating selection pressures is an easily accessible mechanism for traversing fitness landscapes in ALE experiments, and provide theoretical and practical frameworks for implementation.
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Affiliation(s)
- Alexander C. Carpenter
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
| | - Adam M. Feist
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Fergus S.M. Harrison
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
| | - Thomas C. Williams
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
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Sage RF, Edwards EJ, Heyduk K, Cushman JC. Crassulacean acid metabolism (CAM) at the crossroads: a special issue to honour 50 years of CAM research by Klaus Winter. ANNALS OF BOTANY 2023; 132:553-561. [PMID: 37856823 PMCID: PMC10799977 DOI: 10.1093/aob/mcad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Affiliation(s)
- Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5R3C6, Canada
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada–Reno, Reno, NV 89557, USA
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Sage RF, Gilman IS, Smith JAC, Silvera K, Edwards EJ. Atmospheric CO2 decline and the timing of CAM plant evolution. ANNALS OF BOTANY 2023; 132:753-770. [PMID: 37642245 PMCID: PMC10799994 DOI: 10.1093/aob/mcad122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/19/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS CAM photosynthesis is hypothesized to have evolved in atmospheres of low CO2 concentration in recent geological time because of its ability to concentrate CO2 around Rubisco and boost water use efficiency relative to C3 photosynthesis. We assess this hypothesis by compiling estimates of when CAM clades arose using phylogenetic chronograms for 73 CAM clades. We further consider evidence of how atmospheric CO2 affects CAM relative to C3 photosynthesis. RESULTS Where CAM origins can be inferred, strong CAM is estimated to have appeared in the past 30 million years in 46 of 48 examined clades, after atmospheric CO2 had declined from high (near 800 ppm) to lower (<450 ppm) values. In turn, 21 of 25 clades containing CAM species (but where CAM origins are less certain) also arose in the past 30 million years. In these clades, CAM is probably younger than the clade origin. We found evidence for repeated weak CAM evolution during the higher CO2 conditions before 30 million years ago, and possible strong CAM origins in the Crassulaceae during the Cretaceous period prior to atmospheric CO2 decline. Most CAM-specific clades arose in the past 15 million years, in a similar pattern observed for origins of C4 clades. CONCLUSIONS The evidence indicates strong CAM repeatedly evolved in reduced CO2 conditions of the past 30 million years. Weaker CAM can pre-date low CO2 and, in the Crassulaceae, strong CAM may also have arisen in water-limited microsites under relatively high CO2. Experimental evidence from extant CAM species demonstrates that elevated CO2 reduces the importance of nocturnal CO2 fixation by increasing the contribution of C3 photosynthesis to daily carbon gain. Thus, the advantage of strong CAM would be reduced in high CO2, such that its evolution appears less likely and restricted to more extreme environments than possible in low CO2.
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Affiliation(s)
- Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - J Andrew C Smith
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Katia Silvera
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
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Edwards EJ. Reconciling continuous and discrete models of C4 and CAM evolution. ANNALS OF BOTANY 2023; 132:717-725. [PMID: 37675944 PMCID: PMC10799980 DOI: 10.1093/aob/mcad125] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/11/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND A current argument in the CAM biology literature has focused on the nature of the CAM evolutionary trajectory: whether there is a smooth continuum of phenotypes between plants with C3 and CAM photosynthesis or whether there are discrete steps of phenotypic evolutionary change such as has been modelled for the evolution of C4 photosynthesis. A further implication is that a smooth continuum would increase the evolvability of CAM, whereas discrete changes would make the evolutionary transition from C3 to CAM more difficult. SCOPE In this essay, I attempt to reconcile these two viewpoints, because I think in many ways this is a false dichotomy that is constraining progress in understanding how both CAM and C4 evolved. In reality, the phenotypic space connecting C3 species and strong CAM/C4 species is both a continuum of variably expressed quantitative traits and yet also contains certain combinations of traits that we are able to identify as discrete, recognizable phenotypes. In this sense, the evolutionary mechanics of CAM origination are no different from those of C4 photosynthesis, nor from the evolution of any other complex trait assemblage. CONCLUSIONS To make progress, we must embrace the concept of discrete phenotypic phases of CAM evolution, because their delineation will force us to articulate what aspects of phenotypic variation we think are significant. There are some current phenotypic gaps that are limiting our ability to build a complete CAM evolutionary model: the first is how a rudimentary CAM biochemical cycle becomes established, and the second is how the 'accessory' CAM cycle in C3+CAM plants is recruited into a primary metabolism. The connections to the C3 phenotype we are looking for are potentially found in the behaviour of C3 plants when undergoing physiological stress - behaviour that, strangely enough, remains essentially unexplored in this context.
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Affiliation(s)
- Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
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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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Alenazi AS, Bianconi ME, Middlemiss E, Milenkovic V, Curran EV, Sotelo G, Lundgren MR, Nyirenda F, Pereira L, Christin PA, Dunning LT, Osborne CP. Leaf anatomy explains the strength of C 4 activity within the grass species Alloteropsis semialata. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37184423 DOI: 10.1111/pce.14607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/23/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Abstract
C4 photosynthesis results from anatomical and biochemical characteristics that together concentrate CO2 around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), increasing productivity in warm conditions. This complex trait evolved through the gradual accumulation of components, and particular species possess only some of these, resulting in weak C4 activity. The consequences of adding C4 components have been modelled and investigated through comparative approaches, but the intraspecific dynamics responsible for strengthening the C4 pathway remain largely unexplored. Here, we evaluate the link between anatomical variation and C4 activity, focusing on populations of the photosynthetically diverse grass Alloteropsis semialata that fix various proportions of carbon via the C4 cycle. The carbon isotope ratios in these populations range from values typical of C3 to those typical of C4 plants. This variation is statistically explained by a combination of leaf anatomical traits linked to the preponderance of bundle sheath tissue. We hypothesize that increased investment in bundle sheath boosts the strength of the intercellular C4 pump and shifts the balance of carbon acquisition towards the C4 cycle. Carbon isotope ratios indicating a stronger C4 pathway are associated with warmer, drier environments, suggesting that incremental anatomical alterations can lead to the emergence of C4 physiology during local adaptation within metapopulations.
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Affiliation(s)
- Ahmed S Alenazi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Biological Sciences, Northern Border University, Arar, Saudi Arabia
| | - Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Ella Middlemiss
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Emma V Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Marjorie R Lundgren
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
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Zhou H, Akçay E, Helliker B. Optimal coordination and reorganization of photosynthetic properties in C 4 grasses. PLANT, CELL & ENVIRONMENT 2023; 46:796-811. [PMID: 36478594 DOI: 10.1111/pce.14506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Each of >20 independent evolutions of C4 photosynthesis in grasses required reorganization of the Calvin-Benson-cycle (CB-cycle) within the leaf, along with coordination of C4 -cycle enzymes with the CB-cycle to maximize CO2 assimilation. Considering the vast amount of time over which C4 evolved, we hypothesized (i) trait divergences exist within and across lineages with both C4 and closely related C3 grasses, (ii) trends in traits after C4 evolution yield the optimization of C4 through time, and (iii) the presence/absence of trends in coordination between the CB-cycle and C4 -cycle provides information on the strength of selection. To address these hypotheses, we used a combination of optimality modelling, physiological measurements and phylogenetic-comparative-analysis. Photosynthesis was optimized after the evolution of C4 causing diversification in maximal assimilation, electron transport, Rubisco carboxylation, phosphoenolpyruvate carboxylase and chlorophyll within C4 lineages. Both theory and measurements indicated a higher light-reaction to CB-cycle ratio (Jatpmax /Vcmax ) in C4 than C3 . There were no evolutionary trends with photosynthetic coordination between the CB-cycle, light reactions and the C4 -cycle, suggesting strong initial selection for coordination. The coordination of CB-C4 -cycles (Vpmax /Vcmax ) was optimal for CO2 of 200 ppm, not to current conditions. Our model indicated that a higher than optimal Vpmax /Vcmax affects assimilation minimally, thus lessening recent selection to decrease Vpmax /Vcmax .
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Affiliation(s)
- Haoran Zhou
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
- School of the Environment, Yale University, New Haven, Connecticut, USA
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brent Helliker
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Prochetto S, Studer AJ, Reinheimer R. De novo transcriptome assemblies of C 3 and C 4 non-model grass species reveal key differences in leaf development. BMC Genomics 2023; 24:64. [PMID: 36747121 PMCID: PMC9901097 DOI: 10.1186/s12864-022-08995-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 11/06/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND C4 photosynthesis is a mechanism that plants have evolved to reduce the rate of photorespiration during the carbon fixation process. The C4 pathway allows plants to adapt to high temperatures and light while more efficiently using resources, such as water and nitrogen. Despite decades of studies, the evolution of the C4 pathway from a C3 ancestor remains a biological enigma. Interestingly, species with C3-C4 intermediates photosynthesis are usually found closely related to the C4 lineages. Indeed, current models indicate that the assembly of C4 photosynthesis was a gradual process that included the relocalization of photorespiratory enzymes, and the establishment of intermediate photosynthesis subtypes. More than a third of the C4 origins occurred within the grass family (Poaceae). In particular, the Otachyriinae subtribe (Paspaleae tribe) includes 35 American species from C3, C4, and intermediates taxa making it an interesting lineage to answer questions about the evolution of photosynthesis. RESULTS To explore the molecular mechanisms that underpin the evolution of C4 photosynthesis, the transcriptomic dynamics along four different leaf segments, that capture different stages of development, were compared among Otachyriinae non-model species. For this, leaf transcriptomes were sequenced, de novo assembled, and annotated. Gene expression patterns of key pathways along the leaf segments showed distinct differences between photosynthetic subtypes. In addition, genes associated with photorespiration and the C4 cycle were differentially expressed between C4 and C3 species, but their expression patterns were well preserved throughout leaf development. CONCLUSIONS New, high-confidence, protein-coding leaf transcriptomes were generated using high-throughput short-read sequencing. These transcriptomes expand what is currently known about gene expression in leaves of non-model grass species. We found conserved expression patterns of C4 cycle and photorespiratory genes among C3, intermediate, and C4 species, suggesting a prerequisite for the evolution of C4 photosynthesis. This dataset represents a valuable contribution to the existing genomic resources and provides new tools for future investigation of photosynthesis evolution.
