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Mohanta TK, Mohanta YK, Kaushik P, Kumar J. Physiology, genomics, and evolutionary aspects of desert plants. J Adv Res 2024; 58:63-78. [PMID: 37160225 PMCID: PMC10982872 DOI: 10.1016/j.jare.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture. AIM OF THE REVIEW The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture. KEY SCIENTIFIC CONCEPTS OF REVIEW This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 611, Oman.
| | - Yugal Kishore Mohanta
- Dept. of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya 793101, India
| | - Prashant Kaushik
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, United States
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Weraduwage SM, Whitten D, Kulke M, Sahu A, Vermaas JV, Sharkey TD. The isoprene-responsive phosphoproteome provides new insights into the putative signalling pathways and novel roles of isoprene. PLANT, CELL & ENVIRONMENT 2024; 47:1099-1117. [PMID: 38038355 DOI: 10.1111/pce.14776] [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: 08/01/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023]
Abstract
Many plants, especially trees, emit isoprene in a highly light- and temperature-dependent manner. The advantages for plants that emit, if any, have been difficult to determine. Direct effects on membranes have been disproven. New insights have been obtained by RNA sequencing, proteomic and metabolomic studies. We determined the responses of the phosphoproteome to exposure of Arabidopsis leaves to isoprene in the gas phase for either 1 or 5 h. Isoprene effects that were not apparent from RNA sequencing and other methods but were apparent in the phosphoproteome include effects on chloroplast movement proteins and membrane remodelling proteins. Several receptor kinases were found to have altered phosphorylation levels. To test whether potential isoprene receptors could be identified, we used molecular dynamics simulations to test for proteins that might have strong binding to isoprene and, therefore might act as receptors. Although many Arabidopsis proteins were found to have slightly higher binding affinities than a reference set of Homo sapiens proteins, no specific receptor kinase was found to have a very high binding affinity. The changes in chloroplast movement, photosynthesis capacity and so forth, found in this work, are consistent with isoprene responses being especially useful in the upper canopy of trees.
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Affiliation(s)
- Sarathi M Weraduwage
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Departments of Biology and Biochemistry, Bishop's University, Sherbrooke, Quebec, Canada
| | - Douglas Whitten
- Research Technology Support Facility-Proteomics Core, Michigan State University, East Lansing, Michigan, USA
| | - Martin Kulke
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- School of Natural Sciences, Technische Universität München, Munich, Germany
| | - Abira Sahu
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Thomas D Sharkey
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
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Perron N, Kirst M, Chen S. Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate. PLANT COMMUNICATIONS 2024; 5:100772. [PMID: 37990498 PMCID: PMC10943566 DOI: 10.1016/j.xplc.2023.100772] [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: 06/20/2023] [Revised: 07/27/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis. A considerable challenge in the coming years will be to develop crops that can cope with the consequences of declining freshwater resources and changing temperatures. One approach to meeting this challenge may lie in our understanding of plant photosynthetic adaptations and water use efficiency. Plants from various taxa have evolved crassulacean acid metabolism (CAM), a water-conserving adaptation of photosynthetic carbon dioxide fixation that enables plants to thrive under semi-arid or seasonally drought-prone conditions. Although past research on CAM has led to a better understanding of the inner workings of plant resilience and adaptation to stress, successful introduction of this pathway into C3 or C4 plants has not been reported. The recent revolution in molecular, systems, and synthetic biology, as well as innovations in high-throughput data generation and mining, creates new opportunities to uncover the minimum genetic tool kit required to introduce CAM traits into drought-sensitive crops. Here, we propose four complementary research avenues to uncover this tool kit. First, genomes and computational methods should be used to improve understanding of the nature of variations that drive CAM evolution. Second, single-cell 'omics technologies offer the possibility for in-depth characterization of the mechanisms that trigger environmentally controlled CAM induction. Third, the rapid increase in new 'omics data enables a comprehensive, multimodal exploration of CAM. Finally, the expansion of functional genomics methods is paving the way for integration of CAM into farming systems.
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Affiliation(s)
- Noé Perron
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32608, USA
| | - Matias Kirst
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32608, USA; School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32603, USA.
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677-1848, USA.
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Sato R, Kondo Y, Agarie S. The first released available genome of the common ice plant ( Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C 3-CAM photosynthetic conversion, and halophilism. F1000Res 2024; 12:448. [PMID: 38618020 PMCID: PMC11016173 DOI: 10.12688/f1000research.129958.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2024] [Indexed: 04/16/2024] Open
Abstract
Background The common ice plant ( Mesembryanthemum crystallinum L.) is an annual herb belonging to the genus Mesembryanthemum of the family Aizoaceae, native to Southern Africa. Methods We performed shotgun genome paired-end sequencing using the Illumina platform to determine the genome sequence of the ice plants. We assembled the whole genome sequences using the genome assembler "ALGA" and "Redundans", then released them as available genomic information. Finally, we mainly estimated the potential genomic function by the homology search method. Results A draft genome was generated with a total length of 286 Mb corresponding to 79.2% of the estimated genome size (361 Mb), consisting of 49,782 contigs. It encompassed 93.49% of the genes of terrestrial higher plants, 99.5% of the ice plant transcriptome, and 100% of known DNA sequences. In addition, 110.9 Mb (38.8%) of repetitive sequences and untranslated regions, 971 tRNA, and 100 miRNA loci were identified, and their effects on stress tolerance and photosynthesis were investigated. Molecular phylogenetic analysis based on ribosomal DNA among 26 kinds of plant species revealed genetic similarity between the ice plant and poplar, which have salt tolerance. Overall, 35,702 protein-coding regions were identified in the genome, of which 56.05% to 82.59% were annotated and submitted to domain searches and gene ontology (GO) analyses, which found that eighteen GO terms stood out among five plant species. These terms were related to biological defense, growth, reproduction, transcription, post-transcription, and intermembrane transportation, regarded as one of the fundamental results of using the utilized ice plant genome. Conclusions The information that we characterized is useful for elucidation of the mechanism of growth promotion under salinity and reversible conversion of the photosynthetic type from C3 to Crassulacean Acid Metabolism (CAM).
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Affiliation(s)
- Ryoma Sato
- Graduate school of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka Nishi-ku Fukuoka, 819-0395, Japan
| | - Yuri Kondo
- Graduate school of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka Nishi-ku Fukuoka, 819-0395, Japan
| | - Sakae Agarie
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku Fukuoka, 819-0395, Japan
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Chang H, Chen YT, Huang HE, Ger MJ. Overexpressing plant ferredoxin-like protein enhances photosynthetic efficiency and carbohydrates accumulation in Phalaenopsis. Transgenic Res 2023; 32:547-560. [PMID: 37851307 DOI: 10.1007/s11248-023-00370-w] [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: 04/03/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023]
Abstract
Crassulacean acid metabolism (CAM) is one of three major models of carbon dioxide assimilation pathway with better water-use efficiency and slower photosynthetic efficiency in photosynthesis. Previous studies indicated that the gene of sweet pepper plant ferredoxin-like protein (PFLP) shows high homology to the ferredoxin-1(Fd-1) family that belongs to photosynthetic type Fd and involves in photosystem I. It is speculated that overexpressing pflp in the transgenic plant may enhance photosynthetic efficiency through the electron transport chain (ETC). To reveal the function of PFLP in photosynthetic efficiency, pflp transgenic Phalaenopsis, a CAM plant, was generated to analyze photosynthetic markers. Transgenic plants exhibited 1.2-folds of electron transport rate than that of wild type (WT), and higher CO2 assimilation rates up to 1.6 and 1.5-folds samples at 4 pm and 10 pm respectively. Enzyme activity of phosphoenolpyruvate carboxylase (PEPC) was increased to 5.9-folds in Phase III, and NAD+-linked malic enzyme (NAD+-ME) activity increased 1.4-folds in Phase IV in transgenic plants. The photosynthesis products were analyzed between transgenic plants and WT. Soluble sugars contents such as glucose, fructose, and sucrose were found to significantly increase to 1.2, 1.8, and 1.3-folds higher in transgenic plants. The starch grains were also accumulated up to 1.4-folds in transgenic plants than that of WT. These results indicated that overexpressing pflp in transgenic plants increases carbohydrates accumulation by enhancing electron transport flow during photosynthesis. This is the first evidence for the PFLP function in CAM plants. Taken altogether, we suggest that pflp is an applicable gene for agriculture application that enhances electron transport chain efficiency during photosynthesis.
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Affiliation(s)
- Hsiang Chang
- Department of Biotechnology and Pharmaceutical Technology, Yuanpei University of Medical Technology, Hsinchu, 30015, Taiwan
| | - Yen-Ting Chen
- Institute of Biotechnology, National University of Kaohsiung, Kaohsiung, 81148, Taiwan
| | - Hsiang-En Huang
- Department of Life Sciences, National Taitung University, Taitung, 95002, Taiwan
| | - Mang-Jye Ger
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, 81148, Taiwan.
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Yamaga-Hatakeyama Y, Okutani M, Hatakeyama Y, Yabiku T, Yukawa T, Ueno O. Photosynthesis and leaf structure of F1 hybrids between Cymbidium ensifolium (C3) and C. bicolor subsp. pubescens (CAM). ANNALS OF BOTANY 2023; 132:895-907. [PMID: 36579478 PMCID: PMC10799985 DOI: 10.1093/aob/mcac157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/17/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS The introduction of crassulacean acid metabolism (CAM) into C3 crops has been considered as a means of improving water-use efficiency. In this study, we investigated photosynthetic and leaf structural traits in F1 hybrids between Cymbidium ensifolium (female C3 parent) and C. bicolor subsp. pubescens (male CAM parent) of the Orchidaceae. METHODS Seven F1 hybrids produced through artificial pollination and in vitro culture were grown in a greenhouse with the parent plants. Structural, biochemical and physiological traits involved in CAM in their leaves were investigated. KEY RESULTS Cymbidium ensifolium accumulated very low levels of malate without diel fluctuation, whereas C. bicolor subsp. pubescens showed nocturnal accumulation and diurnal consumption of malate. The F1s also accumulated malate at night, but much less than C. bicolor subsp. pubescens. This feature was consistent with low nocturnal fixation of atmospheric CO2 in the F1s. The δ13C values of the F1s were intermediate between those of the parents. Leaf thickness was thicker in C. bicolor subsp. pubescens than in C. ensifolium, and those of the F1s were more similar to that of C. ensifolium. This was due to the difference in mesophyll cell size. The chloroplast coverage of mesophyll cell perimeter adjacent to intercellular air spaces of C. bicolor subsp. pubescens was lower than that of C. ensifolium, and that of the F1s was intermediate between them. Interestingly, one F1 had structural and physiological traits more similar to those of C. bicolor subsp. pubescens than the other F1s. Nevertheless, all F1s contained intermediate levels of phosphoenolpyruvate carboxylase but as much pyruvate, Pi dikinase as C. bicolor subsp. pubescens. CONCLUSIONS CAM traits were intricately inherited in the F1 hybrids, the level of CAM expression varied widely among F1 plants, and the CAM traits examined were not necessarily co-ordinately transmitted to the F1s.
