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Xu H, Pang T, Zhang L, Liu J. Photosynthetic performance of the red algae Gracilariopsis lemaneiformis under high seawater pH: Excess reactive oxygen production due to carbon limitation. Photochem Photobiol 2024. [PMID: 39032084 DOI: 10.1111/php.13968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 07/22/2024]
Abstract
The red algae Gracilariopsis lemaneiformis is extensively cultivated at high densities, leading to significant increases in regional seawater pH due to its photosynthetic removal of inorganic carbon. We conducted a study on G. lemaneiformis cultured under various pH conditions (normal pH, pH 9.3, and pH 9.6) and light levels (dark and 100 μmol photons m-2 s-1) to investigate how high pH seawater environments affect the metabolic processes of G. lemaneiformis. The high pH did not directly damage the photosynthetic light reactions or the Calvin cycle. Instead, the observed reduction in photosynthetic rates was primarily due to CO2 limitation. However, under illuminated conditions, a high pH environment leads to a decrease in electron transport efficiency (ETo/RC) and reaction center density (RC/CSo), while simultaneously increasing the levels of hydrogen peroxide (H2O2), malondialdehyde (MDA), and the activity of antioxidant enzymes. Under illuminated conditions, the limitation of inhibit the photosynthetic electron transport process, leading to energy imbalance and excessive production of reactive oxygen species, which in turn resulted in lipid peroxidation of the cell membrane. This might be one of the inducing factors responsible for the bleaching in sea-farmed G. lemaneiformis plants.
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Affiliation(s)
- Hongjun Xu
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tong Pang
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Litao Zhang
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jianguo Liu
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
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2
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Wang S, Chen L, Li S, Hu F. Uncovering proteome variations and concomitant quality changes of differently drying-treated rape (Brassica napus) bee pollen by label-free quantitative proteomics. Food Chem 2024; 434:137559. [PMID: 37748288 DOI: 10.1016/j.foodchem.2023.137559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
High moisture content of fresh bee pollen makes it difficult to preserve and thus makes drying a necessary process during the bee pollen production. Drying treatment will affect its quality and the effects of sun drying, hot-air drying and freeze drying on the proteome of rape (Brassica napus) bee pollen have been evaluated using label-free quantitative proteomics by liquid chromatography-tandem mass spectrometer (LC-MS/MS). A total of 8377 proteins are identified, among which the most abundant differential proteins were found in freeze drying-treated samples. Also freeze-drying treatment maximizes the content of antioxidant, antibacterial and anemic bioactive pollen protein. Besides, rape bee pollen is found to adjust its metabolism to protect itself during the drying process. These results can be favorable to evaluate the effects of drying treatment on the nutrition and function of processed rape bee pollen and insight into how rape bee pollen proteins respond to dehydration.
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Affiliation(s)
- Shuyue Wang
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liang Chen
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shanshan Li
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fuliang Hu
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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3
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Launay H, Avilan L, Gérard C, Parsiegla G, Receveur-Brechot V, Gontero B, Carriere F. Location of the photosynthetic carbon metabolism in microcompartments and separated phases in microalgal cells. FEBS Lett 2023; 597:2853-2878. [PMID: 37827572 DOI: 10.1002/1873-3468.14754] [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: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Carbon acquisition, assimilation and storage in eukaryotic microalgae and cyanobacteria occur in multiple compartments that have been characterised by the location of the enzymes involved in these functions. These compartments can be delimited by bilayer membranes, such as the chloroplast, the lumen, the peroxisome, the mitochondria or monolayer membranes, such as lipid droplets or plastoglobules. They can also originate from liquid-liquid phase separation such as the pyrenoid. Multiple exchanges exist between the intracellular microcompartments, and these are reviewed for the CO2 concentration mechanism, the Calvin-Benson-Bassham cycle, the lipid metabolism and the cellular energetic balance. Progress in microscopy and spectroscopic methods opens new perspectives to characterise the molecular consequences of the location of the proteins involved, including intrinsically disordered proteins.
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Affiliation(s)
- Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Luisana Avilan
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Cassy Gérard
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
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4
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Meloni M, Gurrieri L, Fermani S, Velie L, Sparla F, Crozet P, Henri J, Zaffagnini M. Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate. FRONTIERS IN PLANT SCIENCE 2023; 14:1130430. [PMID: 36875598 PMCID: PMC9978339 DOI: 10.3389/fpls.2023.1130430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
The Calvin-Benson-Bassham (CBB) cycle comprises the metabolic phase of photosynthesis and is responsible for carbon fixation and the production of sugar phosphates. The first step of the cycle involves the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) which catalyzes the incorporation of inorganic carbon into 3-phosphoglyceric acid (3PGA). The following steps include ten enzymes that catalyze the regeneration of ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco. While it is well established that Rubisco activity acts as a limiting step of the cycle, recent modeling studies and experimental evidence have shown that the efficiency of the pathway is also impacted by the regeneration of the Rubisco substrate itself. In this work, we review the current understanding of the structural and catalytic features of the photosynthetic enzymes that catalyze the last three steps of the regeneration phase, namely ribose-5-phosphate isomerase (RPI), ribulose-5-phosphate epimerase (RPE), and phosphoribulokinase (PRK). In addition, the redox- and metabolic-based regulatory mechanisms targeting the three enzymes are also discussed. Overall, this review highlights the importance of understudied steps in the CBB cycle and provides direction for future research aimed at improving plant productivity.
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Affiliation(s)
- Maria Meloni
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Libero Gurrieri
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Simona Fermani
- Department of Chemistry “G. Ciamician”, University of Bologna, Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, Bologna, Italy
| | - Lauren Velie
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Francesca Sparla
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Pierre Crozet
- Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Julien Henri
- Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
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5
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Wang J, Sun Z, Wang X, Tang Y, Li X, Ren C, Ren J, Wang X, Jiang C, Zhong C, Zhao S, Zhang H, Liu X, Kang S, Zhao X, Yu H. Transcriptome-based analysis of key pathways relating to yield formation stage of foxtail millet under different drought stress conditions. FRONTIERS IN PLANT SCIENCE 2023; 13:1110910. [PMID: 36816479 PMCID: PMC9937063 DOI: 10.3389/fpls.2022.1110910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Although foxtail millet, as small Panicoid crop, is of drought resilient, drought stress has a significant effect on panicle of foxtail millet at the yield formation stage. In this study, the changes of panicle morphology, photosynthesis, antioxidant protective enzyme system, reactive oxygen species (ROS) system, and osmotic regulatory substance and RNA-seq of functional leaves under light drought stress (LD), heavy drought stress (HD), light drought control (LDCK) and heavy drought control (HDCK) were studied to get a snap-shot of specific panicle morphological changes, physiological responses and related molecular mechanisms. The results showed that the length and weight of panicle had decreased, but with increased empty abortive rate, and then yield dropped off 14.9% and 36.9%, respectively. The photosynthesis of millet was significantly decreased, like net photosynthesis rate, stomatal conductance and transpiration rate, especially under HD treatment with reluctant recovery from rehydration. Under LD and HD treatment, the peroxidase (POD) was increased by 34% and 14% and the same as H2O2 by 34.7% and 17.2% compared with LDCK and HDCK. The ability to produce and inhibit O2- free radicals under LD treatment was higher than HD. The content of soluble sugar was higher under LD treatment but the proline was higher under HD treatment. Through RNA-seq analysis, there were 2,393 and 3,078 different genes expressed under LD and HD treatment. According to the correlation analysis between weighted gene coexpression network analysis (WGCNA) and physiological traits, the co-expression network of several modules with high correlation was constructed, and some hub genes of millet in response to drought stress were found. The expression changes relating to carbon fixation, sucrose and starch synthesis, lignin synthesis, gibberellin synthesis, and proline synthesis of millet were specifically analyzed. These findings provide a full perspective on how drought affects the yield formation of foxtail millet by constructing one work model thereby providing theoretical foundation for hub genes exploration and drought resistance breeding of foxtail millet.
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Wang L, Yang C, Shan Q, Zhao M, Yu J, Li YF. Transcriptome-wide profiling of mRNA N 6-methyladenosine modification in rice panicles and flag leaves. Genomics 2023; 115:110542. [PMID: 36535337 DOI: 10.1016/j.ygeno.2022.110542] [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: 09/03/2022] [Revised: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
N6-methyladenosine (m6A) modification is essential for plant growth and development. Exploring m6A methylation patterns in rice tissues is fundamental to understanding the regulatory effects of this modification. Here, we profiled the transcriptome-wide m6A landscapes of rice panicles at the booting stage (PB) and flowering stage (PF), and of flag leaves at the flowering stage (LF). The global m6A level differed significantly among the three tissues and was closely associated with the expression of writer and eraser genes. The methylated gene ratio was higher in the flag leaves than in the panicles. Compared with commonly methylated genes, tissue-specific methylated genes showed lower levels of both m6A modification and expression, and a preference for m6A deposition in the coding sequence region. The m6A profiles of the two organs had more distinct differences than the profiles of the same organ at different stages. A negative correlation between m6A levels and gene expression was observed in PF vs. PB but not in PF vs. LF, indicting the complicated regulatory effect of m6A on gene expression. The distinct expression patterns of m6A reader genes in different tissues indicate that readers may affect gene stability through binding. Overall, our findings demonstrated that m6A modification influences tissue function by regulating gene expression. Our findings provide valuable insights on the regulation and biological functions of m6A modifications in rice.
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Affiliation(s)
- Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China.
| | - Chenhui Yang
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Qianru Shan
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China.
