1
|
Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
Collapse
Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
2
|
Bouvier JW, Emms DM, Kelly S. Rubisco is evolving for improved catalytic efficiency and CO 2 assimilation in plants. Proc Natl Acad Sci U S A 2024; 121:e2321050121. [PMID: 38442173 PMCID: PMC10945770 DOI: 10.1073/pnas.2321050121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that rbcL is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO2/O2 specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO2 assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO2 assimilation in plants.
Collapse
Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - David M Emms
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| |
Collapse
|
3
|
Ito K, Sugawara S, Kageyama S, Sawaguchi N, Hyotani T, Miyazawa SI, Makino A, Suzuki Y. Equisetum praealtum and E. hyemale have abundant Rubisco with a high catalytic turnover rate and low CO 2 affinity. JOURNAL OF PLANT RESEARCH 2024; 137:255-264. [PMID: 38112982 DOI: 10.1007/s10265-023-01514-z] [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: 10/02/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
The kinetic properties of Rubisco, a key enzyme for photosynthesis, have been examined in numerous plant species. However, this information on some plant groups, such as ferns, is scarce. This study examined Rubisco carboxylase activity and leaf Rubisco levels in seven ferns, including four Equisetum plants (E. arvense, E. hyemale, E. praealtum, and E. variegatum), considered living fossils. The turnover rates of Rubisco carboxylation (kcatc) in E. praealtum and E. hyemale were comparable to those in the C4 plants maize (Zea mays) and sorghum (Sorghum bicolor), whose kcatc values are high. Rubisco CO2 affinity, estimated from the percentage of Rubisco carboxylase activity under CO2 unsaturated conditions in kcatc in these Equisetum plants, was low and also comparable to that in maize and sorghum. In contrast, kcatc and CO2 affinities of Rubisco in other ferns, including E. arvense and E. variegatum were comparable with those in C3 plants. The N allocation to Rubisco in the ferns examined was comparable to that in the C3 plants. These results indicate that E. praealtum and E. hyemale have abundant Rubisco with high kcatc and low CO2 affinity, whereas the carboxylase activity and abundance of Rubisco in other ferns were similar to those in C3 plants. Herein, the Rubisco properties of E. praealtum and E. hyemale were discussed regarding their evolution and physiological implications.
Collapse
Affiliation(s)
- Kana Ito
- Graduate School of Arts and Sciences, Iwate University, Morioka, Japan
| | | | - Sota Kageyama
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Naoki Sawaguchi
- Graduate School of Arts and Sciences, Iwate University, Morioka, Japan
| | - Takuro Hyotani
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | | | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Present address: Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Yuji Suzuki
- Faculty of Agriculture, Iwate University, Morioka, Japan.
| |
Collapse
|
4
|
Yogadasan N, Doxey AC, Chuong SDX. A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information. Genome Biol Evol 2023; 15:evad129. [PMID: 37462292 PMCID: PMC10368328 DOI: 10.1093/gbe/evad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
C4 photosynthesis is known to have at least 61 independent origins across plant lineages making it one of the most notable examples of convergent evolution. Of the >60 independent origins, a predicted 22-24 origins, encompassing greater than 50% of all known C4 species, exist within the Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) clade of the Poaceae family. This clade is therefore primed with species ideal for the study of genomic changes associated with the acquisition of the C4 photosynthetic trait. In this study, we take advantage of the growing availability of sequenced plastid genomes and employ a machine learning (ML) approach to screen for plastid genes harboring C3 and C4 distinguishing information in PACMAD species. We demonstrate that certain plastid-encoded protein sequences possess distinguishing and informative sequence information that allows them to train accurate ML C3/C4 classification models. Our RbcL-trained model, for example, informs a C3/C4 classifier with greater than 99% accuracy. Accurate prediction of photosynthetic type from individual sequences suggests biologically relevant, and potentially differing roles of these sequence products in C3 versus C4 metabolism. With this ML framework, we have identified several key sequences and sites that are most predictive of C3/C4 status, including RbcL, subunits of the NAD(P)H dehydrogenase complex, and specific residues within, further highlighting their potential significance in the evolution and/or maintenance of C4 photosynthetic machinery. This general approach can be applied to uncover intricate associations between other similar genotype-phenotype relationships.
Collapse
Affiliation(s)
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Simon D X Chuong
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| |
Collapse
|
5
|
Chen L, Yang Y, Zhao Z, Lu S, Lu Q, Cui C, Parry MAJ, Hu YG. Genome-wide identification and comparative analyses of key genes involved in C 4 photosynthesis in five main gramineous crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1134170. [PMID: 36993845 PMCID: PMC10040670 DOI: 10.3389/fpls.2023.1134170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Compared to C3 species, C4 plants showed higher photosynthetic capacity as well as water and nitrogen use efficiency due to the presence of the C4 photosynthetic pathway. Previous studies have shown that all genes required for the C4 photosynthetic pathway exist in the genomes of C3 species and are expressed. In this study, the genes encoding six key C4 photosynthetic pathway enzymes (β-CA, PEPC, ME, MDH, RbcS, and PPDK) in the genomes of five important gramineous crops (C4: maize, foxtail millet, and sorghum; C3: rice and wheat) were systematically identified and compared. Based on sequence characteristics and evolutionary relationships, their C4 functional gene copies were distinguished from non-photosynthetic functional gene copies. Furthermore, multiple sequence alignment revealed important sites affecting the activities of PEPC and RbcS between the C3 and C4 species. Comparisons of expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among species, while C4 gene copies in C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that may affect C4 gene expression and subcellular localization were found in the coding and promoter regions. Our work emphasized the diversity of the evolution of different genes in the C4 photosynthetic pathway and confirmed that the specific high expression in the leaf and appropriate intracellular distribution were the keys to the evolution of C4 photosynthesis. The results of this study will help determine the evolutionary mechanism of the C4 photosynthetic pathway in Gramineae and provide references for the transformation of C4 photosynthetic pathways in wheat, rice, and other major C3 cereal crops.
Collapse
Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yang Yang
- College of Agriculture, Shannxi Agricultural University (Institute of Crop Sciences), Taiyuan, Shanxi, China
| | - Zhangchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiumei Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunge Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Martin A. J. Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
6
|
Capó-Bauçà S, Galmés J, Aguiló-Nicolau P, Ramis-Pozuelo S, Iñiguez C. Carbon assimilation in upper subtidal macroalgae is determined by an inverse correlation between Rubisco carboxylation efficiency and CO 2 concentrating mechanism effectiveness. THE NEW PHYTOLOGIST 2023; 237:2027-2038. [PMID: 36385703 DOI: 10.1111/nph.18623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Seaweeds have a wide ecophysiological and phylogenetic diversity with species expressing different Rubisco forms that frequently coexist with biophysical CO2 concentrating mechanisms (CCMs), an adaptation that overcomes the low CO2 availability and gas diffusion in seawater. Here, we assess the possible coevolution between the Rubisco catalysis and the type and effectiveness of CCMs present in six upper subtidal macroalgal species belonging to three phylogenetic groups of seaweeds. A wide diversity in the Rubisco kinetic traits was found across the analyzed species, although the specificity factor was the only parameter explained by the expressed Rubisco form. Differences in the catalytic trade-offs were found between Rubisco forms, indicating that ID Rubiscos could be better adapted to the intracellular O2 : CO2 ratio found in marine organisms during steady-state photosynthesis. The biophysical components of the CCMs also differed among macroalgal species, resulting in different effectiveness to concentrate CO2 around Rubisco active sites. Interestingly, an inverse relationship was found between the effectiveness of CCMs and the in vitro Rubisco carboxylation efficiency, which possibly led to a similar carboxylation potential across the analyzed macroalgal species. Our results demonstrate a coevolution between Rubisco kinetics and CCMs across phylogenetically distant marine macroalgal species sharing the same environment.
