1
|
Zhang B, Ma Z, Guo H, Chen S, Liu J. Single-cell RNA-sequencing provides new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass leaf blades. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108857. [PMID: 38905728 DOI: 10.1016/j.plaphy.2024.108857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
As an important warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) flourishes in warm areas around the world due to the existence of the C4 photosynthetic pathway. However, how C4 photosynthesis operates in bermudagrass leaves is still poorly understood. In this study, we performed single-cell RNA-sequencing on 5296 cells from bermudagrass leaf blades. Eight cell clusters corresponding to mesophyll, bundle sheath, epidermis and vascular bundle cells were successfully identified using known cell marker genes. Expression profiling indicated that genes encoding NADP-dependent malic enzymes (NADP-MEs) were highly expressed in bundle sheath cells, whereas NAD-ME genes were weakly expressed in all cell types, suggesting C4 photosynthesis of bermudagrass leaf blades might be NADP-ME type rather than NAD-ME type. The results also indicated that starch synthesis-related genes showed preferential expression in bundle sheath cells, whereas starch degradation-related genes were highly expressed in mesophyll cells, which agrees with the observed accumulation of starch-filled chloroplasts in bundle sheath cells. Gene co-expression analysis further revealed that different families of transcription factors were co-expressed with multiple C4 photosynthesis-related genes, suggesting a complex transcription regulatory network of C4 photosynthesis might exist in bermudagrass leaf blades. These findings collectively provided new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass.
Collapse
Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Ziyan Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Si Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| |
Collapse
|
2
|
Ludwig M, Hartwell J, Raines CA, Simkin AJ. The Calvin-Benson-Bassham cycle in C 4 and Crassulacean acid metabolism species. Semin Cell Dev Biol 2024; 155:10-22. [PMID: 37544777 DOI: 10.1016/j.semcdb.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023]
Abstract
The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.
Collapse
Affiliation(s)
- Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Andrew J Simkin
- University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| |
Collapse
|
3
|
Zhang Q, Tian S, Chen G, Tang Q, Zhang Y, Fleming AJ, Zhu XG, Wang P. Regulatory NADH dehydrogenase-like complex optimizes C 4 photosynthetic carbon flow and cellular redox in maize. THE NEW PHYTOLOGIST 2024; 241:82-101. [PMID: 37872738 DOI: 10.1111/nph.19332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 09/20/2023] [Indexed: 10/25/2023]
Abstract
C4 plants typically operate a CO2 concentration mechanism from mesophyll (M) cells into bundle sheath (BS) cells. NADH dehydrogenase-like (NDH) complex is enriched in the BS cells of many NADP-malic enzyme (ME) type C4 plants and is more abundant in C4 than in C3 plants, but to what extent it is involved in the CO2 concentration mechanism remains to be experimentally investigated. We created maize and rice mutants deficient in NDH function and then used a combination of transcriptomic, proteomic, and metabolomic approaches for comparative analysis. Considerable decreases in growth, photosynthetic activities, and levels of key photosynthetic proteins were observed in maize but not rice mutants. However, transcript abundance for many cyclic electron transport (CET) and Calvin-Benson cycle components, as well as BS-specific C4 enzymes, was increased in maize mutants. Metabolite analysis of the maize ndh mutants revealed an increased NADPH : NADP ratio, as well as malate, ribulose 1,5-bisphosphate (RuBP), fructose 1,6-bisphosphate (FBP), and photorespiration intermediates. We suggest that by optimizing NADPH and malate levels and adjusting NADP-ME activity, NDH functions to balance metabolic and redox states in the BS cells of maize (in addition to ATP supply), coordinating photosynthetic transcript abundance and protein content, thus directly regulating the carbon flow in the two-celled C4 system of maize.
Collapse
Affiliation(s)
- Qiqi Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shilong Tian
- University of Chinese Academy of Sciences, Beijing, China
| | - Genyun Chen
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiming Tang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Andrew J Fleming
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Xin-Guang Zhu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Peng Wang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
4
|
Han SY, Kim WY, Kim JS, Hwang I. Comparative transcriptomics reveals the role of altered energy metabolism in the establishment of single-cell C 4 photosynthesis in Bienertia sinuspersici. FRONTIERS IN PLANT SCIENCE 2023; 14:1202521. [PMID: 37476170 PMCID: PMC10354284 DOI: 10.3389/fpls.2023.1202521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/31/2023] [Indexed: 07/22/2023]
Abstract
Single-cell C4 photosynthesis (SCC4) in terrestrial plants without Kranz anatomy involves three steps: initial CO2 fixation in the cytosol, CO2 release in mitochondria, and a second CO2 fixation in central chloroplasts. Here, we investigated how the large number of mechanisms underlying these processes, which occur in three different compartments, are orchestrated in a coordinated manner to establish the C4 pathway in Bienertia sinuspersici, a SCC4 plant. Leaves were subjected to transcriptome analysis at three different developmental stages. Functional enrichment analysis revealed that SCC4 cycle genes are coexpressed with genes regulating cyclic electron flow and amino/organic acid metabolism, two key processes required for the production of energy molecules in C3 plants. Comparative gene expression profiling of B. sinuspersici and three other species (Suaeda aralocaspica, Amaranthus hypochondriacus, and Arabidopsis thaliana) showed that the direction of metabolic flux was determined via an alteration in energy supply in peripheral chloroplasts and mitochondria via regulation of gene expression in the direction of the C4 cycle. Based on these results, we propose that the redox homeostasis of energy molecules via energy metabolism regulation is key to the establishment of the SCC4 pathway in B. sinuspersici.