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Reduction in Phosphoribulokinase Amount and Re-Routing Metabolism in Chlamydomonas reinhardtii CP12 Mutants. Int J Mol Sci 2022; 23:ijms23052710. [PMID: 35269851 PMCID: PMC8910624 DOI: 10.3390/ijms23052710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
The chloroplast protein CP12 is involved in the dark/light regulation of the Calvin–Benson–Bassham cycle, in particular, in the dark inhibition of two enzymes: glyceraldehyde−3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), but other functions related to stress have been proposed. We knocked out the unique CP12 gene to prevent its expression in Chlamydomonas reinhardtii (ΔCP12). The growth rates of both wild-type and ΔCP12 cells were nearly identical, as was the GAPDH protein abundance and activity in both cell lines. On the contrary, the abundance of PRK and its specific activity were significantly reduced in ΔCP12, as revealed by relative quantitative proteomics. Isolated PRK lost irreversibly its activity over-time in vitro, which was prevented in the presence of recombinant CP12 in a redox-independent manner. We have identified amino acid residues in the CP12 protein that are required for this new function preserving PRK activity. Numerous proteins involved in redox homeostasis and stress responses were more abundant and the expressions of various metabolic pathways were also increased or decreased in the absence of CP12. These results highlight CP12 as a moonlighting protein with additional functions beyond its well-known regulatory role in carbon metabolism.
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8
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Zhang Y, Fernie AR. Stable and Temporary Enzyme Complexes and Metabolons Involved in Energy and Redox Metabolism. Antioxid Redox Signal 2021; 35:788-807. [PMID: 32368925 DOI: 10.1089/ars.2019.7981] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Significance: Alongside well-characterized permanent multimeric enzymes and multienzyme complexes, relatively unstable transient enzyme-enzyme assemblies, including metabolons, provide an important mechanism for the regulation of energy and redox metabolism. Critical Issues: Despite the fact that enzyme-enzyme assemblies have been proposed for many decades and experimentally analyzed for at least 40 years, there are very few pathways for which unequivocal evidence for the presence of metabolite channeling, the most frequently evoked reason for their formation, has been provided. Further, in contrast to the stronger, permanent interactions for which a deep understanding of the subunit interface exists, the mechanism(s) underlying transient enzyme-enzyme interactions remain poorly studied. Recent Advances: The widespread adoption of proteomic and cell biological approaches to characterize protein-protein interaction is defining an ever-increasing number of enzyme-enzyme assemblies as well as enzyme-protein interactions that likely identify factors which stabilize such complexes. Moreover, the use of microfluidic technologies provided compelling support of a role for substrate-specific chemotaxis in complex assemblies. Future Directions: Embracing current and developing technologies should render the delineation of metabolons from other enzyme-enzyme complexes more facile. In parallel, attempts to confirm that the findings reported in microfluidic systems are, indeed, representative of the cellular situation will be critical to understanding the physiological circumstances requiring and evoking dynamic changes in the levels of the various transient enzyme-enzyme assemblies of the cell. Antioxid. Redox Signal. 35, 788-807.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
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9
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Smythers AL, Iannetta AA, Hicks LM. Crosslinking mass spectrometry unveils novel interactions and structural distinctions in the model green alga Chlamydomonas reinhardtii. Mol Omics 2021; 17:917-928. [PMID: 34499065 DOI: 10.1039/d1mo00197c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interactomics is an emerging field that seeks to identify both transient and complex-bound protein interactions that are essential for metabolic functions. Crosslinking mass spectrometry (XL-MS) has enabled untargeted global analysis of these protein networks, permitting largescale simultaneous analysis of protein structure and interactions. Increased commercial availability of highly specific, cell permeable crosslinkers has propelled the study of these critical interactions forward, with the development of MS-cleavable crosslinkers further increasing confidence in identifications. Herein, the global interactome of the unicellular alga Chlamydomonas reinhardtii was analyzed via XL-MS by implementing the MS-cleavable disuccinimidyl sulfoxide (DSSO) crosslinker and enriching for crosslinks using strong cation exchange chromatography. Gentle lysis via repeated freeze-thaw cycles facilitated in vitro analysis of 157 protein-protein crosslinks (interlinks) and 612 peptides linked to peptides of the same protein (intralinks) at 1% FDR throughout the C. reinhardtii proteome. The interlinks confirmed known protein relationships across the cytosol and chloroplast, including coverage on 42% and 38% of the small and large ribosomal subunits, respectively. Of the 157 identified interlinks, 92% represent the first empirical evidence of interaction observed in C. reinhardtii. Several of these crosslinks point to novel associations between proteins, including the identification of a previously uncharacterized Mg-chelatase associated protein (Cre11.g477733.t1.2) bound to seven distinct lysines on Mg-chelatase (Cre06.g306300.t1.2). Additionally, the observed intralinks facilitated characterization of novel protein structures across the C. reinhardtii proteome. Together, these data establish a framework of protein-protein interactions that can be further explored to facilitate understanding of the dynamic protein landscape in C. reinhardtii.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan Laboratories, 125 South Road, CB#3290, Chapel Hill, NC 27599-3290, USA.
| | - Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan Laboratories, 125 South Road, CB#3290, Chapel Hill, NC 27599-3290, USA.
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan Laboratories, 125 South Road, CB#3290, Chapel Hill, NC 27599-3290, USA.
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CP12 Is Involved in Protection against High Light Intensity by Suppressing the ROS Generation in Synechococcus elongatus PCC7942. PLANTS 2021; 10:plants10071275. [PMID: 34201575 PMCID: PMC8309167 DOI: 10.3390/plants10071275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/17/2022]
Abstract
We previously reported that CP12 formed a complex with GAPDH and PRK and regulated the activities of these enzymes and the Calvin-Benson cycle under dark conditions as the principal regulatory system in cyanobacteria. More interestingly, we found that the cyanobacterial CP12 gene-disrupted strain was more sensitive to photo-oxidative stresses such as under high light conditions and paraquat treatment. When a mutant strain that grew normally under low light was subjected to high light conditions, decreases in chlorophyll and photosynthetic activity were observed. Furthermore, a large amount of ROS was accumulated in the cells of the CP12 gene-disrupted strain. These data suggest that CP12 also functions under light conditions and may be involved in protection against oxidative stress by controlling the flow of electrons from Photosystem I to NADPH.
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Coelho AC, Pires R, Schütz G, Santa C, Manadas B, Pinto P. Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach. PLoS One 2021; 16:e0245148. [PMID: 33481834 PMCID: PMC7822296 DOI: 10.1371/journal.pone.0245148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
The pathological interaction between oak trees and Phytophthora cinnamomi has implications in the cork oak decline observed over the last decades in the Iberian Peninsula. During host colonization, the phytopathogen secretes effector molecules like elicitins to increase disease effectiveness. The objective of this study was to unravel the proteome changes associated with the cork oak immune response triggered by P. cinnamomi inoculation in a long-term assay, through SWATH-MS quantitative proteomics performed in the oak leaves. Using the Arabidopis proteome database as a reference, 424 proteins were confidently quantified in cork oak leaves, of which 80 proteins showed a p-value below 0.05 or a fold-change greater than 2 or less than 0.5 in their levels between inoculated and control samples being considered as altered. The inoculation of cork oak roots with P. cinnamomi increased the levels of proteins associated with protein-DNA complex assembly, lipid oxidation, response to endoplasmic reticulum stress, and pyridine-containing compound metabolic process in the leaves. In opposition, several proteins associated with cellular metabolic compound salvage and monosaccharide catabolic process had significantly decreased abundances. The most significant abundance variations were observed for the Ribulose 1,5-Bisphosphate Carboxylase small subunit (RBCS1A), Heat Shock protein 90–1 (Hsp90-1), Lipoxygenase 2 (LOX2) and Histone superfamily protein H3.3 (A8MRLO/At4G40030) revealing a pertinent role for these proteins in the host-pathogen interaction mechanism. This work represents the first SWATH-MS analysis performed in cork oak plants inoculated with P. cinnamomi and highlights host proteins that have a relevant action in the homeostatic states that emerge from the interaction between the oomycete and the host in the long term and in a distal organ.
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Affiliation(s)
- Ana Cristina Coelho
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Escola Superior de Educação e Comunicação (ESEC), University of Algarve, Faro, Portugal
- * E-mail:
| | - Rosa Pires
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
| | - Gabriela Schütz
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Instituto Superior de Engenharia, University of Algarve, Faro, Portugal
| | - Cátia Santa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Patrícia Pinto
- Center for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
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12
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Zhang Y, Fernie AR. Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism. PLANT COMMUNICATIONS 2021; 2:100081. [PMID: 33511342 PMCID: PMC7816073 DOI: 10.1016/j.xplc.2020.100081] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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13
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Zhao W, Liu H, Zhang L, Hu Z, Liu J, Hua W, Xu S, Liu J. Genome-Wide Identification and Characterization of FBA Gene Family in Polyploid Crop Brassica napus. Int J Mol Sci 2019; 20:E5749. [PMID: 31731804 PMCID: PMC6888112 DOI: 10.3390/ijms20225749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022] Open
Abstract
Fructose-1,6-bisphosphate aldolase (FBA) is a versatile metabolic enzyme involved in multiple important processes of glycolysis, gluconeogenesis, and Calvin cycle. Despite its significance in plant biology, the identity of this gene family in oil crops is lacking. Here, we performed genome-wide identification and characterization of FBAs in an allotetraploid species, oilseed rape Brassica napus. Twenty-two BnaFBA genes were identified and divided into two groups based on integrative analyses of functional domains, phylogenetic relationships, and gene structures. Twelve and ten B. napus FBAs (BnaFBAs) were predicted to be localized in the chloroplast and cytoplasm, respectively. Notably, synteny analysis revealed that Brassica-specific triplication contributed to the expansion of the BnaFBA gene family during the evolution of B. napus. Various cis-acting regulatory elements pertinent to abiotic and biotic stresses, as well as phytohormone responses, were detected. Intriguingly, each of the BnaFBA genes exhibited distinct sequence polymorphisms. Among them, six contained signatures of selection, likely having experienced breeding selection during adaptation and domestication. Importantly, BnaFBAs showed diverse expression patterns at different developmental stages and were preferentially highly expressed in photosynthetic tissues. Our data thus provided the foundation for further elucidating the functional roles of individual BnaFBA and also potential targets for engineering to improve photosynthetic productivity in B. napus.