Collapse
Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Sonia Ramis-Pozuelo
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, 07122, Balearic Islands, Spain
| |
Collapse
|
7
|
Cavanagh AP, Slattery R, Kubien DS. Temperature-induced changes in Arabidopsis Rubisco activity and isoform expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:651-663. [PMID: 36124740 PMCID: PMC9833042 DOI: 10.1093/jxb/erac379] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/16/2022] [Indexed: 06/06/2023]
Abstract
In many plant species, expression of the nuclear encoded Rubisco small subunit (SSu) varies with environmental changes, but the functional role of any changes in expression remains unclear. In this study, we investigated the impact of differential expression of Rubisco SSu isoforms on carbon assimilation in Arabidopsis. Using plants grown at contrasting temperatures (10 °C and 30 °C), we confirm the previously reported temperature response of the four RbcS genes and extend this to protein expression, finding that warm-grown plants produce Rubisco containing ~65% SSu-B and cold-grown plants produce Rubisco with ~65% SSu-A as a proportion of the total pool of subunits. We find that these changes in isoform concentration are associated with kinetic changes to Rubisco in vitro: warm-grown plants produce a Rubisco having greater CO2 affinity (i.e. higher SC/O and lower KC) but lower kcatCO2 at warm measurement temperatures. Although warm-grown plants produce 38% less Rubisco than cold-grown plants on a leaf area basis, warm-grown plants can maintain similar rates of photosynthesis to cold-grown plants at ambient CO2 and 30 °C, indicating that the carboxylation capacity of warm-grown Rubisco is enhanced at warmer measurement temperatures, and is able to compensate for the lower Rubisco content in warm-grown plants. This association between SSu isoform expression and maintenance of Rubisco activity at high temperature suggests that SSu isoform expression could impact the temperature response of C3 photosynthesis.
Collapse
Affiliation(s)
| | - Rebecca Slattery
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David S Kubien
- Department of Biology, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
| |
Collapse
|
8
|
Iqbal WA, Lisitsa A, Kapralov MV. Predicting plant Rubisco kinetics from RbcL sequence data using machine learning. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:638-650. [PMID: 36094849 PMCID: PMC9833099 DOI: 10.1093/jxb/erac368] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for the conversion of atmospheric CO2 to organic carbon during photosynthesis, and often acts as a rate limiting step in the later process. Screening the natural diversity of Rubisco kinetics is the main strategy used to find better Rubisco enzymes for crop engineering efforts. Here, we demonstrate the use of Gaussian processes (GPs), a family of Bayesian models, coupled with protein encoding schemes, for predicting Rubisco kinetics from Rubisco large subunit (RbcL) sequence data. GPs trained on published experimentally obtained Rubisco kinetic datasets were applied to over 9000 sequences encoding RbcL to predict Rubisco kinetic parameters. Notably, our predicted kinetic values were in agreement with known trends, e.g. higher carboxylation turnover rates (Kcat) for Rubisco enzymes from C4 or crassulacean acid metabolism (CAM) species, compared with those found in C3 species. This is the first study demonstrating machine learning approaches as a tool for screening and predicting Rubisco kinetics, which could be applied to other enzymes.
Collapse
Affiliation(s)
- Wasim A Iqbal
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Alexei Lisitsa
- Department of Computer Science, University of Liverpool, Liverpool, L69 3BX, United Kingdom
| | | |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Zecca G, Panzeri D, Grassi F. Detecting signals of adaptive evolution in grape plastomes with a focus on the Cretaceous-Palaeogene (K/Pg) transition. ANNALS OF BOTANY 2022; 130:965-980. [PMID: 36282948 PMCID: PMC9851337 DOI: 10.1093/aob/mcac128] [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: 07/15/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Although plastid genes are widely used in phylogenetic studies, signals of positive selection have been scarcely investigated in the grape family. The plastomes from 91 accessions of Vitaceae were examined to understand the extent to which positive selection is present and to identify which genes are involved. Moreover, the changes through time of genes under episodic positive selection were investigated and the hypothesis of an adaptive process following the Cretaceous-Palaeogene (K/Pg) transition about 66 million years ago was tested. METHODS Different codon-substitution models were used to assess pervasive and episodic positive selection events on 70 candidate plastid genes. Divergence times between lineages were estimated and stochastic character mapping analysis was used to simulate variation over time of the genes found to be under episodic positive selection. KEY RESULTS A total of 20 plastid genes (29 %) showed positive selection. Among them, 14 genes showed pervasive signatures of positive selection and nine genes showed episodic signatures of positive selection. In particular, four of the nine genes (psbK, rpl20, rpoB, rps11) exhibited a similar pattern showing an increase in the rate of variation close to the K/Pg transition. CONCLUSION Multiple analyses have shown that the grape family has experienced ancient and recent positive selection events and that the targeted genes are involved in essential functions such as photosynthesis, self-replication and metabolism. Our results are consistent with the idea that the K/Pg transition has favoured an increased rate of change in some genes. Intense environmental perturbations have influenced the rapid diversification of certain lineages, and new mutations arising on some plastid genes may have been fixed by natural selection over the course of many generations.
Collapse
Affiliation(s)
- Giovanni Zecca
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
| | - Davide Panzeri
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
| | - Fabrizio Grassi
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
- NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| |
Collapse
|
11
|
Medeiros DB, Ishihara H, Guenther M, Rosado de Souza L, Fernie AR, Stitt M, Arrivault S. 13CO2 labeling kinetics in maize reveal impaired efficiency of C4 photosynthesis under low irradiance. PLANT PHYSIOLOGY 2022; 190:280-304. [PMID: 35751609 PMCID: PMC9434203 DOI: 10.1093/plphys/kiac306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 06/01/2023]
Abstract
C4 photosynthesis allows faster photosynthetic rates and higher water and nitrogen use efficiency than C3 photosynthesis, but at the cost of lower quantum yield due to the energy requirement of its biochemical carbon concentration mechanism. It has also been suspected that its operation may be impaired in low irradiance. To investigate fluxes under moderate and low irradiance, maize (Zea mays) was grown at 550 µmol photons m-2 s-l and 13CO2 pulse-labeling was performed at growth irradiance or several hours after transfer to 160 µmol photons m-2 s-1. Analysis by liquid chromatography/tandem mass spectrometry or gas chromatography/mass spectrometry provided information about pool size and labeling kinetics for 32 metabolites and allowed estimation of flux at many steps in C4 photosynthesis. The results highlighted several sources of inefficiency in low light. These included excess flux at phosphoenolpyruvate carboxylase, restriction of decarboxylation by NADP-malic enzyme, and a shift to increased CO2 incorporation into aspartate, less effective use of metabolite pools to drive intercellular shuttles, and higher relative and absolute rates of photorespiration. The latter provides evidence for a lower bundle sheath CO2 concentration in low irradiance, implying that operation of the CO2 concentration mechanism is impaired in this condition. The analyses also revealed rapid exchange of carbon between the Calvin-Benson cycle and the CO2-concentration shuttle, which allows rapid adjustment of the balance between CO2 concentration and assimilation, and accumulation of large amounts of photorespiratory intermediates in low light that provides a major carbon reservoir to build up C4 metabolite pools when irradiance increases.
Collapse
Affiliation(s)
- David B Medeiros
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Hirofumi Ishihara
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Manuela Guenther
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| |
Collapse
|
12
|
Lin MT, Salihovic H, Clark FK, Hanson MR. Improving the efficiency of Rubisco by resurrecting its ancestors in the family Solanaceae. SCIENCE ADVANCES 2022; 8:eabm6871. [PMID: 35427154 PMCID: PMC9012466 DOI: 10.1126/sciadv.abm6871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants and photosynthetic organisms have a remarkably inefficient enzyme named Rubisco that fixes atmospheric CO2 into organic compounds. Understanding how Rubisco has evolved in response to past climate change is important for attempts to adjust plants to future conditions. In this study, we developed a computational workflow to assemble de novo both large and small subunits of Rubisco enzymes from transcriptomics data. Next, we predicted sequences for ancestral Rubiscos of the (nightshade) family Solanaceae and characterized their kinetics after coexpressing them in Escherichia coli. Predicted ancestors of C3 Rubiscos were identified that have superior kinetics and excellent potential to help plants adapt to anthropogenic climate change. Our findings also advance understanding of the evolution of Rubisco's catalytic traits.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Tcherkez G, Farquhar GD. Rubisco catalytic adaptation is mostly driven by photosynthetic conditions - Not by phylogenetic constraints. JOURNAL OF PLANT PHYSIOLOGY 2021; 267:153554. [PMID: 34749030 DOI: 10.1016/j.jplph.2021.153554] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The prevalence of phylogenetic constraints in Rubisco evolution has been emphasised recently by (Bouvier et al., 2021), who argued that phylogenetic inheritance limits Rubisco adaptation much more than the biochemical trade-off between specificity, CO2 affinity and turn-over. In this Opinion, we have critically examined how a phylogenetic signal can be computed with Rubisco kinetic properties and phylogenetic trees, and we arrive at a different conclusion. In particular, Rubisco's adaptation is partly driven by C4 vs. C3 photosynthetic conditions in Angiosperms, apparent phylogenetic signals being mostly due to either homoplasy, computation artefacts or the use of nearly identical sister species. While phylogenetic inheritance of an ancestral enzyme form probably has some role in Rubisco's adaptation landscape, it is a minor player, at least compared to microenvironmental conditions such as CO2 and O2 concentrations.
