1
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Daems S, Shameer S, Ceusters N, Sweetlove L, Ceusters J. Metabolic modelling identifies mitochondrial Pi uptake and pyruvate efflux as key aspects of daytime metabolism and proton homeostasis in crassulacean acid metabolism leaves. THE NEW PHYTOLOGIST 2024; 244:159-175. [PMID: 39113419 DOI: 10.1111/nph.20032] [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: 05/18/2024] [Accepted: 07/15/2024] [Indexed: 09/17/2024]
Abstract
Crassulacean acid metabolism (CAM) leaves are characterized by nocturnal acidification and diurnal deacidification processes related with the timed actions of phosphoenolpyruvate carboxylase and Rubisco, respectively. How CAM leaves manage cytosolic proton homeostasis, particularly when facing massive diurnal proton effluxes from the vacuole, remains unclear. A 12-phase flux balance analysis (FBA) model was constructed for a mature malic enzyme-type CAM mesophyll cell in order to predict diel kinetics of intracellular proton fluxes. The charge- and proton-balanced FBA model identified the mitochondrial phosphate carrier (PiC, Pi/H+ symport), which provides Pi to the matrix to sustain ATP biosynthesis, as a major consumer of cytosolic protons during daytime (> 50%). The delivery of Pi to the mitochondrion, co-transported with protons, is required for oxidative phosphorylation and allows sufficient ATP to be synthesized to meet the high energy demand during CAM Phase III. Additionally, the model predicts that mitochondrial pyruvate originating from decarboxylation of malate is exclusively exported to the cytosol, probably via a pyruvate channel mechanism, to fuel gluconeogenesis. In this biochemical cycle, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) acts as another important cytosolic proton consumer. Overall, our findings emphasize the importance of mitochondria in CAM and uncover a hitherto unappreciated role in metabolic proton homeostasis.
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Affiliation(s)
- Stijn Daems
- Research Group for Sustainable Crop Production & Protection, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Geel, 2440, Belgium
- KU Leuven Plant Institute (LPI), KU Leuven, Leuven, 3000, Belgium
| | - Sanu Shameer
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
- Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Nathalie Ceusters
- Research Group for Sustainable Crop Production & Protection, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Geel, 2440, Belgium
| | - Lee Sweetlove
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Johan Ceusters
- Research Group for Sustainable Crop Production & Protection, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Geel, 2440, Belgium
- KU Leuven Plant Institute (LPI), KU Leuven, Leuven, 3000, Belgium
- Centre for Environmental Sciences, Environmental Biology, UHasselt, Diepenbeek, 3590, Belgium
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2
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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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3
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Ludwig M, Hartwell J, Raines CA, Simkin AJ. The Calvin-Benson-Bassham cycle in C 4 and Crassulacean acid metabolism species. Semin Cell Dev Biol 2024; 155:10-22. [PMID: 37544777 DOI: 10.1016/j.semcdb.2023.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023]
Abstract
The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.
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Affiliation(s)
- Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Andrew J Simkin
- University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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4
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Leverett A, Borland AM. Elevated nocturnal respiratory rates in the mitochondria of CAM plants: current knowledge and unanswered questions. ANNALS OF BOTANY 2023; 132:855-867. [PMID: 37638861 PMCID: PMC10799998 DOI: 10.1093/aob/mcad119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/14/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
Crassulacean acid metabolism (CAM) is a metabolic adaptation that has evolved convergently in 38 plant families to aid survival in water-limited niches. Whilst primarily considered a photosynthetic adaptation, CAM also has substantial consequences for nocturnal respiratory metabolism. Here, we outline the history, current state and future of nocturnal respiration research in CAM plants, with a particular focus on the energetics of nocturnal respiratory oxygen consumption. Throughout the 20th century, research interest in nocturnal respiration occurred alongside initial discoveries of CAM, although the energetic and mechanistic implications of nocturnal oxygen consumption and links to the operation of the CAM cycle were not fully understood. Recent flux balance analysis (FBA) models have provided new insights into the role that mitochondria play in the CAM cycle. Several FBA models have predicted that CAM requires elevated nocturnal respiratory rates, compared to C3 species, to power vacuolar malic acid accumulation. We provide physiological data, from the genus Clusia, to corroborate these modelling predictions, thereby reinforcing the importance of elevated nocturnal respiratory rates for CAM. Finally, we outline five unanswered questions pertaining to nocturnal respiration which must be addressed if we are to fully understand and utilize CAM plants in a hotter, drier world.
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Affiliation(s)
- Alistair Leverett
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge CB2 3EA, UK
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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5
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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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6
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Heyduk K, McAssey EV, Field R, Leebens-Mack J. The Agavoideae: an emergent model clade for CAM evolutionary biology. ANNALS OF BOTANY 2023; 132:727-737. [PMID: 37191440 PMCID: PMC10799990 DOI: 10.1093/aob/mcad062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/16/2023] [Accepted: 05/15/2023] [Indexed: 05/17/2023]
Abstract
Crassulacean acid metabolism - or CAM photosynthesis - was described in the early to mid-20th century, and our understanding of this metabolic pathway was later expanded upon through detailed biochemical analyses of carbon balance. Soon after, scientists began to study the ecophysiological implications of CAM, and a large part of this early work was conducted in the genus Agave, in the subfamily Agavoideae of the family Asparagaceae. Today, the Agavoideae continues to be important for the study of CAM photosynthesis, from the ecophysiology of CAM species, to the evolution of the CAM phenotype and to the genomics underlying CAM traits. Here we review past and current work on CAM in the Agavoideae, in particular highlighting the work of Park Nobel in Agave, and focusing on the powerful comparative system the Agavoideae has become for studying the origins of CAM. We also highlight new genomics research and the potential for studying intraspecific variation within species of the Agavoideae, particularly species in the genus Yucca. The Agavoideae has served as an important model clade for CAM research for decades, and undoubtedly will continue to help push our understanding of CAM biology and evolution in the future.
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Affiliation(s)
- Karolina Heyduk
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Edward V McAssey
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Richard Field
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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7
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de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
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Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
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8
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Zhao M, Nakamura T, Nakamura Y, Munemasa S, Mori IC, Murata Y. The effect of exogenous dihydroxyacetone and methylglyoxal on growth, anthocyanin accumulation, and the glyoxalase system in Arabidopsis. Biosci Biotechnol Biochem 2023; 87:1323-1331. [PMID: 37553179 DOI: 10.1093/bbb/zbad109] [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: 06/29/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
Dihydroxyacetone (DHA) occurs in wide-ranging organisms, including plants, and can undergo spontaneous conversion to methylglyoxal (MG). While the toxicity of MG to plants is well-known, the toxicity of DHA to plants remains to be elucidated. We investigated the effects of DHA and MG on Arabidopsis. Exogenous DHA at up to 10 mm did not affect the radicle emergence, the expansion of green cotyledons, the seedling growth, or the activity of glyoxalase II, while DHA at 10 mm inhibited the root elongation and increased the activity of glyoxalase I. Exogenous MG at 1.0 mm inhibited these physiological responses and increased both activities. Dihydroxyacetone at 10 mm increased the MG content in the roots. These results indicate that DHA is not so toxic as MG in Arabidopsis seeds and seedlings and suggest that the toxic effect of DHA at high concentrations is attributed to MG accumulation by the conversion to MG.