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Affiliation(s)
| | - Masamitsu Okutani
- School of Agriculture, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuto Hatakeyama
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takayuki Yabiku
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, Tsukuba, Ibaraki 305-0005, Japan
| | - Osamu Ueno
- Faculty of Agriculture, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Chomthong M, Griffiths H. Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches. ANNALS OF BOTANY 2023; 132:583-596. [PMID: 37742290 PMCID: PMC10799989 DOI: 10.1093/aob/mcad142] [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: 03/26/2023] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND AND SCOPE This review summarizes recent advances in our understanding of Crassulacean Acid Metabolism (CAM) by integrating evolutionary, ecological, physiological, metabolic and molecular perspectives. A number of key control loops which moderate the expression of CAM phases, and their metabolic and molecular control, are explored. These include nocturnal stomatal opening, activation of phosphoenolpyruvate carboxylase by a specific protein kinase, interactions with circadian clock control, as well as daytime decarboxylation and activation of Rubisco. The vacuolar storage and release of malic acid and the interplay between the supply and demand for carbohydrate reserves are also key metabolic control points. FUTURE OPPORTUNITIES We identify open questions and opportunities, with experimentation informed by top-down molecular modelling approaches allied with bottom-up mechanistic modelling systems. For example, mining transcriptomic datasets using high-speed systems approaches will help to identify targets for future genetic manipulation experiments to define the regulation of CAM (whether circadian or metabolic control). We emphasize that inferences arising from computational approaches or advanced nuclear sequencing techniques can identify potential genes and transcription factors as regulatory targets. However, these outputs then require systematic evaluation, using genetic manipulation in key model organisms over a developmental progression, combining gene silencing and metabolic flux analysis and modelling to define functionality across the CAM day-night cycle. From an evolutionary perspective, the origins and function of CAM succulents and responses to water deficits are set against the mesophyll and hydraulic limitations imposed by cell and tissue succulence in contrasting morphological lineages. We highlight the interplay between traits across shoots (3D vein density, mesophyll conductance and cell shrinkage) and roots (xylem embolism and segmentation). Thus, molecular, biophysical and biochemical processes help to curtail water losses and exploit rapid rehydration during restorative rain events. In the face of a changing climate, we hope such approaches will stimulate opportunities for future research.
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Affiliation(s)
- Methawi Chomthong
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Li C, Huang W, Han X, Zhao G, Zhang W, He W, Nie B, Chen X, Zhang T, Bai W, Zhang X, He J, Zhao C, Fernie AR, Tschaplinski TJ, Yang X, Yan S, Wang L. Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis. PLANT COMMUNICATIONS 2023; 4:100594. [PMID: 36960529 PMCID: PMC10504562 DOI: 10.1016/j.xplc.2023.100594] [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: 10/27/2022] [Revised: 02/19/2023] [Accepted: 03/20/2023] [Indexed: 05/29/2023]
Abstract
Crassulacean acid metabolism (CAM) has high water-use efficiency (WUE) and is widely recognized to have evolved from C3 photosynthesis. Different plant lineages have convergently evolved CAM, but the molecular mechanism that underlies C3-to-CAM evolution remains to be clarified. Platycerium bifurcatum (elkhorn fern) provides an opportunity to study the molecular changes underlying the transition from C3 to CAM photosynthesis because both modes of photosynthesis occur in this species, with sporotrophophyll leaves (SLs) and cover leaves (CLs) performing C3 and weak CAM photosynthesis, respectively. Here, we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs differed from those in strong CAM species. We investigated the diel dynamics of the metabolome, proteome, and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental conditions. We found that multi-omic diel dynamics in P. bifurcatum exhibit both tissue and diel effects. Our analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway (TCA cycle), CAM pathway, and stomatal movement in CLs compared with SLs. We also confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) exhibits convergence in gene expression among highly divergent CAM lineages. Gene regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal movement. Taken together, our results provide new insights into weak CAM photosynthesis and new avenues for CAM bioengineering.
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Affiliation(s)
- Cheng Li
- 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, China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxu Han
- 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, China
| | - Guohua Zhao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Wenyang Zhang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Weijun He
- 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, China
| | - Bao Nie
- 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, China
| | - Xufeng Chen
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Taijie Zhang
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Wenhui Bai
- 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, China
| | - Xiaopeng Zhang
- 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, China
| | - Jingjing He
- 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, China
| | - Cheng Zhao
- 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, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
| | - Li Wang
- 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, China; Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China.
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Miszalski Z, Kaszycki P, Śliwa-Cebula M, Kaczmarczyk A, Gieniec M, Supel P, Kornaś A. Plasticity of Plantago lanceolata L. in Adaptation to Extreme Environmental Conditions. Int J Mol Sci 2023; 24:13605. [PMID: 37686411 PMCID: PMC10487448 DOI: 10.3390/ijms241713605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
This study aimed at characterizing some adaptive changes in Plantago lanceolata L. exposed to harsh conditions of a desert-like environment generating physiological stress of limited water availability and exposure to strong light. It was clearly shown that the plants were capable of adapting their root system and vascular tissues to enable efficient vegetative performance. Soil analyses, as well as nitrogen isotope discrimination data show that P. lanceolata leaves in a desert-like environment had better access to nitrogen (nitrite/nitrate) and were able to fix it efficiently, as compared to the plants growing in the surrounding forest. The arbuscular mycorrhiza was also shown to be well-developed, and this was accompanied by higher bacterial frequency in the root zone, which might further stimulate plant growth. A closer look at the nitrogen content and leaf veins with a higher number of vessels and a greater vessel diameter made it possible to define the changes developed by the plants populating sandy habitats as compared with the vegetation sites located in the nearby forest. A determination of the photosynthesis parameters indicates that the photochemical apparatus in P. lanceolata inhabiting the desert areas adapted slightly to the desert-like environment and the time of day, with some changes of the reaction center (RC) size (photosystem II, PSII), while the plants' photochemical activity was at a similar level. No differences between the two groups of plants were observed in the dissipation of light energy. The exposure of plants to harsh conditions of a desert-like environment increased the water use efficiency (WUE) value in parallel with possible stimulation of the β-carboxylation pathway.
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Affiliation(s)
- Zbigniew Miszalski
- The W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland; (Z.M.); (A.K.); (M.G.)
| | - Paweł Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland; (P.K.); (M.Ś.-C.); (P.S.)
| | - Marta Śliwa-Cebula
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland; (P.K.); (M.Ś.-C.); (P.S.)
| | - Adriana Kaczmarczyk
- The W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland; (Z.M.); (A.K.); (M.G.)
| | - Miron Gieniec
- The W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland; (Z.M.); (A.K.); (M.G.)
| | - Paulina Supel
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland; (P.K.); (M.Ś.-C.); (P.S.)
| | - Andrzej Kornaś
- Institute of Biology and Earth Sciences, Pedagogical University of Krakow, Podchorążych 2, 30-084 Kraków, Poland
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Wang Y, Smith JAC, Zhu XG, Long SP. Rethinking the potential productivity of crassulacean acid metabolism by integrating metabolic dynamics with shoot architecture, using the example of Agave tequilana. THE NEW PHYTOLOGIST 2023; 239:2180-2196. [PMID: 37537720 DOI: 10.1111/nph.19128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/04/2023] [Indexed: 08/05/2023]
Abstract
Terrestrial CAM plants typically occur in hot semiarid regions, yet can show high crop productivity under favorable conditions. To achieve a more mechanistic understanding of CAM plant productivity, a biochemical model of diel metabolism was developed and integrated with 3-D shoot morphology to predict the energetics of light interception and photosynthetic carbon assimilation. Using Agave tequilana as an example, this biochemical model faithfully simulated the four diel phases of CO2 and metabolite dynamics during the CAM rhythm. After capturing the 3-D form over an 8-yr production cycle, a ray-tracing method allowed the prediction of the light microclimate across all photosynthetic surfaces. Integration with the biochemical model thereby enabled the simulation of plant and stand carbon uptake over daily and annual courses. The theoretical maximum energy conversion efficiency of Agave spp. is calculated at 0.045-0.049, up to 7% higher than for C3 photosynthesis. Actual light interception, and biochemical and anatomical limitations, reduced this to 0.0069, or 15.6 Mg ha-1 yr-1 dry mass annualized over an 8-yr cropping cycle, consistent with observation. This is comparable to the productivity of many C3 crops, demonstrating the potential of CAM plants in climates where little else may be grown while indicating strategies that could raise their productivity.
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Affiliation(s)
- Yu Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA
| | - J Andrew C Smith
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Xin-Guang Zhu
- Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Stephen P Long
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
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11
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Ouyang K, Liang Q, Miao L, Zhang Z, Li Z. Genome-wide mapping of DNase I hypersensitive sites in pineapple leaves. Front Genet 2023; 14:1086554. [PMID: 37470036 PMCID: PMC10352800 DOI: 10.3389/fgene.2023.1086554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Pineapple [Ananas comosus (L.) Merr.] is the most economically important crop possessing crassulacean acid metabolism (CAM) photosynthesis which has a higher water use efficiency by control of nocturnal opening and diurnal closure of stomata. To provide novel insights into the diel regulatory landscape in pineapple leaves, we performed genome-wide mapping of DNase I hypersensitive sites (DHSs) in pineapple leaves at day (2a.m.) and night (10a.m.) using a simplified DNase-seq method. As a result, totally 33340 and 28753 DHSs were found in green-tip tissue, and 29597 and 40068 were identified in white-base tissue at 2a.m. and 10a.m., respectively. We observed that majority of the pineapple genes occupied less than two DHSs with length shorter than 1 kb, and the promotor DHSs showed a proximal trend to the transcription start site (>77% promotor DHSs within 1 kb). In addition, more intergenic DHSs were identified around transcription factors or transcription co-regulators (TFs/TCs) than other functional genes, indicating complex regulatory contexts around TFs/TCs. Through combined analysis of tissue preferential DHSs and genes, we respectively found 839 and 888 coordinately changed genes in green-tip at 2a.m. and 10a.m. (AcG2 and AcG10). Furthermore, AcG2-specific, AcG10-specific and common accessible DHSs were dissected from the total photosynthetic preferential DHSs, and the regulatory networks indicated dynamic regulations with multiple cis-regulatory elements occurred to genes preferentially expressed in photosynthetic tissues. Interestingly, binding motifs of several cycling TFs were identified in the DHSs of key CAM genes, revealing a circadian regulation to CAM coordinately diurnal expression. Our results provide a chromatin regulatory landscape in pineapple leaves during the day and night. This will provide important information to assist with deciphering the circadian regulation of CAM photosynthesis.