Collapse
Affiliation(s)
- Guillaume Tcherkez
- Institut de Recherche and Horticulture et Semences, INRAe Angers, Université D'Angers, 42 Rue Georges Morel, 49070, Beaucouzé, France; Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia.
| | - Graham D Farquhar
- Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia
| |
Collapse
|
16
|
Sales CRG, Wang Y, Evers JB, Kromdijk J. Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5942-5960. [PMID: 34268575 PMCID: PMC8411859 DOI: 10.1093/jxb/erab327] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source-sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.
Collapse
Affiliation(s)
- Cristina R G Sales
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Yu Wang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jochem B Evers
- Centre for Crops Systems Analysis (WUR), Wageningen University, Wageningen, The Netherlands
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
17
|
Stitt M, Luca Borghi G, Arrivault S. Targeted metabolite profiling as a top-down approach to uncover interspecies diversity and identify key conserved operational features in the Calvin-Benson cycle. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5961-5986. [PMID: 34473300 PMCID: PMC8411860 DOI: 10.1093/jxb/erab291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/21/2021] [Indexed: 05/02/2023]
Abstract
Improving photosynthesis is a promising avenue to increase crop yield. This will be aided by better understanding of natural variance in photosynthesis. Profiling of Calvin-Benson cycle (CBC) metabolites provides a top-down strategy to uncover interspecies diversity in CBC operation. In a study of four C4 and five C3 species, principal components analysis separated C4 species from C3 species and also separated different C4 species. These separations were driven by metabolites that reflect known species differences in their biochemistry and pathways. Unexpectedly, there was also considerable diversity between the C3 species. Falling atmospheric CO2 and changing temperature, nitrogen, and water availability have driven evolution of C4 photosynthesis in multiple lineages. We propose that analogous selective pressures drove lineage-dependent evolution of the CBC in C3 species. Examples of species-dependent variation include differences in the balance between the CBC and the light reactions, and in the balance between regulated steps in the CBC. Metabolite profiles also reveal conserved features including inactivation of enzymes in low irradiance, and maintenance of CBC metabolites at relatively high levels in the absence of net CO2 fixation. These features may be important for photosynthetic efficiency in low light, fluctuating irradiance, and when stomata close due to low water availability.
Collapse
Affiliation(s)
- Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - 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
| |
Collapse
|
18
|
Lin MT, Orr DJ, Worrall D, Parry MAJ, Carmo-Silva E, Hanson MR. A procedure to introduce point mutations into the Rubisco large subunit gene in wild-type plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:876-887. [PMID: 33576096 DOI: 10.1111/tpj.15196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 01/22/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic inefficiencies limit the productivity and sustainability of crop production and the resilience of agriculture to future societal and environmental challenges. Rubisco is a key target for improvement as it plays a central role in carbon fixation during photosynthesis and is remarkably inefficient. Introduction of mutations to the chloroplast-encoded Rubisco large subunit rbcL is of particular interest for improving the catalytic activity and efficiency of the enzyme. However, manipulation of rbcL is hampered by its location in the plastome, with many species recalcitrant to plastome transformation, and by the plastid's efficient repair system, which can prevent effective maintenance of mutations introduced with homologous recombination. Here we present a system where the introduction of a number of silent mutations into rbcL within the model plant Nicotiana tabacum facilitates simplified screening via additional restriction enzyme sites. This system was used to successfully generate a range of transplastomic lines from wild-type N. tabacum with stable point mutations within rbcL in 40% of the transformants, allowing assessment of the effect of these mutations on Rubisco assembly and activity. With further optimization the approach offers a viable way forward for mutagenic testing of Rubisco function in planta within tobacco and modification of rbcL in other crops where chloroplast transformation is feasible. The transformation strategy could also be applied to introduce point mutations in other chloroplast-encoded genes.
Collapse
Affiliation(s)
- Myat T Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Dawn Worrall
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Elizabete Carmo-Silva
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| |
Collapse
|
19
|
Formation of Proto-Kranz in C3 Rice Induced by Spike-Stalk Injection Method. Int J Mol Sci 2021; 22:ijms22094305. [PMID: 33919137 PMCID: PMC8122280 DOI: 10.3390/ijms22094305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 01/08/2023] Open
Abstract
Introduction of C4 photosynthetic traits into C3 crops is an important strategy for improving photosynthetic capacity and productivity. Here, we report the research results of a variant line of sorghum-rice (SR) plant with big panicle and high spikelet density by introducing sorghum genome DNA into rice by spike-stalk injection. The whole-genome resequencing showed that a few sorghum genes could be integrated into the rice genome. Gene expression was confirmed for two C4 photosynthetic enzymes containing pyruvate, orthophosphate dikinase and phosphoenolpyruvate carboxykinase. Exogenous sorghum DNA integration induced a series of key traits associated with the C4 pathway called "proto-Kranz" anatomy, including leaf thickness, bundle sheath number and size, and chloroplast size in bundle sheath cells. Significantly, transgenic plants exhibited enhanced photosynthetic capacity resulting from both photosynthetic CO2-concentrating effect and improved energy balance, which led to an increase in carbohydrate levels and productivity. Furthermore, such rice plant exhibited delayed leaf senescence. In summary, this study provides a proof for the feasibility of inducing the transition from C3 leaf anatomy to proto-Kranz by spike-stalk injection to achieve efficient photosynthesis and increase productivity.
Collapse
|
20
|
Loeuille B, Thode V, Siniscalchi C, Andrade S, Rossi M, Pirani JR. Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera. PeerJ 2021; 9:e10886. [PMID: 33665028 PMCID: PMC7912680 DOI: 10.7717/peerj.10886] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/12/2021] [Indexed: 01/23/2023] Open
Abstract
Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.
Collapse
Affiliation(s)
- Benoit Loeuille
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Verônica Thode
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carolina Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States of America
| | - Sonia Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - José Rubens Pirani
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| |
Collapse
|
21
|
Cummins PL. The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:662425. [PMID: 34539685 PMCID: PMC8440988 DOI: 10.3389/fpls.2021.662425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/26/2021] [Indexed: 05/20/2023]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO) is the carbon-fixing enzyme present in most photosynthetic organisms, converting CO2 into organic matter. Globally, photosynthetic efficiency in terrestrial plants has become increasingly challenged in recent decades due to a rapid increase in atmospheric CO2 and associated changes toward warmer and dryer environments. Well adapted for these new climatic conditions, the C4 photosynthetic pathway utilizes carbon concentrating mechanisms to increase CO2 concentrations surrounding RuBisCO, suppressing photorespiration from the oxygenase catalyzed reaction with O2. The energy efficiency of C3 photosynthesis, from which the C4 pathway evolved, is thought to rely critically on an uninterrupted supply of chloroplast CO2. Part of the homeostatic mechanism that maintains this constancy of supply involves the CO2 produced as a byproduct of photorespiration in a negative feedback loop. Analyzing the database of RuBisCO kinetic parameters, we suggest that in genera (Flaveria and Panicum) for which both C3 and C4 examples are available, the C4 pathway evolved only from C3 ancestors possessing much lower than the average carboxylase specificity relative to that of the oxygenase reaction (S C/O=S C/S O), and hence, the higher CO2 levels required for development of the photorespiratory CO2 pump (C2 photosynthesis) essential in the initial stages of C4 evolution, while in the later stage (final optimization phase in the Flaveria model) increased CO2 turnover may have occurred, which would have been supported by the higher CO2 levels. Otherwise, C4 RuBisCO kinetic traits remain little changed from the ancestral C3 species. At the opposite end of the spectrum, C3 plants (from Limonium) with higher than average S C/O, which may be associated with the ability of increased CO2, relative to O2, affinity to offset reduced photorespiration and chloroplast CO2 levels, can tolerate high stress environments. It is suggested that, instead of inherently constrained by its kinetic mechanism, RuBisCO possesses the extensive kinetic plasticity necessary for adaptation to changes in photorespiration that occur in the homeostatic regulation of CO2 supply under a broad range of abiotic environmental conditions.