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Affiliation(s)
- Santiago Prochetto
- grid.10798.370000 0001 2172 9456Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe, Argentina
| | - Anthony J. Studer
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, University of Illinois, 1201 West Gregory Drive, Edward R. Madigan Laboratory #289, Urbana, IL 61801 USA
| | - Renata Reinheimer
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, FCA, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe, Argentina.
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11
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Amy Lyu MJ, Tang Q, Wang Y, Essemine J, Chen F, Ni X, Chen G, Zhu XG. Evolution of gene regulatory network of C 4 photosynthesis in the genus Flaveria reveals the evolutionary status of C 3-C 4 intermediate species. PLANT COMMUNICATIONS 2023; 4:100426. [PMID: 35986514 PMCID: PMC9860191 DOI: 10.1016/j.xplc.2022.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/16/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
C4 photosynthesis evolved from ancestral C3 photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4 metabolic pathway have been intensively studied and well documented; however, the transcription factors (TFs) that regulate these C4 metabolic genes are not yet well understood. In particular, how the TF regulatory network of C4 metabolic genes was rewired during the evolutionary process is unclear. Here, we constructed gene regulatory networks (GRNs) for four closely evolutionarily related species from the genus Flaveria, which represent four different evolutionary stages of C4 photosynthesis: C3 (F. robusta), type I C3-C4 (F. sonorensis), type II C3-C4 (F. ramosissima), and C4 (F. trinervia). Our results show that more than half of the co-regulatory relationships between TFs and core C4 metabolic genes are species specific. The counterparts of the C4 genes in C3 species were already co-regulated with photosynthesis-related genes, whereas the required TFs for C4 photosynthesis were recruited later. The TFs involved in C4 photosynthesis were widely recruited in the type I C3-C4 species; nevertheless, type II C3-C4 species showed a divergent GRN from C4 species. In line with these findings, a 13CO2 pulse-labeling experiment showed that the CO2 initially fixed into C4 acid was not directly released to the Calvin-Benson-Bassham cycle in the type II C3-C4 species. Therefore, our study uncovered dynamic changes in C4 genes and TF co-regulation during the evolutionary process; furthermore, we showed that the metabolic pathway of the type II C3-C4 species F. ramosissima represents an alternative evolutionary solution to the ammonia imbalance in C3-C4 intermediate species.
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Affiliation(s)
- Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiming Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Yanjie Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Jemaa Essemine
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Faming Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxiang Ni
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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12
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Adachi S, Stata M, Martin DG, Cheng S, Liu H, Zhu XG, Sage RF. The Evolution of C4 Photosynthesis in Flaveria (Asteraceae): Insights from the Flaveria linearis Complex. PLANT PHYSIOLOGY 2023; 191:233-251. [PMID: 36200882 PMCID: PMC9806627 DOI: 10.1093/plphys/kiac467] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Flaveria is a leading model for C4 plant evolution due to the presence of a dozen C3-C4 intermediate species, many of which are associated with a phylogenetic complex centered around Flaveria linearis. To investigate C4 evolution in Flaveria, we updated the Flaveria phylogeny and evaluated gas exchange, starch δ13C, and activity of C4 cycle enzymes in 19 Flaveria species and 28 populations within the F. linearis complex. A principal component analysis identified six functional clusters: (1) C3, (2) sub-C2, (3) full C2, (4) enriched C2, (5) sub-C4, and (6) fully C4 species. The sub-C2 species lacked a functional C4 cycle, while a gradient was present in the C2 clusters from little to modest C4 cycle activity as indicated by δ13C and enzyme activities. Three Yucatan populations of F. linearis had photosynthetic CO2 compensation points equivalent to C4 plants but showed little evidence for an enhanced C4 cycle, indicating they have an optimized C2 pathway that recaptures all photorespired CO2 in the bundle sheath (BS) tissue. All C2 species had enhanced aspartate aminotransferase activity relative to C3 species and most had enhanced alanine aminotransferase activity. These aminotransferases form aspartate and alanine from glutamate and in doing so could help return photorespiratory nitrogen (N) from BS to mesophyll cells, preventing glutamate feedback onto photorespiratory N assimilation. Their use requires upregulation of parts of the C4 metabolic cycle to generate carbon skeletons to sustain N return to the mesophyll, and thus could facilitate the evolution of the full C4 photosynthetic pathway.
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Affiliation(s)
- Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Matt Stata
- Department of Ecology and Evolution, The University of Toronto, Toronto, Ontario M5S3B2, Canada
| | - Duncan G Martin
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongbing Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xin-Guang Zhu
- Center of Excellence for Molecular Plant Sciences, Institute for Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032 China
| | - Rowan F Sage
- Department of Ecology and Evolution, The University of Toronto, Toronto, Ontario M5S3B2, Canada
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13
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Riaz A, Deng F, Chen G, Jiang W, Zheng Q, Riaz B, Mak M, Zeng F, Chen ZH. Molecular Regulation and Evolution of Redox Homeostasis in Photosynthetic Machinery. Antioxidants (Basel) 2022; 11:antiox11112085. [PMID: 36358456 PMCID: PMC9686623 DOI: 10.3390/antiox11112085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 01/14/2023] Open
Abstract
The recent advances in plant biology have significantly improved our understanding of reactive oxygen species (ROS) as signaling molecules in the redox regulation of complex cellular processes. In plants, free radicals and non-radicals are prevalent intra- and inter-cellular ROS, catalyzing complex metabolic processes such as photosynthesis. Photosynthesis homeostasis is maintained by thiol-based systems and antioxidative enzymes, which belong to some of the evolutionarily conserved protein families. The molecular and biological functions of redox regulation in photosynthesis are usually to balance the electron transport chain, photosystem II, photosystem I, mesophyll and bundle sheath signaling, and photo-protection regulating plant growth and productivity. Here, we review the recent progress of ROS signaling in photosynthesis. We present a comprehensive comparative bioinformatic analysis of redox regulation in evolutionary distinct photosynthetic cells. Gene expression, phylogenies, sequence alignments, and 3D protein structures in representative algal and plant species revealed conserved key features including functional domains catalyzing oxidation and reduction reactions. We then discuss the antioxidant-related ROS signaling and important pathways for achieving homeostasis of photosynthesis. Finally, we highlight the importance of plant responses to stress cues and genetic manipulation of disturbed redox status for balanced and enhanced photosynthetic efficiency and plant productivity.
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Affiliation(s)
- Adeel Riaz
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 414000, China
| | - Fenglin Deng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 414000, China
| | - Guang Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wei Jiang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 414000, China
| | - Qingfeng Zheng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 414000, China
| | - Bisma Riaz
- Department of Biotechnology, University of Okara, Okara, Punjab 56300, Pakistan
| | - Michelle Mak
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Fanrong Zeng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 414000, China
- Correspondence: (F.Z.); (Z.-H.C.)
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
- Correspondence: (F.Z.); (Z.-H.C.)
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14
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Pradhan B, Panda D, Bishi SK, Chakraborty K, Muthusamy SK, Lenka SK. Progress and prospects of C 4 trait engineering in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:920-931. [PMID: 35727191 DOI: 10.1111/plb.13446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Incorporating C4 photosynthetic traits into C3 crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C3 , C4 , and C3 -C4 intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C4 photosynthetic traits in C3 crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C3 crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C3 crops for sustaining food, fibre and fuel production around the globe.