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Affiliation(s)
- Kai Ouyang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qifu Liang
- Fujian Key Laboratory of Agro-Products Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Li Miao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiliang Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhanjie Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Pérez-López J, Feria AB, Gandullo J, de la Osa C, Jiménez-Guerrero I, Echevarría C, Monreal JA, García-Mauriño S. Silencing of Sb PPCK1-3 Negatively Affects Development, Stress Responses and Productivity in Sorghum. PLANTS (BASEL, SWITZERLAND) 2023; 12:2426. [PMID: 37446987 DOI: 10.3390/plants12132426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays central roles in photosynthesis, respiration, amino acid synthesis, and seed development. PEPC is regulated by different post-translational modifications. Between them, the phosphorylation by PEPC-kinase (PEPCk) is widely documented. In this work, we simultaneously silenced the three sorghum genes encoding PEPCk (SbPPCK1-3) by RNAi interference, obtaining 12 independent transgenic lines (Ppck1-12 lines), showing different degrees of SbPPCK1-3 silencing. Among them, two T2 homozygous lines (Ppck-2 and Ppck-4) were selected for further evaluation. Expression of SbPPCK1 was reduced by 65% and 83% in Ppck-2 and Ppck-4 illuminated leaves, respectively. Expression of SbPPCK2 was higher in roots and decreased by 50% in Ppck-2 and Ppck-4 in this tissue. Expression of SbPPCK3 was low and highly variable. Despite the incomplete gene silencing, it decreased the degree of phosphorylation of PEPC in illuminated leaves, P-deficient plants, and NaCl-treated plants. Both leaves and seeds of Ppck lines had altered metabolic profiles and a general decrease in amino acid content. In addition, Ppck lines showed delayed flowering, and 20% of Ppck-4 plants did not produce flowers at all. The total amount of seeds was lowered by 50% and 36% in Ppck-2 and Ppck-4 lines, respectively. The quality of seeds was lower in Ppck lines: lower amino acid content, including Lys, and higher phytate content. These data confirm the relevance of the phosphorylation of PEPC in sorghum development, stress responses, yield, and quality of seeds.
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Affiliation(s)
- Jesús Pérez-López
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Ana B Feria
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Jacinto Gandullo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Clara de la Osa
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Irene Jiménez-Guerrero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Cristina Echevarría
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - José A Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Sofía García-Mauriño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
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13
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Moreno-Villena JJ, Zhou H, Gilman IS, Tausta SL, Cheung CYM, Edwards EJ. Spatial resolution of an integrated C 4+CAM photosynthetic metabolism. SCIENCE ADVANCES 2022; 8:eabn2349. [PMID: 35930634 PMCID: PMC9355352 DOI: 10.1126/sciadv.abn2349] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/22/2022] [Indexed: 05/27/2023]
Abstract
C4 and CAM photosynthesis have repeatedly evolved in plants over the past 30 million years. Because both repurpose the same set of enzymes but differ in their spatial and temporal deployment, they have long been considered as distinct and incompatible adaptations. Portulaca contains multiple C4 species that perform CAM when droughted. Spatially explicit analyses of gene expression reveal that C4 and CAM systems are completely integrated in Portulaca oleracea, with CAM and C4 carbon fixation occurring in the same cells and CAM-generated metabolites likely incorporated directly into the C4 cycle. Flux balance analysis corroborates the gene expression findings and predicts an integrated C4+CAM system under drought. This first spatially explicit description of a C4+CAM photosynthetic metabolism presents a potential new blueprint for crop improvement.
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Affiliation(s)
- Jose J. Moreno-Villena
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Haoran Zhou
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
- School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Ian S. Gilman
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - S. Lori Tausta
- Department of Molecular Biophysics and Biochemistry, Yale University, 600 West Campus, West Haven, CT 06516, USA
| | | | - Erika J. Edwards
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
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14
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Shu JP, Yan YH, Wang RJ. Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C 4 and crassulacean acid metabolism plants. PeerJ 2022; 10:e12828. [PMID: 35116203 PMCID: PMC8784020 DOI: 10.7717/peerj.12828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/03/2022] [Indexed: 01/10/2023] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
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Affiliation(s)
- Jiang-Ping Shu
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Jiang Wang
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,University of Chinese Academy of Sciences, Beijing, China
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15
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Hurtado-Gaitán E, Sellés-Marchart S, Hartwell J, Martínez-Esteso MJ, Bru-Martínez R. Down-Regulation of Phosphoenolpyruvate Carboxylase Kinase in Grapevine Cell Cultures and Leaves Is Linked to Enhanced Resveratrol Biosynthesis. Biomolecules 2021; 11:1641. [PMID: 34827639 PMCID: PMC8615455 DOI: 10.3390/biom11111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
In grapevine, trans-Resveratrol (tR) is produced as a defence mechanism against stress or infection. tR is also considered to be important for human health, which increases its interest to the scientific community. Transcriptomic analysis in grapevine cell cultures treated with the defence response elicitor methyl-β-cyclodextrin (CD) revealed that both copies of PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) were down-regulated significantly. A role for PPCK in the defence response pathway has not been proposed previously. We therefore analysed the control of PPCK transcript levels in grapevine cell cultures and leaves elicited with CD. Moreover, phosphoenolpyruvate carboxylase (PPC), stilbene synthase (STS), and the transcription factors MYB14 and WRKY24, which are involved in the activation of STS transcription, were also analysed by RT-qPCR. The results revealed that under CD elicitation conditions PPCK down-regulation, increased stilbene production and loss of PPC activity occurs in both tissues. Moreover, STS transcripts were co-induced with MYB14 and WRKY24 in cell cultures and leaves. These genes have not previously been reported to respond to CD in grape leaves. Our findings thus support the hypothesis that PPCK is involved in diverting metabolism towards stilbene biosynthesis, both for in vitro cell culture and whole leaves. We thus provide new evidence for PEP being redirected between primary and secondary metabolism to support tR production and the stress response.
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Affiliation(s)
- Elías Hurtado-Gaitán
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK;
| | - Maria José Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
- Instituto de Investigación Sanitaria y Biomédica de Alicante ISABIAL-Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO, 03010 Alicante, Spain
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16
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van Tongerlo E, Trouwborst G, Hogewoning SW, van Ieperen W, Dieleman JA, Marcelis LFM. Crassulacean acid metabolism species differ in the contribution of C 3 and C 4 carboxylation to end of day CO 2 fixation. PHYSIOLOGIA PLANTARUM 2021; 172:134-145. [PMID: 33305855 PMCID: PMC8246577 DOI: 10.1111/ppl.13312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Crassulacean acid metabolism (CAM) is a photosynthetic pathway that temporally separates the nocturnal CO2 uptake, via phosphoenolpyruvate carboxylase (PEPC, C4 carboxylation), from the diurnal refixation by Rubisco (C3 carboxylation). At the end of the day (CAM-Phase IV), when nocturnally stored CO2 has depleted, stomata reopen and allow additional CO2 uptake, which can be fixed by Rubisco or by PEPC. This work examined the CO2 uptake via C3 and C4 carboxylation in phase IV in the CAM species Phalaenopsis "Sacramento" and Kalanchoe blossfeldiana "Saja." Short blackout periods during phase IV caused a sharp drop in CO2 uptake in K. blossfeldiana but not in Phalaenopsis, indicating strong Rubisco activity only in K. blossfeldiana. Chlorophyll fluorescence revealed a progressive decrease in ΦPSII in Phalaenopsis, implying decreasing Rubisco activity, while ΦPSII remained constant in phase IV in K. blossfeldiana. However, short switching to 2% O2 indicated the presence of photorespiration and thus Rubisco activity in both species throughout phase IV. Lastly, in Phalaenopsis, accumulation of starch in phase IV occurred. These results indicate that in Phalaenopsis, PEPC was the main carboxylase in phase IV, although Rubisco remained active throughout the whole phase. This will lead to double carboxylation (futile cycling) but may help to avoid photoinhibition.
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Affiliation(s)
- Evelien van Tongerlo
- Horticulture and Product Physiology, Department of Plant SciencesWageningen University and ResearchWageningenThe Netherlands
| | | | | | - Wim van Ieperen
- Horticulture and Product Physiology, Department of Plant SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Janneke A. Dieleman
- Greenhouse HorticultureWageningen University and ResearchWageningenThe Netherlands
| | - Leo F. M. Marcelis
- Horticulture and Product Physiology, Department of Plant SciencesWageningen University and ResearchWageningenThe Netherlands
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17
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Ceusters N, Borland AM, Ceusters J. How to resolve the enigma of diurnal malate remobilisation from the vacuole in plants with crassulacean acid metabolism? THE NEW PHYTOLOGIST 2021; 229:3116-3124. [PMID: 33159327 DOI: 10.1111/nph.17070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/02/2020] [Indexed: 06/11/2023]
Abstract
Opening of stomata in plants with crassulacean acid metabolism (CAM) is mainly shifted to the night period when atmospheric CO2 is fixed by phosphoenolpyruvate carboxylase and stored as malic acid in the vacuole. As such, CAM plants ameliorate transpirational water losses and display substantially higher water-use efficiency compared with C3 and C4 plants. In the past decade significant technical advances have allowed an unprecedented exploration of genomes, transcriptomes, proteomes and metabolomes of CAM plants and efforts are ongoing to engineer the CAM pathway in C3 plants. Whilst research efforts have traditionally focused on nocturnal carboxylation, less information is known regarding the drivers behind diurnal malate remobilisation from the vacuole that liberates CO2 to be fixed by RuBisCo behind closed stomata. To shed more light on this process, we provide a stoichiometric analysis to identify potentially rate-limiting steps underpinning diurnal malate mobilisation and help direct future research efforts. Within this remit we address three key questions: Q1 Does light-dependent assimilation of CO2 via RuBisCo dictate the rate of malate mobilisation? Q2: Do the enzymes responsible for malate decarboxylation limit daytime mobilisation from the vacuole? Q3: Does malate efflux from the vacuole set the pace of decarboxylation?
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Affiliation(s)
- Nathalie Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, Geel, 2440, Belgium
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne,, NE1 7RU, UK
| | - Johan Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, Geel, 2440, Belgium
- Centre for Environmental Sciences, Environmental Biology, UHasselt, Campus Diepenbeek, Agoralaan Building D, Diepenbeek, 3590, Belgium
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18
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Santos MG, Davey PA, Hofmann TA, Borland A, Hartwell J, Lawson T. Stomatal Responses to Light, CO 2, and Mesophyll Tissue in Vicia faba and Kalanchoë fedtschenkoi. FRONTIERS IN PLANT SCIENCE 2021; 12:740534. [PMID: 34777422 PMCID: PMC8579043 DOI: 10.3389/fpls.2021.740534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/22/2021] [Indexed: 05/14/2023]
Abstract
The responses of stomatal aperture to light intensity and CO2 concentration were studied in both Vicia faba (C3) and Kalanchoë fedtschenkoi (Crassulacean acid metabolism; CAM), in material sampled from both light and dark periods. Direct comparison was made between intact leaf segments, epidermises grafted onto exposed mesophyll, and isolated epidermal peels, including transplantations between species and between diel periods. We reported the stomatal opening in response to darkness in isolated CAM peels from the light period, but not from the dark. Furthermore, we showed that C3 mesophyll has stimulated CAM stomata in transplanted peels to behave as C3 in response to light and CO2. By using peels and mesophyll from plants sampled in the dark and the light period, we provided clear evidence that CAM stomata behaved differently from C3. This might be linked to stored metabolites/ions and signalling pathway components within the guard cells, and/or a mesophyll-derived signal. Overall, our results provided evidence for both the involvement of guard cell metabolism and mesophyll signals in stomatal responses in both C3 and CAM species.