Collapse
Affiliation(s)
- Sang-Yun Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21+) and Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung Sun Kim
- Genomic Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| |
Collapse
|
5
|
Boussardon C, Carrie C, Keech O. Comparing plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad133. [PMID: 37026385 PMCID: PMC10400147 DOI: 10.1093/jxb/erad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Indexed: 06/19/2023]
Abstract
Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, proplasts to only cite a few denominations. Over the past decades, methods based on density gradients and differential centrifugations have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the TOC64 gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis thaliana using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, and allowed the identification of 1672 proteins, among which 1342 were predicted plastidial, and 705 were fully confirmed according to SUBA5. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NDC1, VTE1, PGL34, ABC1K1) and cyclic electron flow in plastids originating from vascular tissues. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.
Collapse
Affiliation(s)
- Clément Boussardon
- Department of Plant Physiology, Umeå Plant Science, Umeå University, S-90187 Umeå, Sweden
| | - Chris Carrie
- School of Biological Sciences, University of Auckland, 3A Symonds St, Auckland,1142, New Zealand
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science, Umeå University, S-90187 Umeå, Sweden
| |
Collapse
|
6
|
Wu JX, Pascovici D, Wu Y, Walker AK, Mirzaei M. Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data. Methods Mol Biol 2023; 2426:375-390. [PMID: 36308698 DOI: 10.1007/978-1-0716-1967-4_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this protocol we describe our workflow for analyzing complex, multi-condition quantitative proteomic experiments, with the aim to extract biological insights. The tool we use is an R package, PloGO2, contributed to Bioconductor, which we can optionally precede by running correlation network analysis with WGCNA. We describe the data required and the steps we take, including detailed code examples and outputs explanation. The package was designed to generate gene ontology or pathway summaries for many data subsets at the same time, visualize protein abundance summaries for each biological category examined, help determine enriched protein subsets by comparing them all to a reference set, and suggest key highly correlated hub proteins, if the optional network analysis is employed.
Collapse
Affiliation(s)
- Jemma X Wu
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia.
| | | | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
7
|
A Changing Light Environment Induces Significant Lateral CO 2 Diffusion within Maize Leaves. Int J Mol Sci 2022; 23:ijms232314530. [PMID: 36498855 PMCID: PMC9736261 DOI: 10.3390/ijms232314530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
A leaf structure with high porosity is beneficial for lateral CO2 diffusion inside the leaves. However, the leaf structure of maize is compact, and it has long been considered that lateral CO2 diffusion is restricted. Moreover, lateral CO2 diffusion is closely related to CO2 pressure differences (ΔCO2). Therefore, we speculated that enlarging the ΔCO2 between the adjacent regions inside maize leaves may result in lateral diffusion when the diffusion resistance is kept constant. Thus, the leaf structure and gas exchange of maize (C4), cotton (C3), and other species were explored. The results showed that maize and sorghum leaves had a lower mesophyll porosity than cotton and cucumber leaves. Similar to cotton, the local photosynthetic induction resulted in an increase in the ΔCO2 between the local illuminated and the adjacent unilluminated regions, which significantly reduced the respiration rate of the adjacent unilluminated region. Further analysis showed that when the adjacent region in the maize leaves was maintained under a steady high light, the photosynthesis induction in the local regions not only gradually reduced the ΔCO2 between them but also progressively increased the steady photosynthetic rate in the adjacent region. Under field conditions, the ΔCO2, respiration, and photosynthetic rate of the adjacent region were also markedly changed by fluctuating light in local regions in the maize leaves. Consequently, we proposed that enlarging the ΔCO2 between the adjacent regions inside the maize leaves results in the lateral CO2 diffusion and supports photosynthesis in adjacent regions to a certain extent under fluctuating light.