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Affiliation(s)
- B Pradhan
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Kolkata, India
| | - D Panda
- Department of Biodiversity & Conservation of Natural Resources, Central University of Odisha, Koraput, India
| | - S K Bishi
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - K Chakraborty
- Department of Plant Physiology, ICAR-National Rice Research Institute, Cuttack, India
| | - S K Muthusamy
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - S K Lenka
- Department of Plant Biotechnology, Gujarat Biotechnology University, Gujarat, India
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15
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Rangan P, Wankhede DP, Subramani R, Chinnusamy V, Malik SK, Baig MJ, Singh K, Henry R. Evolution of an intermediate C 4 photosynthesis in the non-foliar tissues of the Poaceae. PHOTOSYNTHESIS RESEARCH 2022; 153:125-134. [PMID: 35648247 DOI: 10.1007/s11120-022-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Carbon concentrating mechanisms (CCMs) in plants are abaptive features that have evolved to sustain plant growth in unfavorable environments, especially at low atmospheric carbon levels and high temperatures. Uptake of CO2 and its storage in the aerenchyma tissues of Lycopsids and diurnal acidity fluctuation in aquatic plants during the Palaeozoic era (ca. 300 Ma.) would represent the earliest evolution of a CCM. The CCM parts of the dark reactions of photosynthesis have evolved many times, while the light reactions are conserved across plant lineages. A C4 type CCM, leaf C4 photosynthesis is evolved in the PACMAD clade of the Poaceae family. The evolution of C4 photosynthesis from C3 photosynthesis was an abaptation. Photosynthesis in reproductive tissues of sorghum and maize (PACMAD clade) has been shown to be of a weaker C4 type (high CO2 compensation point, low carbon isotope discrimination, and lack of Rubisco compartmentalization, when compared to the normal C4 types) than that in the leaves (normal C4 type). However, this does not fit well with the character polarity concept from an evolutionary perspective. In a recent model proposed for CCM evolution, the development of a rudimentary CCM prior to the evolution of a more efficient CCM (features contrasting to a weaker C4 type, leading to greater biomass production rate) has been suggested. An intermediate crassulacean acid metabolism (CAM) type of CCM (rudimentary) was reported in the genera, Brassia, Coryanthes, Eriopsis, Peristeria, of the orchids (well-known group of plants that display the CAM pathway). Similarly, we propose here the evolution of a rudimentary CCM (C4-like type pathway) in the non-foliar tissues of the Poaceae, prior to the evolution of the C4 pathway as identified in the leaves of the C4 species of the PACMAD clade.
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Affiliation(s)
- Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.
| | | | - Rajkumar Subramani
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | | | - Surendra K Malik
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | | | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
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16
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Zhao YY, Lyu MA, Miao F, Chen G, Zhu XG. The evolution of stomatal traits along the trajectory toward C4 photosynthesis. PLANT PHYSIOLOGY 2022; 190:441-458. [PMID: 35652758 PMCID: PMC9434244 DOI: 10.1093/plphys/kiac252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/21/2022] [Indexed: 05/03/2023]
Abstract
C4 photosynthesis optimizes plant carbon and water relations, allowing high photosynthetic rates with low stomatal conductance. Stomata have long been considered a part of the C4 syndrome. However, it remains unclear how stomatal traits evolved along the path from C3 to C4. Here, we examined stomata in the Flaveria genus, a model used for C4 evolutionary study. Comparative, transgenic, and semi-in vitro experiments were performed to study the molecular basis that underlies the changes of stomatal traits in C4 evolution. The evolution from C3 to C4 species is accompanied by a gradual rather than an abrupt change in stomatal traits. The initial change appears near the Type I intermediate stage. Co-evolution of the photosynthetic pathway and stomatal traits is supported. On the road to C4, stomata tend to be fewer in number but larger in size and stomatal density dominates changes in anatomical maximum stomatal conductance (gsmax). Reduction of FSTOMAGEN expression underlies decreased gsmax in Flaveria and likely occurs in other C4 lineages. Decreased gsmax contributes to the increase in intrinsic water-use efficiency in C4 evolution. This work highlights the stomatal traits in the current C4 evolutionary model. Our study provides insights into the pattern, mechanism, and role of stomatal evolution along the road toward C4.
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Affiliation(s)
- Yong-Yao Zhao
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingju Amy Lyu
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - FenFen Miao
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Genyun Chen
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Mercado MA, Studer AJ. Meeting in the Middle: Lessons and Opportunities from Studying C 3-C 4 Intermediates. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:43-65. [PMID: 35231181 DOI: 10.1146/annurev-arplant-102720-114201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The discovery of C3-C4 intermediate species nearly 50 years ago opened up a new avenue for studying the evolution of photosynthetic pathways. Intermediate species exhibit anatomical, biochemical, and physiological traits that range from C3 to C4. A key feature of C3-C4 intermediates that utilize C2 photosynthesis is the improvement in photosynthetic efficiency compared with C3 species. Although the recruitment of some core enzymes is shared across lineages, there is significant variability in gene expression patterns, consistent with models that suggest numerous evolutionary paths from C3 to C4 photosynthesis. Despite the many evolutionary trajectories, the recruitment of glycine decarboxylase for C2 photosynthesis is likely required. As technologies enable high-throughput genotyping and phenotyping, the discovery of new C3-C4 intermediates species will enrich comparisons between evolutionary lineages. The investigation of C3-C4 intermediate species will enhance our understanding of photosynthetic mechanisms and evolutionary processes and will potentially aid in crop improvement.
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Affiliation(s)
| | - Anthony J Studer
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA; ,
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18
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Bianconi ME, Sotelo G, Curran EV, Milenkovic V, Samaritani E, Dunning LT, Bertolino LT, Osborne CP, Christin PA. Upregulation of C 4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. PLANT, CELL & ENVIRONMENT 2022. [PMID: 35201618 DOI: 10.1101/2021.08.10.455822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
C4 photosynthesis is thought to have evolved via intermediate stages, with changes towards the C4 phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C4 components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C4 and non-C4 populations. Here, we analyse F1 hybrids between C3 and C4 , and C3 +C4 and C4 genotypes to determine whether the acquisition of C4 characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C4 gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C4 cycle coexists with C3 carbon fixation in the hybrids. This partial C4 phenotype is associated with C4 -like photosynthetic efficiency in C3 +C4 × C4 , but not in C3 × C4 hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C4 characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C4 components is thus constrained, with C3 +C4 species providing an essential step for C4 evolution.
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Affiliation(s)
- Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Emma V Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Emanuela Samaritani
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Lígia T Bertolino
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
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19
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Bianconi ME, Sotelo G, Curran EV, Milenkovic V, Samaritani E, Dunning LT, Bertolino LT, Osborne CP, Christin P. Upregulation of C 4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. PLANT, CELL & ENVIRONMENT 2022; 45:1398-1411. [PMID: 35201618 PMCID: PMC9314825 DOI: 10.1111/pce.14301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/20/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
C4 photosynthesis is thought to have evolved via intermediate stages, with changes towards the C4 phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C4 components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C4 and non-C4 populations. Here, we analyse F1 hybrids between C3 and C4 , and C3 +C4 and C4 genotypes to determine whether the acquisition of C4 characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C4 gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C4 cycle coexists with C3 carbon fixation in the hybrids. This partial C4 phenotype is associated with C4 -like photosynthetic efficiency in C3 +C4 × C4 , but not in C3 × C4 hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C4 characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C4 components is thus constrained, with C3 +C4 species providing an essential step for C4 evolution.
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Affiliation(s)
- Matheus E. Bianconi
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Emma V. Curran
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Emanuela Samaritani
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Lígia T. Bertolino
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Colin P. Osborne
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Pascal‐Antoine Christin
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
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20
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Abstract
Metabolism relies on a small class of molecules (coenzymes) that serve as universal donors and acceptors of key chemical groups and electrons. Although metabolic networks crucially depend on structurally redundant coenzymes [e.g., NAD(H) and NADP(H)] associated with different enzymes, the criteria that led to the emergence of this redundancy remain poorly understood. Our combination of modeling and structural and sequence analysis indicates that coenzyme redundancy may not be essential for metabolism but could rather constitute an evolved strategy promoting efficient usage of enzymes when biochemical reactions are near equilibrium. Our work suggests that early metabolism may have operated with fewer coenzymes and that adaptation for metabolic efficiency may have driven the rise of coenzyme diversity in living systems. Coenzymes distribute a variety of chemical moieties throughout cellular metabolism, participating in group (e.g., phosphate and acyl) and electron transfer. For a variety of reactions requiring acceptors or donors of specific resources, there often exist degenerate sets of molecules [e.g., NAD(H) and NADP(H)] that carry out similar functions. Although the physiological roles of various coenzyme systems are well established, it is unclear what selective pressures may have driven the emergence of coenzyme redundancy. Here, we use genome-wide metabolic modeling approaches to decompose the selective pressures driving enzymatic specificity for either NAD(H) or NADP(H) in the metabolic network of Escherichia coli. We found that few enzymes are thermodynamically constrained to using a single coenzyme, and in principle a metabolic network relying on only NAD(H) is feasible. However, structural and sequence analyses revealed widespread conservation of residues that retain selectivity for either NAD(H) or NADP(H), suggesting that additional forces may shape specificity. Using a model accounting for the cost of oxidoreductase enzyme expression, we found that coenzyme redundancy universally reduces the minimal amount of protein required to catalyze coenzyme-coupled reactions, inducing individual reactions to strongly prefer one coenzyme over another when reactions are near thermodynamic equilibrium. We propose that protein minimization generically promotes coenzyme redundancy and that coenzymes typically thought to exist in a single pool (e.g., coenzyme A [CoA]) may exist in more than one form (e.g., dephospho-CoA).