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Affiliation(s)
- Mauro G. Santos
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, United Kingdom
| | - Phillip A. Davey
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, United Kingdom
| | | | - Anne Borland
- School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, United Kingdom
- *Correspondence: Tracy Lawson
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Baena G, Feria AB, Hernández-Huertas L, Gandullo J, Echevarría C, Monreal JA, García-Mauriño S. Genetic and Pharmacological Inhibition of Autophagy increases the Monoubiquitination of Non-Photosynthetic Phospho enolpyruvate Carboxylase. PLANTS 2020; 10:plants10010012. [PMID: 33374865 PMCID: PMC7823769 DOI: 10.3390/plants10010012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an enzyme with key roles in carbon and nitrogen metabolisms. The mechanisms that control enzyme stability and turnover are not well known. This paper investigates the degradation of PEPC via selective autophagy, including the role of the monoubiquitination of the enzyme in this process. In Arabidopsis, the genetic inhibition of autophagy increases the amount of monoubiquitinated PEPC in the atg2, atg5, and atg18a lines. The same is observed in nbr1, which is deficient in a protein that recruits monoubiquitinated substrates for selective autophagy. In cultured tobacco cells, the chemical inhibition of the degradation of autophagic substrates increases the quantity of PEPC proteins. When the formation of the autophagosome is blocked with 3-methyladenine (3-MA), monoubiquitinated PEPC accumulates as a result. Finally, pull-down experiments with a truncated version of NBR1 demonstrate the recovery of intact and/or fragmented PEPC in Arabidopsis leaves and roots, as well as cultured tobacco cells. Taken together, the results show that a fraction of PEPC is cleaved via selective autophagy and that the monoubiquitination of the enzyme has a role in its recruitment towards this pathway. Although autophagy seems to be a minor pathway, the results presented here increase the knowledge about the role of monoubiquitination and the regulation of PEPC degradation.
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Nomura K, Sakurai Y, Dozono M. Molecular Cloning of Novel-Type Phospho enolpyruvate Carboxylase Isoforms in Pitaya ( Hylocereus undatus). PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091241. [PMID: 32967083 PMCID: PMC7569800 DOI: 10.3390/plants9091241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme involved in the initial CO2 fixation of crassulacean acid metabolism (CAM) photosynthesis. To understand the cultivation characteristics of a CAM plant pitaya, it is necessary to clarify the characteristics of PEPC in this species. Here, we cloned three PEPC cDNAs in pitaya, HuPPC1, HuPPC2, and HuPPC3, which encode 942, 934, and 966 amino acid residues, respectively. Phylogenetic analysis indicated that these PEPC belonged to plant-type PEPC (PTPC), although HuPPC1 and HuPPC2 have no Ser-phosphorylation motif in N-terminal region, which is a crucial regulation site in PTPC and contributes to CAM periodicity. HuPPC1 and HuPPC2 phylogenetically unique to the Cactaceae family, whereas HuPPC3 was included in a CAM clade. Two isoforms were partially purified at the protein level and were assigned as HuPPC2 and HuPPC3 using MASCOT analysis. The most distinct difference in enzymatic properties between the two was sensitivity to malate and aspartate, both of which are allosteric inhibitors of PEPC. With 2 mM malate, HuPPC3 was inhibited to 10% of the initial activity, whereas HuPPC2 activity was maintained at 70%. Aspartate inhibited HuPPC3 activity by approximately 50% at 5 mM; however, such inhibition was not observed for HuPPC2 at 10 mM. These results suggest that HuPPC3 corresponds to a general CAM-related PEPC, whereas HuPPC1 and HuPPC2 are related to carbon and/or nitrogen metabolism, with a characteristic regulation mechanism similar to those of Cactaceae plants.
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Affiliation(s)
- Keiichi Nomura
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Yuho Sakurai
- Faculty of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Mayu Dozono
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
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21
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Scholl J, Dengler L, Bader L, Forchhammer K. Phosphoenolpyruvate carboxylase from the cyanobacterium Synechocystis sp. PCC 6803 is under global metabolic control by P II signaling. Mol Microbiol 2020; 114:292-307. [PMID: 32274833 DOI: 10.1111/mmi.14512] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is the second major carbon-fixing enzyme in photoautotrophic organisms. PEPC is required for the synthesis of amino acids of the glutamate and aspartate family by replenishing the TCA cycle. Furthermore, in cyanobacteria, PEPC, together with malate dehydrogenase and malic enzyme, forms a metabolic shunt for the synthesis of pyruvate from PEP. During this process, CO2 is first fixed and later released again. Due to its central metabolic position, it is crucial to fully understand the regulation of PEPC. Here, we identify PEPC from the cyanobacterium Synechocystis sp. PCC 6803 (PEPC) as a novel interaction partner for the global signal transduction protein PII . In addition to an extensive characterization of PEPC, we demonstrate specific PII -PEPC complex formation and its enzymatic consequences. PEPC activity is tuned by the metabolite-sensing properties of PII : Whereas in the absence of PII, PEPC is subjected to ATP inhibition, it is activated beyond its basal activity in the presence of PII . Furthermore, PII -PEPC complex formation is inhibited by ADP and PEPC activation by PII -ATP is mitigated in the presence of 2-OG, linking PEPC regulation to the cell's global carbon/nitrogen status. Finally, physiological relevance of the in vitro measurements was proven by metabolomic analyses of Synechocystis wild-type and PII -deficient cells.
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Affiliation(s)
- Jörg Scholl
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Lisa Dengler
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Laura Bader
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
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22
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Chomthong M, Griffiths H. Model approaches to advance crassulacean acid metabolism system integration. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:951-963. [PMID: 31943394 DOI: 10.1111/tpj.14691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
This review summarises recent progress in understanding crassulacean acid metabolism (CAM) systems and the integration of internal and external stimuli to maximise water-use efficiency. Complex CAM traits have been reduced to their minimum and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large-scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address the evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water-use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co-expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that the resultant improvements of bottom-up, mechanistic modelling systems can enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.
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Affiliation(s)
- Methawi Chomthong
- Department of Plant Sciences, University of Cambridge, Downing street, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing street, Cambridge, CB2 3EA, UK
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23
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Heyduk K, Ray JN, Ayyampalayam S, Moledina N, Borland A, Harding SA, Tsai CJ, Leebens-Mack J. Shared expression of crassulacean acid metabolism (CAM) genes pre-dates the origin of CAM in the genus Yucca. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6597-6609. [PMID: 30870557 PMCID: PMC6883266 DOI: 10.1093/jxb/erz105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/20/2019] [Indexed: 05/05/2023]
Abstract
Crassulacean acid metabolism (CAM) is a carbon-concentrating mechanism that has evolved numerous times across flowering plants and is thought to be an adaptation to water-limited environments. CAM has been investigated from physiological and biochemical perspectives, but little is known about how plants evolve from C3 to CAM at the genetic or metabolic level. Here we take a comparative approach in analyzing time-course data of C3, CAM, and C3+CAM intermediate Yucca (Asparagaceae) species. RNA samples were collected over a 24 h period from both well-watered and drought-stressed plants, and were clustered based on time-dependent expression patterns. Metabolomic data reveal differences in carbohydrate metabolism and antioxidant response between the CAM and C3 species, suggesting that changes to metabolic pathways are important for CAM evolution and function. However, all three species share expression profiles of canonical CAM pathway genes, regardless of photosynthetic pathway. Despite differences in transcript and metabolite profiles between the C3 and CAM species, shared time-structured expression of CAM genes in both CAM and C3Yucca species suggests that ancestral expression patterns required for CAM may have pre-dated its origin in Yucca.
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Affiliation(s)
- Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Jeremy N Ray
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | - Nida Moledina
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Anne Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK
| | - Scott A Harding
- Department of Genetics, University of Georgia, Athens, GA, USA
- Warnell School of Forestry, University of Georgia, Athens, GA, USA
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, GA, USA
- Warnell School of Forestry, University of Georgia, Athens, GA, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, USA
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24
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Zhao Y, Guo A, Wang Y, Hua J. Evolution of PEPC gene family in Gossypium reveals functional diversification and GhPEPC genes responding to abiotic stresses. Gene 2019; 698:61-71. [PMID: 30825597 DOI: 10.1016/j.gene.2019.02.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 02/10/2019] [Accepted: 02/23/2019] [Indexed: 12/24/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) family genes play important roles in regulating plant growth and abiotic stress response. Based on the sequenced Gossypium genomes, we performed comprehensive analysis of PEPC homolog genes in cotton, which six, six, eleven and ten PEPC genes were identified in Gossypium arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2), respectively. These genes were divided into six subgroups: PEPC-i, PEPC-ii, PEPC-iii, PEPC-iv, PEPC-v and PEPC-vi; PEPC genes in each subgroup displayed conserved gene structure and motifs. Segmental duplication and whole genome duplication (WGD) events yielded the expansion of PEPC genes. Expression assays showed that the duplicated PEPC genes displayed diverse expression patterns, indicating that they experienced functional divergence. Of which, genes in PEPC-iv subgroup played crucial role for substrate distribution in cottonseed. Cis-elements, putative miRNAs and expression analyses showed that GhPEPC homologs might respond to abiotic stresses, expression levels of GhPEPC1 and GhPEPC2/GhPEPC2D genes were larger induced than other GhPEPC genes under cold, heat, salt, and drought stresses, indicating the crucial roles in abiotic stresses response. Present study serves new information to decipher the evolution and function of PEPC genes in Gossypium.
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Affiliation(s)
- Yanpeng Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Yumei Wang
- Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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Heyduk K, Hwang M, Albert V, Silvera K, Lan T, Farr K, Chang TH, Chan MT, Winter K, Leebens-Mack J. Altered Gene Regulatory Networks Are Associated With the Transition From C 3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae). FRONTIERS IN PLANT SCIENCE 2019; 9:2000. [PMID: 30745906 PMCID: PMC6360190 DOI: 10.3389/fpls.2018.02000] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/24/2018] [Indexed: 05/21/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here, we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.