Collapse
|
8
|
Tao S, Zhang W. Network and epigenetic characterization of subsets of genes specifically expressed in maize bundle sheath cells. Comput Struct Biotechnol J 2022; 20:3581-3590. [PMID: 35860403 PMCID: PMC9287181 DOI: 10.1016/j.csbj.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/21/2022] Open
Abstract
Bundle sheath (BS) cells exhibit dramatically structural differences and functional variations at physiological, biochemical and epigenetic levels as compared to mesophyll (M) cells in maize. The regulatory mechanisms controlling functional divergences between M and BS have been extensively investigated. However, BS cell-related regulatory networks are still not completely characterized. To address this, we herein conducted WGCNA-related co-expression assays using bulk M and BS cell RNA-seq data sets and identified a module containing 384 genes highly expressed in BS cells (including 20 hub TFs) instead of M cells. According to the hub TF centered regulatory network, we found that Dof22 and Dof30 might act as key regulators in the regulation of expression of BS-specific genes, and several MYB TFs exhibited a high collaboration with Dof TFs. By comparing the enrichment levels of histone modifications, we found that genes in the aforementioned module were more enriched with histone acetylation as compared to other BS-enriched DEGs with similar expression levels. Moreover, we found that a subset of genes functioning in photosynthesis, protein auto processing and enzymatic activities were significantly enriched with broad H3K4me3. Thus, our study provides evidence showing that regulatory network and histone modifications may play vital roles in the regulation of a subset of genes with important functions in BS cells.
Collapse
Affiliation(s)
- Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| |
Collapse
|
9
|
Gilman IS, Moreno-Villena JJ, Lewis ZR, Goolsby EW, Edwards EJ. Gene co-expression reveals the modularity and integration of C4 and CAM in Portulaca. PLANT PHYSIOLOGY 2022; 189:735-753. [PMID: 35285495 PMCID: PMC9157154 DOI: 10.1093/plphys/kiac116] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/17/2022] [Indexed: 05/17/2023]
Abstract
C4 photosynthesis and Crassulacean acid metabolism (CAM) have been considered as largely independent adaptations despite sharing key biochemical modules. Portulaca is a geographically widespread clade of over 100 annual and perennial angiosperm species that primarily use C4 but facultatively exhibit CAM when drought stressed, a photosynthetic system known as C4 + CAM. It has been hypothesized that C4 + CAM is rare because of pleiotropic constraints, but these have not been deeply explored. We generated a chromosome-level genome assembly of Portulaca amilis and sampled mRNA from P. amilis and Portulaca oleracea during CAM induction. Gene co-expression network analyses identified C4 and CAM gene modules shared and unique to both Portulaca species. A conserved CAM module linked phosphoenolpyruvate carboxylase to starch turnover during the day-night transition and was enriched in circadian clock regulatory motifs in the P. amilis genome. Preservation of this co-expression module regardless of water status suggests that Portulaca constitutively operate a weak CAM cycle that is transcriptionally and posttranscriptionally upregulated during drought. C4 and CAM mostly used mutually exclusive genes for primary carbon fixation, and it is likely that nocturnal CAM malate stores are shuttled into diurnal C4 decarboxylation pathways, but we found evidence that metabolite cycling may occur at low levels. C4 likely evolved in Portulaca through co-option of redundant genes and integration of the diurnal portion of CAM. Thus, the ancestral CAM system did not strongly constrain C4 evolution because photosynthetic gene networks are not co-regulated for both daytime and nighttime functions.
Collapse
Affiliation(s)
- Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Author for correspondence:
| | - Jose J Moreno-Villena
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Zachary R Lewis
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Eric W Goolsby
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
10
|
Zhu Y, Jin L, Shi R, Li J, Wang Y, Zhang L, Liang CZ, Narayana VK, De Souza DP, Thorne RF, Zhang LR, Zhang XD, Wu M. The long noncoding RNA glycoLINC assembles a lower glycolytic metabolon to promote glycolysis. Mol Cell 2022; 82:542-554.e6. [PMID: 35081364 DOI: 10.1016/j.molcel.2021.11.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 08/03/2021] [Accepted: 11/15/2021] [Indexed: 01/27/2023]
Abstract
Non-covalent complexes of glycolytic enzymes, called metabolons, were postulated in the 1970s, but the concept has been controversial. Here we show that a c-Myc-responsive long noncoding RNA (lncRNA) that we call glycoLINC (gLINC) acts as a backbone for metabolon formation between all four glycolytic payoff phase enzymes (PGK1, PGAM1, ENO1, and PKM2) along with lactate dehydrogenase A (LDHA). The gLINC metabolon enhances glycolytic flux, increases ATP production, and enables cell survival under serine deprivation. Furthermore, gLINC overexpression in cancer cells promotes xenograft growth in mice fed a diet deprived of serine, suggesting that cancer cells employ gLINC during metabolic reprogramming. We propose that gLINC makes a functional contribution to cancer cell adaptation and provide the first example of a lncRNA-facilitated metabolon.
Collapse
Affiliation(s)
- Youming Zhu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei 230032, China
| | - Lei Jin
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; School of Medicine and Public Health, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Ronghua Shi
- The Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Cell and Molecular Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Jinming Li
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China
| | - Yan Wang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei 230031, China
| | - Chao-Zhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei 230031, China
| | - Vinod K Narayana
- Bio21 Institute and Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia; Metabolomics Australia, University of Melbourne, Parkville, VIC 3010, Australia
| | - David P De Souza
- Bio21 Institute and Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia; Metabolomics Australia, University of Melbourne, Parkville, VIC 3010, Australia
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; School of Environmental and Life Sciences, The University of Newcastle, Newcastle, NSW 2258, Australia
| | - Li Rong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China.