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21
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Borghi GL, Arrivault S, Günther M, Barbosa Medeiros D, Dell’Aversana E, Fusco GM, Carillo P, Ludwig M, Fernie AR, Lunn JE, Stitt M. Metabolic profiles in C3, C3-C4 intermediate, C4-like, and C4 species in the genus Flaveria. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1581-1601. [PMID: 34910813 PMCID: PMC8890617 DOI: 10.1093/jxb/erab540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/14/2021] [Indexed: 05/22/2023]
Abstract
C4 photosynthesis concentrates CO2 around Rubisco in the bundle sheath, favouring carboxylation over oxygenation and decreasing photorespiration. This complex trait evolved independently in >60 angiosperm lineages. Its evolution can be investigated in genera such as Flaveria (Asteraceae) that contain species representing intermediate stages between C3 and C4 photosynthesis. Previous studies have indicated that the first major change in metabolism probably involved relocation of glycine decarboxylase and photorespiratory CO2 release to the bundle sheath and establishment of intercellular shuttles to maintain nitrogen stoichiometry. This was followed by selection for a CO2-concentrating cycle between phosphoenolpyruvate carboxylase in the mesophyll and decarboxylases in the bundle sheath, and relocation of Rubisco to the latter. We have profiled 52 metabolites in nine Flaveria species and analysed 13CO2 labelling patterns for four species. Our results point to operation of multiple shuttles, including movement of aspartate in C3-C4 intermediates and a switch towards a malate/pyruvate shuttle in C4-like species. The malate/pyruvate shuttle increases from C4-like to complete C4 species, accompanied by a rise in ancillary organic acid pools. Our findings support current models and uncover further modifications of metabolism along the evolutionary path to C4 photosynthesis in the genus Flaveria.
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Affiliation(s)
- Gian Luca Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- Correspondence:
| | - Manuela Günther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - David Barbosa Medeiros
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Emilia Dell’Aversana
- Universitá degli Studi della Campania, Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Via Vivaldi 43, 81100 Caserta, Italy
| | - Giovanna Marta Fusco
- Universitá degli Studi della Campania, Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Via Vivaldi 43, 81100 Caserta, Italy
| | - Petronia Carillo
- Universitá degli Studi della Campania, Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Via Vivaldi 43, 81100 Caserta, Italy
| | - Martha Ludwig
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, 6009 Perth, Australia
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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22
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Casola C, Li J. Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C 4 plants. PeerJ 2022; 10:e12791. [PMID: 35127287 PMCID: PMC8801178 DOI: 10.7717/peerj.12791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/22/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL. METHODS Our study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages. RESULTS The reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacements in C4 lineages, with both RbcL and RpoC1 (the RNA polymerase beta' subunit 1) showing a significantly higher convergent/non-convergent replacements ratio in C4 branches. Notably, more C4:C4 reference branches showed higher numbers of convergent vs. non-convergent replacements than C3:C3 and C3:C4 branches. Our results suggest that, in the PACMAD clade, C4 grasses experienced higher levels of molecular convergence than C3 species across multiple chloroplast genes. These findings have important implications for our understanding of the evolution of the C4 photosynthesis pathway.
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Affiliation(s)
- Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
- Interdisciplinary Graduate Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, United States of America
| | - Jingjia Li
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
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23
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Parma DF, Vaz MGMV, Falquetto P, Silva JC, Clarindo WR, Westhoff P, van Velzen R, Schlüter U, Araújo WL, Schranz ME, Weber APM, Nunes-Nesi A. New Insights Into the Evolution of C 4 Photosynthesis Offered by the Tarenaya Cluster of Cleomaceae. FRONTIERS IN PLANT SCIENCE 2022; 12:756505. [PMID: 35116048 PMCID: PMC8803641 DOI: 10.3389/fpls.2021.756505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/16/2021] [Indexed: 05/04/2023]
Abstract
Cleomaceae is closely related to Brassicaceae and includes C3, C3-C4, and C4 species. Thus, this family represents an interesting system for studying the evolution of the carbon concentrating mechanism. However, inadequate genetic information on Cleomaceae limits their research applications. Here, we characterized 22 Cleomaceae accessions [3 genera (Cleoserrata, Gynandropsis, and Tarenaya) and 11 species] in terms of genome size; molecular phylogeny; as well as anatomical, biochemical, and photosynthetic traits. We clustered the species into seven groups based on genome size. Interestingly, despite clear differences in genome size (2C, ranging from 0.55 to 1.3 pg) in Tarenaya spp., this variation was not consistent with phylogenetic grouping based on the internal transcribed spacer (ITS) marker, suggesting the occurrence of multiple polyploidy events within this genus. Moreover, only G. gynandra, which possesses a large nuclear genome, exhibited the C4 metabolism. Among the C3-like species, we observed intra- and interspecific variation in nuclear genome size as well as in biochemical, physiological, and anatomical traits. Furthermore, the C3-like species had increased venation density and bundle sheath cell size, compared to C4 species, which likely predisposed the former lineages to C4 photosynthesis. Accordingly, our findings demonstrate the potential of Cleomaceae, mainly members of Tarenaya, in offering novel insights into the evolution of C4 photosynthesis.
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Affiliation(s)
- Daniele F. Parma
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Marcelo G. M. V. Vaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Priscilla Falquetto
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Jéssica C. Silva
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Philipp Westhoff
- Plant Metabolism and Metabolomics Laboratory, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Robin van Velzen
- Biosystematics Group, Wageningen University & Research, Wageningen, Netherlands
| | - Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University & Research, Wageningen, Netherlands
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
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24
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Shameer S, Wang Y, Bota P, Ratcliffe RG, Long SP, Sweetlove LJ. A hybrid kinetic and constraint-based model of leaf metabolism allows predictions of metabolic fluxes in different environments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:295-313. [PMID: 34699645 DOI: 10.1111/tpj.15551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
While flux balance analysis (FBA) provides a framework for predicting steady-state leaf metabolic network fluxes, it does not readily capture the response to environmental variables without being coupled to other modelling formulations. To address this, we coupled an FBA model of 903 reactions of soybean (Glycine max) leaf metabolism with e-photosynthesis, a dynamic model that captures the kinetics of 126 reactions of photosynthesis and associated chloroplast carbon metabolism. Successful coupling was achieved in an iterative formulation in which fluxes from e-photosynthesis were used to constrain the FBA model and then, in turn, fluxes computed from the FBA model used to update parameters in e-photosynthesis. This process was repeated until common fluxes in the two models converged. Coupling did not hamper the ability of the kinetic module to accurately predict the carbon assimilation rate, photosystem II electron flux, and starch accumulation of field-grown soybean at two CO2 concentrations. The coupled model also allowed accurate predictions of additional parameters such as nocturnal respiration, as well as analysis of the effect of light intensity and elevated CO2 on leaf metabolism. Predictions included an unexpected decrease in the rate of export of sucrose from the leaf at high light, due to altered starch-sucrose partitioning, and altered daytime flux modes in the tricarboxylic acid cycle at elevated CO2 . Mitochondrial fluxes were notably different between growing and mature leaves, with greater anaplerotic, tricarboxylic acid cycle and mitochondrial ATP synthase fluxes predicted in the former, primarily to provide carbon skeletons and energy for protein synthesis.
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Affiliation(s)
- Sanu Shameer
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Yu Wang
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pedro Bota
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Stephen P Long
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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25
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Washburn JD, Strable J, Dickinson P, Kothapalli SS, Brose JM, Covshoff S, Conant GC, Hibberd JM, Pires JC. Distinct C 4 sub-types and C 3 bundle sheath isolation in the Paniceae grasses. PLANT DIRECT 2021; 5:e373. [PMID: 34988355 PMCID: PMC8711749 DOI: 10.1002/pld3.373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
In C4 plants, the enzymatic machinery underpinning photosynthesis can vary, with, for example, three distinct C4 acid decarboxylases being used to release CO2 in the vicinity of RuBisCO. For decades, these decarboxylases have been used to classify C4 species into three biochemical sub-types. However, more recently, the notion that C4 species mix and match C4 acid decarboxylases has increased in popularity, and as a consequence, the validity of specific biochemical sub-types has been questioned. Using five species from the grass tribe Paniceae, we show that, although in some species transcripts and enzymes involved in multiple C4 acid decarboxylases accumulate, in others, transcript abundance and enzyme activity is almost entirely from one decarboxylase. In addition, the development of a bundle sheath isolation procedure for a close C3 species in the Paniceae enables the preliminary exploration of C4 sub-type evolution.
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Affiliation(s)
- Jacob D. Washburn
- Plant Genetics Research Unit, USDA‐ARSUniversity of MissouriColumbiaMOUSA
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Josh Strable
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | | | | | - Julia M. Brose
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Sarah Covshoff
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Gavin C. Conant
- Program in Genetics, Bioinformatics Research Center, Department of Biological SciencesNorth Carolina State UniversityRaleighNCUSA
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26
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Johnson JE, Field CB, Berry JA. The limiting factors and regulatory processes that control the environmental responses of C 3, C 3-C 4 intermediate, and C 4 photosynthesis. Oecologia 2021; 197:841-866. [PMID: 34714387 PMCID: PMC8591018 DOI: 10.1007/s00442-021-05062-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Abstract
Here, we describe a model of C3, C3-C4 intermediate, and C4 photosynthesis that is designed to facilitate quantitative analysis of physiological measurements. The model relates the factors limiting electron transport and carbon metabolism, the regulatory processes that coordinate these metabolic domains, and the responses to light, carbon dioxide, and temperature. It has three unique features. First, mechanistic expressions describe how the cytochrome b6f complex controls electron transport in mesophyll and bundle sheath chloroplasts. Second, the coupling between the mesophyll and bundle sheath expressions represents how feedback regulation of Cyt b6f coordinates electron transport and carbon metabolism. Third, the temperature sensitivity of Cyt b6f is differentiated from that of the coupling between NADPH, Fd, and ATP production. Using this model, we present simulations demonstrating that the light dependence of the carbon dioxide compensation point in C3-C4 leaves can be explained by co-occurrence of light saturation in the mesophyll and light limitation in the bundle sheath. We also present inversions demonstrating that population-level variation in the carbon dioxide compensation point in a Type I C3-C4 plant, Flaveria chloraefolia, can be explained by variable allocation of photosynthetic capacity to the bundle sheath. These results suggest that Type I C3-C4 intermediate plants adjust pigment and protein distributions to optimize the glycine shuttle under different light and temperature regimes, and that the malate and aspartate shuttles may have originally functioned to smooth out the energy supply and demand associated with the glycine shuttle. This model has a wide range of potential applications to physiological, ecological, and evolutionary questions.