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Affiliation(s)
- Maoxiang Zhao
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Toshiyuki Nakamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yoshimasa Nakamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Shintaro Munemasa
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Izumi C Mori
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Yoshiyuki Murata
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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9
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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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10
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Fan W, He ZS, Zhe M, Feng JQ, Zhang L, Huang Y, Liu F, Huang JL, Ya JD, Zhang SB, Yang JB, Zhu A, Li DZ. High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes. PLANT COMMUNICATIONS 2023; 4:100564. [PMID: 36809882 PMCID: PMC10504564 DOI: 10.1016/j.xplc.2023.100564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Epiphytes with crassulacean acid metabolism (CAM) photosynthesis are widespread among vascular plants, and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation. However, we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes. Here, we report a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii (Orchidaceae). The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27 192 annotated genes was organized into 20 pseudochromosomes, 82.8% of which consisted of repetitive elements. Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids. We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics, proteomics, and metabolomics data collected across a CAM diel cycle. Patterns of rhythmically oscillating metabolites, especially CAM-related products, reveal circadian rhythmicity in metabolite accumulation in epiphytes. Genome-wide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism. Notably, we observed diurnal expression of several core CAM genes (especially βCA and PPC) that may be involved in temporal fixation of carbon sources. Our study provides a valuable resource for investigating post-transcription and translation scenarios in C. mannii, an Orchidaceae model for understanding the evolution of innovative traits in epiphytes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mengqing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Qiu Feng
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yiwei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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11
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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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12
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Tan B, Chen S. Defining Mechanisms of C 3 to CAM Photosynthesis Transition toward Enhancing Crop Stress Resilience. Int J Mol Sci 2023; 24:13072. [PMID: 37685878 PMCID: PMC10487458 DOI: 10.3390/ijms241713072] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Global climate change and population growth are persistently posing threats to natural resources (e.g., freshwater) and agricultural production. Crassulacean acid metabolism (CAM) evolved from C3 photosynthesis as an adaptive form of photosynthesis in hot and arid regions. It features the nocturnal opening of stomata for CO2 assimilation, diurnal closure of stomata for water conservation, and high water-use efficiency. To cope with global climate challenges, the CAM mechanism has attracted renewed attention. Facultative CAM is a specialized form of CAM that normally employs C3 or C4 photosynthesis but can shift to CAM under stress conditions. It not only serves as a model for studying the molecular mechanisms underlying the CAM evolution, but also provides a plausible solution for creating stress-resilient crops with facultative CAM traits. This review mainly discusses the recent research effort in defining the C3 to CAM transition of facultative CAM plants, and highlights challenges and future directions in this important research area with great application potential.
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Affiliation(s)
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA;
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13
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Bryant N, Engle N, Tschaplinski T, Pu Y, Ragauskas AJ. Variable lignin structure revealed in Populus leaves. RSC Adv 2023; 13:20187-20197. [PMID: 37416906 PMCID: PMC10320358 DOI: 10.1039/d3ra03142j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/25/2023] [Indexed: 07/08/2023] Open
Abstract
Lignin has long been a trait of interest, especially in bioenergy feedstocks such as Populus. While the stem lignin of Populus is well studied, foliar lignin has received significantly less consideration. To this end, leaves from 11 field grown, natural variant Populus trichocarpa genotypes were investigated by NMR, FTIR, and GC-MS. Five of these genotypes were sufficiently irrigated, and the other six genotypes were irrigated at a reduced rate (59% of the potential evapotranspiration for the site) to induce drought treatment. Analysis by HSQC NMR revealed highly variable lignin structure among the samples, especially for the syringyl/guaiacyl (S/G) ratio, which ranged from 0.52-11.9. Appreciable levels of a condensed syringyl lignin structure were observed in most samples. The same genotype subjected to different treatments exhibited similar levels of condensed syringyl lignin, suggesting this was not a response to stress. A cross peak of δC/δH 74.6/5.03, consistent with the erythro form of the β-O-4 linkage, was observed in genotypes where significant syringyl units were present. Principle component analysis revealed that FTIR absorbances associated with syringyl units (830 cm-1, 1317 cm-1) greatly contributed to variability between samples. Additionally, the ratio of 830/1230 cm-1 peak intensities were reasonably correlated (p-value < 0.05) with the S/G ratio determined by NMR. Analysis by GC-MS revealed significant variability of secondary metabolites such as tremuloidin, trichocarpin, and salicortin. Additionally, salicin derivatives were found to be well correlated with NMR results, which has been previously hypothesized. These results highlight previously unexplored nuance and variability associated with foliage tissue of poplar.
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Affiliation(s)
- Nathan Bryant
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville Tennessee 37996 USA
| | - Nancy Engle
- BioEnergy Science Center & Center for Bioenergy Innovation, Biosciences Division, University of Tennessee-Oak Ridge National Laboratory Joint Institute for Biological Science, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Timothy Tschaplinski
- BioEnergy Science Center & Center for Bioenergy Innovation, Biosciences Division, University of Tennessee-Oak Ridge National Laboratory Joint Institute for Biological Science, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center & Center for Bioenergy Innovation, Biosciences Division, University of Tennessee-Oak Ridge National Laboratory Joint Institute for Biological Science, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville Tennessee 37996 USA
- BioEnergy Science Center & Center for Bioenergy Innovation, Biosciences Division, University of Tennessee-Oak Ridge National Laboratory Joint Institute for Biological Science, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Center for Renewable Carbon, Department of Forestry, Wildlife, and Fisheries, University of Tennessee Institute of Agriculture Knoxville TN 37996 USA
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14
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Wang X, Huang X, Chen L, Xie Z, Tan S, Qin X, Chen T, Huang Y, Xi J, Chen H, Yi K. Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave. PLANTS (BASEL, SWITZERLAND) 2023; 12:2020. [PMID: 37653937 PMCID: PMC10222593 DOI: 10.3390/plants12102020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/06/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Agave species are widely planted for fiber production. However, the molecular basis of agave fiber development has not been well understood. In this study, we performed a transcriptomic analysis in A. amaniensi, a well-known variety with high-quality fiber production. Approximately 43.87 million clean reads were obtained using Illumina sequencing. The de novo assembly produced 66,746 unigrams, 54% of which were annotated in a public database. In the Nr database, 21,490 unigenes of A. amaniensis were shown to be most closely related to Asparagus officinalis. Nine expansin A orthologs with full coding regions were obtained, which were named EXP1a, EXP1b, EXP2, EXP3, EXP4a, EXP4b, EXP11, EXP12, and EXP13. The maximum likelihood phylogenetic tree revealed the species-specific expansion of expansin genes in Arabidopsis, rice and agave. The expression analysis suggested the negative correlation between the expression of expansin genes and the leaf growth rate, except AhEXP11. Moreover, expansin genes were differentially affected by abiotic and biotic stresses. Notably, AhEXP2 expression level was highly upgraded after the infection of Phytophthora nicotiana. Nutrient deficiency also influent expansin genes expression. Together, our research will benefit future studies related to fiber development, disease resistance and nutrient usage in agave.
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Affiliation(s)
- Xuxia Wang
- Urban Construction College, Wuchang Shouyi University, Wuhan 430064, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Lisha Chen
- Quality Supervision, Inspection and Testing Center of Sisal and Products, Ministry of Agriculture and Rural Affairs, Zhanjiang 524022, China
| | - Zhouli Xie
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Yanlei Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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15
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Chowrasia S, Nishad J, Mahato R, Kiran K, Rajkumari N, Panda AK, Rawal HC, Barman M, Mondal TK. Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01350-8. [PMID: 37184674 DOI: 10.1007/s11103-023-01350-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/02/2023] [Indexed: 05/16/2023]
Abstract
Soil salinity stress is one of the major bottlenecks for crop production. Although, allantoin is known to be involved in nitrogen metabolism in plants, yet several reports in recent time indicate its involvement in various abiotic stress responses including salinity stress. However, the detail mechanism of allantoin involvement in salinity stress tolerance in plants is not studied well. Moreover, we demonstrated the role of exogenous application of allantoin as well as increased concentration of endogenous allantoin in rendering salinity tolerance in rice and Arabidopsis respectively, via., induction of abscisic acid (ABA) and brassinosteroid (BR) biosynthesis pathways. Exogenous application of allantoin (10 µM) provides salt-tolerance to salt-sensitive rice genotype (IR-29). Transcriptomic data after exogenous supplementation of allantoin under salinity stress showed induction of ABA (OsNCED1) and BR (Oscytochrome P450) biosynthesis genes in IR-29. Further, the key gene of allantoin biosynthesis pathway i.e., urate oxidase of the halophytic species Oryza coarctata was also found to induce ABA and BR biosynthesis genes when over-expressed in transgenic Arabidopsis. Thus, indicating that ABA and BR biosynthesis pathways were involved in allantoin mediated salinity tolerance in both rice and Arabidopsis. Additionally, it has been found that several physio-chemical parameters such as biomass, Na+/K+ ratio, MDA, soluble sugar, proline, allantoin and chlorophyll contents were also associated with the allantoin-mediated salinity tolerance in urate oxidase overexpressed lines of Arabidopsis. These findings depicted the functional conservation of allantoin for salinity tolerance in both plant clades.