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Affiliation(s)
- Wei Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Hongfang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Zhiyong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Jun Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Shouming Xu
- Henan key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
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Arefian M, Vessal S, Malekzadeh-Shafaroudi S, Siddique KHM, Bagheri A. Comparative proteomics and gene expression analyses revealed responsive proteins and mechanisms for salt tolerance in chickpea genotypes. BMC PLANT BIOLOGY 2019; 19:300. [PMID: 31288738 PMCID: PMC6617847 DOI: 10.1186/s12870-019-1793-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/22/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Salinity is a major abiotic stress that limits the growth, productivity, and geographical distribution of plants. A comparative proteomics and gene expression analysis was performed to better understand salinity tolerance mechanisms in chickpea. RESULTS Ten days of NaCl treatments resulted in the differential expression of 364 reproducible spots in seedlings of two contrasting chickpea genotypes, Flip 97-43c (salt tolerant, T1) and Flip 97-196c (salt susceptible, S1). Notably, after 3 days of salinity, 80% of the identified proteins in T1 were upregulated, while only 41% in S2 had higher expression than the controls. The proteins were classified into eight functional categories, and three groups of co-expression profile. The second co-expressed group of proteins had higher and/or stable expression in T1, relative to S2, suggesting coordinated regulation and the importance of some processes involved in salinity acclimation. This group was mainly enriched in proteins associated with photosynthesis (39%; viz. chlorophyll a-b binding protein, oxygen-evolving enhancer protein, ATP synthase, RuBisCO subunits, carbonic anhydrase, and fructose-bisphosphate aldolase), stress responsiveness (21%; viz. heat shock 70 kDa protein, 20 kDa chaperonin, LEA-2 and ascorbate peroxidase), and protein synthesis and degradation (14%; viz. zinc metalloprotease FTSH 2 and elongation factor Tu). Thus, the levels and/or early and late responses in the activation of targeted proteins explained the variation in salinity tolerance between genotypes. Furthermore, T1 recorded more correlations between the targeted transcripts and their corresponding protein expression profiles than S2. CONCLUSIONS This study provides insight into the proteomic basis of a salt-tolerance mechanism in chickpea, and offers unexpected and poorly understood molecular resources as reliable starting points for further dissection.
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Affiliation(s)
- Mohammad Arefian
- Plant Biotechnology and Breeding Department, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Saeedreza Vessal
- Research Center for Plant Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Saeid Malekzadeh-Shafaroudi
- Plant Biotechnology and Breeding Department, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Abdolreza Bagheri
- Plant Biotechnology and Breeding Department, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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15
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Simkin AJ, López-Calcagno PE, Raines CA. Feeding the world: improving photosynthetic efficiency for sustainable crop production. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1119-1140. [PMID: 30772919 PMCID: PMC6395887 DOI: 10.1093/jxb/ery445] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 05/18/2023]
Abstract
A number of recent studies have provided strong support demonstrating that improving the photosynthetic processes through genetic engineering can provide an avenue to improve yield potential. The major focus of this review is on improvement of the Calvin-Benson cycle and electron transport. Consideration is also given to how altering regulatory process may provide an additional route to increase photosynthetic efficiency. Here we summarize some of the recent successes that have been observed through genetic manipulation of photosynthesis, showing that, in both the glasshouse and the field, yield can be increased by >40%. These results provide a clear demonstration of the potential for increasing yield through improvements in photosynthesis. In the final section, we consider the need to stack improvement in photosynthetic traits with traits that target the yield gap in order to provide robust germplasm for different crops across the globe.
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Affiliation(s)
- Andrew J Simkin
- NIAB EMR, New Road, East Malling, Kent, UK
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| | | | - Christine A Raines
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
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Jiang J, Gai Z, Wang Y, Fan K, Sun L, Wang H, Ding Z. Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition. BMC Genomics 2018; 19:840. [PMID: 30477445 PMCID: PMC6258439 DOI: 10.1186/s12864-018-5250-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 11/14/2018] [Indexed: 02/02/2023] Open
Abstract
Background Nε-Acetylation of lysine residues, a frequently occurring post-translational modification, plays important functions in regulating physiology and metabolism. However, the information of global overview of protein acetylome under nitrogen-starvation/resupply in tea (Camellia sinensis) leaves was limited. And the full function of lysine acetylated proteins of tea plants in nitrogen absorption and assimilation remains unclear. Results Here, we performed the global review of lysine acetylome in tea leaves under nitrogen (N)-starvation/resupply, using peptide prefractionation, immunoaffinity enrichment, and coupling with high sensitive LC-MS/MS combined with affinity purification analysis. Altogether, 2229 lysine acetylation sites on 1286 proteins were identified, of which 16 conserved motifs in E*KacK, Kac*K, Kac*R, Kac*HK, Kac*N, Kac*S, Kac*T, Kac*D, were extracted from 2180 acetylated peptides. Approximately, 36.76% of the acetylated lysines were located in the regions of ordered secondary structures. The most of the identified lysine acetylation proteins were located in the chloroplast (39%) and cytoplasm (29%). The largest group of acetylated proteins consisted of many enzymes, such as ATP synthase, ribosomal proteins and malate dehydrogenase [NADP], which were related to metabolism (38%) in the biological process. These acetylated proteins were mainly enriched in three primary protein complexes of photosynthesis: photosystem I, photosystem II and the cytochrome b6/f complex. And some acetylated proteins related to glycolysis and secondary metabolite biosynthesis were increased/decreased under N-resupply. Moreover, the PPI (protein-protein interaction) analysis revealed that the diverse interactions of identified acetylated proteins mainly involved in photosynthesis and ribosome. Conclusion The results suggested that lysine acetylated proteins might play regulating roles in metabolic process in tea leaves. The critical regulatory roles mainly involved in diverse aspects of metabolic processes, especially in photosynthesis, glycolysis and secondary metabolism. A lot of proteins related to the photosynthesis and glycolysis were found to be acetylated, including LHCA1, LHCA3, LHCB6, psaE, psaD, psaN, GAPDH, PEPC, ENL and petC. And some proteins related to flavonoids were also found to be acetylated, including PAL, DFR, naringenin 3-dioxygenase and CHI. The provided data may serve as important resources for exploring the physiological, biochemical, and genetic role of lysine acetylation in tea plants. Data are available via ProteomeXchange with identifier PXD008931. Electronic supplementary material The online version of this article (10.1186/s12864-018-5250-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jutang Jiang
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Zhongshuai Gai
- College of Life Science, Yantai University, Yantai, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Kai Fan
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Hui Wang
- Rizhao Tea Research Institute of Shandong, Rizhao, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China.
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Kumari A, Pandey-Rai S. Enhanced arsenic tolerance and secondary metabolism by modulation of gene expression and proteome profile in Artemisia annua L. after application of exogenous salicylic acid. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:590-602. [PMID: 30326438 DOI: 10.1016/j.plaphy.2018.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 05/19/2023]
Abstract
This study was designed to investigate the effect of exogenous application of salicylic acid (SA) on proteins pattern and secondary metabolites in arsenic (As) stressed Artemisia annua. A. annua was treated by As 100 μM, SA 100 μM and combined treatment of SA 100 μM + As 100 μM upto 3 days. Significant accumulation of As was observed in roots than shoots at As 100 μM treatment. Under As treatment, oxidative stress was induced as indicated by increased TBARS content. Biomass, carotenoid, flavonoids were enhanced whereas total chlorophyll pigment was reduced under As treatment. Combined treatment of SA 100 μM + As 100 μM was more effective for increment of biomass, total chlorophyll content, and flavonoids as compared to As 100 μM treatment. Protein profiling revealed 20 differentially abundant proteins by 2-DE PAGE and MALDI-TOF-MS analysis. Identified proteins were related to photosynthesis, energy metabolism, transcriptional regulators, secondary metabolism, lipid metabolism, transport proteins and unknown/hypothetical proteins. All identified proteins were significantly increased in abundance under combined treatments of SA 100 μM + As 100 μM. The expression analysis of key genes involved in biosynthesis of lipid metabolism, signal molecule, transcriptional regulators, artemisinin biosynthetic genes, isoprenoids pathway, terpenes and flavonoids pathway were significantly upregulated under combined treatments of SA 100 μM + As 100 μM, suggesting a fine linkage in regulation of primary and secondary metabolism to modulate tolerance capacity and to improve phytoremediation property of A. annua against arsenic toxicity.