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Affiliation(s)
- Jennifer E Johnson
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA.
| | - Christopher B Field
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA.,Stanford Woods Institute for the Environment, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA
| | - Joseph A Berry
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
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27
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Sundermann EM, Lercher MJ, Heckmann D. Modeling photosynthetic resource allocation connects physiology with evolutionary environments. Sci Rep 2021; 11:15979. [PMID: 34354112 PMCID: PMC8342476 DOI: 10.1038/s41598-021-94903-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/15/2021] [Indexed: 11/12/2022] Open
Abstract
The regulation of resource allocation in biological systems observed today is the cumulative result of natural selection in ancestral and recent environments. To what extent are observed resource allocation patterns in different photosynthetic types optimally adapted to current conditions, and to what extent do they reflect ancestral environments? Here, we explore these questions for C3, C4, and C3–C4 intermediate plants of the model genus Flaveria. We developed a detailed mathematical model of carbon fixation, which accounts for various environmental parameters and for energy and nitrogen partitioning across photosynthetic components. This allows us to assess environment-dependent plant physiology and performance as a function of resource allocation patterns. Models of C4 plants optimized for conditions experienced by evolutionary ancestors perform better than models accounting for experimental growth conditions, indicating low phenotypic plasticity. Supporting this interpretation, the model predicts that C4 species need to re-allocate more nitrogen between photosynthetic components than C3 species to adapt to new environments. We thus hypothesize that observed resource distribution patterns in C4 plants still reflect optimality in ancestral environments, allowing the quantitative inference of these environments from today’s plants. Our work allows us to quantify environmental effects on photosynthetic resource allocation and performance in the light of evolutionary history.
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Affiliation(s)
- Esther M Sundermann
- Institute for Computer Science and Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Martin J Lercher
- Institute for Computer Science and Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - David Heckmann
- Institute for Computer Science and Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
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28
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Huang CF, Liu WY, Jade Lu MY, Chen YH, Ku MSB, Li WH. Whole genome duplication facilitated the evolution of C4 photosynthesis in Gynandropsis gynandra. Mol Biol Evol 2021; 38:4715-4731. [PMID: 34191030 PMCID: PMC8557433 DOI: 10.1093/molbev/msab200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In higher plants, whole-genome duplication (WGD) is thought to facilitate the evolution of C4 photosynthesis from C3 photosynthesis. To understand this issue, we used new and existing leaf-development transcriptomes to construct two coding sequence databases for C4Gynandropsis gynandra and C3Tarenaya hassleriana, which shared a WGD before their divergence. We compared duplicated genes in the two species and found that the WGD contributed to four aspects of the evolution of C4 photosynthesis in G. gynandra. First, G. gynandra has retained the duplicates of ALAAT (alanine aminotransferase) and GOGAT (glutamine oxoglutarate aminotransferase) for nitrogen recycling to establish a photorespiratory CO2 pump in bundle sheath (BS) cells for increasing photosynthesis efficiency, suggesting that G. gynandra experienced a C3–C4 intermediate stage during the C4 evolution. Second, G. gynandra has retained almost all known vein-development-related paralogous genes derived from the WGD event, likely contributing to the high vein complexity of G. gynandra. Third, the WGD facilitated the evolution of C4 enzyme genes and their recruitment into the C4 pathway. Fourth, several genes encoding photosystem I proteins were derived from the WGD and are upregulated in G. gynandra, likely enabling the NADH dehydrogenase-like complex to produce extra ATPs for the C4 CO2 concentration mechanism. Thus, the WGD apparently played an enabler role in the evolution of C4 photosynthesis in G. gynandra. Importantly, an ALAAT duplicate became highly expressed in BS cells in G. gynandra, facilitating nitrogen recycling and transition to the C4 cycle. This study revealed how WDG may facilitate C4 photosynthesis evolution.
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Affiliation(s)
- Chi-Fa Huang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Yu Liu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Maurice S B Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 600, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.,Department of Ecology and Evolution, University of Chicago, Chicago, 60637, USA
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29
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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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30
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Russ Monson and the evolution of C 4 photosynthesis. Oecologia 2021; 197:823-840. [PMID: 33661402 DOI: 10.1007/s00442-021-04883-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
Early in his career, Russ Monson produced a series of influential eco-physiological papers that helped lay the foundation for the study of C4 plant evolution. Among the most important was a 1984 paper with Maurice Ku and Gerry Edwards that outlined the pathway for the evolutionary bridge from C3 to C4 photosynthesis. This model proposed C4 photosynthesis arose out of a shuttle that imported photorespiratory metabolites into bundle sheath (BS) cells, where glycine decarboxylase cleaved off CO2, allowing it to accumulate and be efficiently refixed by BS Rubisco. By the mid-1990's, Monson's research focus had shifted away from C4 plants, save for one 2003 paper on C3 versus C4 stomatal control with Travis Huxman, and a series of critical reviews on C4 evolution. These reviews heavily influenced the modern synthesis of C4 evolutionary studies, which incorporates phylogenomic understanding with physiological, molecular, and structural characterizations of trait shifts in multiple evolutionary lineages. Subsequent research supported the Monson et al. model from 1984, by showing a glycine shuttle occurs in nearly all C3-C4 intermediate species identified. Monson also examined the physiological controls over the ecological distribution of C3, C3-C4 intermediate, and C4 photosynthesis, building our understanding of the fitness value of the intermediate and C4 pathway in relevant microenvironments. By establishing the foundation for discoveries that followed, Russ Monson can rightly be considered a leading pioneer contributing to the evolutionary biology of C4 photosynthesis.
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31
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Kopriva S, Weber APM. Genetic encoding of complex traits. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1-3. [PMID: 33471904 PMCID: PMC7816844 DOI: 10.1093/jxb/eraa498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Stanislav Kopriva
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Correspondence: or
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
- Correspondence: or
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32
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Rojas-Pirela M, Andrade-Alviárez D, Rojas V, Kemmerling U, Cáceres AJ, Michels PA, Concepción JL, Quiñones W. Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. Open Biol 2020; 10:200302. [PMID: 33234025 PMCID: PMC7729029 DOI: 10.1098/rsob.200302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phosphoglycerate kinase (PGK) is a glycolytic enzyme that is well conserved among the three domains of life. PGK is usually a monomeric enzyme of about 45 kDa that catalyses one of the two ATP-producing reactions in the glycolytic pathway, through the conversion of 1,3-bisphosphoglycerate (1,3BPGA) to 3-phosphoglycerate (3PGA). It also participates in gluconeogenesis, catalysing the opposite reaction to produce 1,3BPGA and ADP. Like most other glycolytic enzymes, PGK has also been catalogued as a moonlighting protein, due to its involvement in different functions not associated with energy metabolism, which include pathogenesis, interaction with nucleic acids, tumorigenesis progression, cell death and viral replication. In this review, we have highlighted the overall aspects of this enzyme, such as its structure, reaction kinetics, activity regulation and possible moonlighting functions in different protistan organisms, especially both free-living and parasitic Kinetoplastea. Our analysis of the genomes of different kinetoplastids revealed the presence of open-reading frames (ORFs) for multiple PGK isoforms in several species. Some of these ORFs code for unusually large PGKs. The products appear to contain additional structural domains fused to the PGK domain. A striking aspect is that some of these PGK isoforms are predicted to be catalytically inactive enzymes or ‘dead’ enzymes. The roles of PGKs in kinetoplastid parasites are analysed, and the apparent significance of the PGK gene duplication that gave rise to the different isoforms and their expression in Trypanosoma cruzi is discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Verónica Rojas
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Universidad de Chile, Facultad de Medicina, Santiago de Chile 8380453, Santigo de Chile
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Paul A Michels
- Centre for Immunity, Infection and Evolution, The King's Buildings, Edinburgh EH9 3FL, UK.,Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
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33
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Khoshravesh R, Stata M, Adachi S, Sage TL, Sage RF. Evolutionary Convergence of C 4 Photosynthesis: A Case Study in the Nyctaginaceae. FRONTIERS IN PLANT SCIENCE 2020; 11:578739. [PMID: 33224166 PMCID: PMC7667235 DOI: 10.3389/fpls.2020.578739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/06/2020] [Indexed: 05/27/2023]
Abstract
C4 photosynthesis evolved over 65 times, with around 24 origins in the eudicot order Caryophyllales. In the Caryophyllales family Nyctaginaceae, the C4 pathway is known in three genera of the tribe Nyctagineae: Allionia, Okenia and Boerhavia. Phylogenetically, Allionia and Boerhavia/Okenia are separated by three genera whose photosynthetic pathway is uncertain. To clarify the distribution of photosynthetic pathways in the Nyctaginaceae, we surveyed carbon isotope ratios of 159 species of the Nyctaginaceae, along with bundle sheath (BS) cell ultrastructure, leaf gas exchange, and C4 pathway biochemistry in five species from the two C4 clades and closely related C3 genera. All species in Allionia, Okenia and Boerhavia are C4, while no C4 species occur in any other genera of the family, including three that branch between Allionia and Boerhavia. This demonstrates that C4 photosynthesis evolved twice in Nyctaginaceae. Boerhavia species use the NADP-malic enzyme (NADP-ME) subtype of C4 photosynthesis, while Allionia species use the NAD-malic enzyme (NAD-ME) subtype. The BS cells of Allionia have many more mitochondria than the BS of Boerhavia. Bundle sheath mitochondria are closely associated with chloroplasts in Allionia which facilitates CO2 refixation following decarboxylation by mitochondrial NAD-ME. The close relationship between Allionia and Boerhavia could provide insights into why NADP-ME versus NAD-ME subtypes evolve, particularly when coupled to analysis of their respective genomes. As such, the group is an excellent system to dissect the organizational hierarchy of convergent versus divergent traits produced by C4 evolution, enabling us to understand when convergence is favored versus when divergent modifications can result in a common phenotype.