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Affiliation(s)
- Soni Chowrasia
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Jyoti Nishad
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rekha Mahato
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kanti Kiran
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Nitasana Rajkumari
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Alok Kumar Panda
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Hukam C Rawal
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Mandira Barman
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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16
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Rapid screening of secondary aromatic metabolites in Populus trichocarpa leaves. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:41. [PMID: 36899393 PMCID: PMC9999501 DOI: 10.1186/s13068-023-02287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND High-throughput metabolomics analytical methodology is needed for population-scale studies of bioenergy-relevant feedstocks such as poplar (Populus sp.). Here, the authors report the relative abundance of extractable aromatic metabolites in Populus trichocarpa leaves rapidly estimated using pyrolysis-molecular beam mass spectrometry (py-MBMS). Poplar leaves were analyzed in conjunction with and validated by GC/MS analysis of extracts to determine key spectral features used to build PLS models to predict the relative composition of extractable aromatic metabolites in whole poplar leaves. RESULTS The Pearson correlation coefficient for the relative abundance of extractable aromatic metabolites based on ranking between GC/MS analysis and py-MBMS analysis of the Boardman leaf set was 0.86 with R2 = 0.76 using a simplified prediction approach from select ions in MBMS spectra. Metabolites most influential to py-MBMS spectral features in the Clatskanie set included the following compounds: catechol, salicortin, salicyloyl-coumaroyl-glucoside conjugates, α-salicyloylsalicin, tremulacin, as well as other salicylates, trichocarpin, salicylic acid, and various tremuloidin conjugates. Ions in py-MBMS spectra with the highest correlation to the abundance of extractable aromatic metabolites as determined by GC/MS analysis of extracts, included m/z 68, 71, 77, 91, 94, 105, 107, 108, and 122, and were used to develop the simplified prediction approach without PLS models or a priori measurements. CONCLUSIONS The simplified py-MBMS method is capable of rapidly screening leaf tissue for relative abundance of extractable aromatic secondary metabolites to enable prioritization of samples in large populations requiring comprehensive metabolomics that will ultimately inform plant systems biology models and advance the development of optimized biomass feedstocks for renewable fuels and chemicals.
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17
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Yang Z, Gao C, Zhang Y, Yan Q, Hu W, Yang L, Wang Z, Li F. Recent progression and future perspectives in cotton genomic breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:548-569. [PMID: 36226594 DOI: 10.1111/jipb.13388] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/11/2022] [Indexed: 05/26/2023]
Abstract
Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.
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Affiliation(s)
- Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yihao Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qingdi Yan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572000, China
- Sanya Institute, Zhengzhou University, Sanya, 572000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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18
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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19
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Hu R, Zhang J, Jawdy S, Sreedasyam A, Lipzen A, Wang M, Ng V, Daum C, Keymanesh K, Liu D, Lu H, Ranjan P, Chen JG, Muchero W, Tschaplinski TJ, Tuskan GA, Schmutz J, Yang X. Comparative genomics analysis of drought response between obligate CAM and C 3 photosynthesis plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153791. [PMID: 36027837 DOI: 10.1016/j.jplph.2022.153791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/16/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) plants exhibit elevated drought and heat tolerance compared to C3 and C4 plants through an inverted pattern of day/night stomatal closure and opening for CO2 assimilation. However, the molecular responses to water-deficit conditions remain unclear in obligate CAM species. In this study, we presented genome-wide transcription sequencing analysis using leaf samples of an obligate CAM species Kalanchoë fedtschenkoi under moderate and severe drought treatments at two-time points of dawn (2-h before the start of light period) and dusk (2-h before the dark period). Differentially expressed genes were identified in response to environmental drought stress and a whole genome wide co-expression network was created as well. We found that the expression of CAM-related genes was not regulated by drought stimuli in K. fedtschenkoi. Our comparative analysis revealed that CAM species (K. fedtschenkoi) and C3 species (Arabidopsis thaliana, Populus deltoides 'WV94') share some common transcriptional changes in genes involved in multiple biological processes in response to drought stress, including ABA signaling and biosynthesis of secondary metabolites.
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Affiliation(s)
- Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Jin Zhang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA; State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Avinash Sreedasyam
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA.
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94589, USA.
| | - Mei Wang
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94589, USA.
| | - Vivian Ng
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94589, USA.
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94589, USA.
| | - Keykhosrow Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94589, USA.
| | - Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Jin-Gui Chen
- 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.
| | - Wellington Muchero
- 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.
| | - 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.
| | - Gerald A Tuskan
- 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.
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94589, 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.
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20
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Xin H, Wang Y, Li Q, Wan T, Hou Y, Liu Y, Gichuki DK, Zhou H, Zhu Z, Xu C, Zhou Y, Liu Z, Li R, Liu B, Lu L, Jiang H, Zhang J, Wan J, Aryal R, Hu G, Chen Z, Gituru RW, Liang Z, Wen J, Wang Q. A genome for Cissus illustrates features underlying its evolutionary success in dry savannas. HORTICULTURE RESEARCH 2022; 9:uhac208. [PMID: 36467268 PMCID: PMC9715578 DOI: 10.1093/hr/uhac208] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/08/2022] [Indexed: 06/17/2023]
Abstract
Cissus is the largest genus in Vitaceae and is mainly distributed in the tropics and subtropics. Crassulacean acid metabolism (CAM), a photosynthetic adaptation to the occurrence of succulent leaves or stems, indicates that convergent evolution occurred in response to drought stress during species radiation. Here we provide the chromosomal level assembly of Cissus rotundifolia (an endemic species in Eastern Africa) and a genome-wide comparison with grape to understand genome divergence within an ancient eudicot family. Extensive transcriptome data were produced to illustrate the genetics underpinning C. rotundifolia's ecological adaption to seasonal aridity. The modern karyotype and smaller genome of C. rotundifolia (n = 12, 350.69 Mb/1C), which lack further whole-genome duplication, were mainly derived from gross chromosomal rearrangements such as fusions and segmental duplications, and were sculpted by a very recent burst of retrotransposon activity. Bias in local gene amplification contributed to its remarkable functional divergence from grape, and the specific proliferated genes associated with abiotic and biotic responses (e.g. HSP-20, NBS-LRR) enabled C. rotundifolia to survive in a hostile environment. Reorganization of existing enzymes of CAM characterized as diurnal expression patterns of relevant genes further confer the ability to thrive in dry savannas.
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Affiliation(s)
| | | | | | | | - Yujun Hou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanshuang Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duncan Kiragu Gichuki
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huimin Zhou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenfei Zhu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Xu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yadong Zhou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhiming Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - Rongjun Li
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bing Liu
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Limin Lu
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Hongsheng Jiang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junnan Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Guangwan Hu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhiduan Chen
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Robert Wahiti Gituru
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, 62000-00200, Nairobi, Kenya
| | | | - Jun Wen
- Corresponding authors. E-mail: ; ;
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21
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Heyduk K, McAssey EV, Leebens‐Mack J. Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae). THE NEW PHYTOLOGIST 2022; 235:2111-2126. [PMID: 35596719 PMCID: PMC9796715 DOI: 10.1111/nph.18267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis has evolved repeatedly across the plant tree of life, however our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well watered and drought-stressed treatments. We further assessed gene expression and the molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. By contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms. Together the physiological and transcriptomic comparison of closely related C3 and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.