Collapse
|
22
|
Lin MT, Stone WD, Chaudhari V, Hanson MR. Small subunits can determine enzyme kinetics of tobacco Rubisco expressed in Escherichia coli. NATURE PLANTS 2020; 6:1289-1299. [PMID: 32929197 DOI: 10.1038/s41477-020-00761-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/28/2020] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) catalyses the first step in carbon fixation and is a strategic target for improving photosynthetic efficiency. In plants, Rubisco is composed of eight large and eight small subunits, and its biogenesis requires multiple chaperones. Here, we optimized a system to produce tobacco Rubisco in Escherichia coli by coexpressing chaperones in autoinduction medium. We successfully assembled tobacco Rubisco in E. coli with each small subunit that is normally encoded by the nuclear genome. Even though each enzyme carries only a single type of small subunit in E. coli, the enzymes exhibit carboxylation kinetics that are very similar to the carboxylation kinetics of the native Rubisco. Tobacco Rubisco assembled with a recently discovered trichome small subunit has a higher catalytic rate and a lower CO2 affinity compared with Rubisco complexes that are assembled with other small subunits. Our E. coli expression system will enable the analysis of features of both subunits of Rubisco that affect its kinetic properties.
Collapse
Affiliation(s)
- Myat T Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - William D Stone
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA
| | | | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
23
|
Goudet MMM, Orr DJ, Melkonian M, Müller KH, Meyer MT, Carmo-Silva E, Griffiths H. Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae. THE NEW PHYTOLOGIST 2020; 227:810-823. [PMID: 32249430 DOI: 10.1111/nph.16577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO2 uptake (K0.5 ), carbon isotope discrimination (δ13 C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ13 C and pyrenoid ultrastructure between high and low CO2 conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.
Collapse
Affiliation(s)
- Myriam M M Goudet
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, 50674, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, 45141, Essen, Germany
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | | | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| |
Collapse
|
24
|
Mehmood F, Abdullah, Ubaid Z, Shahzadi I, Ahmed I, Waheed MT, Poczai P, Mirza B. Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco ( Nicotiana rustica). PeerJ 2020; 8:e9552. [PMID: 32775052 PMCID: PMC7382938 DOI: 10.7717/peerj.9552] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323-25,369 bp each) separated by a large single-copy (LSC) region (86,510-86,716 bp) and a small single-copy (SSC) region (18,441-18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65-0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.
Collapse
Affiliation(s)
- Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zartasha Ubaid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iram Shahzadi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Bushra Mirza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
25
|
Shi W, Yue L, Guo J, Wang J, Yuan X, Dong S, Guo J, Guo P. Identification and evolution of C 4 photosynthetic pathway genes in plants. BMC PLANT BIOLOGY 2020; 20:132. [PMID: 32228460 PMCID: PMC7106689 DOI: 10.1186/s12870-020-02339-x] [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: 11/21/2019] [Accepted: 03/11/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND NADP-malic enzyme (NAPD-ME), and pyruvate orthophosphate dikinase (PPDK) are important enzymes that participate in C4 photosynthesis. However, the evolutionary history and forces driving evolution of these genes in C4 plants are not completely understood. RESULTS We identified 162 NADP-ME and 35 PPDK genes in 25 species and constructed respective phylogenetic trees. We classified NADP-ME genes into four branches, A1, A2, B1 and B2, whereas PPDK was classified into two branches in which monocots were in branch I and dicots were in branch II. Analyses of selective pressure on the NAPD-ME and PPDK gene families identified four positively selected sites, including 94H and 196H in the a5 branch of NADP-ME, and 95A and 559E in the e branch of PPDK at posterior probability thresholds of 95%. The positively selected sites were located in the helix and sheet regions. Quantitative RT-PCR (qRT-PCR) analyses revealed that expression levels of 6 NADP-ME and 2 PPDK genes from foxtail millet were up-regulated after exposure to light. CONCLUSION This study revealed that positively selected sites of NADP-ME and PPDK evolution in C4 plants. It provides information on the classification and positive selection of plant NADP-ME and PPDK genes, and the results should be useful in further research on the evolutionary history of C4 plants.
Collapse
Affiliation(s)
- Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Linqi Yue
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Jiahui Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Jianming Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Shuqi Dong
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Jie Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China.
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China.
| |
Collapse
|
26
|
Iñiguez C, Capó-Bauçà S, Niinemets Ü, Stoll H, Aguiló-Nicolau P, Galmés J. Evolutionary trends in RuBisCO kinetics and their co-evolution with CO 2 concentrating mechanisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:897-918. [PMID: 31820505 DOI: 10.1111/tpj.14643] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/15/2019] [Accepted: 11/27/2019] [Indexed: 05/19/2023]
Abstract
RuBisCO-catalyzed CO2 fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO2 concentrating mechanisms (CCMs) and/or the evolution of a more CO2 -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO2 /O2 concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO2 specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.
Collapse
Affiliation(s)
- Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia
| | - Heather Stoll
- Department of Earth Sciences, ETH Zürich, Sonnegstrasse 5, 8092, Zürich, Switzerland
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| |
Collapse
|
27
|
Busch FA. Photorespiration in the context of Rubisco biochemistry, CO 2 diffusion and metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:919-939. [PMID: 31910295 DOI: 10.1111/tpj.14674] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 05/11/2023]
Abstract
Photorespiratory metabolism is essential for plants to maintain functional photosynthesis in an oxygen-containing environment. Because the oxygenation reaction of Rubisco is followed by the loss of previously fixed carbon, photorespiration is often considered a wasteful process and considerable efforts are aimed at minimizing the negative impact of photorespiration on the plant's carbon uptake. However, the photorespiratory pathway has also many positive aspects, as it is well integrated within other metabolic processes, such as nitrogen assimilation and C1 metabolism, and it is important for maintaining the redox balance of the plant. The overall effect of photorespiratory carbon loss on the net CO2 fixation of the plant is also strongly influenced by the physiology of the leaf related to CO2 diffusion. This review outlines the distinction between Rubisco oxygenation and photorespiratory CO2 release as a basis to evaluate the costs and benefits of photorespiration.
Collapse
Affiliation(s)
- Florian A Busch
- Research School of Biology and ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Acton, ACT, 2601, Australia
| |
Collapse
|
28
|
Hermida-Carrera C, Fares MA, Font-Carrascosa M, Kapralov MV, Koch MA, Mir A, Molins A, Ribas-Carbó M, Rocha J, Galmés J. Exploring molecular evolution of Rubisco in C 3 and CAM Orchidaceae and Bromeliaceae. BMC Evol Biol 2020; 20:11. [PMID: 31969115 PMCID: PMC6977233 DOI: 10.1186/s12862-019-1551-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 11/29/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The CO2-concentrating mechanism associated to Crassulacean acid metabolism (CAM) alters the catalytic context for Rubisco by increasing CO2 availability and provides an advantage in particular ecological conditions. We hypothesized about the existence of molecular changes linked to these particular adaptations in CAM Rubisco. We investigated molecular evolution of the Rubisco large (L-) subunit in 78 orchids and 144 bromeliads with C3 and CAM photosynthetic pathways. The sequence analyses were complemented with measurements of Rubisco kinetics in some species with contrasting photosynthetic mechanism and differing in the L-subunit sequence. RESULTS We identified potential positively selected sites and residues with signatures of co-adaptation. The implementation of a decision tree model related Rubisco specific variable sites to the leaf carbon isotopic composition of the species. Differences in the Rubisco catalytic traits found among C3 orchids and between strong CAM and C3 bromeliads suggested Rubisco had evolved in response to differing CO2 concentration. CONCLUSIONS The results revealed that the variability in the Rubisco L-subunit sequence in orchids and bromeliads is composed of coevolving sites under potential positive adaptive signal. The sequence variability was related to δ13C in orchids and bromeliads, however it could not be linked to the variability found in the kinetic properties of the studied species.