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Affiliation(s)
- Roxana Khoshravesh
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
- Department of Biology, The University of New Mexico, Albuquerque, NM, United States
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
| | - Shunsuke Adachi
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tammy L. Sage
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
| | - Rowan F. Sage
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto, ON, Canada
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Tronconi MA, Hüdig M, Schranz ME, Maurino VG. Independent Recruitment of Duplicated β-Subunit-Coding NAD-ME Genes Aided the Evolution of C4 Photosynthesis in Cleomaceae. FRONTIERS IN PLANT SCIENCE 2020; 11:572080. [PMID: 33123181 PMCID: PMC7573226 DOI: 10.3389/fpls.2020.572080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/14/2020] [Indexed: 05/21/2023]
Abstract
In different lineages of C4 plants, the release of CO2 by decarboxylation of a C4 acid near rubisco is catalyzed by NADP-malic enzyme (ME) or NAD-ME, and the facultative use of phosphoenolpyruvate carboxykinase. The co-option of gene lineages during the evolution of C4-NADP-ME has been thoroughly investigated, whereas that of C4-NAD-ME has received less attention. In this work, we aimed at elucidating the mechanism of recruitment of NAD-ME for its function in the C4 pathway by focusing on the eudicot family Cleomaceae. We identified a duplication of NAD-ME in vascular plants that generated the two paralogs lineages: α- and β-NAD-ME. Both gene lineages were retained across seed plants, and their fixation was likely driven by a degenerative process of sub-functionalization, which resulted in a NAD-ME operating primarily as a heteromer of α- and β-subunits. We found most angiosperm genomes maintain a 1:1 β-NAD-ME/α-NAD-ME (β/α) relative gene dosage, but with some notable exceptions mainly due to additional duplications of β-NAD-ME subunits. For example, a significantly high proportion of species with C4-NAD-ME-type photosynthesis have a non-1:1 ratio of β/α. In the Brassicales, we found C4 species with a 2:1 ratio due to a β-NAD-ME duplication (β1 and β2); this was also observed in the C3 Tarenaya hassleriana and Brassica crops. In the independently evolved C4 species, Gynandropsis gynandra and Cleome angustifolia, all three genes were affected by C4 evolution with α- and β1-NAD-ME driven by adaptive selection. In particular, the β1-NAD-MEs possess many differentially substituted amino acids compared with other species and the β2-NAD-MEs of the same species. Five of these amino acids are identically substituted in β1-NAD-ME of G. gynandra and C. angustifolia, two of them were identified as positively selected. Using synteny analysis, we established that β-NAD-ME duplications were derived from ancient polyploidy events and that α-NAD-ME is in a unique syntenic context in both Cleomaceae and Brassicaceae. We discuss our hypotheses for the evolution of NAD-ME and its recruitment for C4 photosynthesis. We propose that gene duplications provided the basis for the recruitment of NAD-ME in C4 Cleomaceae and that all members of the NAD-ME gene family have been adapted to fit the C4-biochemistry. Also, one of the β-NAD-ME gene copies was independently co-opted for its function in the C4 pathway.
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Affiliation(s)
- Marcos A. Tronconi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Meike Hüdig
- Abteilung Molekulare Pflanzenphysiologie, Institut für Molekulare Physiologie und Biotechnologie der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - Veronica G. Maurino
- Abteilung Molekulare Pflanzenphysiologie, Institut für Molekulare Physiologie und Biotechnologie der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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Jobe TO, Rahimzadeh Karvansara P, Zenzen I, Kopriva S. Ensuring Nutritious Food Under Elevated CO 2 Conditions: A Case for Improved C 4 Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:1267. [PMID: 33013946 PMCID: PMC7461923 DOI: 10.3389/fpls.2020.01267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/03/2020] [Indexed: 05/04/2023]
Abstract
Global climate change is a challenge for efforts to ensure food security for future generations. It will affect crop yields through changes in temperature and precipitation, as well as the nutritional quality of crops. Increased atmospheric CO2 leads to a penalty in the content of proteins and micronutrients in most staple crops, with the possible exception of C4 crops. It is essential to understand the control of nutrient homeostasis to mitigate this penalty. However, despite the importance of mineral nutrition for plant performance, comparably less is known about the regulation of nutrient uptake and homeostasis in C4 plants than in C3 plants and mineral nutrition has not been a strong focus of the C4 research. Here we review what is known about C4 specific features of nitrogen and sulfur assimilation as well as of homeostasis of other essential elements. We identify the major knowledge gaps and urgent questions for future research. We argue that adaptations in mineral nutrition were an integral part of the evolution of C4 photosynthesis and should be considered in the attempts to engineer C4 photosynthetic mechanisms into C3 crops.
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Affiliation(s)
- Timothy O Jobe
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Parisa Rahimzadeh Karvansara
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Ivan Zenzen
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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Moody NR, Christin PA, Reid JD. Kinetic Modifications of C 4 PEPC Are Qualitatively Convergent, but Larger in Panicum Than in Flaveria. FRONTIERS IN PLANT SCIENCE 2020; 11:1014. [PMID: 32719709 PMCID: PMC7350407 DOI: 10.3389/fpls.2020.01014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
C4 photosynthesis results from a set of anatomical features and biochemical components that act together to concentrate CO2 within the leaf and boost productivity. This complex trait evolved independently many times, resulting in various realizations of the phenotype, but in all C4 plants the primary fixation of atmospheric carbon is catalyzed by phosphoenolpyruvate carboxylase. Comparisons of C4 and non-C4 PEPC from a few closely related species suggested that the enzyme was modified to meet the demands of the C4 cycle. However, very few C4 groups have been investigated, hampering general conclusions. To test the hypothesis that distant C4 lineages underwent convergent biochemical changes, we compare the kinetic variation between C4 and non-C4 PEPC from a previously assessed young lineage (Flaveria, Asteraceae) with those from an older lineage found within the distantly related grass family (Panicum). Despite the evolutionary distance, the kinetic changes between the non-C4 and C4 PEPC are qualitatively similar, with a decrease in sensitivity for inhibitors, an increased specificity (k cat/K m) for bicarbonate, and a decreased specificity (k cat/K m) for PEP. The differences are more pronounced in the older lineage Panicum, which might indicate that optimization of PEPC for the C4 context increases with evolutionary time.
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Affiliation(s)
- Nicholas R. Moody
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | | | - James D. Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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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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Kohli A, Miro B, Balié J, d’A Hughes J. Photosynthesis research: a model to bridge fundamental science, translational products, and socio-economic considerations in agriculture. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2281-2298. [PMID: 32076700 PMCID: PMC7135011 DOI: 10.1093/jxb/eraa087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/19/2020] [Indexed: 05/04/2023]
Abstract
Despite impressive success in molecular physiological understanding of photosynthesis, and preliminary evidence on its potential for quantum shifts in agricultural productivity, the question remains of whether increased photosynthesis, without parallel fine-tuning of the associated processes, is enough. There is a distinct lack of formal socio-economic impact studies that address the critical questions of product profiling, cost-benefit analysis, environmental trade-offs, and technological and market forces in product acceptability. When a relatively well understood process gains enough traction for translational value, its broader scientific and technical gap assessment, in conjunction with its socio-economic impact assessment for success, should be a prerequisite. The successes in the upstream basic understanding of photosynthesis should be integrated with a gap analysis for downstream translational applications to impact the farmers' and customers' lifestyles and livelihoods. The purpose of this review is to assess how the laboratory, the field, and the societal demands from photosynthesis could generate a transformative product. Two crucial recommendations from the analysis of the state of knowledge and potential ways forward are (i) the formulation of integrative mega-projects, which span the multistakeholder spectrum, to ensure rapid success in harnessing the transformative power of photosynthesis; and (ii) stipulating spatiotemporal, labour, and economic criteria to stage-gate deliverables.