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Affiliation(s)
- Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
| | - Jim Leebens‐Mack
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
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22
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Heyduk K. Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future. PLANT PHYSIOLOGY 2022; 190:19-30. [PMID: 35748752 PMCID: PMC9434201 DOI: 10.1093/plphys/kiac303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) is a mode of photosynthesis that evolved in response to decreasing CO2 levels in the atmosphere some 20 million years ago. An elevated ratio of O2 relative to CO2 caused many plants to face increasing stress from photorespiration, a process exacerbated for plants living under high temperatures or in water-limited environments. Today, our climate is again rapidly changing and plants' ability to cope with and adapt to these novel environments is critical for their success. This review focuses on CAM plant responses to abiotic stressors likely to dominate in our changing climate: increasing CO2 levels, increasing temperatures, and greater variability in drought. Empirical studies that have assessed CAM responses are reviewed, though notably these are concentrated in relatively few CAM lineages. Other aspects of CAM biology, including the effects of abiotic stress on the light reactions and the role of leaf succulence, are also considered in the context of climate change. Finally, more recent studies using genomic techniques are discussed to link physiological changes in CAM plants with the underlying molecular mechanism. Together, the body of work reviewed suggests that CAM plants will continue to thrive in certain environments under elevated CO2. However, how CO2 interacts with other environmental factors, how those interactions affect CAM plants, and whether all CAM plants will be equally affected remain outstanding questions regarding the evolution of CAM on a changing planet.
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23
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Barros J, Shrestha HK, Serrani-Yarce JC, Engle NL, Abraham PE, Tschaplinski TJ, Hettich RL, Dixon RA. Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon. THE PLANT CELL 2022; 34:3339-3363. [PMID: 35670759 PMCID: PMC9421481 DOI: 10.1093/plcell/koac171] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/23/2022] [Indexed: 05/30/2023]
Abstract
Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary and secondary metabolism in land plants. Here, we used a systems biology approach to investigate the global metabolic responses to lignin pathway perturbations in the model grass Brachypodium distachyon. We identified the lignin biosynthetic protein families and found that ammonia-lyases (ALs) are among the most abundant proteins in lignifying tissues in grasses. Integrated metabolomic and proteomic data support a link between lignin biosynthesis and primary metabolism mediated by the ammonia released from ALs that is recycled for the synthesis of amino acids via glutamine. RNA interference knockdown of lignin genes confirmed that the route of the canonical pathway using shikimate ester intermediates is not essential for lignin formation in Brachypodium, and there is an alternative pathway from Tyr via sinapic acid for the synthesis of syringyl lignin involving yet uncharacterized enzymatic steps. Our findings support a model in which plant ALs play a central role in coordinating the allocation of carbon for lignin synthesis and the nitrogen available for plant growth. Collectively, these data also emphasize the value of integrative multiomic analyses to advance our understanding of plant metabolism.
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Affiliation(s)
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - Juan C Serrani-Yarce
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76201, USA
| | - Nancy L Engle
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76201, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Paul E Abraham
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Timothy J Tschaplinski
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Robert L Hettich
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
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24
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Reyna-Llorens I, Aubry S. As right as rain: deciphering drought-related metabolic flexibility in the C4-CAM Portulaca. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4615-4619. [PMID: 35950459 PMCID: PMC9366322 DOI: 10.1093/jxb/erac179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article comments on: Ferrari RC, Kawabata AB, Ferreira SS, Hartwell J, Freschi L. 2022. A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism gene expression in Portulaca oleracea. Journal of Experimental Botany 73,4867–4885.
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25
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Shahzad S, Hussain M, Munir H, Arfan M. Proximate composition and spatio-temporal heterogeneity of phytochemicals in Agave sisalana Perrine (sisal) adapted in different agro-ecological zones of Punjab, Pakistan. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:48869-48879. [PMID: 35199269 DOI: 10.1007/s11356-022-19260-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Exploring extractable phytochemicals from locally adapted sisal plant vegetation vary seasonally at different locations. This study elaborated proximate composition and phytochemical heterogeneity in sisal due to varying environmental conditions analyzed from five districts, i.e., Chakwal, Khushab, Rawalpindi, Faisalabad, and Layyah in Punjab, Pakistan. Extensive surveying and plant sampling across 2 years 2017-2018 and 2018-2019, during mid-spring, summer, autumn, and winter seasons were carried out for understanding the seasonal impact on sisal. The present study was designed in a randomized complete block design (RCBD) and analyzed considering seasonal, yearly, and locational impact. The spatial differences in phytochemicals concentration were strongly associated with environmental conditions prevailing in different seasons. Autumn season reflected saponins, tannins, and flavonoids in higher concentrations during 2018-2019 while steroids and terpenoids were higher during spring 2018-2019. Spatio-temporal variations in the proximate analysis were more apparent in different samples collected from different districts. Data recorded for the Khushab district and autumn season reflected the higher composition of a proximate analysis and phytochemical contents as compared to other seasons. Overall, the spatial differences in phytochemicals concentration were strongly associated with soils and environmental conditions prevailing in different seasons in selected districts.
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Affiliation(s)
- Sobia Shahzad
- Department of Botany, University of Agriculture, Faisalabad, 38000, Pakistan.
| | - Mumtaz Hussain
- Department of Botany, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Hassan Munir
- Department of Agronomy, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Arfan
- Department of Botany, University of Agriculture, Faisalabad, 38000, Pakistan
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26
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Maceda-López LF, Góngora-Castillo EB, Ibarra-Laclette E, Morán-Velázquez DC, Girón Ramírez A, Bourdon M, Villalpando-Aguilar JL, Toomer G, Tang JZ, Azadi P, Santamaría JM, López-Rosas I, López MG, Simpson J, Alatorre-Cobos F. Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111496. [PMID: 35684270 PMCID: PMC9182668 DOI: 10.3390/plants11111496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 05/08/2023]
Abstract
Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.
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Affiliation(s)
- Luis F. Maceda-López
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Elsa B. Góngora-Castillo
- CONACYT-Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico;
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C. Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Mexico;
| | - Dalia C. Morán-Velázquez
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Amaranta Girón Ramírez
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK;
| | - José L. Villalpando-Aguilar
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Gabriela Toomer
- Division of Microbiology and Molecular Biology, IIT Research Institute, Chicago, IL 60616, USA;
| | - John Z. Tang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Jorge M. Santamaría
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Itzel López-Rosas
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
| | - Mercedes G. López
- Departmento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - Fulgencio Alatorre-Cobos
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
- Correspondence:
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27
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Marone MP, Campanari MFZ, Raya FT, Pereira GAG, Carazzolle MF. Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions. PeerJ 2022; 10:e13252. [PMID: 35529479 PMCID: PMC9070324 DOI: 10.7717/peerj.13252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Abstract
Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting point to the study of the potential uses of agaves' fungi as biotechnological tools.
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Affiliation(s)
- Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Fabio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
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28
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Villalobos Solis MI, Engle NL, Spangler MK, Cottaz S, Fort S, Maeda J, Ané JM, Tschaplinski TJ, Labbé JL, Hettich RL, Abraham PE, Rush TA. Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:808578. [PMID: 37746234 PMCID: PMC10512320 DOI: 10.3389/ffunb.2022.808578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 09/26/2023]
Abstract
The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor, the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO4), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor. Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.