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Affiliation(s)
- Anjana Kumari
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Shashi Pandey-Rai
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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Li K, Qiu H, Zhou M, Lin Y, Guo Z, Lu S. Chloroplast Protein 12 Expression Alters Growth and Chilling Tolerance in Tropical Forage Stylosanthes guianensis (Aublet) Sw. FRONTIERS IN PLANT SCIENCE 2018; 9:1319. [PMID: 30237807 PMCID: PMC6135879 DOI: 10.3389/fpls.2018.01319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/22/2018] [Indexed: 05/29/2023]
Abstract
Stylosanthes guianensis (Aublet) Sw. is a tropical forage legume with soil acidity tolerance and excellent adaptation to infertile soils, but sensitive to chilling. To understand the molecular responses of S. guianensis to chilling, differentially expressed genes between a chilling tolerant mutant 7-1 and the wild type were identified using suppression subtractive hybridization, and eight of them were confirmed and the regulation pattern were analyzed using quantitative reverse transcription PCR (qRT-PCR). Chloroplast protein 12 (CP12) functions to regulate the Calvin cycle by forming a ternary complex with glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK). SgCP12 transcript was induced by chilling in both plants, and higher levels were observed in 7-1 than in the wild type, implying a potential role of SgCP12 in chilling tolerance. To confirm this, transgenic S. guianensis plants over-expressing or down-regulating SgCP12 were generated, respectively. Higher Fv/Fm and survival rate and lower ion leakage were observed in transgenic plants overexpressing SgCP12 as compared with the wild type after chilling treatment, while lower Fv/Fm and survival rate and higher ion leakage were found in SgCP12 antisense plants. SgCP12 overexpression plants showed promoted growth with increased plant height and fresh weight, while the antisense plants exhibited reduced growth with decreased plant height and fresh weight as compared with the wild type. The results indicated that regulation of SgCP12 expression alters plant growth and chilling tolerance in S. guianensis. In addition, higher levels of net photosynthetic rate (Pn), GAPDH and PRK activities were observed in SgCP12 overexpression transgenic plants, while lower levels in antisense plants than in the wild type under both control and chilling conditions, indicating that altered activities of GAPDH and PRK were associated with the changed Pn in transgenic S. guianensis. Our results suggest that SgCP12 regulates GAPDH and PRK activities, Pn, and chilling tolerance in S. guianensis.
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Affiliation(s)
- Kailong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Grassland Science Engineering Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hong Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Grassland Science Engineering Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Min Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Grassland Science Engineering Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Grassland Science Engineering Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Shaoyun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Grassland Science Engineering Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, China
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Cai B, Li Q, Liu F, Bi H, Ai X. Decreasing fructose-1,6-bisphosphate aldolase activity reduces plant growth and tolerance to chilling stress in tomato seedlings. PHYSIOLOGIA PLANTARUM 2018; 163:247-258. [PMID: 29230823 DOI: 10.1111/ppl.12682] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 10/23/2017] [Accepted: 12/07/2017] [Indexed: 05/23/2023]
Abstract
In northern China, low temperature is the most common abiotic stresses for tomato plants cultivated in solar-greenhouse in winter. We recently found that the expression and enzyme activity of fructose-1,6-bisphosphate aldolases (FBAs) in tomato, which are important enzymes in the Calvin-Benson cycle (CBC), were significantly altered in tomato seedlings subjected to heat/cold stresses. In order to study the role of FBA in photosynthesis and in regulating cold stress responses of tomato seedlings (Solanum lycopersicum), we transformed a tomato inbred line (FF) with RNA interference (RNAi) vector containing SlFBA7 reverse tandem repeat sequence. We found that the decreased SlFBA7 expression led to the decreased activities of FBA, as well as the activities of other main enzymes in the CBC. We also noticed a decrease in net photosynthetic rate, ribulose-1,5-bisphosphate and soluble sugar content, stem diameter, dry weight and seed size in RNAi SlFBA7 plants compared to wild-type. However, there are no changes in starch contents in the RNAi transgenic plants. RNAi SlFBA7 plants showed a decreased germination rate, and an increased levels of superoxide anions (O2·- ) and hydrogen peroxide (H2 O2 ) under low temperature (8/5°C) and low-light intensity (100 μmol m-2 s-1 photon flux density) growth conditions. These findings demonstrated the important role of SlFBA7 in regulating growth and chilling tolerance of tomato seedlings, and suggested that the catalytic activity of FBA in the CBC is sensitive to temperature.
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Affiliation(s)
- Bingbing Cai
- State Key Laboratory of Crop Biology/Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qiang Li
- State Key Laboratory of Crop Biology/Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Fengjiao Liu
- State Key Laboratory of Crop Biology/Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Huangai Bi
- State Key Laboratory of Crop Biology/Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xizhen Ai
- State Key Laboratory of Crop Biology/Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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20
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Li X, Xu J, Duan S, Bian C, Hu J, Shen H, Li G, Jin L. Pedigree-Based Deciphering of Genome-Wide Conserved Patterns in an Elite Potato Parental Line. FRONTIERS IN PLANT SCIENCE 2018; 9:690. [PMID: 29875792 PMCID: PMC5974212 DOI: 10.3389/fpls.2018.00690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/04/2018] [Indexed: 05/26/2023]
Abstract
Elite parental lines are more likely to breed fine varieties, but knowledge about elite parents and their genetic backgrounds is limited. In this paper, we investigated the pedigree relationships of potato varieties bred worldwide and in China. Several elite parents were identified, and these parents were more frequently used as parents in breeding programs across different time periods and countries. We next used 2b-RAD, a reduced-representation sequencing method, to genotype the elite parent Mira and 24 of its offspring. These cultivars span 5 generations, making this lineage the longest continuous pedigree among Chinese bred potatoes. A total of 47,314 tetraploid single nucleotide polymorphisms (SNPs) identified by FreeBayes were used to trace the conserved segments of the Mira genome. The conserved segments had identical or similar allele-specific SNPs across the analyzed genotypes. In Mira, 3,788 segments comprising over 10,000 bp, or 20.8% of the genome, were defined as conserved segments. These segments contain genes involved in crucial biological processes that are of special interest to breeders. These regions, which have been conserved across generations of highly selective breeding, may be helpful for further breeding and performing genome-wide breeding by design.
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Affiliation(s)
- Xiaochuan Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China
- College of Horticulture, China Agricultural University, Beijing, China
- Bijie Institute of Agricultural Sciences, Bijie, China
| | - Jianfei Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China
| | - Shaoguang Duan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China
| | - Chunsong Bian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China
| | - Jun Hu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China
| | - Huolin Shen
- College of Horticulture, China Agricultural University, Beijing, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China
| | - Liping Jin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China
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Zhang Y, Launay H, Liu F, Lebrun R, Gontero B. Interaction between adenylate kinase 3 and glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii. FEBS J 2018; 285:2495-2503. [PMID: 29727516 DOI: 10.1111/febs.14494] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/22/2018] [Accepted: 04/26/2018] [Indexed: 01/21/2023]
Abstract
The critical and ubiquitous enzyme adenylate kinase (ADK) catalyzes the nucleotide phosphoryl exchange reaction: 2ADP ↔ ATP + AMP. The ADK3 in the chloroplasts of the green alga Chlamydomonas reinhardtii, bears an unusual C-terminal extension that is similar to the C-terminal end of the intrinsically disordered protein CP12. In this study, we report that this enzyme, when oxidized but not when reduced, is able to interact with the chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) forming a stable complex as shown by native electrophoresis and mass spectrometry. In this bienzyme complex, the activity of ADK3 is unchanged while the NADPH-dependent activity of GAPDH is significantly inhibited. Moreover ADK3, like CP12, can protect GAPDH against thermal inactivation and aggregation. The ADK3-GAPDH bienzyme complex is unable to recruit phosphoribulokinase (PRK), in contrast with the ternary complex formed between GAPDH-CP12 and PRK. The interaction between ADK3 and GAPDH might be a mechanism to regulate the crucial ATP: NADPH ratio within chloroplasts to optimize the Calvin-Benson cycle during rapid fluctuation in environmental resources. ENZYMES Adenylate kinase (EC 2.7.4.3), glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.13), phosphoribulokinase (PRK, EC 2.7.1.19).
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Affiliation(s)
- Yizhi Zhang
- Aix Marseille Univ, CNRS, BIP, UMR 7281, Marseille, France
| | - Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR 7281, Marseille, France
| | - Fan Liu
- Aix Marseille Univ, CNRS, BIP, UMR 7281, Marseille, France.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, China
| | - Régine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IMM, FR 3479, CNRS, Marseille, France
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Cryptic Disorder Out of Disorder: Encounter between Conditionally Disordered CP12 and Glyceraldehyde-3-Phosphate Dehydrogenase. J Mol Biol 2018; 430:1218-1234. [PMID: 29501381 DOI: 10.1016/j.jmb.2018.02.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 01/14/2023]
Abstract
Among intrinsically disordered proteins, conditionally disordered proteins undergo dramatic structural disorder rearrangements upon environmental changes and/or post-translational modifications that directly modulate their function. Quantifying the dynamics of these fluctuating proteins is extremely challenging but paramount to understanding the regulation of their function. The chloroplast protein CP12 is a model of such proteins and acts as a redox switch by formation/disruption of its two disulfide bridges. It regulates the Calvin cycle by forming, in oxidized conditions, a supramolecular complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and then phosphoribulokinase. In this complex, both enzymes are inactive. The highly dynamic nature of CP12 has so far hindered structural characterization explaining its mode of action. Thanks to a synergistic combination of small-angle X-ray scattering, nuclear magnetic resonance and circular dichroism that drove the molecular modeling of structural ensembles, we deciphered the structural behavior of Chlamydomonas reinhardtii oxidized CP12 alone and in the presence of GAPDH. Contrary to sequence-based structural predictions, the N-terminal region is unstable, oscillates at the ms timescale between helical and random conformations, and is connected through a disordered linker to its C-terminus, which forms a stable helical turn. Upon binding to GAPDH, oxidized CP12 undergoes an induced unfolding of its N-terminus. This phenomenon called cryptic disorder contributes to decrease the entropy cost and explains CP12 unusual high affinity for its partners.
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Chen Y, Zhou B, Li J, Tang H, Tang J, Yang Z. Formation and Change of Chloroplast-Located Plant Metabolites in Response to Light Conditions. Int J Mol Sci 2018; 19:E654. [PMID: 29495387 PMCID: PMC5877515 DOI: 10.3390/ijms19030654] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 11/16/2022] Open
Abstract
Photosynthesis is the central energy conversion process for plant metabolism and occurs within mature chloroplasts. Chloroplasts are also the site of various metabolic reactions involving amino acids, lipids, starch, and sulfur, as well as where the production of some hormones takes place. Light is one of the most important environmental factors, acting as an essential energy source for plants, but also as an external signal influencing their growth and development. Plants experience large fluctuations in the intensity and spectral quality of light, and many attempts have been made to improve or modify plant metabolites by treating them with different light qualities (artificial lighting) or intensities. In this review, we discuss how changes in light intensity and wavelength affect the formation of chloroplast-located metabolites in plants.