Collapse
Affiliation(s)
- Carmen Hermida-Carrera
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Mario A. Fares
- Integrative and Systems Biology Group, Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas (CSIC–UPV), 46022 Valencia, Spain
- Department of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Marcel Font-Carrascosa
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Maxim V. Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU United Kingdom
| | - Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 9120 Heidelberg, Germany
| | - Arnau Mir
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, 07122 Palma, Illes Balears Spain
| | - Arántzazu Molins
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Miquel Ribas-Carbó
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| | - Jairo Rocha
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, 07122 Palma, Illes Balears Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Ctra. Valldemossa km. 7.5, 07122 Palma, Illes Balears Spain
| |
Collapse
|
29
|
Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution. Gene 2020; 732:144355. [PMID: 31935501 DOI: 10.1016/j.gene.2020.144355] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/13/2023]
Abstract
Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.
Collapse
|
30
|
Yamada K, Davydov II, Besnard G, Salamin N. Duplication history and molecular evolution of the rbcS multigene family in angiosperms. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6127-6139. [PMID: 31498865 PMCID: PMC6859733 DOI: 10.1093/jxb/erz363] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/12/2019] [Indexed: 05/22/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the main enzyme determining the rate of photosynthesis. The small subunit of the protein, encoded by the rbcS gene, has been shown to influence the catalytic efficiency, CO2 specificity, assembly, activity, and stability of RuBisCO. However, the evolution of the rbcS gene remains poorly studied. We inferred the phylogenetic tree of the rbcS gene in angiosperms using the nucleotide sequences and found that it is composed of two lineages that may have existed before the divergence of land plants. Although almost all species sampled carry at least one copy of lineage 1, genes of lineage 2 were lost in most angiosperm species. We found the specific residues that have undergone positive selection during the evolution of the rbcS gene. We detected intensive coevolution between each rbcS gene copy and the rbcL gene encoding the large subunit of RuBisCO. We tested the role played by each rbcS gene copy on the stability of the RuBisCO protein through homology modelling. Our results showed that this evolutionary constraint could limit the level of divergence seen in the rbcS gene, which leads to the similarity among the rbcS gene copies of lineage 1 within species.
Collapse
Affiliation(s)
- Kana Yamada
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Iakov I Davydov
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174), CNRS-UPS-IRD, University of Toulouse III, Toulouse Cedex, France
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
31
|
Yao X, Tan YH, Yang JB, Wang Y, Corlett RT, Manen JF. Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae). BMC Evol Biol 2019; 19:192. [PMID: 31638910 PMCID: PMC6805373 DOI: 10.1186/s12862-019-1521-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/27/2019] [Indexed: 12/26/2022] Open
Abstract
Background The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range. Results The rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (> 3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common. Conclusions This study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.
Collapse
Affiliation(s)
- Xin Yao
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yun-Hong Tan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yan Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Jean-François Manen
- Laboratoire de Systématique Végétale et Biodiversité, University of Geneva (retired), Chemin de l'Impératrice 1, CH-1292, Chambésy, Switzerland.
| |
Collapse
|
32
|
Rickaby REM, Eason Hubbard MR. Upper ocean oxygenation, evolution of RuBisCO and the Phanerozoic succession of phytoplankton. Free Radic Biol Med 2019; 140:295-304. [PMID: 31075497 PMCID: PMC6856715 DOI: 10.1016/j.freeradbiomed.2019.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/10/2019] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
Abstract
Evidence is compiled to demonstrate a redox scale within Earth's photosynthesisers that correlates the specificity of their RuBisCO with organismal metabolic tolerance to anoxia, and ecological selection by dissolved O2/CO2 and nutrients. The Form 1B RuBisCO found in the chlorophyte green algae, has a poor selectivity between the two dissolved substrates, O2 and CO2, at the active site. This enzyme appears adapted to lower O2/CO2 ratios, or more "anoxic" conditions and therefore requires additional energetic or nutrient investment in a carbon concentrating mechanism (CCM) to boost the intracellular CO2/O2 ratio and maintain competitive carboxylation rates under increasingly high O2/CO2 conditions in the environment. By contrast the coccolithophores and diatoms evolved containing the more selective Rhodophyte Form 1D RuBisCO, better adapted to a higher O2/CO2 ratio, or more oxic conditions. This Form 1D RuBisCO requires lesser energetic or nutrient investment in a CCM to attain high carboxylation rates under environmentally high O2/CO2 ratios. Such a physiological relationship may underpin the succession of phytoplankton in the Phanerozoic oceans: the coccolithophores and diatoms took over the oceanic realm from the incumbent cyanobacteria and green algae when the upper ocean became persistently oxygenated, alkaline and more oligotrophic. The facultatively anaerobic green algae, able to tolerate the anoxic conditions of the water column and a periodically inundated soil, were better poised to adapt to the fluctuating anoxia associated with periods of submergence and emergence and transition onto the land. The induction of a CCM may exert a natural limit to the improvement of RuBisCO efficiency over Earth history. Rubisco specificity appears to adapt on the timescale of ∼100 Myrs. So persistent elevation of CO2/O2 ratios in the intracellular environment around the enzyme, may induce a relaxation in RuBisCO selectivity for CO2 relative to O2. The most efficient RuBisCO for net carboxylation is likely to be found in CCM-lacking algae that have been exposed to hyperoxic conditions for at least 100 Myrs, such as intertidal brown seaweeds.
Collapse
Affiliation(s)
- Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK.
| | - M R Eason Hubbard
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| |
Collapse
|
33
|
Ma WJ, Santos del Blanco L, Pannell JR. A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology and hybrid sterility. ANNALS OF BOTANY 2019; 124:165-178. [PMID: 31098610 PMCID: PMC6676388 DOI: 10.1093/aob/mcz058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND AIMS Polyploidy has played a major role in the origin of new plant species, probably because of the expansion of polyploid populations in the species' ecological niche, and because reproductive isolation can be established between a new polyploid population and its diploid progenitor species. It is well established that most polyploid species are polyphyletic, with multiple independent origins, and that polyploid genomes may undergo rapid change after their duplication and hybridization associated with their origin. We considered whether multiple independent origins and rapid genomic change might lead to reproductive isolation between polyploid populations of the same ploidy but with potentially different evolutionary histories. METHODS We tested our hypothesis by assessing differences in DNA content and morphology, the evolution of reproductive isolation, and the phylogenetic placement of two broadly sympatric hexaploid lineages of the wind-pollinated annual plant Mercurialis annua hitherto regarded as populations of the same species. KEY RESULTS The two hexaploid lineages of M. annua have slightly divergent DNA content, and distinct inflorescence morphology. They also fall into largely different clades of a chloroplast phylogeny and are reproductively isolated from one another. CONCLUSIONS The distinct evolutionary histories of the two hexaploid lineages of M. annua have contributed to the remarkable reproductive diversity of the species complex. It seems likely that reproductive interference between them will eventually lead to the displacement of one lineage by the other via pollen swamping. Thus, whereas polyploidization can contribute to speciation, diversification might also be compromised by reproductive interference.