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Affiliation(s)
| | - Nancy L. Engle
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Margaret K. Spangler
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sylvain Cottaz
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Sébastien Fort
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Jesse L. Labbé
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Paul E. Abraham
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Tomás A. Rush
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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29
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Winter K, Smith JAC. CAM photosynthesis: the acid test. THE NEW PHYTOLOGIST 2022; 233:599-609. [PMID: 34637529 PMCID: PMC9298356 DOI: 10.1111/nph.17790] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 05/04/2023]
Abstract
There is currently considerable interest in the prospects for bioengineering crassulacean acid metabolism (CAM) photosynthesis - or key elements associated with it, such as increased water-use efficiency - into C3 plants. Resolving how CAM photosynthesis evolved from the ancestral C3 pathway could provide valuable insights into the targets for such bioengineering efforts. It has been proposed that the ability to accumulate organic acids at night may be common among C3 plants, and that the transition to CAM might simply require enhancement of pre-existing fluxes, without the need for changes in circadian or diurnal regulation. We show, in a survey encompassing 40 families of vascular plants, that nocturnal acidification is a feature entirely restricted to CAM species. Although many C3 species can synthesize malate during the light period, we argue that the switch to night-time malic acid accumulation requires a fundamental metabolic reprogramming that couples glycolytic breakdown of storage carbohydrate to the process of net dark CO2 fixation. This central element of the CAM pathway, even when expressed at a low level, represents a biochemical capability not seen in C3 plants, and so is better regarded as a discrete evolutionary innovation than as part of a metabolic continuum between C3 and CAM.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research InstitutePO Box 0843‐03092BalboaAncónRepublic of Panama
| | - J. Andrew C. Smith
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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30
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Qiao Z, Yates TB, Shrestha HK, Engle NL, Flanagan A, Morrell‐Falvey JL, Sun Y, Tschaplinski TJ, Abraham PE, Labbé J, Wang Z, Hettich RL, Tuskan GA, Muchero W, Chen J. Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinase. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2454-2468. [PMID: 34272801 PMCID: PMC8633507 DOI: 10.1111/pbi.13671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 05/22/2023]
Abstract
Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole-genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor-like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor-root colonization by the ectomycorrhizal fungus Laccaria bicolor. By introducing PtLecRLK1 into a perennial grass known to be a non-host of L. bicolor, switchgrass (Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro-PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non-host to a host of L. bicolor. Furthermore, transcriptomic and proteomic analyses on inoculated-transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defence pathway, consistent with the view that pathogenic defence response is down-regulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N-containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non-host to enhance plant productivity and fitness on marginal lands.
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Affiliation(s)
- Zhenzhen Qiao
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Timothy B. Yates
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTNUSA
| | - Him K. Shrestha
- Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy L. Engle
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Yali Sun
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Paul E. Abraham
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jessy Labbé
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Robert L. Hettich
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
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Wickell D, Kuo LY, Yang HP, Dhabalia Ashok A, Irisarri I, Dadras A, de Vries S, de Vries J, Huang YM, Li Z, Barker MS, Hartwick NT, Michael TP, Li FW. Underwater CAM photosynthesis elucidated by Isoetes genome. Nat Commun 2021; 12:6348. [PMID: 34732722 PMCID: PMC8566536 DOI: 10.1038/s41467-021-26644-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.
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Affiliation(s)
- David Wickell
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Amra Dhabalia Ashok
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences, University of Goettingen, Goettingen, Germany
| | | | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Nolan T Hartwick
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Todd P Michael
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Fay-Wei Li
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
- Boyce Thompson Institute, Ithaca, NY, USA.
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32
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Shrestha HK, Solis MIV, Jawdy SS, Tuskan GA, Yang X, Abraham PE. Temporal dynamics of protein and post-translational modification abundances in Populus leaf across a diurnal period. Proteomics 2021; 21:e2100127. [PMID: 34482644 DOI: 10.1002/pmic.202100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/09/2022]
Abstract
Populus spp. are dedicated woody biomass feedstocks for advanced biofuels and bioproducts. Proper growth and fitness of poplar as a sustainable feedstock depends on timely perception and response to environmental signals (e.g., light, temperature, water). Poplar leaves, like other C3 photosynthesis plants, have evolved oscillating or circadian rhythms that play important roles in synchronizing biological processes with external cues. To characterize this phenomenon at a molecular level, we employed bottom-up proteomics using high-resolution mass spectrometry and de novo-assisted database searching to identify abundance changes in proteins and post-translational modifications in poplar leaf tissue sampled across a 12/12-hour light/dark diurnal period.
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Affiliation(s)
- Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | | | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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33
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Moseley RC, Motta F, Tuskan GA, Haase SB, Yang X. Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi. Cells 2021; 10:2217. [PMID: 34571864 PMCID: PMC8471846 DOI: 10.3390/cells10092217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023] Open
Abstract
The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.
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Affiliation(s)
- Robert C. Moseley
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
| | - Francis Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Gerald A. Tuskan
- 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
| | - Steven B. Haase
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
- Department of Medicine, Duke University, Durham, NC 27708, 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
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1H-NMR profile of mezcal and its distillation fractions using two sample preparation methods: direct analysis and solid-phase extraction. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01660-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Crassulacean acid metabolism (CAM) has evolved from a C3 ground state to increase water use efficiency of photosynthesis. During CAM evolution, selective pressures altered the abundance and expression patterns of C3 genes and their regulators to enable the trait. The circadian pattern of CO2 fixation and the stomatal opening pattern observed in CAM can be explained largely with a regulatory architecture already present in C3 plants. The metabolic CAM cycle relies on enzymes and transporters that exist in C3 plants and requires tight regulatory control to avoid futile cycles between carboxylation and decarboxylation. Ecological observations and modeling point to mesophyll conductance as a major factor during CAM evolution. The present state of knowledge enables suggestions for genes for a minimal CAM cycle for proof-of-concept engineering, assuming altered regulation of starch synthesis and degradation are not critical elements of CAM photosynthesis and sufficient malic acid export from the vacuole is possible.
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Affiliation(s)
- Katharina Schiller
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
| | - Andrea Bräutigam
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
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36
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Hu Z, Nie Z, Yan C, Huang H, Ma X, Wang Y, Ye N, Tuskan GA, Yang X, Yin H. Transcriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnieriana. Cells 2021; 10:1526. [PMID: 34204368 PMCID: PMC8233840 DOI: 10.3390/cells10061526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 11/16/2022] Open
Abstract
Crassulacean acid metabolism (CAM) is an important photosynthetic pathway for plant adaptation to dry environments. CAM plants feature a coordinated interaction between mesophyll and epidermis functions that involves refined regulations of gene expression. Plant microRNAs (miRNAs) are crucial post-transcription regulators of gene expression, however, their roles underlying the CAM pathway remain poorly investigated. Here, we present a study characterizing the expression of miRNAs in an obligate CAM species Kalanchoë marnieriana. Through sequencing of transcriptome and degradome in mesophyll and epidermal tissues under the drought treatments, we identified differentially expressed miRNAs that were potentially involved in the regulation of CAM. In total, we obtained 84 miRNA genes, and eight of them were determined to be Kalanchoë-specific miRNAs. It is widely accepted that CAM pathway is regulated by circadian clock. We showed that miR530 was substantially downregulated in epidermal peels under drought conditions; miR530 targeted two tandem zinc knuckle/PLU3 domain encoding genes (TZPs) that were potentially involved in light signaling and circadian clock pathways. Our work suggests that the miR530-TZPs module might play a role of regulating CAM-related gene expression in Kalanchoë.
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Affiliation(s)
- Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Z.H.); (Z.N.); (H.H.); (X.M.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (N.Y.)
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Ziyan Nie
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Z.H.); (Z.N.); (H.H.); (X.M.)
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Chao Yan
- Experimental Center for Subtropical Forestry, Chinese Academy of Forestry, Fenyi 336600, China;
| | - Hu Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Z.H.); (Z.N.); (H.H.); (X.M.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (N.Y.)
| | - Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Z.H.); (Z.N.); (H.H.); (X.M.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (N.Y.)