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, NSW 2308, Australia.
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; The Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Cell and Molecular Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.
| |
Collapse
|
11
|
Lande NV, Barua P, Gayen D, Wardhan V, Jeevaraj T, Kumar S, Chakraborty S, Chakraborty N. Dehydration-responsive chickpea chloroplast protein, CaPDZ1, confers dehydration tolerance by improving photosynthesis. PHYSIOLOGIA PLANTARUM 2022; 174:e13613. [PMID: 35199362 DOI: 10.1111/ppl.13613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 05/27/2023]
Abstract
The screening of a dehydration-responsive chloroplast proteome of chickpea led us to identify and investigate the functional importance of an uncharacterized protein, designated CaPDZ1. In all, we identified 14 CaPDZs, and phylogenetic analysis revealed that these belong to photosynthetic eukaryotes. Sequence analyses of CaPDZs indicated that CaPDZ1 is a unique member, which harbours a TPR domain besides a PDZ domain. The global expression analysis showed that CaPDZs are intimately associated with various stresses such as dehydration and oxidative stress along with certain phytohormone responses. The CaPDZ1-overexpressing chickpea seedlings exhibited distinct phenotypic and molecular responses, particularly increased photosystem (PS) efficiency, ETR and qP that validated its participation in PSII complex assembly and/or repair. The investigation of CaPDZ1 interacting proteins through Y2H library screening and co-IP analysis revealed the interacting partners to be PSII associated CP43, CP47, D1, D2 and STN8. These findings supported the earlier hypothesis regarding the role of direct or indirect involvement of PDZ proteins in PS assembly or repair. Moreover, the GUS-promoter analysis demonstrated the preferential expression of CaPDZ1 specifically in photosynthetic tissues. We classified CaPDZ1 as a dehydration-responsive chloroplast intrinsic protein with multi-fold abundance under dehydration stress, which may participate synergistically with other chloroplast proteins in the maintenance of the photosystem.
Collapse
Affiliation(s)
- Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| | - Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| | - Dipak Gayen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| | - Vijay Wardhan
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| | - Theboral Jeevaraj
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| | - Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi, India
| |
Collapse
|
12
|
Calace P, Tonetti T, Margarit E, Figueroa CM, Lobertti C, Andreo CS, Gerrard Wheeler MC, Saigo M. The C4 cycle and beyond: diverse metabolic adaptations accompany dual-cell photosynthetic functions in Setaria. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7876-7890. [PMID: 34402880 DOI: 10.1093/jxb/erab381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
C4 photosynthesis is typically characterized by the spatial compartmentalization of the photosynthetic reactions into mesophyll (M) and bundle sheath (BS) cells. Initial carbon fixation within M cells gives rise to C4 acids, which are transported to the BS cells. There, C4 acids are decarboxylated so that the resulting CO2 is incorporated into the Calvin cycle. This work is focused on the study of Setaria viridis, a C4 model plant, closely related to several major feed and bioenergy grasses. First, we performed the heterologous expression and biochemical characterization of Setaria isoforms for chloroplastic NADP-malic enzyme (NADP-ME) and mitochondrial NAD-malic enzyme (NAD-ME). The kinetic parameters obtained agree with a major role for NADP-ME in the decarboxylation of the C4 acid malate in the chloroplasts of BS cells. In addition, mitochondria-located NAD-ME showed regulatory properties that could be important in the context of the operation of the C4 carbon shuttle. Secondly, we compared the proteomes of M and BS compartments and found 825 differentially accumulated proteins that could support different metabolic scenarios. Most interestingly, we found evidence of metabolic strategies to insulate the C4 core avoiding the leakage of intermediates by either up-regulation or down-regulation of chloroplastic, mitochondrial, and peroxisomal proteins. Overall, the results presented in this work provide novel data concerning the complexity of C4 metabolism, uncovering future lines of research that will undoubtedly contribute to the expansion of knowledge on this topic.
Collapse
Affiliation(s)
- Paula Calace
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Tonetti
- Instituto de Agrobiotecnología del Litoral (IAL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Ezequiel Margarit
- Grupo de Calidad de Frutos Cítricos, Bayas y Mejoramiento Forestal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (IAL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Carlos Lobertti
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Laboratorio de Patogénesis Bacteriana, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Centro Científico Tecnológico Rosario, Rosario, Argentina
| | - Carlos S Andreo
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariel C Gerrard Wheeler
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariana Saigo
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| |
Collapse
|
13
|
Urban A, Rogowski P, Wasilewska-Dębowska W, Romanowska E. Understanding Maize Response to Nitrogen Limitation in Different Light Conditions for the Improvement of Photosynthesis. PLANTS 2021; 10:plants10091932. [PMID: 34579465 PMCID: PMC8471034 DOI: 10.3390/plants10091932] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022]
Abstract
The photosynthetic capacity of leaves is determined by their content of nitrogen (N). Nitrogen involved in photosynthesis is divided between soluble proteins and thylakoid membrane proteins. In C4 plants, the photosynthetic apparatus is partitioned between two cell types: mesophyll cells and bundle sheath. The enzymes involved in the C4 carbon cycle and assimilation of nitrogen are localized in a cell-specific manner. Although intracellular distribution of enzymes of N and carbon assimilation is variable, little is known about the physiological consequences of this distribution caused by light changes. Light intensity and nitrogen concentration influence content of nitrates in leaves and can induce activity of the main enzymes involved in N metabolism, and changes that reduce the photosynthesis rate also reduce photosynthetic N use efficiency. In this review, we wish to highlight and discuss how/whether light intensity can improve photosynthesis in maize during nitrogen limitation. We described the general regulation of changes in the main photosynthetic and nitrogen metabolism enzymes, their quantity and localization, thylakoid protein abundance, intracellular transport of organic acids as well as specific features connected with C4 photosynthesis, and addressed the major open questions related to N metabolism and effects of light on photosynthesis in C4 plants.