Collapse
Affiliation(s)
- Wen-Juan Ma
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
34
|
Xie DF, Yu HX, Price M, Xie C, Deng YQ, Chen JP, Yu Y, Zhou SD, He XJ. Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome. FRONTIERS IN PLANT SCIENCE 2019; 10:460. [PMID: 31114591 PMCID: PMC6503222 DOI: 10.3389/fpls.2019.00460] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
Collapse
Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuan Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi-Qi Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jun-Pei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
35
|
Arrivault S, Alexandre Moraes T, Obata T, Medeiros DB, Fernie AR, Boulouis A, Ludwig M, Lunn JE, Borghi GL, Schlereth A, Guenther M, Stitt M. Metabolite profiles reveal interspecific variation in operation of the Calvin-Benson cycle in both C4 and C3 plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1843-1858. [PMID: 30773587 PMCID: PMC6436152 DOI: 10.1093/jxb/erz051] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/29/2019] [Indexed: 05/18/2023]
Abstract
Low atmospheric CO2 in recent geological time led to the evolution of carbon-concentrating mechanisms (CCMs) such as C4 photosynthesis in >65 terrestrial plant lineages. We know little about the impact of low CO2 on the Calvin-Benson cycle (CBC) in C3 species that did not evolve CCMs, representing >90% of terrestrial plant species. Metabolite profiling provides a top-down strategy to investigate the operational balance in a pathway. We profiled CBC intermediates in a panel of C4 (Zea mays, Setaria viridis, Flaveria bidentis, and F. trinervia) and C3 species (Oryza sativa, Triticium aestivum, Arabidopsis thaliana, Nicotiana tabacum, and Manihot esculenta). Principal component analysis revealed differences between C4 and C3 species that were driven by many metabolites, including lower ribulose 1,5-bisphosphate in C4 species. Strikingly, there was also considerable variation between C3 species. This was partly due to different chlorophyll and protein contents, but mainly to differences in relative levels of metabolites. Correlation analysis indicated that one contributory factor was the balance between fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, phosphoribulokinase, and Rubisco. Our results point to the CBC having experienced different evolutionary trajectories in C3 species since the ancestors of modern plant lineages diverged. They underline the need to understand CBC operation in a wide range of species.
Collapse
Affiliation(s)
- Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | | | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
- Present address: Department of Biochemistry, Center for Plant Science Innovation, University of Nebraska-Lincoln, 1901 Vine Str, Lincoln, NE 68588, USA
| | - David B Medeiros
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Alix Boulouis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
- Present address: Institut de Biologie Physico-Chimique, CNRS - Sorbonne Université, Paris, France
| | - Martha Ludwig
- School of Molecular Sciences, The University of Western Australia, Crawley WA, Australia
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Gian Luca Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Armin Schlereth
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Manuela Guenther
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
- Correspondence:
| |
Collapse
|
36
|
Iñiguez C, Galmés J, Gordillo FJL. Rubisco carboxylation kinetics and inorganic carbon utilization in polar versus cold-temperate seaweeds. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1283-1297. [PMID: 30576461 PMCID: PMC6382342 DOI: 10.1093/jxb/ery443] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/07/2018] [Indexed: 05/07/2023]
Abstract
Despite the high productivity and ecological importance of seaweeds in polar coastal regions, little is known about their carbon utilization mechanisms, especially the kinetics of the CO2-fixing enzyme Rubisco. We analyzed Rubisco carboxylation kinetics at 4 °C and 25 °C in 12 diverse polar seaweed species (including cold-temperate populations of the same species) and the relationship with their ability to use bicarbonate, by using 13C isotope discrimination and pH drift experiments. We observed a large variation in Rubisco carboxylation kinetics among the selected species, although no correlation was found between either the Michaelis-Menten constant for CO2 (Kc) or Rubisco content per total soluble protein ([Rubisco]/[TSP]) and the ability to use bicarbonate for non-green seaweeds. This study reports intraspecific Rubisco cold adaptation by means of either higher Rubisco carboxylation turnover rate (kcatc) and carboxylase efficiency (kcatc/Kc) at 4 °C or higher [Rubisco]/[TSP] in some of the analyzed species. Our data point to a widespread ability for photosynthetic bicarbonate usage among polar seaweeds, despite the higher affinity of Rubisco for CO2 and higher dissolved CO2 concentration in cold seawater. Moreover, the reported catalytic variation within form ID Rubisco might avert the canonical trade-off previously observed between Kc and kcatc for plant Rubiscos.
Collapse
Affiliation(s)
- Concepción Iñiguez
- Department of Ecology, Faculty of Sciences, University of Malaga, Boulevard Louis Pasteur s/n, Málaga, Spain
- Research Group in Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Carretera de Valldemossa, Palma, Illes Balears, Spain
| | - Jeroni Galmés
- Research Group in Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Carretera de Valldemossa, Palma, Illes Balears, Spain
| | - Francisco J L Gordillo
- Department of Ecology, Faculty of Sciences, University of Malaga, Boulevard Louis Pasteur s/n, Málaga, Spain
| |
Collapse
|
37
|
Sedelnikova OV, Hughes TE, Langdale JA. Understanding the Genetic Basis of C 4 Kranz Anatomy with a View to Engineering C 3 Crops. Annu Rev Genet 2018; 52:249-270. [PMID: 30208293 DOI: 10.1146/annurev-genet-120417-031217] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One of the most remarkable examples of convergent evolution is the transition from C3 to C4 photosynthesis, an event that occurred on over 60 independent occasions. The evolution of C4 is particularly noteworthy because of the complexity of the developmental and metabolic changes that took place. In most cases, compartmentalized metabolic reactions were facilitated by the development of a distinct leaf anatomy known as Kranz. C4 Kranz anatomy differs from ancestral C3 anatomy with respect to vein spacing patterns across the leaf, cell-type specification around veins, and cell-specific organelle function. Here we review our current understanding of how Kranz anatomy evolved and how it develops, with a focus on studies that are dissecting the underlying genetic mechanisms. This research field has gained prominence in recent years because understanding the genetic regulation of Kranz may enable the C3-to-C4 transition to be engineered, an endeavor that would significantly enhance crop productivity.
Collapse
Affiliation(s)
- Olga V Sedelnikova
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom; , ,
| | - Thomas E Hughes
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom; , ,
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom; , ,
| |
Collapse
|
38
|
Yin H, Guo HB, Weston DJ, Borland AM, Ranjan P, Abraham PE, Jawdy SS, Wachira J, Tuskan GA, Tschaplinski TJ, Wullschleger SD, Guo H, Hettich RL, Gross SM, Wang Z, Visel A, Yang X. Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. BMC Genomics 2018; 19:588. [PMID: 30081833 PMCID: PMC6090859 DOI: 10.1186/s12864-018-4964-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in genus Agave is largely unknown. Results Using an approach that integrated genomics, gene co-expression networks, comparative genomics and protein structure analyses, we investigated the molecular evolution of CAM as exemplified in Agave. Comparative genomics analyses among C3, C4 and CAM species revealed that core metabolic components required for CAM have ancient genomic origins traceable to non-vascular plants while regulatory proteins required for diel re-programming of metabolism have a more recent origin shared among C3, C4 and CAM species. We showed that accelerated evolution of key functional domains in proteins responsible for primary metabolism and signaling, together with a diel re-programming of the transcription of genes involved in carbon fixation, carbohydrate processing, redox homeostasis, and circadian control is required for the evolution of CAM in Agave. Furthermore, we highlighted the potential candidates contributing to the adaptation of CAM functional modules. Conclusions This work provides evidence of adaptive evolution of CAM related pathways. We showed that the core metabolic components required for CAM are shared by non-vascular plants, but regulatory proteins involved in re-reprogramming of carbon fixation and metabolite transportation appeared more recently. We propose that the accelerated evolution of key proteins together with a diel re-programming of gene expression were required for CAM evolution from C3 ancestors in Agave. Electronic supplementary material The online version of this article (10.1186/s12864-018-4964-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Present address: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Hao-Bo Guo
- Department of Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Paul E Abraham
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Wachira
- Department of Biology, Morgan State University, Baltimore, MD, 21251, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hong Guo
- Department of Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert L Hettich
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA
| | - Stephen M Gross
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Present address: Illumina, Inc., San Diego, CA, 92122, USA
| | - Zhong Wang
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. .,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| |
Collapse
|
39
|
Piot A, Hackel J, Christin PA, Besnard G. One-third of the plastid genes evolved under positive selection in PACMAD grasses. PLANTA 2018; 247:255-266. [PMID: 28956160 DOI: 10.1007/s00425-017-2781-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/18/2017] [Indexed: 05/10/2023]
Abstract
We demonstrate that rbcL underwent strong positive selection during the C 3 -C 4 photosynthetic transitions in PACMAD grasses, in particular the 3' end of the gene. In contrast, selective pressures on other plastid genes vary widely and environmental drivers remain to be identified. Plastid genomes have been widely used to infer phylogenetic relationships among plants, but the selective pressures driving their evolution have not been systematically investigated. In our study, we analyse all protein-coding plastid genes from 113 species of PACMAD grasses (Poaceae) to evaluate the selective pressures driving their evolution. Our analyses confirm that the gene encoding the large subunit of RubisCO (rbcL) evolved under strong positive selection after C3-C4 photosynthetic transitions. We highlight new codons in rbcL that underwent parallel changes, in particular those encoding the C-terminal part of the protein. C3-C4 photosynthetic shifts did not significantly affect the evolutionary dynamics of other plastid genes. Instead, while two-third of the plastid genes evolved under purifying selection or neutrality, 25 evolved under positive selection across the PACMAD clade. This set of genes encode for proteins involved in diverse functions, including self-replication of plastids and photosynthesis. Our results suggest that plastid genes widely adapt to changing ecological conditions, but factors driving this evolution largely remain to be identified.