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Affiliation(s)
- Yiyong Chen
- Tea Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou 510640, China.
| | - Bo Zhou
- Tea Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou 510640, China.
| | - Jianlong Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou 510640, China.
| | - Hao Tang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou 510640, China.
| | - Jinchi Tang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou 510640, China.
| | - Ziyin Yang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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Kamies R, Farrant JM, Tadele Z, Cannarozzi G, Rafudeen MS. A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef. Proteomes 2017; 5:E32. [PMID: 29140297 PMCID: PMC5748567 DOI: 10.3390/proteomes5040032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/20/2017] [Accepted: 11/10/2017] [Indexed: 01/13/2023] Open
Abstract
The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins.
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Affiliation(s)
- Rizqah Kamies
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
| | - Gina Cannarozzi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
| | - Mohammed Suhail Rafudeen
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
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Elena López-Calcagno P, Omar Abuzaid A, Lawson T, Anne Raines C. Arabidopsis CP12 mutants have reduced levels of phosphoribulokinase and impaired function of the Calvin-Benson cycle. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2285-2298. [PMID: 28430985 PMCID: PMC5447874 DOI: 10.1093/jxb/erx084] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
CP12 is a small, redox-sensitive protein, the most detailed understanding of which is the thioredoxin-mediated regulation of the Calvin-Benson cycle, where it facilitates the formation of a complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) in response to changes in light intensity. In most organisms, CP12 proteins are encoded by small multigene families, where the importance of each individual CP12 gene in vivo has not yet been reported. We used Arabidopsis thaliana T-DNA mutants and RNAi transgenic lines with reduced levels of CP12 transcript to determine the relative importance of each of the CP12 genes. We found that single cp12-1, cp12-2, and cp12-3 mutants do not develop a severe photosynthetic or growth phenotype. In contrast, reductions of both CP12-1 and CP12-2 transcripts lead to reductions in photosynthetic capacity and to slower growth and reduced seed yield. No clear phenotype for CP12-3 was evident. Additionally, the levels of PRK protein are reduced in the cp12-1, cp12-1/2, and multiple mutants. Our results suggest that there is functional redundancy between CP12-1 and CP12-2 in Arabidopsis where these proteins have a role in determining the level of PRK in mature leaves and hence photosynthetic capacity.
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Affiliation(s)
| | - Amani Omar Abuzaid
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Tracy Lawson
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Christine Anne Raines
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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Abstract
Purpose of Review We provide an overview of the current knowledge on cytochrome P450-mediated metabolism organized as metabolons and factors that facilitate their stabilization. Essential parameters will be discussed including those that are commonly disregarded using the dhurrin metabolon from Sorghum bicolor as a case study. Recent Findings Sessile plants control their metabolism to prioritize their resources between growth and development, or defense. This requires fine-tuned complex dynamic regulation of the metabolic networks involved. Within the recent years, numerous studies point to the formation of dynamic metabolons playing a major role in controlling the metabolic fluxes within such networks. Summary We propose that P450s and their partners interact and associate dynamically with POR, which acts as a charging station possibly in concert with Cytb5. Solvent environment, lipid composition, and non-catalytic proteins guide metabolon formation and thereby activity, which have important implications for synthetic biology approaches aiming to produce high-value specialized metabolites in heterologous hosts.
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Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
- Carlsberg Research Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark
| | - Tomas Laursen
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608 USA
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Kriechbaumer V, Botchway SW, Hawes C. Localization and interactions between Arabidopsis auxin biosynthetic enzymes in the TAA/YUC-dependent pathway. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4195-207. [PMID: 27208541 DOI: 10.1093/jxb/erw195] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The growth regulator auxin is involved in all key developmental processes in plants. A complex network of a multiplicity of potential biosynthetic pathways as well as transport, signalling plus conjugation and deconjugation lead to a complex and multifaceted system system for auxin function. This raises the question how such a system can be effectively organized and controlled. Here we report that a subset of auxin biosynthetic enzymes in the TAA/YUC route of auxin biosynthesis is localized to the endoplasmic reticulum (ER). ER microsomal fractions also contain a significant percentage of auxin biosynthetic activity. This could point toward a model of auxin function using ER membrane location and subcellular compartmentation for supplementary layers of regulation. Additionally we show specific protein-protein interactions between some of the enzymes in the TAA/YUC route of auxin biosynthesis.
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Affiliation(s)
- Verena Kriechbaumer
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0QX, UK
| | - Chris Hawes
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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Schönhals EM, Ortega F, Barandalla L, Aragones A, Ruiz de Galarreta JI, Liao JC, Sanetomo R, Walkemeier B, Tacke E, Ritter E, Gebhardt C. Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:767-785. [PMID: 26825382 PMCID: PMC4799268 DOI: 10.1007/s00122-016-2665-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 01/09/2016] [Indexed: 05/23/2023]
Abstract
SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker-trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker-trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.
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Affiliation(s)
- E M Schönhals
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | | | | | - J-C Liao
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - R Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - B Walkemeier
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - C Gebhardt
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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Dastmalchi M, Bernards MA, Dhaubhadel S. Twin anchors of the soybean isoflavonoid metabolon: evidence for tethering of the complex to the endoplasmic reticulum by IFS and C4H. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:689-706. [PMID: 26856401 DOI: 10.1111/tpj.13137] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 05/02/2023]
Abstract
Isoflavonoids are specialized plant metabolites, almost exclusive to legumes, and their biosynthesis forms a branch of the diverse phenylpropanoid pathway. Plant metabolism may be coordinated at many levels, including formation of protein complexes, or 'metabolons', which represent the molecular level of organization. Here, we have confirmed the existence of the long-postulated isoflavonoid metabolon by identifying elements of the complex, their subcellular localizations and their interactions. Isoflavone synthase (IFS) and cinnamate 4-hydroxylase (C4H) have been shown to be tandem P450 enzymes that are anchored in the ER, interacting with soluble enzymes of the phenylpropanoid and isoflavonoid pathways (chalcone synthase, chalcone reductase and chalcone isomerase). The soluble enzymes of these pathways, whether localized to the cytoplasm or nucleus, are tethered to the ER through interaction with these P450s. The complex is also held together by interactions between the soluble elements. We provide evidence for IFS interaction with upstream and non-consecutive enzymes. The existence of such a protein complex suggests a possible mechanism for flux of metabolites into the isoflavonoid pathway. Further, through interaction studies, we identified several candidates that are associated with GmIFS2, an isoform of IFS, in soybean hairy roots. This list provides additional candidates for various biosynthetic and structural elements that are involved in isoflavonoid production. Our interaction studies provide valuable information about isoform specificity among isoflavonoid enzymes, which may guide future engineering of the pathway in legumes or help overcome bottlenecks in heterologous expression.
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Affiliation(s)
- Mehran Dastmalchi
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Mark A Bernards
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Sangeeta Dhaubhadel
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
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A Metabolic Probe-Enabled Strategy Reveals Uptake and Protein Targets of Polyunsaturated Aldehydes in the Diatom Phaeodactylum tricornutum. PLoS One 2015; 10:e0140927. [PMID: 26496085 PMCID: PMC4619725 DOI: 10.1371/journal.pone.0140927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/01/2015] [Indexed: 01/12/2023] Open
Abstract
Diatoms are unicellular algae of crucial importance as they belong to the main primary producers in aquatic ecosystems. Several diatom species produce polyunsaturated aldehydes (PUAs) that have been made responsible for chemically mediated interactions in the plankton. PUA-effects include chemical defense by reducing the reproductive success of grazing copepods, allelochemical activity by interfering with the growth of competing phytoplankton and cell to cell signaling. We applied a PUA-derived molecular probe, based on the biologically highly active 2,4-decadienal, with the aim to reveal protein targets of PUAs and affected metabolic pathways. By using fluorescence microscopy, we observed a substantial uptake of the PUA probe into cells of the diatom Phaeodactylum tricornutum in comparison to the uptake of a structurally closely related control probe based on a saturated aldehyde. The specific uptake motivated a chemoproteomic approach to generate a qualitative inventory of proteins covalently targeted by the α,β,γ,δ-unsaturated aldehyde structure element. Activity-based protein profiling revealed selective covalent modification of target proteins by the PUA probe. Analysis of the labeled proteins gave insights into putative affected molecular functions and biological processes such as photosynthesis including ATP generation and catalytic activity in the Calvin cycle or the pentose phosphate pathway. The mechanism of action of PUAs involves covalent reactions with proteins that may result in protein dysfunction and interference of involved pathways.
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32
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De la Fuente IM. Elements of the cellular metabolic structure. Front Mol Biosci 2015; 2:16. [PMID: 25988183 PMCID: PMC4428431 DOI: 10.3389/fmolb.2015.00016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/12/2015] [Indexed: 12/19/2022] Open
Abstract
A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra,” Consejo Superior de Investigaciones CientíficasGranada, Spain
- Department of Mathematics, University of the Basque Country, UPV/Euskal Herriko UnibertsitateaLeioa, Spain
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Tamoi M, Shigeoka S. Diversity of regulatory mechanisms of photosynthetic carbon metabolism in plants and algae. Biosci Biotechnol Biochem 2015; 79:870-6. [PMID: 25776275 DOI: 10.1080/09168451.2015.1020754] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
To clarify the regulatory mechanisms of the Calvin cycle in algae, we analyzed the molecular properties of the enzymes involved in this cycle. We demonstrated that these enzymes were not regulated by redox modulation through the ferredoxin/thioredoxin system under light/dark conditions and were not sensitive to treatments with hydrogen peroxide in vitro, unlike the chloroplastic thiol-modulated enzymes of plants. On the other hand, we found that cyanobacteria possessed a unique enzyme involved in the Calvin cycle. The CP12 protein played an important role in regulating carbon metabolism in the Calvin cycle in cyanobacteria and eukaryotic algae. This review described the regulatory mechanisms of the Calvin cycle in algae and also the effects of alterations to photosynthetic carbon metabolism on plant productivity, carbon partitioning, and the carbon/nitrogen balance using transgenic plants expressing algal genes.