Collapse
|
14
|
Chotewutmontri P, Barkan A. Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize. PLANT PHYSIOLOGY 2021; 187:59-72. [PMID: 34618144 PMCID: PMC8418429 DOI: 10.1093/plphys/kiab272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/10/2021] [Indexed: 05/20/2023]
Abstract
The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic, and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS), and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize (Zea mays) and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS- and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 182 genes exhibiting cell type-dependent differences in translational efficiency, 31 of which encode proteins with core roles in C4 photosynthesis. Our results suggest that non-AUG start codons are used preferentially in upstream open reading frames of BS cells, revealed mRNA sequence motifs that correlate with cell type-dependent translation, and identified potential translational regulators that are differentially expressed. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.
Collapse
Affiliation(s)
- Prakitchai Chotewutmontri
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 USA
- Author for communication:
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 USA
| |
Collapse
|
15
|
Hotto AM, Salesse-Smith C, Lin M, Busch FA, Simpson I, Stern DB. Rubisco production in maize mesophyll cells through ectopic expression of subunits and chaperones. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4930-4937. [PMID: 33928359 DOI: 10.1093/jxb/erab189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
C4 plants, such as maize, strictly compartmentalize Rubisco to bundle sheath chloroplasts. The molecular basis for the restriction of Rubisco from the more abundant mesophyll chloroplasts is not fully understood. Mesophyll chloroplasts transcribe the Rubisco large subunit gene and, when normally quiescent transcription of the nuclear Rubisco small subunit gene family is overcome by ectopic expression, mesophyll chloroplasts still do not accumulate measurable Rubisco. Here we show that a combination of five ubiquitin promoter-driven nuclear transgenes expressed in maize leads to mesophyll accumulation of assembled Rubisco. These encode the Rubisco large and small subunits, Rubisco assembly factors 1 and 2, and the assembly factor Bundle sheath defective 2. In these plants, Rubisco large subunit accumulates in mesophyll cells, and appears to be assembled into a holoenzyme capable of binding the substrate analog CABP (carboxyarabinitol bisphosphate). Isotope discrimination assays suggest, however, that mesophyll Rubisco is not participating in carbon assimilation in these plants, most probably due to a lack of the substrate ribulose 1,5-bisphosphate and/or Rubisco activase. Overall, this work defines a minimal set of Rubisco assembly factors in planta and may help lead to methods of regulating the C4 pathway.
Collapse
Affiliation(s)
| | | | - Myat Lin
- Cornell University, Ithaca, NY, USA
| | - Florian A Busch
- School of Biosciences, and Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, UK
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | | | | |
Collapse
|
16
|
Photosynthetic Linear Electron Flow Drives CO 2 Assimilation in Maize Leaves. Int J Mol Sci 2021; 22:ijms22094894. [PMID: 34063101 PMCID: PMC8124781 DOI: 10.3390/ijms22094894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 12/24/2022] Open
Abstract
Photosynthetic organisms commonly develop the strategy to keep the reaction center chlorophyll of photosystem I, P700, oxidized for preventing the generation of reactive oxygen species in excess light conditions. In photosynthesis of C4 plants, CO2 concentration is kept at higher levels around ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) by the cooperation of the mesophyll and bundle sheath cells, which enables them to assimilate CO2 at higher rates to survive under drought stress. However, the regulatory mechanism of photosynthetic electron transport for P700 oxidation is still poorly understood in C4 plants. Here, we assessed gas exchange, chlorophyll fluorescence, electrochromic shift, and near infrared absorbance in intact leaves of maize (a NADP-malic enzyme C4 subtype species) in comparison with mustard, a C3 plant. Instead of the alternative electron sink due to photorespiration in the C3 plant, photosynthetic linear electron flow was strongly suppressed between photosystems I and II, dependent on the difference of proton concentration across the thylakoid membrane (ΔpH) in response to the suppression of CO2 assimilation in maize. Linear relationships among CO2 assimilation rate, linear electron flow, P700 oxidation, ΔpH, and the oxidation rate of ferredoxin suggested that the increase of ΔpH for P700 oxidation was caused by the regulation of proton conductance of chloroplast ATP synthase but not by promoting cyclic electron flow. At the scale of intact leaves, the ratio of PSI to PSII was estimated almost 1:1 in both C3 and C4 plants. Overall, the photosynthetic electron transport was regulated for P700 oxidation in maize through the same strategies as in C3 plants only except for the capacity of photorespiration despite the structural and metabolic differences in photosynthesis between C3 and C4 plants.