Collapse
Affiliation(s)
- Anthony Piot
- Laboratoire Evolution and Diversité Biologique (EDB, UMR 5174), CNRS/ENSFEA/IRD/Université Toulouse III, 118 Route de Narbonne, 31062, Toulouse, France.
| | - Jan Hackel
- Laboratoire Evolution and Diversité Biologique (EDB, UMR 5174), CNRS/ENSFEA/IRD/Université Toulouse III, 118 Route de Narbonne, 31062, Toulouse, France
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB, UMR 5174), CNRS/ENSFEA/IRD/Université Toulouse III, 118 Route de Narbonne, 31062, Toulouse, France.
| |
Collapse
|
40
|
Hermida-Carrera C, Fares MA, Fernández Á, Gil-Pelegrín E, Kapralov MV, Mir A, Molins A, Peguero-Pina JJ, Rocha J, Sancho-Knapik D, Galmés J. Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. PLoS One 2017; 12:e0183970. [PMID: 28859145 PMCID: PMC5578625 DOI: 10.1371/journal.pone.0183970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/15/2017] [Indexed: 12/29/2022] Open
Abstract
Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML.
Collapse
Affiliation(s)
- Carmen Hermida-Carrera
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Mario A. Fares
- Integrative and Systems Biology Group, Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas (CSIC–UPV), Valencia, Spain
- Department of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - Ángel Fernández
- Unidad de Recursos Forestales, C.I.T.A. de Aragón, Zaragoza, Spain
| | | | - Maxim V. Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-Upon-Tyne, United Kingdom
| | - Arnau Mir
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, Palma, Balearic Islands, Spain
| | - Arántzazu Molins
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | | | - Jairo Rocha
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, Palma, Balearic Islands, Spain
| | | | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| |
Collapse
|
41
|
Yerramsetty P, Agar EM, Yim WC, Cushman JC, Berry JO. An rbcL mRNA-binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4635-4649. [PMID: 28981775 PMCID: PMC5853808 DOI: 10.1093/jxb/erx264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Nuclear-encoded RLSB protein binds chloroplastic rbcL mRNA encoding the Rubisco large subunit. RLSB is highly conserved across all groups of land plants and is associated with positive post-transcriptional regulation of rbcL expression. In C3 leaves, RLSB and Rubisco occur in all chlorenchyma cell chloroplasts, while in C4 leaves these accumulate only within bundle sheath (BS) chloroplasts. RLSB's role in rbcL expression makes modification of its localization a likely prerequisite for the evolutionary restriction of Rubisco to BS cells. Taking advantage of evolutionarily conserved RLSB orthologs in several C3, C3-C4, C4-like, and C4 photosynthetic types within the genus Flaveria, we show that low level RLSB sequence divergence and modification to BS specificity coincided with ontogeny of Rubisco specificity and Kranz anatomy during C3 to C4 evolution. In both C3 and C4 species, Rubisco production reflected RLSB production in all cell types, tissues, and conditions examined. Co-localization occurred only in photosynthetic tissues, and both proteins were co-ordinately induced by light at post-transcriptional levels. RLSB is currently the only mRNA-binding protein to be associated with rbcL gene regulation in any plant, with variations in sequence and acquisition of cell type specificity reflecting the progression of C4 evolution within the genus Flaveria.
Collapse
Affiliation(s)
- Pradeep Yerramsetty
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Erin M Agar
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - James O Berry
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| |
Collapse
|
42
|
Young JN, Hopkinson BM. The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3751-3762. [PMID: 28645158 DOI: 10.1093/jxb/erx130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Diatoms are a diverse group of unicellular algae that contribute significantly to global photosynthetic carbon fixation and export in the modern ocean, and are an important source of microfossils for paleoclimate reconstructions. Because of their importance in the environment, diatoms have been a focus of study on the physiology and ecophysiology of carbon fixation, in particular their CO2-concentrating mechanisms (CCMs) and Rubisco characteristics. While carbon fixation in diatoms is not as well understood as in certain model aquatic photoautotrophs, a greater number of species have been examined in diatoms. Recent work has highlighted a large diversity in the function, physiology, and kinetics of both the CCM and Rubisco between different diatom species. This diversity was unexpected since it has generally been assumed that CCMs and Rubiscos were similar within major algal lineages as the result of selective events deep in evolutionary history, and suggests a more recent co-evolution between the CCM and Rubisco within diatoms. This review explores our current understanding of the diatom CCM and highlights the diversity of both the CCM and Rubisco kinetics. We will suggest possible environmental, physiological, and evolutionary drivers for the co-evolution of the CCM and Rubisco in diatoms.
Collapse
Affiliation(s)
- Jodi N Young
- University of Washington, School of Oceanography, Seattle, WA 98105, USA
| | | |
Collapse
|
43
|
Tonti-Filippini J, Nevill PG, Dixon K, Small I. What can we do with 1000 plastid genomes? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:808-818. [PMID: 28112435 DOI: 10.1111/tpj.13491] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 05/21/2023]
Abstract
The plastid genome of plants is the smallest and most gene-rich of the three genomes in each cell and the one generally present in the highest copy number. As a result, obtaining plastid DNA sequence is a particularly cost-effective way of discovering genetic information about a plant. Until recently, the sequence information gathered in this way was generally limited to small portions of the genome amplified by polymerase chain reaction, but recent advances in sequencing technology have stimulated a substantial rate of increase in the sequencing of complete plastid genomes. Within the last year, the number of complete plastid genomes accessible in public sequence repositories has exceeded 1000. This sudden flood of data raises numerous challenges in data analysis and interpretation, but also offers the keys to potential insights across large swathes of plant biology. We examine what has been learnt so far, what more could be learnt if we look at the data in the right way, and what we might gain from the tens of thousands more genome sequences that will surely arrive in the next few years. The most exciting new discoveries are likely to be made at the interdisciplinary interfaces between molecular biology and ecology.
Collapse
Affiliation(s)
- Julian Tonti-Filippini
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Paul G Nevill
- Department of Environment and Agriculture, ARC Centre for Mine Site Restoration, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Kingsley Dixon
- Department of Environment and Agriculture, ARC Centre for Mine Site Restoration, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| |
Collapse
|
44
|
Lu L, Cox CJ, Mathews S, Wang W, Wen J, Chen Z. Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae). Cladistics 2017; 34:57-77. [DOI: 10.1111/cla.12191] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2017] [Indexed: 12/25/2022] Open
Affiliation(s)
- Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Cymon J. Cox
- Centro de Ciências do Mar Universidade do Algarve Gambelas Faro 8005‐319 Portugal
| | - Sarah Mathews
- CSIRO National Research Collections Australian National Herbarium Canberra ACT 2601 Australia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Jun Wen
- Department of Botany National Museum of Natural History MRC166, Smithsonian Institution Washington DC 20013‐7012 USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| |
Collapse
|
45
|
Sharwood RE, Crous KY, Whitney SM, Ellsworth DS, Ghannoum O. Linking photosynthesis and leaf N allocation under future elevated CO2 and climate warming in Eucalyptus globulus. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1157-1167. [PMID: 28064178 PMCID: PMC5444472 DOI: 10.1093/jxb/erw484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Leaf-level photosynthetic processes and their environmental dependencies are critical for estimating CO2 uptake from the atmosphere. These estimates use biochemical-based models of photosynthesis that require accurate Rubisco kinetics. We investigated the effects of canopy position, elevated atmospheric CO2 [eC; ambient CO2 (aC)+240 ppm] and elevated air temperature (eT; ambient temperature (aT)+3 °C) on Rubisco content and activity together with the relationship between leaf N and Vcmax (maximal Rubisco carboxylation rate) of 7 m tall, soil-grown Eucalyptus globulus trees. The kinetics of E. globulus and tobacco Rubisco at 25 °C were similar. In vitro estimates of Vcmax derived from measures of E. globulus Rubisco content and kinetics were consistent, although slightly lower, than the in vivo rates extrapolated from gas exchange. In E. globulus, the fraction of N invested in Rubisco was substantially lower than for crop species and varied with treatments. Photosynthetic acclimation of E. globulus leaves to eC was underpinned by reduced leaf N and Rubisco contents; the opposite occurred in response to eT coinciding with growth resumption in spring. Our findings highlight the adaptive capacity of this key forest species to allocate leaf N flexibly to Rubisco and other photosynthetic proteins across differing canopy positions in response to future, warmer and elevated [CO2] climates.