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Affiliation(s)
- Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Michelle Hwang
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Victor Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Katia Silvera
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Kimberly Farr
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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26
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Ping CY, Chen FC, Cheng TC, Lin HL, Lin TS, Yang WJ, Lee YI. Expression Profiles of Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxylase Kinase Genes in Phalaenopsis, Implications for Regulating the Performance of Crassulacean Acid Metabolism. FRONTIERS IN PLANT SCIENCE 2018; 9:1587. [PMID: 30425727 PMCID: PMC6218735 DOI: 10.3389/fpls.2018.01587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/12/2018] [Indexed: 05/26/2023]
Abstract
Phalaenopsis is one of the most important potted plants in the ornamental market of the world. Previous reports implied that crassulacean acid metabolism (CAM) orchids at their young seedling stages might perform C3 or weak CAM photosynthetic pathways, but the detailed molecular evidence is still lacking. In this study, we used a key species in white Phalaenopsis breeding line, Phalaenopsis aphrodite subsp. formosana, to study the ontogenetical changes of CAM performance in Phalaenopsis. Based on the investigations of rhythms of day/night CO2 exchange, malate contents and phosphoenolpyruvate carboxylase (PEPC) activities, it is suggested that a progressive shift from C3 to CAM occurred as the protocorms differentiated the first leaf. To understand the role of phosphoenolpyruvate carboxylase kinase (PEPC kinase) in relation to its target PEPC in CAM performance in Phalaenopsis, the expression profiles of the genes encoding PEPC (PPC) and PEPC kinase (PPCK) were measured in different developmental stages. In Phalaenopsis, two PPC isogenes were constitutively expressed over a 24-h cycle similar to the housekeeping genes in all stages, whereas the significant day/night difference in PaPPCK expression corresponds to the day/night fluctuations in PEPC activity and malate level. These results suggest that the PaPPCK gene product is most likely involved in regulation of CAM performance in different developmental stages of Phalaenopsis seedlings.
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Affiliation(s)
- Chia-Yun Ping
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fure-Chyi Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Teen-Chi Cheng
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Huey-Ling Lin
- Department of Horticulture, National Chung Hsing University, Taichung, Taiwan
| | - Tzong-Shyan Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Wen-Ju Yang
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Yung-I Lee
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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27
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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.
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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.
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Abstract
Nitrogen (N) fertilizer has a major influence on the yield and quality. Understanding and optimising the response of crop plants to nitrogen fertilizer usage is of central importance in enhancing food security and agricultural sustainability. In this study, the analysis of gene regulatory networks reveals multiple genes and biological processes in response to N. Two microarray studies have been used to infer components of the nitrogen-response network. Since they used different array technologies, a map linking the two probe sets to the maize B73 reference genome has been generated to allow comparison. Putative Arabidopsis homologues of maize genes were used to query the Biological General Repository for Interaction Datasets (BioGRID) network, which yielded the potential involvement of three transcription factors (TFs) (GLK5, MADS64 and bZIP108) and a Calcium-dependent protein kinase. An Artificial Neural Network was used to identify influential genes and retrieved bZIP108 and WRKY36 as significant TFs in both microarray studies, along with genes for Asparagine Synthetase, a dual-specific protein kinase and a protein phosphatase. The output from one study also suggested roles for microRNA (miRNA) 399b and Nin-like Protein 15 (NLP15). Co-expression-network analysis of TFs with closely related profiles to known Nitrate-responsive genes identified GLK5, GLK8 and NLP15 as candidate regulators of genes repressed under low Nitrogen conditions, while bZIP108 might play a role in gene activation.
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29
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Liu A, Contador CA, Fan K, Lam HM. Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes. FRONTIERS IN PLANT SCIENCE 2018; 9:1860. [PMID: 30619423 PMCID: PMC6305480 DOI: 10.3389/fpls.2018.01860] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/30/2018] [Indexed: 05/19/2023]
Abstract
Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.
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Affiliation(s)
- Ailin Liu
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Carolina A. Contador
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kejing Fan
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Hon-Ming Lam,
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30
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Functional Anatomical Traits of the Photosynthetic Organs of Plants with Crassulacean Acid Metabolism. THE LEAF: A PLATFORM FOR PERFORMING PHOTOSYNTHESIS 2018. [DOI: 10.1007/978-3-319-93594-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Inoue K, Araki T, Endo M. Circadian clock during plant development. JOURNAL OF PLANT RESEARCH 2018; 131:59-66. [PMID: 29134443 PMCID: PMC5897470 DOI: 10.1007/s10265-017-0991-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/06/2017] [Indexed: 05/14/2023]
Abstract
Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season. Recent genomic studies have demonstrated that polymorphism in circadian clock genes may contribute to local adaptations over a wide range of latitudes in many plant species. In the present review, we summarize the circadian regulation of biological processes throughout the life cycle of plants, and describe the contribution of the circadian clock to local adaptation.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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32
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Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo HB, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen JG, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nat Commun 2017; 8:1899. [PMID: 29196618 PMCID: PMC5711932 DOI: 10.1038/s41467-017-01491-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022] Open
Abstract
Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Deborah A Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jungmin Ha
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert C Moseley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Elisabeth Fitzek
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Zhihao Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Juan D Beltrán
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rebecca Albion
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Travis Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul Peluso
- Pacific Biosciences, Inc., 940 Hamilton Avenue, Menlo Park, CA, 94025, USA
| | - Robert Van Buren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Henrique Cestari De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | | | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Taybi T, Cushman JC, Borland AM. Leaf carbohydrates influence transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in the facultative CAM plant, Mesembryanthemum crystallinum. JOURNAL OF PLANT PHYSIOLOGY 2017; 218:144-154. [PMID: 28822907 DOI: 10.1016/j.jplph.2017.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/19/2017] [Accepted: 07/28/2017] [Indexed: 05/09/2023]
Abstract
Nocturnal degradation of transitory starch is a limiting factor for the optimal function of crassulacean acid metabolism and must be coordinated with phosphoenolypyruvate carboxylase (PEPC)-mediated CO2 uptake to optimise carbon gain over the diel cycle. The aim of this study was to test the hypothesis that nocturnal carboxylation is coordinated with starch degradation in CAM via a mechanism whereby the products of these pathways regulate diel transcript abundance and enzyme activities for both processes. To test this hypothesis, a starch and CAM-deficient mutant of Mesembryanthemum crystallinum was compared with wild type plants under well-watered and saline (CAM-inducing) conditions. Exposure to salinity increased the transcript abundance of genes required for nocturnal carboxylation, starch and sucrose degradation in both wild type and mutant, but the transcript abundance of several of these genes was not sustained over the dark period in the low-carbohydrate, CAM-deficient mutant. The diel pattern of transcript abundance for PEPC mirrored that of PEPC protein, as did the transcripts, protein, and activity of chloroplastic starch phosphorylase in both wild type and mutant, suggesting robust diel coordination of these metabolic processes. Activities of several amylase isoforms were low or lacking in the mutant, whilst the activity of a cytosolic isoform of starch phosphorylase was significantly elevated, indicating contrasting modes of metabolic regulation for the hydrolytic and phosphorylytic routes of starch degradation. Externally supplied sucrose resulted in an increase in nocturnal transcript abundance of genes required for nocturnal carboxylation and starch degradation. These results demonstrate that carbohydrates impact on transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in CAM.
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Affiliation(s)
- Tahar Taybi
- School of Natural & Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557 USA
| | - Anne M Borland
- School of Natural & Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Arias-Baldrich C, de la Osa C, Bosch N, Ruiz-Ballesta I, Monreal JA, García-Mauriño S. Enzymatic activity, gene expression and posttranslational modifications of photosynthetic and non-photosynthetic phosphoenolpyruvate carboxylase in ammonium-stressed sorghum plants. JOURNAL OF PLANT PHYSIOLOGY 2017; 214:39-47. [PMID: 28431276 DOI: 10.1016/j.jplph.2017.03.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 05/24/2023]
Abstract
Sorghum plants grown with 5mM (NH4)2SO4 showed symptoms of stress, such as reduced growth and photosynthesis, leaf chlorosis, and reddish roots. Phosphoenolpyruvate carboxylase (PEPC) activity, by supplying carbon skeletons for ammonium assimilation, plays a pivotal role in tolerance to ammonium stress. This work investigated the effect of ammonium nutrition on PPC and PPCK gene expression, on PEPC activity, and on post-translational modifications (PTMs) of PEPC in leaves and roots of sorghum plants. Ammonium increased PEPC kinase (PEPCk) activity and the phosphorylation state of PEPC in leaves, both in light and in the dark, due to increased PPCK1 expression in leaves. This result resembled the effect of salinity on sorghum leaf PEPC and PEPCk, which is thought to allow a better functioning of PEPC in conditions that limit the income of reduced C. In roots, ammonium increased PEPC activity and the amount of monoubiquitinated PEPC. The first effect was related to increased PPC3 expression in roots. These results highlight the relevance of this specific isoenzyme (PPC3) in sorghum responses to ammonium stress. Although the role of monoubiquitination is not fully understood, it also increased in germinating seeds along with massive mobilization of reserves, a process in which the anaplerotic function of PEPC is of major importance.
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Affiliation(s)
- Cirenia Arias-Baldrich
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012 Seville, Spain.
| | - Clara de la Osa
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012 Seville, Spain.
| | - Nadja Bosch
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012 Seville, Spain; Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain.
| | - Isabel Ruiz-Ballesta
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012 Seville, Spain.
| | - José A Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012 Seville, Spain.
| | - Sofía García-Mauriño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n° 6, 41012 Seville, Spain.
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Shao H, Gontero B, Maberly SC, Jiang HS, Cao Y, Li W, Huang WM. Responses of Ottelia alismoides, an aquatic plant with three CCMs, to variable CO2 and light. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3985-3995. [PMID: 28369629 PMCID: PMC5853927 DOI: 10.1093/jxb/erx064] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/03/2017] [Indexed: 05/29/2023]
Abstract
Ottelia alismoides is a constitutive C4 plant and bicarbonate user, and has facultative crassulacean acid metabolism (CAM) at low CO2. Acclimation to a factorial combination of light and CO2 showed that the ratio of phosphoenolpyruvate carboxylase (PEPC) to ribulose-bisphosphate carboxylase/oxygenase (Rubisco) (>5) is in the range of that of C4 plants. This and short-term response experiments showed that the activity of PEPC and pyruvate phosphate dikinase (PPDK) was high even at the end of the night, consistent with night-time acid accumulation and daytime carbon fixation. The diel acidity change was maximal at high light and low CO2 at 17-25 µequiv g-1 FW. Decarboxylation proceeded at ~2-3 µequiv g-1 FW h-1, starting at the beginning of the photoperiod, but did not occur at high CO2; the rate was greater at high, compared with low light. There was an inverse relationship between starch formation and acidity loss. Acidity changes account for up to 21% of starch production and stimulate early morning photosynthesis, but night-time accumulation of acid traps <6% of respiratory carbon release. Ottelia alismoides is the only known species to operate CAM and C4 in the same tissue, and one of only two known aquatic species to operate CAM and bicarbonate use.