Collapse
|
17
|
Bezrutczyk M, Zöllner NR, Kruse CPS, Hartwig T, Lautwein T, Köhrer K, Frommer WB, Kim JY. Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves. THE PLANT CELL 2021; 33:531-547. [PMID: 33955497 PMCID: PMC8136869 DOI: 10.1093/plcell/koaa055] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/01/2020] [Indexed: 05/22/2023]
Abstract
Leaves are asymmetric, with different functions for adaxial and abaxial tissue. The bundle sheath (BS) of C3 barley (Hordeum vulgare) is dorsoventrally differentiated into three types of cells: adaxial structural, lateral S-type, and abaxial L-type BS cells. Based on plasmodesmatal connections between S-type cells and mestome sheath (parenchymatous cell layer below bundle sheath), S-type cells likely transfer assimilates toward the phloem. Here, we used single-cell RNA sequencing to investigate BS differentiation in C4 maize (Zea mays L.) plants. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c mRNAs were also detected in the phloem parenchyma (PP). We show that maize has acquired a mechanism for phloem loading in which abBS cells provide the main route for apoplasmic sucrose transfer toward the phloem. This putative route predominates in veins responsible for phloem loading (rank-2 intermediate), whereas rank-1 intermediate and major veins export sucrose from the PP adjacent to the sieve element companion cell complex, as in Arabidopsis thaliana. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. These observations provide insights into the unique transport-specific properties of abBS cells and support a modification to the canonical phloem loading pathway in maize.
Collapse
Affiliation(s)
- Margaret Bezrutczyk
- Institute for Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Nora R Zöllner
- Institute for Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Colin P S Kruse
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Thomas Hartwig
- Institute for Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Tobias Lautwein
- Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory (GTL), Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory (GTL), Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Author for correspondence:
| | - Ji-Yun Kim
- Institute for Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| |
Collapse
|
18
|
Ma M, Liu Y, Bai C, Yong JWH. The Significance of Chloroplast NAD(P)H Dehydrogenase Complex and Its Dependent Cyclic Electron Transport in Photosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:661863. [PMID: 33968117 PMCID: PMC8102782 DOI: 10.3389/fpls.2021.661863] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/22/2021] [Indexed: 05/11/2023]
Abstract
Chloroplast NAD(P)H dehydrogenase (NDH) complex, a multiple-subunit complex in the thylakoid membranes mediating cyclic electron transport, is one of the most important alternative electron transport pathways. It was identified to be essential for plant growth and development during stress periods in recent years. The NDH-mediated cyclic electron transport can restore the over-reduction in stroma, maintaining the balance of the redox system in the electron transfer chain and providing the extra ATP needed for the other biochemical reactions. In this review, we discuss the research history and the subunit composition of NDH. Specifically, the formation and significance of NDH-mediated cyclic electron transport are discussed from the perspective of plant evolution and physiological functionality of NDH facilitating plants' adaptation to environmental stress. A better understanding of the NDH-mediated cyclic electron transport during photosynthesis may offer new approaches to improving crop yield.
Collapse
Affiliation(s)
- Mingzhu Ma
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Yifei Liu
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Yifei Liu,
| | - Chunming Bai
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jean Wan Hong Yong
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
19
|
Cruz DF, De Meyer S, Ampe J, Sprenger H, Herman D, Van Hautegem T, De Block J, Inzé D, Nelissen H, Maere S. Using single-plant-omics in the field to link maize genes to functions and phenotypes. Mol Syst Biol 2020; 16:e9667. [PMID: 33346944 PMCID: PMC7751767 DOI: 10.15252/msb.20209667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/29/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.
Collapse
Affiliation(s)
- Daniel Felipe Cruz
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Sam De Meyer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Joke Ampe
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Heike Sprenger
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dorota Herman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Jolien De Block
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Steven Maere
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| |
Collapse
|
20
|
Massange-Sánchez JA, Casados-Vázquez LE, Juarez-Colunga S, Sawers RJH, Tiessen A. The Phosphoglycerate Kinase (PGK) Gene Family of Maize ( Zea mays var. B73). PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9121639. [PMID: 33255472 PMCID: PMC7761438 DOI: 10.3390/plants9121639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 09/08/2020] [Indexed: 05/17/2023]
Abstract
Phosphoglycerate kinase (PGK, E.C. 2.7.2.3) interconverts ADP + 1,3-bisphospho-glycerate (1,3-bPGA) to ATP + 3-phosphoglycerate (3PGA). While most bacteria have a single pgk gene and mammals possess two copies, plant genomes contain three or more PGK genes. In this study, we identified five Pgk genes in the Zea mays var. B73 genome, predicted to encode proteins targeted to different subcellular compartments: ZmPgk1, ZmPgk2, and ZmPgk4 (chloroplast), ZmPgk3 (cytosol), and ZmPgk5 (nucleus). The expression of ZmPgk3 was highest in non-photosynthetic tissues (roots and cobs), where PGK activity was also greatest, consistent with a function in glycolysis. Green tissues (leaf blade and husk leaf) showed intermediate levels of PGK activity, and predominantly expressed ZmPgk1 and ZmPgk2, suggesting involvement in photosynthetic metabolism. ZmPgk5 was weakly expressed and ZmPgk4 was not detected in any tissue. Phylogenetic analysis showed that the photosynthetic and glycolytic isozymes of plants clustered together, but were distinct from PGKs of animals, fungi, protozoa, and bacteria, indicating that photosynthetic and glycolytic isozymes of plants diversified after the divergence of the plant lineage from other groups. These results show the distinct role of each PGK in maize and provide the basis for future studies into the regulation and function of this key enzyme.