Collapse
Affiliation(s)
- Robert E Sharwood
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australia
| | - Kristine Y Crous
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australia
| | - David S Ellsworth
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Oula Ghannoum
- ARC Centre of Excellence for Translational Photosynthesis, Australia
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| |
Collapse
|
46
|
Sharwood RE. Engineering chloroplasts to improve Rubisco catalysis: prospects for translating improvements into food and fiber crops. THE NEW PHYTOLOGIST 2017; 213:494-510. [PMID: 27935049 DOI: 10.1111/nph.14351] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/10/2016] [Indexed: 05/19/2023]
Abstract
494 I. 495 II. 496 III. 496 IV. 499 V. 499 VI. 501 VII. 501 VIII. 502 IX. 505 X. 506 507 References 507 SUMMARY: The uncertainty of future climate change is placing pressure on cropping systems to continue to provide stable increases in productive yields. To mitigate future climates and the increasing threats against global food security, new solutions to manipulate photosynthesis are required. This review explores the current efforts available to improve carbon assimilation within plant chloroplasts by engineering Rubisco, which catalyzes the rate-limiting step of CO2 fixation. Fixation of CO2 and subsequent cycling of 3-phosphoglycerate through the Calvin cycle provides the necessary carbohydrate building blocks for maintaining plant growth and yield, but has to compete with Rubisco oxygenation, which results in photorespiration that is energetically wasteful for plants. Engineering improvements in Rubisco is a complex challenge and requires an understanding of chloroplast gene regulatory pathways, and the intricate nature of Rubisco catalysis and biogenesis, to transplant more efficient forms of Rubisco into crops. In recent times, major advances in Rubisco engineering have been achieved through improvement of our knowledge of Rubisco synthesis and assembly, and identifying amino acid catalytic switches in the L-subunit responsible for improvements in catalysis. Improving the capacity of CO2 fixation in crops such as rice will require further advances in chloroplast bioengineering and Rubisco biogenesis.
Collapse
Affiliation(s)
- Robert E Sharwood
- ARC Center of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| |
Collapse
|
47
|
Schuler ML, Mantegazza O, Weber APM. Engineering C4 photosynthesis into C3 chassis in the synthetic biology age. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:51-65. [PMID: 26945781 DOI: 10.1111/tpj.13155] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 05/21/2023]
Abstract
C4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long-standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon-concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution.
Collapse
Affiliation(s)
- Mara L Schuler
- Institute for Plant Molecular and Developmental Biology, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Otho Mantegazza
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225, Düsseldorf, Germany
| |
Collapse
|
48
|
von Caemmerer S, Furbank RT. Strategies for improving C4 photosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:125-34. [PMID: 27127850 DOI: 10.1016/j.pbi.2016.04.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 05/22/2023]
Abstract
Recent activities to improve photosynthetic performance in crop plants has focused mainly on C3 photosynthesis where there are clear identified targets such as improving Rubisco kinetics, installation of a CO2 concentrating mechanism and alleviating limitations in chloroplast electron transport. Here we address strategies to improve photosynthetic performance in C4 plants, which utilize a CO2 concentrating mechanism, having evolved a complex blend of anatomy and biochemistry to achieve this. While the limitations to photosynthetic flux are not as well studied in C4 plants, work in transgenic Flaveria bidentis, a transformable model C4 dicot, and recent transcriptional analysis of leaves from diverse C4 plants, provides several gene candidates for improvement of carbon metabolism (such as pyruvate orthophosphate dikinase, phosphoenolpyruvate carboxylase and Rubisco) and for access of CO2 to phosphoenolpyruvate carboxylase in the mesophyll cells (such as carbonic anhydrase and CO2 porins). Chloroplast electron transport in C4 plants is shared between the two cell types, providing opportunities not only to alleviate limitations to flux through intersystem electron transport by targeting nuclear encoded proteins in the cytochrome (Cyt) b6/f complex, but in better sharing the harvesting of light energy between mesophyll and bundle sheath chloroplasts. Gene candidates for improvement of C4 photosynthesis could be utilized either through transgenic approaches or via mining natural allelic variation in sequenced populations of crop species.
Collapse
Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Science Division, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia.
| | - Robert T Furbank
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Science Division, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| |
Collapse
|
49
|
Sharwood RE, Ghannoum O, Whitney SM. Prospects for improving CO2 fixation in C3-crops through understanding C4-Rubisco biogenesis and catalytic diversity. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:135-42. [PMID: 27131319 DOI: 10.1016/j.pbi.2016.04.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/30/2016] [Accepted: 04/04/2016] [Indexed: 05/09/2023]
Abstract
By operating a CO2 concentrating mechanism, C4-photosynthesis offers highly successful solutions to remedy the inefficiency of the CO2-fixing enzyme Rubisco. C4-plant Rubisco has characteristically evolved faster carboxylation rates with low CO2 affinity. Owing to high CO2 concentrations in bundle sheath chloroplasts, faster Rubisco enhances resource use efficiency in C4 plants by reducing the energy and carbon costs associated with photorespiration and lowering the nitrogen investment in Rubisco. Here, we show that C4-Rubisco from some NADP-ME species, such as maize, are also of potential benefit to C3-photosynthesis under current and future atmospheric CO2 pressures. Realizing this bioengineering endeavour necessitates improved understanding of the biogenesis requirements and catalytic variability of C4-Rubisco, as well as the development of transformation capabilities to engineer Rubisco in a wider variety of food and fibre crops.
Collapse
Affiliation(s)
- Robert E Sharwood
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia.
| | - Oula Ghannoum
- ARC Centre of Excellence for Translational Photosynthesis, Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Spencer M Whitney
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| |
Collapse
|
50
|
Cytonuclear Coordination Is Not Immediate upon Allopolyploid Formation in Tragopogon miscellus (Asteraceae) Allopolyploids. PLoS One 2015; 10:e0144339. [PMID: 26646761 PMCID: PMC4673006 DOI: 10.1371/journal.pone.0144339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/17/2015] [Indexed: 11/19/2022] Open
Abstract
Allopolyploids, formed by hybridization and chromosome doubling, face the immediate challenge of having duplicated nuclear genomes that interact with the haploid and maternally inherited cytoplasmic (plastid and mitochondrial) genomes. Most of our knowledge of the genomic consequences of allopolyploidy has focused on the fate of the duplicated nuclear genes without regard to their potential interactions with cytoplasmic genomes. As a step toward understanding the fates of nuclear-encoded subunits that are plastid-targeted, here we examine the retention and expression of the gene encoding the small subunit of Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco; rbcS) in multiple populations of allotetraploid Tragopogon miscellus (Asteraceae). These polyploids formed recently (~80 years ago) and repeatedly from T. dubius and T. pratensis in the northwestern United States. Examination of 79 T. miscellus individuals from 10 natural populations, as well as 25 synthetic allotetraploids, including reciprocally formed plants, revealed a low percentage of naturally occurring individuals that show a bias in either gene (homeolog) loss (12%) or expression (16%), usually toward maintaining the maternal nuclear copy of rbcS. For individuals showing loss, seven retained the maternally derived rbcS homeolog only, while three had the paternally derived copy. All of the synthetic polyploid individuals examined (S0 and S1 generations) retained and expressed both parental homeologs. These results demonstrate that cytonuclear coordination does not happen immediately upon polyploid formation in Tragopogon miscellus.
Collapse
|