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Affiliation(s)
- Masahiro Tamoi
- a Faculty of Agriculture, Department of Advanced Bioscience , Kinki University , Nara , Japan
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Moparthi SB, Thieulin-Pardo G, de Torres J, Ghenuche P, Gontero B, Wenger J. FRET analysis of CP12 structural interplay by GAPDH and PRK. Biochem Biophys Res Commun 2015; 458:488-493. [PMID: 25666947 DOI: 10.1016/j.bbrc.2015.01.135] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
Abstract
CP12 is an intrinsically disordered protein playing a key role in the regulation of the Benson-Calvin cycle. Due to the high intrinsic flexibility of CP12, it is essential to consider its structural modulation induced upon binding to the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) enzymes. Here, we report for the first time detailed structural modulation about the wild-type CP12 and its site-specific N-terminal and C-terminal disulfide bridge mutants upon interaction with GAPDH and PRK by Förster resonance energy transfer (FRET). Our results indicate an increase in CP12 compactness when the complex is formed with GAPDH or PRK. In addition, the distributions in FRET histograms show the elasticity and conformational flexibility of CP12 in all supra molecular complexes. Contrarily to previous beliefs, our FRET results importantly reveal that both N-terminal and C-terminal site-specific CP12 mutants are able to form the monomeric (GAPDH-CP12-PRK) complex.
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Affiliation(s)
- Satish Babu Moparthi
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France.
| | - Gabriel Thieulin-Pardo
- Aix Marseille Université, CNRS, UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, 13402 Marseille Cedex 20, France
| | - Juan de Torres
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Petru Ghenuche
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Brigitte Gontero
- Aix Marseille Université, CNRS, UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, 13402 Marseille Cedex 20, France
| | - Jérôme Wenger
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
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Balsera M, Uberegui E, Schürmann P, Buchanan BB. Evolutionary development of redox regulation in chloroplasts. Antioxid Redox Signal 2014; 21:1327-55. [PMID: 24483204 DOI: 10.1089/ars.2013.5817] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE The post-translational modification of thiol groups stands out as a key strategy that cells employ for metabolic regulation and adaptation to changing environmental conditions. Nowhere is this more evident than in chloroplasts-the O2-evolving photosynthetic organelles of plant cells that are fitted with multiple redox systems, including the thioredoxin (Trx) family of oxidoreductases functional in the reversible modification of regulatory thiols of proteins in all types of cells. The best understood member of this family in chloroplasts is the ferredoxin-linked thioredoxin system (FTS) by which proteins are modified via light-dependent disulfide/dithiol (S-S/2SH) transitions. RECENT ADVANCES Discovered in the reductive activation of enzymes of the Calvin-Benson cycle in illuminated chloroplast preparations, recent studies have extended the role of the FTS far beyond its original boundaries to include a spectrum of cellular processes. Together with the NADP-linked thioredoxin reductase C-type (NTRC) and glutathione/glutaredoxin systems, the FTS also plays a central role in the response of chloroplasts to different types of stress. CRITICAL ISSUES The comparisons of redox regulatory networks functional in chloroplasts of land plants with those of cyanobacteria-prokaryotes considered to be the ancestors of chloroplasts-and different types of algae summarized in this review have provided new insight into the evolutionary development of redox regulation, starting with the simplest O2-evolving organisms. FUTURE DIRECTIONS The evolutionary appearance, mode of action, and specificity of the redox regulatory systems functional in chloroplasts, as well as the types of redox modification operating under diverse environmental conditions stand out as areas for future study.
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Affiliation(s)
- Monica Balsera
- 1 Instituto de Recursos Naturales y Agrobiología de Salamanca , Consejo Superior de Investigaciones Científicas, Salamanca, Spain
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Moparthi SB, Thieulin-Pardo G, Mansuelle P, Rigneault H, Gontero B, Wenger J. Conformational modulation and hydrodynamic radii of CP12 protein and its complexes probed by fluorescence correlation spectroscopy. FEBS J 2014; 281:3206-17. [DOI: 10.1111/febs.12854] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/30/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Affiliation(s)
| | - Gabriel Thieulin-Pardo
- Laboratoire de Bioénergétique et Ingénierie des Protéines; Aix Marseille Université; France
| | - Pascal Mansuelle
- Plate-forme Protéomique; Marseille Protéomique; Institut de Microbiologie de la Méditerranée; France
| | - Hervé Rigneault
- Centrale Marseille; Institut Fresnel; Aix Marseille Université; France
| | - Brigitte Gontero
- Laboratoire de Bioénergétique et Ingénierie des Protéines; Aix Marseille Université; France
| | - Jérôme Wenger
- Centrale Marseille; Institut Fresnel; Aix Marseille Université; France
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37
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Mileo E, Lorenzi M, Erales J, Lignon S, Puppo C, Le Breton N, Etienne E, Marque SRA, Guigliarelli B, Gontero B, Belle V. Dynamics of the intrinsically disordered protein CP12 in its association with GAPDH in the green alga Chlamydomonas reinhardtii: a fuzzy complex. MOLECULAR BIOSYSTEMS 2014; 9:2869-76. [PMID: 24056937 DOI: 10.1039/c3mb70190e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CP12 is a widespread regulatory protein of oxygenic photosynthetic organisms that contributes to the regulation of the Calvin cycle by forming a supra-molecular complex with at least two enzymes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK). CP12 shares some similarities with intrinsically disordered proteins (IDPs) depending on its redox state. In this study, site-directed spin labeling (SDSL) combined with EPR spectroscopy was used to probe the dynamic behavior of CP12 from Chlamydomonas reinhardtii upon binding to GAPDH, the first step towards ternary complex formation. The two N-terminal cysteine residues were labeled using the classical approach while the tyrosine located at the C-terminal end of CP12 was modified following an original procedure. The results show that the label grafted at the C-terminal extremity is in the vicinity of the interaction site whereas the N-terminal region remains fully disordered upon binding to GAPDH. In conclusion, GAPDH-CP12 is a fuzzy complex, in which the N-terminal region of CP12 keeps a conformational freedom in the bound form. This fuzziness could be one of the keys to facilitate binding of PRK to CP12-GAPDH and to form the ternary supra-molecular complex.
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Affiliation(s)
- Elisabetta Mileo
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France.
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Marri L, Thieulin-Pardo G, Lebrun R, Puppo R, Zaffagnini M, Trost P, Gontero B, Sparla F. CP12-mediated protection of Calvin–Benson cycle enzymes from oxidative stress. Biochimie 2014; 97:228-37. [DOI: 10.1016/j.biochi.2013.10.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 10/23/2013] [Indexed: 11/28/2022]
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Rao RSP, Thelen JJ, Miernyk JA. In silico analysis of protein Lys-N(𝜀)-acetylation in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:381. [PMID: 25136347 PMCID: PMC4120686 DOI: 10.3389/fpls.2014.00381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/17/2014] [Indexed: 05/08/2023]
Abstract
Among post-translational modifications, there are some conceptual similarities between Lys-N(𝜀)-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. The study of Lys-acetylation of plant proteins has lagged behind studies of mammalian and microbial cells; 1000s of acetylation sites have been identified in mammalian proteins compared with only hundreds of sites in plant proteins. While most previous emphasis was focused on post-translational modifications of histones, more recent studies have addressed metabolic regulation. Being directly coupled with cellular CoA/acetyl-CoA and NAD/NADH, reversible Lys-N(𝜀)-acetylation has the potential to control, or contribute to control, of primary metabolism, signaling, and growth and development.
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Affiliation(s)
- R. Shyama Prasad Rao
- Division of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
| | - Jay J. Thelen
- Division of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
| | - Ján A. Miernyk
- Division of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
- Plant Genetics Research Unit, United States Department of Agriculture – Agricultural Research ServiceColumbia, MO, USA
- *Correspondence: Jan A. Miernyk, Division of Biochemistry, University of Missouri, 102 Curtis Hall, Columbia, MO 65211, USA e-mail:
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Michelet L, Zaffagnini M, Morisse S, Sparla F, Pérez-Pérez ME, Francia F, Danon A, Marchand CH, Fermani S, Trost P, Lemaire SD. Redox regulation of the Calvin-Benson cycle: something old, something new. FRONTIERS IN PLANT SCIENCE 2013; 4:470. [PMID: 24324475 PMCID: PMC3838966 DOI: 10.3389/fpls.2013.00470] [Citation(s) in RCA: 266] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/30/2013] [Indexed: 05/18/2023]
Abstract
Reversible redox post-translational modifications such as oxido-reduction of disulfide bonds, S-nitrosylation, and S-glutathionylation, play a prominent role in the regulation of cell metabolism and signaling in all organisms. These modifications are mainly controlled by members of the thioredoxin and glutaredoxin families. Early studies in photosynthetic organisms have identified the Calvin-Benson cycle, the photosynthetic pathway responsible for carbon assimilation, as a redox regulated process. Indeed, 4 out of 11 enzymes of the cycle were shown to have a low activity in the dark and to be activated in the light through thioredoxin-dependent reduction of regulatory disulfide bonds. The underlying molecular mechanisms were extensively studied at the biochemical and structural level. Unexpectedly, recent biochemical and proteomic studies have suggested that all enzymes of the cycle and several associated regulatory proteins may undergo redox regulation through multiple redox post-translational modifications including glutathionylation and nitrosylation. The aim of this review is to detail the well-established mechanisms of redox regulation of Calvin-Benson cycle enzymes as well as the most recent reports indicating that this pathway is tightly controlled by multiple interconnected redox post-translational modifications. This redox control is likely allowing fine tuning of the Calvin-Benson cycle required for adaptation to varying environmental conditions, especially during responses to biotic and abiotic stresses.