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Affiliation(s)
- Ajay Kohli
- International Rice Research Institute, Los Baños, Philippines
| | - Berta Miro
- International Rice Research Institute, Los Baños, Philippines
| | - Jean Balié
- International Rice Research Institute, Los Baños, Philippines
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Liu Y, Maimaitijiang T, Zhang J, Ma Y, Lan H. The Developmental Enhancement of a C 4 System With Non-Typical C 4 Physiological Characteristics in Salsola ferganica (Kranz Anatomy), an Annual Desert Halophyte. FRONTIERS IN PLANT SCIENCE 2020; 11:152. [PMID: 32210984 PMCID: PMC7069449 DOI: 10.3389/fpls.2020.00152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/31/2020] [Indexed: 05/27/2023]
Abstract
Variations of photosynthetic structures in different tissues or cells are in coordination with changes in various aspects, e.g. physiology, biochemistry, gene expression, etc. Most C4 plant species undergo developmental enhancement of the photosynthetic system, which may present different modes of changes between anatomy and physiology/biochemistry. In the current study, we investigated a Kranz-type C4 species Salsola ferganica with the progressive development of photosynthetic (PS) structure, performance of PS physiology, induction of PS enzymes, and transcriptional and translational regulation of PS genes, results revealed that S. ferganica presented C3 type anatomy in cotyledons but C4 type in leaves (C3/L4), with the C4 system separation of initial carbon fixation in the palisade mesophyll (M) cells and the following incorporation into triosephosphates and sugars in the bundle sheath (BS) cells, respectively. The BS cells continuously surrounded the vascular bundles and water storage cells in leaf anatomic structure. Compared to the single-cell C4 species Suaeda aralocaspica, S. ferganica exhibited similar developmental enhancement of C4 syndrome temporally and spatially in anatomic structures, enzyme activities, and gene expression, which suggests that completion of differentiation of the photosynthetic system is necessary for a C4 assimilation pathway. Besides, S. ferganica also displayed some different characteristics compared to S. aralocaspica in photosynthetic physiology, e.g. a more flexible δ13C value, much lower phosphoenolpyruvate carboxylase (PEPC) activity, and an insensitive response to stimuli, etc., which were not typical C4 characteristics. We speculate that this may suggest a different status of these two species in the evolutionary process of the photosynthesis pathway. Our findings will contribute to further understanding of the diversity of photosynthesis systems in Kranz-type C4 species and the Salsola genus.
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Affiliation(s)
| | | | | | | | - Haiyan Lan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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40
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Using energy-efficient synthetic biochemical pathways to bypass photorespiration. Biochem Soc Trans 2020; 47:1805-1813. [PMID: 31754693 DOI: 10.1042/bst20190322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/24/2019] [Accepted: 10/28/2019] [Indexed: 12/30/2022]
Abstract
Current crop yields will not be enough to sustain today's diets for a growing global population. As plant photosynthetic efficiency has not reached its theoretical maximum, optimizing photosynthesis is a promising strategy to enhance plant productivity. The low productivity of C3 plants is caused in part by the substantial energetic investments necessary to maintain a high flux through the photorespiratory pathway. Accordingly, lowering the energetic costs of photorespiration to enhance the productivity of C3 crops has been a goal of synthetic plant biology for decades. The use of synthetic bypasses to photorespiration in different plants showed an improvement of photosynthetic performance and growth under laboratory and field conditions, even though in silico predictions suggest that the tested synthetic pathways should confer a minimal or even negative energetic advantage over the wild type photorespiratory pathway. Current strategies increasingly utilize theoretical modeling and new molecular techniques to develop synthetic biochemical pathways that bypass photorespiration, representing a highly promising approach to enhance future plant productivity.
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van Rooijen R, Schulze S, Petzsch P, Westhoff P. Targeted misexpression of NAC052, acting in H3K4 demethylation, alters leaf morphological and anatomical traits in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1434-1448. [PMID: 31740936 PMCID: PMC7031063 DOI: 10.1093/jxb/erz509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/18/2019] [Indexed: 05/31/2023]
Abstract
In an effort to identify genetic regulators for the cell ontogeny around the veins in Arabidopsis thaliana leaves, an activation-tagged mutant line with altered leaf morphology and altered bundle sheath anatomy was characterized. This mutant had a small rosette area with wrinkled leaves and chlorotic leaf edges, as well as enhanced chloroplast numbers in the (pre-)bundle sheath tissue. It had a bundle-specific promoter from the gene GLYCINE DECARBOXYLASE SUBUNIT-T from the C4 species Flaveria trinervia (GLDTFt promoter) inserted in the coding region of the transcriptional repressor NAC052, functioning in H3K4 demethylation, in front of an alternative start codon in-frame with the natural start codon. Reconstruction of the mutation event of our activation-tagged line by creating a line expressing an N-terminally truncated sequence of NAC052 under control of the GLDTFt promoter confirmed the involvement of NAC052 in leaf development. Our study not only reveals leaf anatomic and transcriptomic effects of an N-terminally truncated NAC052 under control of the GLDTFt promoter, but also identifies NAC052 as a novel genetic regulator of leaf development.
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Affiliation(s)
- Roxanne van Rooijen
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’, Duesseldorf, Germany
| | - Stefanie Schulze
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Patrick Petzsch
- Biologisch-Medizinisches Forschungszentrum (BMFZ), Genomics & Transcriptomics Labor (GTL), Heinrich-Heine-University, Duesseldorf, Germany
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’, Duesseldorf, Germany
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42
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Wheeler LC, Smith SD. Computational Modeling of Anthocyanin Pathway Evolution: Biases, Hotspots, and Trade-offs. Integr Comp Biol 2020; 59:585-598. [PMID: 31120530 DOI: 10.1093/icb/icz049] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The alteration of metabolic pathways is a common mechanism underlying the evolution of new phenotypes. Flower color is a striking example of the importance of metabolic evolution in a complex phenotype, wherein shifts in the activity of the underlying pathway lead to a wide range of pigments. Although experimental work has identified common classes of mutations responsible for transitions among colors, we lack a unifying model that relates pathway function and activity to the evolution of distinct pigment phenotypes. One challenge in creating such a model is the branching structure of pigment pathways, which may lead to evolutionary trade-offs due to competition for shared substrates. In order to predict the effects of shifts in enzyme function and activity on pigment production, we created a simple kinetic model of a major plant pigmentation pathway: the anthocyanin pathway. This model describes the production of the three classes of blue, purple, and red anthocyanin pigments, and accordingly, includes multiple branches and substrate competition. We first studied the general behavior of this model using a naïve set of parameters. We then stochastically evolved the pathway toward a defined optimum and analyzed the patterns of fixed mutations. This approach allowed us to quantify the probability density of trajectories through pathway state space and identify the types and number of changes. Finally, we examined whether our simulated results qualitatively align with experimental observations, i.e., the predominance of mutations which change color by altering the function of branching genes in the pathway. These analyses provide a theoretical framework that can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.
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Affiliation(s)
- L C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80302, USA
| | - S D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80302, USA
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Blätke MA, Bräutigam A. Evolution of C4 photosynthesis predicted by constraint-based modelling. eLife 2019; 8:e49305. [PMID: 31799932 PMCID: PMC6905489 DOI: 10.7554/elife.49305] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/08/2019] [Indexed: 01/03/2023] Open
Abstract
Constraint-based modelling (CBM) is a powerful tool for the analysis of evolutionary trajectories. Evolution, especially evolution in the distant past, is not easily accessible to laboratory experimentation. Modelling can provide a window into evolutionary processes by allowing the examination of selective pressures which lead to particular optimal solutions in the model. To study the evolution of C4 photosynthesis from a ground state of C3 photosynthesis, we initially construct a C3 model. After duplication into two cells to reflect typical C4 leaf architecture, we allow the model to predict the optimal metabolic solution under various conditions. The model thus identifies resource limitation in conjunction with high photorespiratory flux as a selective pressure relevant to the evolution of C4. It also predicts that light availability and distribution play a role in guiding the evolutionary choice of possible decarboxylation enzymes. The data shows evolutionary CBM in eukaryotes predicts molecular evolution with precision.
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Affiliation(s)
- Mary-Ann Blätke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Andrea Bräutigam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Computational Biology, Faculty of Biology, Bielefeld University, UniversitätsstraßeBielefeldGermany
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44
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Edwards EJ. Evolutionary trajectories, accessibility and other metaphors: the case of C 4 and CAM photosynthesis. THE NEW PHYTOLOGIST 2019; 223:1742-1755. [PMID: 30993711 DOI: 10.1111/nph.15851] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/18/2019] [Indexed: 05/24/2023]
Abstract
Are evolutionary outcomes predictable? Adaptations that show repeated evolutionary convergence across the Tree of Life provide a special opportunity to dissect the context surrounding their origins, and identify any commonalities that may predict why certain traits evolved many times in particular clades and yet never evolved in others. The remarkable convergence of C4 and Crassulacean Acid Metabolism (CAM) photosynthesis in vascular plants makes them exceptional model systems for understanding the repeated evolution of complex phenotypes. This review highlights what we have learned about the recurring assembly of C4 and CAM, focusing on the increasingly predictable stepwise evolutionary integration of anatomy and biochemistry. With the caveat that we currently understand C4 evolution better than we do CAM, I propose a general model that explains and unites C4 and CAM evolutionary trajectories. Available data suggest that anatomical modifications are the 'rate-limiting step' in each trajectory, which in large part determines the evolutionary accessibility of both syndromes. The idea that organismal structure exerts a primary influence on innovation is discussed in the context of other systems. Whether the rate-limiting step occurs early or late in the evolutionary assembly of a new phenotype may have profound implications for its distribution across the Tree of Life.