Collapse
Affiliation(s)
- Julio A. Massange-Sánchez
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
- Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ) Subsede Zapopan, Guadalajara 44270, Mexico
- Correspondence: ; Tel.: +52-(33)-3345-5200 (ext. 1700)
| | - Luz E. Casados-Vázquez
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
- Life Science Division Food Department, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato 36500, Mexico
| | - Sheila Juarez-Colunga
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
| | - Ruairidh J. H. Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA 16801, USA;
| | - Axel Tiessen
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
- Laboratorio Nacional PlanTECC, Ciudad de México C.P. 06020, Mexico
| |
Collapse
|
21
|
Bhuiyan NH, Rowland E, Friso G, Ponnala L, Michel EJS, van Wijk KJ. Autocatalytic Processing and Substrate Specificity of Arabidopsis Chloroplast Glutamyl Peptidase. PLANT PHYSIOLOGY 2020; 184:110-129. [PMID: 32663165 PMCID: PMC7479906 DOI: 10.1104/pp.20.00752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/29/2020] [Indexed: 05/02/2023]
Abstract
Chloroplast proteostasis is governed by a network of peptidases. As a part of this network, we show that Arabidopsis (Arabidopsis thaliana) chloroplast glutamyl peptidase (CGEP) is a homo-oligomeric stromal Ser-type (S9D) peptidase with both exo- and endo-peptidase activity. Arabidopsis CGEP null mutant alleles (cgep) had no visible phenotype but showed strong genetic interactions with stromal CLP protease system mutants, resulting in reduced growth. Loss of CGEP upregulated the chloroplast protein chaperone machinery and 70S ribosomal proteins, but other parts of the proteostasis network were unaffected. Both comparative proteomics and mRNA-based coexpression analyses strongly suggested that the function of CGEP is at least partly involved in starch metabolism regulation. Recombinant CGEP degraded peptides and proteins smaller than ∼25 kD. CGEP specifically cleaved substrates on the C-terminal side of Glu irrespective of neighboring residues, as shown using peptide libraries incubated with recombinant CGEP and mass spectrometry. CGEP was shown to undergo autocatalytic C-terminal cleavage at E946, removing 15 residues, both in vitro and in vivo. A conserved motif (A[S/T]GGG[N/G]PE946) immediately upstream of E946 was identified in dicotyledons, but not monocotyledons. Structural modeling suggested that C-terminal processing increases the upper substrate size limit by improving catalytic cavity access. In vivo complementation with catalytically inactive CGEP-S781R or a CGEP variant with an unprocessed C-terminus in a cgep clpr2-1 background was used to demonstrate the physiological importance of both CGEP peptidase activity and its autocatalytic processing. CGEP homologs of photosynthetic and nonphotosynthetic bacteria lack the C-terminal prosequence, suggesting it is a recent functional adaptation in plants.
Collapse
Affiliation(s)
- Nazmul H Bhuiyan
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Elden Rowland
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Giulia Friso
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | | | - Elena J S Michel
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Klaas J van Wijk
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| |
Collapse
|
22
|
Nguyen J, Schein J, Hunt K, Tippmann-Feightner J, Rapp M, Stoffer-Bittner A, Nalam V, Funk A, Schultes N, Mourad G. The Nicotiana sylvestris nucleobase cation symporter 1 retains a dicot solute specificity profile. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.plgene.2020.100226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
23
|
Abstract
C4 photosynthesis evolved multiple times independently from ancestral C3 photosynthesis in a broad range of flowering land plant families and in both monocots and dicots. The evolution of C4 photosynthesis entails the recruitment of enzyme activities that are not involved in photosynthetic carbon fixation in C3 plants to photosynthesis. This requires a different regulation of gene expression as well as a different regulation of enzyme activities in comparison to the C3 context. Further, C4 photosynthesis relies on a distinct leaf anatomy that differs from that of C3, requiring a differential regulation of leaf development in C4. We summarize recent progress in the understanding of C4-specific features in evolution and metabolic regulation in the context of C4 photosynthesis.