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Affiliation(s)
- Laure Michelet
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Mirko Zaffagnini
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - Samuel Morisse
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Francesca Sparla
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - María Esther Pérez-Pérez
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Francesco Francia
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - Antoine Danon
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Christophe H. Marchand
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Simona Fermani
- Department of Chemistry “G. Ciamician”, University of BolognaBologna, Italy
| | - Paolo Trost
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - Stéphane D. Lemaire
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
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Gaston D, Roger AJ. Functional divergence and convergent evolution in the plastid-targeted glyceraldehyde-3-phosphate dehydrogenases of diverse eukaryotic algae. PLoS One 2013; 8:e70396. [PMID: 23936198 PMCID: PMC3728087 DOI: 10.1371/journal.pone.0070396] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 06/18/2013] [Indexed: 11/19/2022] Open
Abstract
Background Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme of the glycolytic pathway, reversibly catalyzing the sixth step of glycolysis and concurrently reducing the coenzyme NAD+ to NADH. In photosynthetic organisms a GAPDH paralog (Gap2 in Cyanobacteria, GapA in most photosynthetic eukaryotes) functions in the Calvin cycle, performing the reverse of the glycolytic reaction and using the coenzyme NADPH preferentially. In a number of photosynthetic eukaryotes that acquired their plastid by the secondary endosymbiosis of a eukaryotic red alga (Alveolates, haptophytes, cryptomonads and stramenopiles) GapA has been apparently replaced with a paralog of the host’s own cytosolic GAPDH (GapC1). Plastid GapC1 and GapA therefore represent two independent cases of functional divergence and adaptations to the Calvin cycle entailing a shift in subcellular targeting and a shift in binding preference from NAD+ to NADPH. Methods We used the programs FunDi, GroupSim, and Difference Evolutionary-Trace to detect sites involved in the functional divergence of these two groups of GAPDH sequences and to identify potential cases of convergent evolution in the Calvin-cycle adapted GapA and GapC1 families. Sites identified as being functionally divergent by all or some of these programs were then investigated with respect to their possible roles in the structure and function of both glycolytic and plastid-targeted GAPDH isoforms. Conclusions In this work we found substantial evidence for convergent evolution in GapA/B and GapC1. In many cases sites in GAPDHs of these groups converged on identical amino acid residues in specific positions of the protein known to play a role in the function and regulation of plastid-functioning enzymes relative to their cytosolic counterparts. In addition, we demonstrate that bioinformatic software like FunDi are important tools for the generation of meaningful biological hypotheses that can then be tested with direct experimental techniques.
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Affiliation(s)
- Daniel Gaston
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle. Biochem Soc Trans 2013; 40:995-9. [PMID: 22988853 DOI: 10.1042/bst20120097] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many proteins contain disordered regions under physiological conditions and lack specific three-dimensional structure. These are referred to as IDPs (intrinsically disordered proteins). CP12 is a chloroplast protein of approximately 80 amino acids and has a molecular mass of approximately 8.2-8.5 kDa. It is enriched in charged amino acids and has a small number of hydrophobic residues. It has a high proportion of disorder-promoting residues, but has at least two (often four) cysteine residues forming one (or two) disulfide bridge(s) under oxidizing conditions that confers some order. However, CP12 behaves like an IDP. It appears to be universally distributed in oxygenic photosynthetic organisms and has recently been detected in a cyanophage. The best studied role of CP12 is its regulation of the Calvin cycle responsible for CO2 assimilation. Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. Association-dissociation of this complex, induced by the redox state of CP12, allows the Calvin cycle to be inactive in the dark and active in the light. CP12 is promiscuous and interacts with other enzymes such as aldolase and malate dehydrogenase. It also plays other roles in plant metabolism such as protecting GAPDH from inactivation and scavenging metal ions such as copper and nickel, and it is also linked to stress responses. Thus CP12 seems to be involved in many functions in photosynthetic cells and behaves like a jack of all trades as well as being a master of the Calvin cycle.
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Avilan L, Puppo C, Erales J, Woudstra M, Lebrun R, Gontero B. CP12 residues involved in the formation and regulation of the glyceraldehyde-3-phosphate dehydrogenase-CP12-phosphoribulokinase complex in Chlamydomonas reinhardtii. MOLECULAR BIOSYSTEMS 2013; 8:2994-3002. [PMID: 22955105 DOI: 10.1039/c2mb25244a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CP12, a member of the intrinsically disordered protein family, forms a stable complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK). To understand the function of conserved residues of CP12 in the formation of the GAPDH-CP12-PRK complex and in the regulation of the enzymes within this complex, we have produced mutants of CP12 by site-directed mutagenesis. The GAPDH, CP12 and PRK recombinant proteins are able to reconstitute spontaneously the ternary complex that has been described in Chlamydomonas reinhardtii. Our analysis reveals that the central part ((35)WXXVEE(47)) of CP12 is required to form the GAPDH-CP12-PRK complex. Using the same series of single amino acid replacements, we have identified individual residues, which seem to represent also contact points for GAPDH. Most notably, substitution of glutamate 74 prevents the binding of GAPDH to CP12. This is similar to the mutant C66S, with which the GAPDH-CP12-PRK complex is not formed. In contrast, replacement of the three last residues ((78)YED(80)) of CP12 has no effect on the formation of the ternary supra-molecular complex. However, our findings strongly suggest that Y78 and D80 are involved in the regulation of the GAPDH activity within the supra-molecular complex, since the mutants, D80K and Y78S, do not down-regulate the activity of GAPDH. The replacement of the amino acid E79 weakens the interaction between GAPDH and CP12 as no GAPDH-CP12 sub-complex is formed. In this case, nevertheless, the supra-molecular complex is formed when PRK is present indicating that PRK strengthens the interaction between GAPDH and CP12 within the supra-molecular complex.
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Affiliation(s)
- Luisana Avilan
- Laboratoire de Bioénergétique et Ingénierie des Protéines CNRS-UMR 7281-Aix-Marseille Université. Institut de Microbiologie de la Méditerranée, CNRS, 31 Chemin Joseph Aiguier, BP71, 13 402 Marseille Cedex 20, France
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Kaaki W, Woudstra M, Gontero B, Halgand F. Exploration of CP12 conformational changes and of quaternary structural properties using electrospray ionization traveling wave ion mobility mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:179-186. [PMID: 23239332 DOI: 10.1002/rcm.6442] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 10/10/2012] [Accepted: 10/16/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE CP12 is a small chloroplast protein involved in the Benson-Calvin cycle. Since it was demonstrated that the CP12 protein shared different conformational properties between reduced and oxidized states we took advantage of the segregational properties of the Traveling Wave Ion Mobility (TWIM) guide to study subtle conformational changes related to redox changes. METHODS Electrospray ionization mass (ESI-MS) spectra of the CP12 protein were recorded in the positive ion mode using an ESI source fitted on a quadrupole time-of-flight (QToF) hybrid mass spectrometer equipped with a TWIM cell (Synapt HDMS G1, Waters Corp., Manchester) under non-denaturing conditions. Non-covalent experiments were performed using the same instrument without the use of the TWIM device. RESULTS Whatever the CP12 form studied, our results showed that CP12 protein was represented by two conformers in equilibrium that displayed very slight differences. These observations led us to propose that CP12 protein structure is rather undergoing transient subtle structural changes than having two different conformational populations in solution. In addition, using non-denaturing experiments, NAD and CP12 stoichiometry were determined with respect to the GAPDH tetramer and the redox state of CP12. CONCLUSIONS In this study we showed that the use of the segregational property of the ion mobility (TWIM, Synapt G1 HDMS, Waters, Manchester, UK) allowed differentiation of subtle conformational changes between redox states of the CP12 protein. Standard non-denaturing experiments revealed different binding stoichiometry according to the redox state of the CP12 protein.
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Affiliation(s)
- Wassim Kaaki
- Unité de Bioénergétique et Ingénierie des Protéines (UMR 7281), Institut de Microbiologie de la Méditerranée, CNRS & AMU Aix-Marseille Univ, France
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Kane K, Moheb A, Fukushi Y, Roy R, Hüner NPA, Ibrahim RK, Sarhan F. Daphnetin methylation stabilizes the activity of phosphoribulokinase in wheat during cold acclimation. Biochem Cell Biol 2012; 90:657-66. [PMID: 22827600 DOI: 10.1139/o2012-023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The methylation of daphnetin (7,8-dihydroxycoumarin) to its 8-methyl derivative is catalyzed by a wheat (Triticum aestivum L.) O-methyltransferase (TaOMT1). This enzyme is regulated by cold and photosystem II excitation pressure (plastid redox state). Here, we investigated the biological significance of this methylation and its potential role in modulating the activity of kinases in wheat. To identify the potential kinases that may interact with daphnetin in wheat, the soluble protein extract from aerial parts of cold-acclimated wheat was purified by DEAE-cellulose separation and affinity chromatography on a daphnetin derivative (7,8-dihydroxy-4-coumarin acetic acid)-EAH sepharose column. Mass spectrometric analysis indicated that wheat phosphoribulokinase (TaPRK) is the major kinase that binds to daphnetin. This TaPRK plays an important role in regulating the flow of carbon through the Calvin cycle, by catalyzing the final step in the regeneration of ribulose 1,5-bisphosphate from ribulose-5-phosphate (Ru5P) and ATP. The activities of TaPRK, endogenous or recombinant, are inhibited by daphnetin in a specific and dose-dependent manner, but not by its monomethyl derivative (7-methyl, 8-hydroxycoumarin). Furthermore, HPLC-MS analysis of wheat extracts reveals that 7,8-dimethoxycoumarin is more abundant than its monomethyl derivative. The results also show that cold acclimation does not alter the level of TaPRK mRNA or its enzyme activity, and thus ensures the stable generation of ribulose 1,5-biphosphate.