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Affiliation(s)
- Hui Shao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Brigitte Gontero
- Aix Marseille Univ CNRS, BIP UMR, IMM, FR, Chemin Joseph Aiguier, Marseille Cedex, France
| | - Stephen C Maberly
- Lake Ecosystems Group, Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, UK
| | - Hong Sheng Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Aix Marseille Univ CNRS, BIP UMR, IMM, FR, Chemin Joseph Aiguier, Marseille Cedex, France
| | - Yu Cao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Wei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Wen Min Huang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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Jones MA. Interplay of Circadian Rhythms and Light in the Regulation of Photosynthesis-Derived Metabolism. PROGRESS IN BOTANY VOL. 79 2017:147-171. [PMID: 0 DOI: 10.1007/124_2017_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Wang N, Zhong X, Cong Y, Wang T, Yang S, Li Y, Gai J. Genome-wide Analysis of Phosphoenolpyruvate Carboxylase Gene Family and Their Response to Abiotic Stresses in Soybean. Sci Rep 2016; 6:38448. [PMID: 27924923 PMCID: PMC5141416 DOI: 10.1038/srep38448] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/07/2016] [Indexed: 11/09/2022] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays an important role in assimilating atmospheric CO2 during C4 and crassulacean acid metabolism photosynthesis, and also participates in various non-photosynthetic processes, including fruit ripening, stomatal opening, supporting carbon-nitrogen interactions, seed formation and germination, and regulation of plant tolerance to stresses. However, a comprehensive analysis of PEPC family in Glycine max has not been reported. Here, a total of ten PEPC genes were identified in soybean and denominated as GmPEPC1-GmPEPC10. Based on the phylogenetic analysis of the PEPC proteins from 13 higher plant species including soybean, PEPC family could be classified into two subfamilies, which was further supported by analyses of their conserved motifs and gene structures. Nineteen cis-regulatory elements related to phytohormones, abiotic and biotic stresses were identified in the promoter regions of GmPEPC genes, indicating their roles in soybean development and stress responses. GmPEPC genes were expressed in various soybean tissues and most of them responded to the exogenously applied phytohormones. GmPEPC6, GmPEPC8 and GmPEPC9 were significantly induced by aluminum toxicity, cold, osmotic and salt stresses. In addition, the enzyme activities of soybean PEPCs were also up-regulated by these treatments, suggesting their potential roles in soybean response to abiotic stresses.
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Affiliation(s)
- Ning Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiujuan Zhong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yahui Cong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Tingting Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Songnan Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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Kandoi D, Mohanty S, Tripathy BC. Towards efficient photosynthesis: overexpression of Zea mays phosphoenolpyruvate carboxylase in Arabidopsis thaliana. PHOTOSYNTHESIS RESEARCH 2016; 130:47-72. [PMID: 26897549 DOI: 10.1007/s11120-016-0224-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/25/2016] [Indexed: 05/26/2023]
Abstract
Plants with C4 photosynthesis are efficient in carbon assimilation and have an advantage over C3 photosynthesis. In C4 photosynthesis, the primary CO2 fixation is catalyzed by phosphoenolpyruvate carboxylase (PEPC). Here, we show that overexpression of Zea mays PEPC cDNA, under the control of 35S promoter, in Arabidopsis thaliana resulted in ~7-10 fold higher protein abundance and ~7-10 fold increase in PEPC activity in the transgenic lines than that in the vector control. We suggest that overexpression of PEPC played an anaplerotic role to increase the supply of 4-carbon carboxylic acids, which provided carbon skeletons for increased amino acid and protein synthesis. Higher protein content must have been responsible for increased metabolic processes including chlorophyll biosynthesis, photosynthesis, and respiration. Consequently, the PEPC-overexpressed transgenic plants had higher chlorophyll content, enhanced electron transport rate (ETR), lower non-photochemical quenching (NPQ) of chlorophyll a fluorescence, and a higher performance index (PI) than the vector control. Consistent with these observations, the rate of CO2 assimilation, the starch content, and the dry weight of PEPC-overexpressed plants increased by 14-18 %, 10-18 %, and 6.5-16 %, respectively. Significantly, transgenics were tolerant to salt stress as they had increased ability to synthesize amino acids, including the osmolyte proline. NaCl (150 mM)-treated transgenic plants had higher variable to maximum Chl a fluorescence (F v/F m) ratio, higher PI, higher ETR, and lower NPQ than the salt-treated vector controls. These results suggest that expression of C4 photosynthesis enzyme(s) in a C3 plant can improve its photosynthetic capacity with enhanced tolerance to salinity stress.
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Affiliation(s)
- Deepika Kandoi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- School of Biotechnology, Kalinga Institute of Industrial Technology University, Bhubaneswar, Odisha, 751024, India
| | - Sasmita Mohanty
- School of Biotechnology, Kalinga Institute of Industrial Technology University, Bhubaneswar, Odisha, 751024, India
| | - Baishnab C Tripathy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Xu Z, Li J, Guo X, Jin S, Zhang X. Metabolic engineering of cottonseed oil biosynthesis pathway via RNA interference. Sci Rep 2016; 6:33342. [PMID: 27620452 PMCID: PMC5020431 DOI: 10.1038/srep33342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/15/2016] [Indexed: 11/09/2022] Open
Abstract
Cottonseed oil is recognized as an important oil in food industry for its unique characters: low flavor reversion and the high level of antioxidants (VitaminE) as well as unsaturated fatty acid. However, the cottonseed oil content of cultivated cotton (Gossypium hirsutum) is only around 20%. In this study, we modified the accumulation of oils by the down-regulation of phosphoenolpyruvate carboxylase 1 (GhPEPC1) via RNA interference in transgenic cotton plants. The qRT-PCR and enzyme activity assay revealed that the transcription and expression of GhPEPC1 was dramatically down-regulated in transgenic lines. Consequently, the cottonseed oil content in several transgenic lines showed a significant (P < 0.01) increase (up to 16.7%) without obvious phenotypic changes under filed condition when compared to the control plants. In order to elucidate the molecular mechanism of GhPEPC1 in the regulation of seed oil content, we quantified the expression of the carbon metabolism related genes of transgenic GhPEPC1 RNAi lines by transcriptome analysis. This analysis revealed the decrease of GhPEPC1 expression led to the increase expression of triacylglycerol biosynthesis-related genes, which eventually contributed to the lipid biosynthesis in cotton. This result provides a valuable information for cottonseed oil biosynthesis pathway and shows the potential of creating high cottonseed oil germplasm by RNAi strategy for cotton breeding.
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Affiliation(s)
- Zhongping Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China
| | - Jingwen Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China
| | - Xiaoping Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China
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40
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Chiang CP, Yim WC, Sun YH, Ohnishi M, Mimura T, Cushman JC, Yen HE. Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings. FRONTIERS IN PLANT SCIENCE 2016; 7:1143. [PMID: 27555850 PMCID: PMC4977306 DOI: 10.3389/fpls.2016.01143] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/18/2016] [Indexed: 05/03/2023]
Abstract
The halophyte Mesembryanthemum crystallinum (common or crystalline ice plant) is a useful model for studying molecular mechanisms of salt tolerance. The morphology, physiology, metabolism, and gene expression of ice plant have been studied and large-scale analyses of gene expression profiling have drawn an outline of salt tolerance in ice plant. A rapid root growth to a sudden increase in salinity was observed in ice plant seedlings. Using a fluorescent dye to detect Na(+), we found that ice plant roots respond to an increased flux of Na(+) by either secreting or storing Na(+) in specialized cells. High-throughput sequencing was used to identify small RNA profiles in 3-day-old seedlings treated with or without 200 mM NaCl. In total, 135 conserved miRNAs belonging to 21 families were found. The hairpin precursor of 19 conserved mcr-miRNAs and 12 novel mcr-miRNAs were identified. After 6 h of salt stress, the expression of most mcr-miRNAs showed decreased relative abundance, whereas the expression of their corresponding target genes showed increased mRNA relative abundance. The cognate target genes are involved in a broad range of biological processes: transcription factors that regulate growth and development, enzymes that catalyze miRNA biogenesis for the most conserved mcr-miRNA, and proteins that are involved in ion homeostasis and drought-stress responses for some novel mcr-miRNAs. Analyses of the functions of target genes revealed that cellular processes, including growth and development, metabolism, and ion transport activity are likely to be enhanced in roots under salt stress. The expression of eleven conserved miRNAs and two novel miRNAs were correlated reciprocally with predicted targets within hours after salt stress exposure. Several conserved miRNAs have been known to regulate root elongation, root apical meristem activity, and lateral root formation. Based upon the expression pattern of miRNA and target genes in combination with the observation of Na(+) distribution, ice plant likely responds to increased salinity by using Na(+) as an osmoticum for cell expansion and guard cell opening. Excessive Na(+) could either be secreted through the root epidermis or stored in specialized leaf epidermal cells. These responses are regulated in part at the miRNA-mediated post-transcriptional level.
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Affiliation(s)
- Chih-Pin Chiang
- Department of Life Sciences, National Chung Hsing UniversityTaichung, Taiwan
| | - Won C. Yim
- Department of Biochemistry and Molecular Biology, University of NevadaReno, NV, USA
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung Hsing UniversityTaichung, Taiwan
| | - Miwa Ohnishi
- Graduate School of Science, Kobe UniversityKobe, Japan
| | | | - John C. Cushman
- Department of Biochemistry and Molecular Biology, University of NevadaReno, NV, USA
| | - Hungchen E. Yen
- Department of Life Sciences, National Chung Hsing UniversityTaichung, Taiwan
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Ruiz-Ballesta I, Baena G, Gandullo J, Wang L, She YM, Plaxton WC, Echevarría C. New insights into the post-translational modification of multiple phosphoenolpyruvate carboxylase isoenzymes by phosphorylation and monoubiquitination during sorghum seed development and germination. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3523-36. [PMID: 27194739 PMCID: PMC4892742 DOI: 10.1093/jxb/erw186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC; E.C. 4.1.1.31) was characterized in developing and germinating sorghum seeds, focusing on the transcript and polypeptide abundance of multiple plant-type phosphoenolpyruvate carboxylase (PTPC) genes, and the post-translational modification of each isoenzyme by phosphorylation versus monoubiquitination during germination. We observed high levels of SbPPC4 (Sb07g014960) transcripts during early development (stage I), and extensive transcript abundance of SbPPC2 (Sb02g021090) and SbPPC3 (Sb04g008720) throughout the entire life cycle of the seed. Although tandem mass spectrometry (MS) analysis of immunopurified PTPC indicated that four different PTPC isoenzymes were expressed in the developing and germinating seeds, SbPPC3 was the most abundant isozyme of the developing seed, and of the embryo and the aleurone layer of germinating seeds. In vivo phosphorylation of the different PTPC isoenzymes at their conserved N-terminal seryl phosphorylation site during germination was also established by MS/MS analysis. Furthermore, three of the four isoenzymes were partially monoubiquitinated, with MS/MS pinpointing SbPPC2 and SbPPC3 monoubiquitination at the conserved Lys-630 and Lys-624 residues, respectively. Our results demonstrate that monoubiquitination and phosphorylation simultaneously occur in vivo with different PTPC isozymes during seed germination. In addition, we show that PTPC monoubiquitination in germinating sorghum seeds always increases at stage II (emergence of the radicle), is maintained during the aerobic period of rapid cell division and reserve mobilization, and remains relatively constant until stage IV-V when coleoptiles initiate the formation of the photosynthetic tissues.