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (N.Y.)
| | - Ning Ye
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (N.Y.)
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; (G.A.T.); (X.Y.)
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; (G.A.T.); (X.Y.)
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Z.H.); (Z.N.); (H.H.); (X.M.)
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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37
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Callegari Ferrari R, Pires Bittencourt P, Yumi Nagumo P, Silva Oliveira W, Aurineide Rodrigues M, Hartwell J, Freschi L. Developing Portulaca oleracea as a model system for functional genomics analysis of C 4/CAM photosynthesis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:666-682. [PMID: 33256895 DOI: 10.1071/fp20202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Previously regarded as an intriguing photosynthetic curiosity, the occurrence of C4 and Crassulacean acid metabolism (CAM) photosynthesis within a single organism has recently emerged as a source of information for future biotechnological use. Among C4/CAM facultative species, Portulaca oleracea L. has been used as a model for biochemical and gene expression analysis of C4/CAM under field and laboratory conditions. In the present work, we focussed on developing molecular tools to facilitate functional genomics studies in this species, from the optimisation of RNA isolation protocols to a method for stable genetic transformation. Eleven variations of RNA extraction procedures were tested and compared for RNA quantity and quality. Also, 7 sample sets comprising total RNA from hormonal and abiotic stress treatments, distinct plant organs, leaf developmental stages, and subspecies were used to select, among 12 reference genes, the most stable reference genes for RT-qPCR analysis of each experimental condition. Furthermore, different explant sources, Agrobacterium tumefaciens strains, and regeneration and antibiotic selection media were tested in various combinations to optimise a protocol for stable genetic transformation of P. oleracea. Altogether, we provide essential tools for functional gene analysis in the context of C4/CAM photosynthesis, including an efficient RNA isolation method, preferred reference genes for RT-qPCR normalisation for a range of experimental conditions, and a protocol to produce P. oleracea stable transformants using A. tumefaciens.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Priscila Pires Bittencourt
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Paula Yumi Nagumo
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Willian Silva Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Maria Aurineide Rodrigues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil; and Corresponding author.
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38
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Morreeuw ZP, Escobedo-Fregoso C, Ríos-González LJ, Castillo-Quiroz D, Reyes AG. Transcriptome-based metabolic profiling of flavonoids in Agave lechuguilla waste biomass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110748. [PMID: 33691954 DOI: 10.1016/j.plantsci.2020.110748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 05/23/2023]
Abstract
Agave lechuguilla is one of the most abundant species in arid and semiarid regions of Mexico, and is used to extract fiber. However, 85 % of the harvested plant material is discarded. Previous bioprospecting studies of the waste biomass suggest the presence of bioactive compounds, although the extraction process limited metabolite characterization. This work achieved flavonoid profiling of A. lechuguilla in both processed and non-processed leaf tissues using transcriptomic analysis. Functional annotation of the first de novo transcriptome of A. lechuguilla (255.7 Mbp) allowed identifying genes coding for 33 enzymes and 8 transcription factors involved in flavonoid biosynthesis. The flavonoid metabolic pathway was mostly elucidated by HPLC-MS/MS screening of alcoholic extracts. Key genes of flavonoid synthesis were higher expressed in processed leaf tissues than in non-processed leaves, suggesting a high content of flavonoids and glycoside derivatives in the waste biomass. Targeted HPLC-UV-MS analyses confirmed the concentration of isorhamnetin (1251.96 μg), flavanone (291.51 μg), hesperidin (34.23 μg), delphinidin (24.23 μg), quercetin (15.57 μg), kaempferol (13.71 μg), cyanidin (12.32 μg), apigenin (9.70 μg) and catechin (7.91 μg) per gram of dry residue. Transcriptomic and biochemical profiling concur in the potential of lechuguilla by-products with a wide range of applications in agriculture, feed, food, cosmetics, and pharmaceutical industries.
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Affiliation(s)
- Zoé P Morreeuw
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo Santa Rita Sur, C.P. 23096, La Paz, BCS, Mexico
| | - Cristina Escobedo-Fregoso
- CONACYT-CIBNOR, Av. Instituto Politécnico Nacional 195, Col. Playa Palo Santa Rita Sur, C.P. 23096, La Paz, BCS, Mexico
| | - Leopoldo J Ríos-González
- Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila (UAdeC), Blvd. V. Carranza, Col. Republica Oriente, C.P. 25280, Saltillo, Coahuila, Mexico
| | - David Castillo-Quiroz
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Saltillo, Carretera Saltillo-Zacatecas 9515, Col. Hacienda Buenavista, C.P. 25315, Saltillo, Coahuila, Mexico
| | - Ana G Reyes
- CONACYT-CIBNOR, Av. Instituto Politécnico Nacional 195, Col. Playa Palo Santa Rita Sur, C.P. 23096, La Paz, BCS, Mexico.
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Jiang SC, Engle NL, Banday ZZ, Cecchini NM, Jung HW, Tschaplinski TJ, Greenberg JT. ALD1 accumulation in Arabidopsis epidermal plastids confers local and non-autonomous disease resistance. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2710-2726. [PMID: 33463678 PMCID: PMC8006555 DOI: 10.1093/jxb/eraa609] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/24/2020] [Indexed: 05/10/2023]
Abstract
The Arabidopsis plastid-localized ALD1 protein acts in the lysine catabolic pathway that produces infection-induced pipecolic acid (Pip), Pip derivatives, and basal non-Pip metabolite(s). ALD1 is indispensable for disease resistance associated with Pseudomonas syringae infections of naïve plants as well as those previously immunized by a local infection, a phenomenon called systemic acquired resistance (SAR). Pseudomonas syringae is known to associate with mesophyll as well as epidermal cells. To probe the importance of epidermal cells in conferring bacterial disease resistance, we studied plants in which ALD1 was only detectable in the epidermal cells of specific leaves. Local disease resistance and many features of SAR were restored when ALD1 preferentially accumulated in the epidermal plastids at immunization sites. Interestingly, SAR restoration occurred without appreciable accumulation of Pip or known Pip derivatives in secondary distal leaves. Our findings establish that ALD1 has a non-autonomous effect on pathogen growth and defense activation. We propose that ALD1 is sufficient in the epidermis of the immunized leaves to activate SAR, but basal ALD1 and possibly a non-Pip metabolite(s) are also needed at all infection sites to fully suppress bacterial growth. Thus, epidermal plastids that contain ALD1 play a key role in local and whole-plant immune signaling.
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Affiliation(s)
- Shang-Chuan Jiang
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | | | - Zeeshan Zahoor Banday
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Nicolás M Cecchini
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Ho Won Jung
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | | | - Jean T Greenberg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
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Mode of Action of 1-Naphthylphthalamic Acid in Conspicuous Local Stem Swelling of Succulent Plant, Bryophyllum calycinum: Relevance to the Aspects of Its Histological Observation and Comprehensive Analyses of Plant Hormones. Int J Mol Sci 2021; 22:ijms22063118. [PMID: 33803750 PMCID: PMC8003132 DOI: 10.3390/ijms22063118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/04/2022] Open
Abstract
The mode of action of 1-naphthylphthalamic acid (NPA) to induce conspicuous local stem swelling in the area of its application to the growing internode in intact Bryophyllum calycinum was studied based on the aspects of histological observation and comprehensive analyses of plant hormones. Histological analyses revealed that NPA induced an increase in cell size and numerous cell divisions in the cortex and pith, respectively, compared to untreated stem. In the area of NPA application, vascular tissues had significantly wider cambial zones consisting of 5–6 cell layers, whereas phloem and xylem seemed not to be affected. This indicates that stem swelling in the area of NPA application is caused by stimulation of cell division and cell enlargement mainly in the cambial zone, cortex, and pith. Comprehensive analyses of plant hormones revealed that NPA substantially increased endogenous levels of indole-3-acetic acid (IAA) in the swelling area. NPA also increased endogenous levels of cytokinins, jasmonic acid, and its precursor, 12-oxo-phytodienoic acid, but did not increase abscisic acid and gibberellin levels. It was shown, using radiolabeled 14C-IAA, that NPA applied to the middle of internode segments had little effect on polar auxin transport, while 2,3,5-triiodobenzoic acid substantially inhibited it. These results strongly suggest that NPA induces changes in endogenous levels of plant hormones, such as IAA, cytokinins, and jasmonic acid, and their hormonal crosstalk results in a conspicuous local stem swelling. The possible different mode of action of NPA from other polar auxin transport inhibitors in succulent plants is extensively discussed.