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Affiliation(s)
- Khalil Kane
- Département des Sciences biologiques, Université du Québec à Montréal, C.P 8888, Succ. Centre-Ville, Montréal, QC H2X 3X8, Canada
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Mininno M, Brugière S, Pautre V, Gilgen A, Ma S, Ferro M, Tardif M, Alban C, Ravanel S. Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants. J Biol Chem 2012; 287:21034-44. [PMID: 22547063 PMCID: PMC3375527 DOI: 10.1074/jbc.m112.359976] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 04/28/2012] [Indexed: 11/06/2022] Open
Abstract
In pea (Pisum sativum), the protein-lysine methyltransferase (PsLSMT) catalyzes the trimethylation of Lys-14 in the large subunit (LS) of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), the enzyme catalyzing the CO(2) fixation step during photosynthesis. Homologs of PsLSMT, herein referred to as LSMT-like enzymes, are found in all plant genomes, but methylation of LS Rubisco is not universal in the plant kingdom, suggesting a species-specific protein substrate specificity of the methyltransferase. In this study, we report the biochemical characterization of the LSMT-like enzyme from Arabidopsis thaliana (AtLSMT-L), with a focus on its substrate specificity. We show that, in Arabidopsis, LS Rubisco is not naturally methylated and that the physiological substrates of AtLSMT-L are chloroplastic fructose 1,6-bisphosphate aldolase isoforms. These enzymes, which are involved in the assimilation of CO(2) through the Calvin cycle and in chloroplastic glycolysis, are trimethylated at a conserved lysyl residue located close to the C terminus. Both AtLSMT-L and PsLSMT are able to methylate aldolases with similar kinetic parameters and product specificity. Thus, the divergent substrate specificity of LSMT-like enzymes from pea and Arabidopsis concerns only Rubisco. AtLSMT-L is able to interact with unmethylated Rubisco, but the complex is catalytically unproductive. Trimethylation does not modify the kinetic properties and tetrameric organization of aldolases in vitro. The identification of aldolases as methyl proteins in Arabidopsis and other species like pea suggests a role of protein lysine methylation in carbon metabolism in chloroplasts.
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Affiliation(s)
- Morgane Mininno
- From the INRA, USC1359, F-38054 Grenoble
- CNRS, UMR5168, F-38054 Grenoble
- the Commissariat à l'Energie Atomique, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble
- the Université Joseph Fourier-Grenoble I, UMR5168, F-38041 Grenoble
| | - Sabine Brugière
- the Commissariat à l'Energie Atomique, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble
- INSERM, U1038, F-38054 Grenoble, and
- the Université Joseph Fourier-Grenoble I, U1038, F-38041 Grenoble, France
| | - Virginie Pautre
- From the INRA, USC1359, F-38054 Grenoble
- CNRS, UMR5168, F-38054 Grenoble
- the Commissariat à l'Energie Atomique, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble
- the Université Joseph Fourier-Grenoble I, UMR5168, F-38041 Grenoble
| | - Annabelle Gilgen
- From the INRA, USC1359, F-38054 Grenoble
- CNRS, UMR5168, F-38054 Grenoble
- the Commissariat à l'Energie Atomique, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble
- the Université Joseph Fourier-Grenoble I, UMR5168, F-38041 Grenoble
| | - Sheng Ma
- From the INRA, USC1359, F-38054 Grenoble
- CNRS, UMR5168, F-38054 Grenoble
- the Commissariat à l'Energie Atomique, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble
- the Université Joseph Fourier-Grenoble I, UMR5168, F-38041 Grenoble
| | - Myriam Ferro
- the Commissariat à l'Energie Atomique, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble
- INSERM, U1038, F-38054 Grenoble, and
- the Université Joseph Fourier-Grenoble I, U1038, F-38041 Grenoble, France
| | - Marianne Tardif
- the Commissariat à l'Energie Atomique, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble
- INSERM, U1038, F-38054 Grenoble, and
- the Université Joseph Fourier-Grenoble I, U1038, F-38041 Grenoble, France
| | - Claude Alban
- From the INRA, USC1359, F-38054 Grenoble
- CNRS, UMR5168, F-38054 Grenoble
- the Commissariat à l'Energie Atomique, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble
- the Université Joseph Fourier-Grenoble I, UMR5168, F-38041 Grenoble
| | - Stéphane Ravanel
- From the INRA, USC1359, F-38054 Grenoble
- CNRS, UMR5168, F-38054 Grenoble
- the Commissariat à l'Energie Atomique, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble
- the Université Joseph Fourier-Grenoble I, UMR5168, F-38041 Grenoble
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Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants. J Biotechnol 2012; 162:134-47. [PMID: 22677697 DOI: 10.1016/j.jbiotec.2012.05.006] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/15/2012] [Accepted: 05/21/2012] [Indexed: 11/23/2022]
Abstract
Development of sustainable energy is a pivotal step towards solutions for today's global challenges, including mitigating the progression of climate change and reducing dependence on fossil fuels. Biofuels derived from agricultural crops have already been commercialized. However the impacts on environmental sustainability and food supply have raised ethical questions about the current practices. Cyanobacteria have attracted interest as an alternative means for sustainable energy productions. Being aquatic photoautotrophs they can be cultivated in non-arable lands and do not compete for land for food production. Their rich genetic resources offer means to engineer metabolic pathways for synthesis of valuable bio-based products. Currently the major obstacle in industrial-scale exploitation of cyanobacteria as the economically sustainable production hosts is low yields. Much effort has been made to improve the carbon fixation and manipulating the carbon allocation in cyanobacteria and their evolutionary photosynthetic relatives, algae and plants. This review aims at providing an overview of the recent progress in the bioengineering of carbon fixation and allocation in cyanobacteria; wherever relevant, the progress made in plants and algae is also discussed as an inspiration for future application in cyanobacteria.
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Uematsu K, Suzuki N, Iwamae T, Inui M, Yukawa H. Increased fructose 1,6-bisphosphate aldolase in plastids enhances growth and photosynthesis of tobacco plants. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3001-9. [PMID: 22323273 DOI: 10.1093/jxb/ers004] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The Calvin cycle is the initial pathway of photosynthetic carbon fixation, and several of its reaction steps are suggested to exert rate-limiting influence on the growth of higher plants. Plastid fructose 1,6-bisphosphate aldolase (aldolase, EC 4.1.2.13) is one of the nonregulated enzymes comprising the Calvin cycle and is predicted to have the potential to control photosynthetic carbon flux through the cycle. In order to investigate the effect of overexpression of aldolase, this study generated transgenic tobacco (Nicotiana tabacum L. cv Xanthi) expressing Arabidopsis plastid aldolase. Resultant transgenic plants with 1.4-1.9-fold higher aldolase activities than those of wild-type plants showed enhanced growth, culminating in increased biomass, particularly under high CO₂ concentration (700 ppm) where the increase reached 2.2-fold relative to wild-type plants. This increase was associated with a 1.5-fold elevation of photosynthetic CO₂ fixation in the transgenic plants. The increased plastid aldolase resulted in a decrease in 3-phosphoglycerate and an increase in ribulose 1,5-bisphosphate and its immediate precursors in the Calvin cycle, but no significant changes in the activities of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) or other major enzymes of carbon assimilation. Taken together, these results suggest that aldolase overexpression stimulates ribulose 1,5-bisphosphate regeneration and promotes CO₂ fixation. It was concluded that increased photosynthetic rate was responsible for enhanced growth and biomass yields of aldolase-overexpressing plants.
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Affiliation(s)
- Kimio Uematsu
- Research Institute of Innovative Technology for the Earth-RITE, 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
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Girbig D, Grimbs S, Selbig J. Systematic analysis of stability patterns in plant primary metabolism. PLoS One 2012; 7:e34686. [PMID: 22514655 PMCID: PMC3326025 DOI: 10.1371/journal.pone.0034686] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/06/2012] [Indexed: 11/24/2022] Open
Abstract
Metabolic networks are characterized by complex interactions and regulatory mechanisms between many individual components. These interactions determine whether a steady state is stable to perturbations. Structural kinetic modeling (SKM) is a framework to analyze the stability of metabolic steady states that allows the study of the system Jacobian without requiring detailed knowledge about individual rate equations. Stability criteria can be derived by generating a large number of structural kinetic models (SK-models) with randomly sampled parameter sets and evaluating the resulting Jacobian matrices. Until now, SKM experiments applied univariate tests to detect the network components with the largest influence on stability. In this work, we present an extended SKM approach relying on supervised machine learning to detect patterns of enzyme-metabolite interactions that act together in an orchestrated manner to ensure stability. We demonstrate its application on a detailed SK-model of the Calvin-Benson cycle and connected pathways. The identified stability patterns are highly complex reflecting that changes in dynamic properties depend on concerted interactions between several network components. In total, we find more patterns that reliably ensure stability than patterns ensuring instability. This shows that the design of this system is strongly targeted towards maintaining stability. We also investigate the effect of allosteric regulators revealing that the tendency to stability is significantly increased by including experimentally determined regulatory mechanisms that have not yet been integrated into existing kinetic models.
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Affiliation(s)
- Dorothee Girbig
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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