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Affiliation(s)
- Isabel Ruiz-Ballesta
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avda Reina Mercedes nº 6, 41012 Sevilla, Spain
| | - Guillermo Baena
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avda Reina Mercedes nº 6, 41012 Sevilla, Spain
| | - Jacinto Gandullo
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avda Reina Mercedes nº 6, 41012 Sevilla, Spain
| | - Liqun Wang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, China State Key Laboratory of Crop Genetics and Germplasm Enhancement, Soybean Research Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yi-Min She
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, China
| | | | - Cristina Echevarría
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avda Reina Mercedes nº 6, 41012 Sevilla, Spain
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42
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Rainha N, Medeiros VP, Câmara M, Faustino H, Leite JP, Barreto MDC, Cruz C, Pacheco CA, Ponte D, Bernardes da Silva A. Plasticity of crassulacean acid metabolism at subtropical latitudes: a pineapple case study. PHYSIOLOGIA PLANTARUM 2016; 156:29-39. [PMID: 26362993 DOI: 10.1111/ppl.12386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 06/19/2015] [Accepted: 07/17/2015] [Indexed: 06/05/2023]
Abstract
Plants with the crassulacean acid metabolism (CAM) express high-metabolic plasticity, to adjust to environmental stresses. This article hypothesizes that irradiance and nocturnal temperatures are the major limitations for CAM at higher latitudes such as the Azores (37°45'N). Circadian CAM expression in Ananas comosus L. Merr. (pineapple) was assessed by the diurnal pattern of leaf carbon fixation into l-malate at the solstices and equinoxes, and confirmed by determining maximal phosphoenolpyruvate carboxylase (PEPC) activity in plant material. Metabolic adjustments to environmental conditions were confirmed by gas exchange measurements, and integrated with environmental data to determine CAM's limiting factors: light and temperature. CAM plasticity was observed at the equinoxes, under similar photoperiods, but different environmental conditions. In spring, CAM expression was similar between vegetative and flowering plants, while in autumn, flowering (before anthesis) and fructifying (with fully developed fruit before ripening) plants accumulated more l-malate. Below 100 µmol m(-2) s(-1) , CAM phase I was extended, reducing CAM phase III during the day. Carbon fixation inhibition may occur by two major pathways: nocturnal temperature (<15°C) inhibiting PEPC activity and l-malate accumulation; and low irradiance influencing the interplay between CAM phase I and III, affecting carboxylation and decarboxylation. Both have important consequences for plant development in autumn and winter. Observations were confirmed by flowering time prediction using environmental data, emphasizing that CAM expression had a strong seasonal regulation due to a complex network response to light and temperature, allowing pineapple to survive in environments not suitable for high productivity.
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Affiliation(s)
- Nuno Rainha
- Instituto de Inovação Tecnológica dos Açores (INOVA), Ponta Delgada, Açores, Portugal
- Centro de Ecologia, Evolução e Alterações Climáticas (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Violante P Medeiros
- Instituto de Inovação Tecnológica dos Açores (INOVA), Ponta Delgada, Açores, Portugal
- Departamento de Ciências Tecnológicas e Desenvolvimento, Universidade dos Açores, Ponta Delgada, Portugal
| | - Mariana Câmara
- Instituto de Inovação Tecnológica dos Açores (INOVA), Ponta Delgada, Açores, Portugal
| | - Hélder Faustino
- Instituto de Inovação Tecnológica dos Açores (INOVA), Ponta Delgada, Açores, Portugal
| | - João P Leite
- Instituto de Inovação Tecnológica dos Açores (INOVA), Ponta Delgada, Açores, Portugal
| | - Maria do Carmo Barreto
- Departamento de Ciências Tecnológicas e Desenvolvimento, Universidade dos Açores, Ponta Delgada, Portugal
| | - Cristina Cruz
- Centro de Ecologia, Evolução e Alterações Climáticas (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Vegetal, Universidade de Lisboa, Faculdade de Ciências, Lisboa, Portugal
| | | | - Duarte Ponte
- Instituto de Inovação Tecnológica dos Açores (INOVA), Ponta Delgada, Açores, Portugal
- Departamento de Ciências Tecnológicas e Desenvolvimento, Universidade dos Açores, Ponta Delgada, Portugal
| | - Anabela Bernardes da Silva
- Departamento de Biologia Vegetal, Universidade de Lisboa, Faculdade de Ciências, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Universidade de Lisboa, Faculdade de Ciências, Lisboa, Portugal
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43
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Habibi G, Ajory N. The effect of drought on photosynthetic plasticity in Marrubium vulgare plants growing at low and high altitudes. JOURNAL OF PLANT RESEARCH 2015; 128:987-994. [PMID: 26314352 DOI: 10.1007/s10265-015-0748-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/04/2015] [Indexed: 06/04/2023]
Abstract
Photosynthesis is a biological process most affected by water deficit. Plants have various photosynthetic mechanisms that are matched to specific climatic zones. We studied the photosynthetic plasticity of C3 plants at water deficit using ecotypes of Marrubium vulgare L. from high (2,200 m) and low (1,100 m) elevation sites in the Mishou-Dagh Mountains of Iran. Under experimental drought, high-altitude plants showed more tolerance to water stress based on most of the parameters studied as compared to the low-altitude plants. Increased tolerance in high-altitude plants was achieved by lower levels of daytime stomatal conductance (g s) and reduced damaging effect on maximal quantum yield of photosystem II (PSII) (F v /F m ) coupled with higher levels of carotenoids and non-photochemical quenching (NPQ). High-altitude plants exhibited higher water use efficiency (WUE) than that in low-altitude plants depending on the presence of thick leaves and the reduced daytime stomatal conductance. Additionally, we have studied the oscillation in H(+) content and diel gas exchange patterns to determine the occurrence of C3 or weak CAM (Crassulacean acid metabolism) in M. vulgare through 15 days drought stress. Under water-stressed conditions, low-altitude plants exhibited stomatal conductance and acid fluctuations characteristic of C3 photosynthesis, though high-altitude plants exhibited more pronounced increases in nocturnal acidity and phosphoenolpyruvate carboxylase (PEPC) activity, suggesting photosynthetic flexibility. These results indicated that the regulation of carotenoids, NPQ, stomatal conductance and diel patterns of CO2 exchange presented the larger differences among studied plants at different altitudes and seem to be the protecting mechanisms controlling the photosynthetic performance of M. vulgare plants under drought conditions.
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Affiliation(s)
- Ghader Habibi
- Department of Biology, Payame Noor University, PO BOX 19395-3697, Tehran, Iran.
| | - Neda Ajory
- Department of Biology, Payame Noor University, PO BOX 19395-3697, Tehran, Iran
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44
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Winter K, Holtum JAM, Smith JAC. Crassulacean acid metabolism: a continuous or discrete trait? THE NEW PHYTOLOGIST 2015; 208:73-8. [PMID: 25975197 DOI: 10.1111/nph.13446] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/22/2015] [Indexed: 05/27/2023]
Abstract
The key components of crassulacean acid metabolism (CAM) - nocturnal fixation of atmospheric CO2 and its processing via Rubisco in the subsequent light period - are now reasonably well understood in terms of the biochemical reactions defining this water-saving mode of carbon assimilation. Phenotypically, however, the degree to which plants engage in the CAM cycle relative to regular C3 photosynthesis is highly variable. Depending upon species, ontogeny and environment, the contribution of nocturnal CO2 fixation to 24-h carbon gain can range continuously from close to 0% to 100%. Nevertheless, not all possible combinations of light and dark CO2 fixation appear equally common. Large-scale surveys of carbon-isotope ratios typically show a strongly bimodal frequency distribution, with relatively few intermediate values. Recent research has revealed that many species capable of low-level CAM activity are nested within the peak of C3 -type isotope signatures. While questions remain concerning the adaptive significance of dark CO2 fixation in such species, plants with low-level CAM should prove valuable models for investigating the discrete changes in genetic architecture and gene expression that have enabled the evolutionary transition from C3 to CAM.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - Joseph A M Holtum
- Centre for Tropical Biodiversity and Climate Change, James Cook University, Townsville, QLD, 4811, Australia
| | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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45
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Arias-Baldrich C, Bosch N, Begines D, Feria AB, Monreal JA, García-Mauriño S. Proline synthesis in barley under iron deficiency and salinity. JOURNAL OF PLANT PHYSIOLOGY 2015; 183:121-9. [PMID: 26125122 DOI: 10.1016/j.jplph.2015.05.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 05/07/2023]
Abstract
This work investigates proline synthesis in six barley varieties subjected to iron deficiency, salinity or both stresses. The highest growth under Fe sufficiency corresponded to Belgrano and Shakira. A moderate augment of leaf phosphoenolpyruvate carboxylase (PEPC) activity was observed in all six varieties in response to Fe deficiency, consistently in leaves and sporadically in roots. All six varieties accumulated proline under Fe deficiency, to a higher extent in leaves than in roots. The decrease of Fe supply from 100 μM NaFe(III)-EDTA to 0.5 μM NaFe(III)-EDTA reduced growth and photosynthetic pigments similarly in the six barley varieties. On the contrary, differences between varieties could be observed with respect to increased or, conversely, decreased proline content as a function of the amount of NaFe(III)-EDTA supplied. These two opposite types were represented by Belgrano (higher proline under Fe deficiency) and Shakira (higher proline under Fe sufficiency). Time-course experiments suggested that leaf PEPC activity was not directly responsible for supplying C for proline synthesis under Fe deficiency. High proline levels in the leaves of Fe-deficient Belgrano plants in salinity were associated to a better performance of this variety under these combined stresses.
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Affiliation(s)
- Cirenia Arias-Baldrich
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n6, 41012, Seville, Spain.
| | - Nadja Bosch
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n6, 41012, Seville, Spain.
| | - Digna Begines
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n6, 41012, Seville, Spain.
| | - Ana B Feria
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n6, 41012, Seville, Spain.
| | - José A Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n6, 41012, Seville, Spain.
| | - Sofía García-Mauriño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes n6, 41012, Seville, Spain.