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Liu D, Hu R, Zhang J, Guo HB, Cheng H, Li L, Borland AM, Qin H, Chen JG, Muchero W, Tuskan GA, Yang X. Overexpression of an Agave Phospho enolpyruvate Carboxylase Improves Plant Growth and Stress Tolerance. Cells 2021; 10:582. [PMID: 33800849 PMCID: PMC7999111 DOI: 10.3390/cells10030582] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/29/2022] Open
Abstract
It has been challenging to simultaneously improve photosynthesis and stress tolerance in plants. Crassulacean acid metabolism (CAM) is a CO2-concentrating mechanism that facilitates plant adaptation to water-limited environments. We hypothesized that the ectopic expression of a CAM-specific phosphoenolpyruvate carboxylase (PEPC), an enzyme that catalyzes primary CO2 fixation in CAM plants, would enhance both photosynthesis and abiotic stress tolerance. To test this hypothesis, we engineered a CAM-specific PEPC gene (named AaPEPC1) from Agave americana into tobacco. In comparison with wild-type and empty vector controls, transgenic tobacco plants constitutively expressing AaPEPC1 showed a higher photosynthetic rate and biomass production under normal conditions, along with significant carbon metabolism changes in malate accumulation, the carbon isotope ratio δ13C, and the expression of multiple orthologs of CAM-related genes. Furthermore, AaPEPC1 overexpression enhanced proline biosynthesis, and improved salt and drought tolerance in the transgenic plants. Under salt and drought stress conditions, the dry weight of transgenic tobacco plants overexpressing AaPEPC1 was increased by up to 81.8% and 37.2%, respectively, in comparison with wild-type plants. Our findings open a new door to the simultaneous improvement of photosynthesis and stress tolerance in plants.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hao-Bo Guo
- Department of Computer Science and Engineering, SimCenter, University of Tennessee Chattanooga, Chattanooga, TN 37403, USA; (H.-B.G.); (H.Q.)
| | - Hua Cheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Linling Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Anne M. Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Hong Qin
- Department of Computer Science and Engineering, SimCenter, University of Tennessee Chattanooga, Chattanooga, TN 37403, USA; (H.-B.G.); (H.Q.)
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Uhrig RG, Echevarría‐Zomeño S, Schlapfer P, Grossmann J, Roschitzki B, Koerber N, Fiorani F, Gruissem W. Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome. PLANT, CELL & ENVIRONMENT 2021; 44:821-841. [PMID: 33278033 PMCID: PMC7986931 DOI: 10.1111/pce.13969] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 05/11/2023]
Abstract
Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin-dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.
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Affiliation(s)
- R. Glen Uhrig
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Pascal Schlapfer
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
| | - Jonas Grossmann
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Bernd Roschitzki
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Niklas Koerber
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Fabio Fiorani
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Wilhelm Gruissem
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
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43
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Maceda-López LF, Villalpando-Aguilar JL, García-Hernández E, Ávila de Dios E, Andrade-Canto SB, Morán-Velázquez DC, Rodríguez-López L, Hernández-Díaz D, Chablé-Vega MA, Trejo L, Góngora-Castillo E, López-Rosas I, Simpson J, Alatorre-Cobos F. Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots. 3 Biotech 2021; 11:75. [PMID: 33505830 DOI: 10.1007/s13205-020-02620-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/26/2020] [Indexed: 12/30/2022] Open
Abstract
Together with their undeniable role in the ecology of arid and semiarid ecosystems, Agave species are emerging as a model to dissect the relationships between crassulacean acid metabolism and high efficiency of light and water use, and as an energy crop for bioethanol production. Transcriptome resources from economically valuable Agaves species, such as Agave tequilana and A. salmiana, as well as hybrids for fibers, are now available, and multiple gene expression landscape analyses have been reported. Key components in molecular mechanisms underlying drought tolerance could be uncovered by analyzing gene expression patterns of roots. This study describes an efficient protocol for high-quality total RNA isolation from phenolic compounds-rich Agave roots. Our methodology involves suitable root handling and collecting in the field and using saving-time commercial kits available. RNA isolated from roots free of lignified out-layers and clean cortex showed high values of quality and integrity according to electrophoresis and microfluidics-based platform. Synthesis of long full-length cDNAs and PCR amplification tested the suitability for downstream applications of extracted RNA. The protocol was applied successfully to A. tequilana roots but can be used for other Agave species that also develop lignified epidermis/exodermis in roots.
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Affiliation(s)
- Luis F Maceda-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - José L Villalpando-Aguilar
- Tecnológico Nacional de México, Instituto Tecnológico de Chiná, Calle 11entre 22 y 28, 24050 Chiná, Mexico
| | - Eleazar García-Hernández
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Emmanuel Ávila de Dios
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Silvia B Andrade-Canto
- Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Dalia C Morán-Velázquez
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Lorena Rodríguez-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Demetrio Hernández-Díaz
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Manuel A Chablé-Vega
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Laura Trejo
- CONACYT Research Fellow, Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, UNAM, 90640 Santa Cruz Tlaxcala, Tlaxcala Mexico
| | - Elsa Góngora-Castillo
- CONACYT Research Fellow, Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Itzel López-Rosas
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Fulgencio Alatorre-Cobos
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
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Eguiarte LE, Jiménez Barrón OA, Aguirre-Planter E, Scheinvar E, Gámez N, Gasca-Pineda J, Castellanos-Morales G, Moreno-Letelier A, Souza V. Evolutionary ecology of Agave: distribution patterns, phylogeny, and coevolution (an homage to Howard S. Gentry). AMERICAN JOURNAL OF BOTANY 2021; 108:216-235. [PMID: 33576061 DOI: 10.1002/ajb2.1609] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/29/2020] [Indexed: 06/12/2023]
Abstract
With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in many regions of Mexico and in the southwestern United States, agaves are dominant species. We describe the contributions of H. S. Gentry to the understanding of agaves and review recent advances on the study of the ecology and evolution of the genus. We analyze the present and inferred past distribution patterns of different species in the genus, describing differences in their climatic niche and adaptations to dry conditions. We interpret these patterns using molecular clock data and phylogenetic analyses and information of their coevolving pollinators and from phylogeographic, morphological, and ecological studies and discuss the prospects for their future conservation and management.
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Affiliation(s)
- Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Ofelia A Jiménez Barrón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
- Dirección General de Informática y Telecomunicaciones, Secretaría de Medio Ambiente y Recursos Naturales, Ciudad de México, Mexico
| | - Niza Gámez
- Facultad de Estudios Superiores-Zaragoza, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
- Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Estado de México, Mexico
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa, Villahermosa, Tabasco, Mexico
| | - Alejandra Moreno-Letelier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
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Heyduk K, McAssey EV, Grimwood J, Shu S, Schmutz J, McKain MR, Leebens-Mack J. Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae). FRONTIERS IN PLANT SCIENCE 2021; 11:573767. [PMID: 33519836 PMCID: PMC7843428 DOI: 10.3389/fpls.2020.573767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/17/2020] [Indexed: 05/23/2023]
Abstract
Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ∼11 kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from 41 accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case-Copia LTR transposons-did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. The identification and quantification of transposon families paired with expression evidence paves the way for additional work seeking to link epigenetics with the important trait variation seen in this homoploid hybrid system.