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Affiliation(s)
- Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St, New Haven, CT, 06520-8105, USA
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45
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Jurić I, Hibberd JM, Blatt M, Burroughs NJ. Computational modelling predicts substantial carbon assimilation gains for C3 plants with a single-celled C4 biochemical pump. PLoS Comput Biol 2019; 15:e1007373. [PMID: 31568503 PMCID: PMC6786660 DOI: 10.1371/journal.pcbi.1007373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 10/10/2019] [Accepted: 09/03/2019] [Indexed: 11/29/2022] Open
Abstract
Achieving global food security for the estimated 9 billion people by 2050 is a major scientific challenge. Crop productivity is fundamentally restricted by the rate of fixation of atmospheric carbon. The dedicated enzyme, RubisCO, has a low turnover and poor specificity for CO2. This limitation of C3 photosynthesis (the basic carbon-assimilation pathway present in all plants) is alleviated in some lineages by use of carbon-concentrating-mechanisms, such as the C4 cycle-a biochemical pump that concentrates CO2 near RubisCO increasing assimilation efficacy. Most crops use only C3 photosynthesis, so one promising research strategy to boost their productivity focuses on introducing a C4 cycle. The simplest proposal is to use the cycle to concentrate CO2 inside individual chloroplasts. The photosynthetic efficiency would then depend on the leakage of CO2 out of a chloroplast. We examine this proposal with a 3D spatial model of carbon and oxygen diffusion and C4 photosynthetic biochemistry inside a typical C3-plant mesophyll cell geometry. We find that the cost-efficiency of C4 photosynthesis depends on the gas permeability of the chloroplast envelope, the C4 pathway having higher quantum efficiency than C3 for permeabilities below 300 μm/s. However, at higher permeabilities the C4 pathway still provides a substantial boost to carbon assimilation with only a moderate decrease in efficiency. The gains would be capped by the ability of chloroplasts to harvest light, but even under realistic light regimes a 100% boost to carbon assimilation is possible. This could be achieved in conjunction with lower investment in chloroplasts if their cell surface coverage is also reduced. Incorporation of this C4 cycle into C3 crops could thus promote higher growth rates and better drought resistance in dry, high-sunlight climates.
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Affiliation(s)
- Ivan Jurić
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Julian M. Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Mike Blatt
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow, United Kingdom
| | - Nigel J. Burroughs
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
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46
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Zhou H, Akçay E, Helliker BR. Estimating C 4 photosynthesis parameters by fitting intensive A/C i curves. PHOTOSYNTHESIS RESEARCH 2019; 141:181-194. [PMID: 30758752 DOI: 10.1007/s11120-019-00619-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Measurements of photosynthetic assimilation rate as a function of intercellular CO2 (A/Ci curves) are widely used to estimate photosynthetic parameters for C3 species, yet few parameters have been reported for C4 plants, because of a lack of estimation methods. Here, we extend the framework of widely used estimation methods for C3 plants to build estimation tools by exclusively fitting intensive A/Ci curves (6-8 more sampling points) for C4 using three versions of photosynthesis models with different assumptions about carbonic anhydrase processes and ATP distribution. We use simulation analysis, out of sample tests, existing in vitro measurements and chlorophyll-fluorescence measurements to validate the new estimation methods. Of the five/six photosynthetic parameters obtained, sensitivity analyses show that maximal-Rubisco-carboxylation-rate, electron-transport-rate, maximal-PEP-carboxylation-rate, and carbonic-anhydrase were robust to variation in the input parameters, while day respiration and mesophyll conductance varied. Our method provides a way to estimate carbonic anhydrase activity, a new parameter, from A/Ci curves, yet also shows that models that do not explicitly consider carbonic anhydrase yield approximate results. The two photosynthesis models, differing in whether ATP could freely transport between RuBP and PEP regeneration processes yielded consistent results under high light, but they may diverge under low light intensities. Modeling results show selection for Rubisco of low specificity and high catalytic rate, low leakage of bundle sheath, and high PEPC affinity, which may further increase C4 efficiency.
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Affiliation(s)
- Haoran Zhou
- Department of Biology, University of Pennsylvania, 433 S University Ave., 314 Leidy Labs, Philadelphia, PA, 19104, USA.
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, 433 S University Ave., 314 Leidy Labs, Philadelphia, PA, 19104, USA
| | - Brent R Helliker
- Department of Biology, University of Pennsylvania, 433 S University Ave., 314 Leidy Labs, Philadelphia, PA, 19104, USA
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47
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Bellasio C, Farquhar GD. A leaf-level biochemical model simulating the introduction of C 2 and C 4 photosynthesis in C 3 rice: gains, losses and metabolite fluxes. THE NEW PHYTOLOGIST 2019; 223:150-166. [PMID: 30859576 DOI: 10.1111/nph.15787] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/03/2019] [Indexed: 05/21/2023]
Abstract
This work aims at developing an adequate theoretical basis for comparing assimilation of the ancestral C3 pathway with CO2 concentrating mechanisms (CCM) that have evolved to reduce photorespiratory yield losses. We present a novel model for C3 , C2 , C2 + C4 and C4 photosynthesis simulating assimilatory metabolism, energetics and metabolite traffic at the leaf level. It integrates a mechanistic description of light reactions to simulate ATP and NADPH production, and a variable engagement of cyclic electron flow. The analytical solutions are compact and thus suitable for larger scale simulations. Inputs were derived with a comprehensive gas-exchange experiment. We show trade-offs in the operation of C4 that are in line with ecophysiological data. C4 has the potential to increase assimilation over C3 at high temperatures and light intensities, but this benefit is reversed under low temperatures and light. We apply the model to simulate the introduction of progressively complex levels of CCM into C3 rice, which feeds > 3.5 billion people. Increasing assimilation will require considerable modifications such as expressing the NAD(P)H Dehydrogenase-like complex and upregulating cyclic electron flow, enlarging the bundle sheath, and expressing suitable transporters to allow adequate metabolite traffic. The simpler C2 rice may be a desirable alternative.
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Affiliation(s)
- Chandra Bellasio
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
- University of the Balearic Islands, Palma, Illes Balears, 07122, Spain
- Trees and Timber Institute, National Research Council of Italy, Sesto Fiorentino, Florence, 50019, Italy
| | - Graham D Farquhar
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
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48
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Dunning LT, Moreno-Villena JJ, Lundgren MR, Dionora J, Salazar P, Adams C, Nyirenda F, Olofsson JK, Mapaura A, Grundy IM, Kayombo CJ, Dunning LA, Kentatchime F, Ariyarathne M, Yakandawala D, Besnard G, Quick WP, Bräutigam A, Osborne CP, Christin PA. Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3255-3268. [PMID: 30949663 PMCID: PMC6598098 DOI: 10.1093/jxb/erz149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/19/2019] [Indexed: 05/23/2023]
Abstract
C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: aspartate aminotransferase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxylase. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme pyruvate orthophosphate dikinase. These changes probably created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4 accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous step. These create short bridges across adaptive landscapes that probably facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution.
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Affiliation(s)
- Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Marjorie R Lundgren
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Paolo Salazar
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Claire Adams
- Botany Department, Rhodes University, Grahamstown, South Africa
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Jill K Olofsson
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Isla M Grundy
- Institute of Environmental Studies, University of Zimbabwe, Harare, Zimbabwe
| | | | - Lucy A Dunning
- Department of Social Sciences, University of Sheffield, Sheffield, UK
| | | | - Menaka Ariyarathne
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeiya, Sri Lanka
| | - Deepthi Yakandawala
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeiya, Sri Lanka
| | - Guillaume Besnard
- Laboratoire Évolution et Diversité Biologique (EDB UMR5174), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - W Paul Quick
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | | | - Colin P Osborne
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
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49
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Stata M, Sage TL, Sage RF. Mind the gap: the evolutionary engagement of the C 4 metabolic cycle in support of net carbon assimilation. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:27-34. [PMID: 31150949 DOI: 10.1016/j.pbi.2019.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
C4 photosynthesis evolved dozens of times, with a critical step being the engagement of a C4 metabolic cycle to concentrate CO2 into a bundle sheath-like compartment. While C3-C4 intermediate species show a progressive increase in the activity of a C4 metabolic cycle, the integration of the C4 and C3 biochemical cycles in enhancing photosynthetic carbon gain occurs in a punctuated manner, at an initial C4 cycle activity near 60%. Punctuated integration of the C4 cycle could result from the evolutionary acquisition of traits that coordinate the C3 and C4 biochemical cycles (for example, an enzymatic, regulatory or transport function) or from a sudden reduction in the mesophyll C3 cycle. Alternatively, a punctuated pattern could be an artifact of low numbers of C3-C4 intermediates in the evolutionary space where C4 cycle engagement occurs, due to incomplete sampling of natural diversity or evolutionary dynamics rendering such intermediates unstable. Understanding how the C4 cycle becomes integrated with the C3 cycle could reveal new avenues for engineering the C4 pathway into C3 plants. Such efforts would be facilitated by the generation of hybrids, or the discovery of additional intermediates, that span the transition from low to high C4 cycle engagement.
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Affiliation(s)
- Matt Stata
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, M5S3B2, Canada
| | - Tammy L Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, M5S3B2, Canada
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, M5S3B2, Canada.
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50
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Weber APM. Synthetic evolution of C
4
photosynthesis. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.343.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andreas PM Weber
- Institute of Plant BiochemistryHeinrich Heine UniversityDuesseldorfGermany
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