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46
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Dever LV, Boxall SF, Kneřová J, Hartwell J. Transgenic perturbation of the decarboxylation phase of Crassulacean acid metabolism alters physiology and metabolism but has only a small effect on growth. PLANT PHYSIOLOGY 2015; 167:44-59. [PMID: 25378692 PMCID: PMC4281012 DOI: 10.1104/pp.114.251827] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 10/28/2014] [Indexed: 05/19/2023]
Abstract
Mitochondrial NAD-malic enzyme (ME) and/or cytosolic/plastidic NADP-ME combined with the cytosolic/plastidic pyruvate orthophosphate dikinase (PPDK) catalyze two key steps during light-period malate decarboxylation that underpin secondary CO(2) fixation in some Crassulacean acid metabolism (CAM) species. We report the generation and phenotypic characterization of transgenic RNA interference lines of the obligate CAM species Kalanchoë fedtschenkoi with reduced activities of NAD-ME or PPDK. Transgenic line rNAD-ME1 had 8%, and rPPDK1 had 5% of the wild-type level of activity, and showed dramatic changes in the light/dark cycle of CAM CO(2) fixation. In well-watered conditions, these lines fixed all of their CO(2) in the light; they thus performed C(3) photosynthesis. The alternative malate decarboxylase, NADP-ME, did not appear to compensate for the reduction in NAD-ME, suggesting that NAD-ME was the key decarboxylase for CAM. The activity of other CAM enzymes was reduced as a consequence of knocking out either NAD-ME or PPDK activity, particularly phosphoenolpyruvate carboxylase (PPC) and PPDK in rNAD-ME1. Furthermore, the circadian clock-controlled phosphorylation of PPC in the dark was reduced in both lines, especially in rNAD-ME1. This had the consequence that circadian rhythms of PPC phosphorylation, PPC kinase transcript levels and activity, and the classic circadian rhythm of CAM CO(2) fixation were lost, or dampened toward arrhythmia, under constant light and temperature conditions. Surprisingly, oscillations in the transcript abundance of core circadian clock genes also became arrhythmic in the rNAD-ME1 line, suggesting that perturbing CAM in K. fedtschenkoi feeds back to perturb the central circadian clock.
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Affiliation(s)
- Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jana Kneřová
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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Ceusters J, Borland AM, Taybi T, Frans M, Godts C, De Proft MP. Light quality modulates metabolic synchronization over the diel phases of crassulacean acid metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3705-14. [PMID: 24803500 PMCID: PMC4085966 DOI: 10.1093/jxb/eru185] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Temporal compartmentation of carboxylation processes is a defining feature of crassulacean acid metabolism and involves circadian control of key metabolic and transport steps that regulate the supply and demand for carbon over a 24h cycle. Recent insights on the molecular workings of the circadian clock and its connection with environmental inputs raise new questions on the importance of light quality and, by analogy, certain photoreceptors for synchronizing the metabolic components of CAM. The present work tested the hypothesis that optimal coupling of stomatal conductance, net CO2 uptake, and the reciprocal turnover of carbohydrates and organic acids over the diel CAM cycle requires both blue and red light input signals. Contrasting monochromatic wavelengths of blue, green, and red light (i.e. 475, 530, 630nm) with low fluence rates (10 μmol m(-2) s(-1)) were administered for 16 hours each diel cycle for a total treatment time of 48 hours to the obligate CAM bromeliad, Aechmea 'Maya'. Of the light treatments imposed, low-fluence blue light was a key determinant in regulating stomatal responses, organic acid mobilization from the vacuole, and daytime decarboxylation. However, the reciprocal relationship between starch and organic acid turnover that is typical for CAM was uncoupled under low-fluence blue light. Under low-fluence red or green light, the diel turnover of storage carbohydrates was orchestrated in line with the requirements of CAM, but a consistent delay in acid consumption at dawn compared with plants under white or low-fluence blue light was noted. Consistent with the acknowledged influences of both red and blue light as input signals for the circadian clock, the data stress the importance of both red and blue-light signalling pathways for synchronizing the metabolic and physiological components of CAM over the day/night cycle.
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Affiliation(s)
- Johan Ceusters
- Faculty of Engineering Technology, Department of Microbial and Molecular systems, Bioengineering Technology TC, KU Leuven Campus Geel, Kleinhoefstraat 4, B-2440 Geel, Belgium
| | - Anne M Borland
- School of Biology, Newcastle Institute for Research on Sustainability, Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6407, USA
| | - Tahar Taybi
- School of Biology, Newcastle Institute for Research on Sustainability, Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Mario Frans
- Faculty of Engineering Technology, Department of Microbial and Molecular systems, Bioengineering Technology TC, KU Leuven Campus Geel, Kleinhoefstraat 4, B-2440 Geel, Belgium
| | - Christof Godts
- Faculty of Bioscience Engineering, Department of Biosystems, Division of Crop Biotechnics, KU Leuven, Willem De Croylaan 42, B-3001 Heverlee, Belgium
| | - Maurice P De Proft
- Faculty of Bioscience Engineering, Department of Biosystems, Division of Crop Biotechnics, KU Leuven, Willem De Croylaan 42, B-3001 Heverlee, Belgium
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48
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Aldous SH, Weise SE, Sharkey TD, Waldera-Lupa DM, Stühler K, Mallmann J, Groth G, Gowik U, Westhoff P, Arsova B. Evolution of the Phosphoenolpyruvate Carboxylase Protein Kinase Family in C3 and C4 Flaveria spp. PLANT PHYSIOLOGY 2014; 165:1076-1091. [PMID: 24850859 PMCID: PMC4081323 DOI: 10.1104/pp.114.240283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/20/2014] [Indexed: 05/04/2023]
Abstract
The key enzyme for C4 photosynthesis, Phosphoenolpyruvate Carboxylase (PEPC), evolved from nonphotosynthetic PEPC found in C3 ancestors. In all plants, PEPC is phosphorylated by Phosphoenolpyruvate Carboxylase Protein Kinase (PPCK). However, differences in the phosphorylation pattern exist among plants with these photosynthetic types, and it is still not clear if they are due to interspecies differences or depend on photosynthetic type. The genus Flaveria contains closely related C3, C3-C4 intermediate, and C4 species, which are evolutionarily young and thus well suited for comparative analysis. To characterize the evolutionary differences in PPCK between plants with C3 and C4 photosynthesis, transcriptome libraries from nine Flaveria spp. were used, and a two-member PPCK family (PPCKA and PPCKB) was identified. Sequence analysis identified a number of C3- and C4-specific residues with various occurrences in the intermediates. Quantitative analysis of transcriptome data revealed that PPCKA and PPCKB exhibit inverse diel expression patterns and that C3 and C4 Flaveria spp. differ in the expression levels of these genes. PPCKA has maximal expression levels during the day, whereas PPCKB has maximal expression during the night. Phosphorylation patterns of PEPC varied among C3 and C4 Flaveria spp. too, with PEPC from the C4 species being predominantly phosphorylated throughout the day, while in the C3 species the phosphorylation level was maintained during the entire 24 h. Since C4 Flaveria spp. evolved from C3 ancestors, this work links the evolutionary changes in sequence, PPCK expression, and phosphorylation pattern to an evolutionary phase shift of kinase activity from a C3 to a C4 mode.
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Affiliation(s)
- Sophia H Aldous
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Sean E Weise
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Thomas D Sharkey
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Daniel M Waldera-Lupa
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Kai Stühler
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Julia Mallmann
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Georg Groth
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Udo Gowik
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Peter Westhoff
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
| | - Borjana Arsova
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen (S.H.A., J.M., U.G., P.W., B.A.), Molecular Proteomics Laboratory (D.M.W.-L., K.S.), and Biochemische Pflanzenphysiologie (G.G.), Heinrich-Heine-Universität, 40225 Duesseldorf, Germany;Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.E.W., T.D.S.); andCluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, 40225 Duesseldorf, Germany (K.S., G.G., U.G., P.W., B.A.)
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Owen NA, Griffiths H. A system dynamics model integrating physiology and biochemical regulation predicts extent of crassulacean acid metabolism (CAM) phases. THE NEW PHYTOLOGIST 2013; 200:1116-1131. [PMID: 23992169 DOI: 10.1111/nph.12461] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/19/2013] [Indexed: 06/02/2023]
Abstract
A system dynamics (SD) approach was taken to model crassulacean acid metabolism (CAM) expression from measured biochemical and physiological constants. SD emphasizes state-dependent feedback interaction to describe the emergent properties of a complex system. These mechanisms maintain biological systems with homeostatic limits on a temporal basis. Previous empirical studies on CAM have correlated biological constants (e.g. enzyme kinetic parameters) with expression over the CAM diel cycle. The SD model integrates these constants within the architecture of the CAM 'system'. This allowed quantitative causal connections to be established between biological inputs and the four distinct phases of CAM delineated by gas exchange and malic acid accumulation traits. Regulation at flow junctions (e.g. stomatal and mesophyll conductance, and malic acid transport across the tonoplast) that are subject to feedback control (e.g. stomatal aperture, malic acid inhibition of phosphoenolpyruvate carboxylase, and enzyme kinetics) was simulated. Simulated expression for the leaf-succulent Kalanchoë daigremontiana and more succulent tissues of Agave tequilana showed strong correlation with measured gas exchange and malic acid accumulation (R(2) = 0.912 and 0.937, respectively, for K. daigremontiana and R(2) = 0.928 and 0.942, respectively, for A. tequilana). Sensitivity analyses were conducted to quantitatively identify determinants of diel CO2 uptake. The transition in CAM expression from low to high volume/area tissues (elimination of phase II-IV carbon-uptake signatures) was achieved largely by the manipulation three input parameters.
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Affiliation(s)
- Nick A Owen
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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Aragón C, Pascual P, González J, Escalona M, Carvalho L, Amancio S. The physiology of ex vitro pineapple (Ananas comosus L. Merr. var MD-2) as CAM or C3 is regulated by the environmental conditions: proteomic and transcriptomic profiles. PLANT CELL REPORTS 2013; 32:1807-1818. [PMID: 23959598 DOI: 10.1007/s00299-013-1493-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/30/2013] [Accepted: 08/04/2013] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE Proteomic and transcriptomic profiles of key enzymes were monitored in pineapple plants propagated under C3 and CAM-inducing metabolisms to obtain insight into the CAM-facultative metabolism and the relationship of CAM plants with oxidative stress. ABSTRACT Pineapple is one of the most important tropical crops worldwide. The use of temporary immersion bioreactors for the first stages of pineapple propagation enables precise control of plant growth, increases the rate of plant multiplication, decreases space, energy and labor requirements for pineapple plants in commercial micropropagation. Once the plantlets are ready to be taken from the reactors, they are carefully acclimatized to natural environmental conditions, and a facultative C3/CAM metabolism in the first 2 months of growth is the characteristic of pineapple plants, depending on environmental conditions. We subjected two sets of micropropagated pineapple plants to C3 and CAM-inducing environmental conditions, determined by light intensity/relative humidity (respectively 40 μmol m−2 s−1/85 % and 260 μmol m−2 s−1/50 %). Leaves of pineapple plants grown under CAM-inducing conditions showed higher leaf thickness and more developed cuticles and hypodermic tissue. Proteomic profiles of several proteins, isoenzyme patterns and transcriptomic profiles were also measured. Five major spots were isolated and identified, two of them for the first time in Ananas comosus (OEE 1; OEE 2) and the other three corresponding to small fragments of the large subunit of Rubisco (LSU). PEPC and PEPCK were also detected by immunobloting of 2DE at the end of both ex vitro treatments (C3/CAM) during the dark period. Isoenzymes of SOD and CAT were identified by electrophoresis and the transcript levels of OEE 1 and CAT were associated with CAM metabolism in pineapple plants.
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