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Affiliation(s)
- Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Edward V. McAssey
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Biological Sciences, Quinnipiac University, Hamden, CT, United States
- Department of Biology and Environmental Science, University of New Haven, West Haven, CT, United States
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Shengqiang Shu
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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46
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Martins MCM, Mafra V, Monte-Bello CC, Caldana C. The Contribution of Metabolomics to Systems Biology: Current Applications Bridging Genotype and Phenotype in Plant Science. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:91-105. [DOI: 10.1007/978-3-030-80352-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Lefoulon C, Boxall SF, Hartwell J, Blatt MR. Crassulacean acid metabolism guard cell anion channel activity follows transcript abundance and is suppressed by apoplastic malate. THE NEW PHYTOLOGIST 2020; 227:1847-1857. [PMID: 32367511 DOI: 10.1111/nph.16640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Plants utilising crassulacean acid metabolism (CAM) concentrate CO2 around RuBisCO while reducing transpirational water loss associated with photosynthesis. Unlike stomata of C3 and C4 species, CAM stomata open at night for the mesophyll to fix CO2 into malate (Mal) and store it in the vacuole. CAM plants decarboxylate Mal in the light, generating high CO2 concentrations within the leaf behind closed stomata for refixation by RuBisCO. CO2 may contribute to stomatal closure but additional mechanisms, plausibly including Mal activation of anion channels, ensure closure in the light. In the CAM species Kalanchoë fedtschenkoi, we found that guard cell anion channel activity, recorded under voltage clamp, follows KfSLAC1 and KfALMT12 transcript abundance, declining to near zero by the end of the light period. Unexpectedly, however, we found that extracellular Mal inhibited the anion current of Kalanchoë guard cells, both in wild-type and RNAi mutants with impaired Mal metabolism. We conclude that the diurnal cycle of anion channel gene transcription, rather than the physiological signal of Mal release, is a key factor in the inverted CAM stomatal cycle.
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Affiliation(s)
- Cécile Lefoulon
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - Susanna F Boxall
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool,, L69 7ZB, UK
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool,, L69 7ZB, UK
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
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48
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Ferrari RC, Cruz BC, Gastaldi VD, Storl T, Ferrari EC, Boxall SF, Hartwell J, Freschi L. Exploring C 4-CAM plasticity within the Portulaca oleracea complex. Sci Rep 2020; 10:14237. [PMID: 32859905 PMCID: PMC7455729 DOI: 10.1038/s41598-020-71012-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/29/2020] [Indexed: 11/21/2022] Open
Abstract
Portulaca oleracea is a C4 herb capable of performing CAM under drought stress. It is distributed worldwide and is either considered a polymorphic species or a complex of subspecies, due to its numerous morphological variations. We evaluated CAM plasticity within P. oleracea genotypes since the complexity surrounding this species may be reflected in intraspecific variations in photosynthetic behavior. Eleven subspecies of P. oleracea from distant geographical locations and one cultivar were morphologically and physiologically characterized. C4 and CAM photosynthesis were monitored in plants exposed to well-watered, droughted and rewatered treatments, and data obtained were compared among individual genotypes. All subspecies expressed CAM in a fully-reversible manner. Transcript abundance of C4–CAM signature genes was shown to be a useful indicator of the C4–CAM–C4 switches in all genotypes. C4-related genes were down-regulated and subsequently fully expressed upon drought and rewatering, respectively. CAM-marker genes followed the opposite pattern. A gradient of morphological traits and drought-induced nighttime malate accumulation was observed across genotypes. Therefore, different combinations of CAM expression levels, plant sizes and shapes are available within the P. oleracea complex, which can be a valuable tool in the context of C4/CAM photosynthesis research.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Bruna Coelho Cruz
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | | | - Thalyson Storl
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Elisa Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Susanna F Boxall
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil.
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49
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Kong W, Yoo MJ, Zhu D, Noble JD, Kelley TM, Li J, Kirst M, Assmann SM, Chen S. Molecular changes in Mesembryanthemum crystallinum guard cells underlying the C 3 to CAM transition. PLANT MOLECULAR BIOLOGY 2020; 103:653-667. [PMID: 32468353 DOI: 10.1007/s11103-020-01016-9] [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: 11/18/2019] [Accepted: 05/17/2020] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE: The timing and transcriptomic changes during the C3 to CAM transition of common ice plant support the notion that guard cells themselves can shift from C3 to CAM. Crassulacean acid metabolism (CAM) is a specialized type of photosynthesis: stomata close during the day, enhancing water conservation, and open at night, allowing CO2 uptake. Mesembryanthemum crystallinum (common ice plant) is a facultative CAM species that can shift from C3 photosynthesis to CAM under salt or drought stresses. However, the molecular mechanisms underlying the stress induced transition from C3 to CAM remain unknown. Here we determined the transition time from C3 to CAM in M. crystallinum under salt stress. In parallel, single-cell-type transcriptomic profiling by 3'-mRNA sequencing was conducted in isolated stomatal guard cells to determine the molecular changes in this key cell type during the transition. In total, 495 transcripts showed differential expression between control and salt-treated samples during the transition, including 285 known guard cell genes, seven CAM-related genes, 18 transcription factors, and 185 other genes previously not found to be expressed in guard cells. PEPC1 and PPCK1, which encode key enzymes of CAM photosynthesis, were up-regulated in guard cells after seven days of salt treatment, indicating that guard cells themselves can shift from C3 to CAM. This study provides important information towards introducing CAM stomatal behavior into C3 crops to enhance water use efficiency.
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Affiliation(s)
- Wenwen Kong
- College of Life Sciences, Northeast Agricultural University, Harbin, China
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
- Guangdong Province Key Laboratory for Plant Epigenetics, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Mi-Jeong Yoo
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
| | - Dan Zhu
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
- College of Life Science, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, China
| | - Jerald D Noble
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Theresa M Kelley
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA.
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA.
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50
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Abraham PE, Hurtado Castano N, Cowan-Turner D, Barnes J, Poudel S, Hettich R, Flütsch S, Santelia D, Borland AM. Peeling back the layers of crassulacean acid metabolism: functional differentiation between Kalanchoë fedtschenkoi epidermis and mesophyll proteomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:869-888. [PMID: 32314451 DOI: 10.1111/tpj.14757] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/18/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that offers the potential to engineer improved water-use efficiency (WUE) and drought resilience in C3 plants while sustaining productivity in the hotter and drier climates that are predicted for much of the world. CAM species show an inverted pattern of stomatal opening and closing across the diel cycle, which conserves water and provides a means of maintaining growth in hot, water-limited environments. Recent genome sequencing of the constitutive model CAM species Kalanchoë fedtschenkoi provides a platform for elucidating the ensemble of proteins that link photosynthetic metabolism with stomatal movement, and that protect CAM plants from harsh environmental conditions. We describe a large-scale proteomics analysis to characterize and compare proteins, as well as diel changes in their abundance in guard cell-enriched epidermis and mesophyll cells from leaves of K. fedtschenkoi. Proteins implicated in processes that encompass respiration, the transport of water and CO2 , stomatal regulation, and CAM biochemistry are highlighted and discussed. Diel rescheduling of guard cell starch turnover in K. fedtschenkoi compared with that observed in Arabidopsis is reported and tissue-specific localization in the epidermis and mesophyll of isozymes implicated in starch and malate turnover are discussed in line with the contrasting roles for these metabolites within the CAM mesophyll and stomatal complex. These data reveal the proteins and the biological processes enriched in each layer and provide key information for studies aiming to adapt plants to hot and dry environments by modifying leaf physiology for improved plant sustainability.
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Affiliation(s)
- Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Natalia Hurtado Castano
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Daniel Cowan-Turner
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jeremy Barnes
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Suresh Poudel
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | | | - Diana Santelia
- Institute of Integrative Biology, ETH, Zürich, Switzerland
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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