Collapse
Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
| |
Collapse
|
24
|
Watkins KP, Williams-Carrier R, Chotewutmontri P, Friso G, Teubner M, Belcher S, Ruwe H, Schmitz-Linneweber C, van Wijk KJ, Barkan A. Exploring the proteome associated with the mRNA encoding the D1 reaction center protein of Photosystem II in plant chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:369-382. [PMID: 31793101 DOI: 10.1111/tpj.14629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 05/13/2023]
Abstract
Synthesis of the D1 reaction center protein of Photosystem II is dynamically regulated in response to environmental and developmental cues. In chloroplasts, much of this regulation occurs at the post-transcriptional level, but the proteins responsible are largely unknown. To discover proteins that impact psbA expression, we identified proteins that associate with maize psbA mRNA by: (i) formaldehyde cross-linking of leaf tissue followed by antisense oligonucleotide affinity capture of psbA mRNA; and (ii) co-immunoprecipitation with HCF173, a psbA translational activator that is known to bind psbA mRNA. The S1 domain protein SRRP1 and two RNA Recognition Motif (RRM) domain proteins, CP33C and CP33B, were enriched with both approaches. Orthologous proteins were also among the enriched protein set in a previous study in Arabidopsis that employed a designer RNA-binding protein as a psbA RNA affinity tag. We show here that CP33B is bound to psbA mRNA in vivo, as was shown previously for CP33C and SRRP1. Immunoblot, pulse labeling, and ribosome profiling analyses of mutants lacking CP33B and/or CP33C detected some decreases in D1 protein levels under some conditions, but no change in psbA RNA abundance or translation. However, analogous experiments showed that SRRP1 represses psbA ribosome association in the dark, represses ycf1 ribosome association, and promotes accumulation of ndhC mRNA. As SRRP1 is known to harbor RNA chaperone activity, we postulate that SRRP1 mediates these effects by modulating RNA structures. The uncharacterized proteins that emerged from our analyses provide a resource for the discovery of proteins that impact the expression of psbA and other chloroplast genes.
Collapse
Affiliation(s)
- Kenneth P Watkins
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | | | | | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Marlene Teubner
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115, Berlin, Germany
| | - Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Hannes Ruwe
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115, Berlin, Germany
| | | | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| |
Collapse
|
25
|
Flores-Ortiz C, Alvarez LM, Undurraga A, Arias D, Durán F, Wegener G, Stange C. Differential role of the two ζ-carotene desaturase paralogs in carrot (Daucus carota): ZDS1 is a functional gene essential for plant development and carotenoid synthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110327. [PMID: 31928663 DOI: 10.1016/j.plantsci.2019.110327] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/16/2019] [Accepted: 10/21/2019] [Indexed: 05/22/2023]
Abstract
Daucus carota is a biennale crop that develops an edible storage root. Orange carrots, the most consumed cultivar worldwide, accumulate high levels of β-carotene and α-carotene in the storage root during secondary growth. Genes involved in β-carotene synthesis have been identified in carrots and unlike most species, D. carota has two ζ-carotene desaturase genes, named ZDS1 and ZDS2, that share 91.3 % identity in their coding regions. ZDS1 expression falls during leaf, but not root development, while ZDS2 is induced in leaves and storage roots of a mature plant. In this work, by means of post-transcriptional gene silencing, we determined that ZDS1 is essential for initial carrot development. The suppression of the expression of this gene by RNAi triggered a reduction in the transcript levels of ZDS2 and PSY2 genes, with a concomitant decrease in the carotenoid content in both, leaves and storage roots. On the contrary, transgenic lines with reduced ZDS2 transcript abundance maintain the same levels of expression of endogenous ZDS1 and PSY2 and carotenoid profile as wild-type plants. The simultaneous silencing of ZDS1 and ZDS2 resulted in lines with a negligible leaf and root development, as well as significantly lower endogenous PSY2 expression. Further functional analyses, such as a plastidial subcellular localization of ZDS1:GFP and the increment in carotenoid content in transgenic tobacco plants overexpressing the carrot ZDS1, confirmed that ZDS1 codifies for a functional enzyme. Overall, these results lead us to propose that the main ζ-carotene desaturase activity in carrot is encoded by the ZDS1 gene and ZDS2 gene has a complementary and non essential role.
Collapse
Affiliation(s)
- Carlos Flores-Ortiz
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Ñuñoa, Chile
| | - Lilia M Alvarez
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Ñuñoa, Chile
| | - Alejandro Undurraga
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Ñuñoa, Chile
| | - Daniela Arias
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Ñuñoa, Chile
| | - Felipe Durán
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Ñuñoa, Chile
| | - Guillermo Wegener
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Ñuñoa, Chile
| | - Claudia Stange
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Ñuñoa, Chile.
| |
Collapse
|
26
|
Li Y, Tu M, Feng Y, Wang W, Messing J. Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:274. [PMID: 31832097 PMCID: PMC6868837 DOI: 10.1186/s13068-019-1612-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/09/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Sorghum bicolor (L.) is an important bioenergy source. The stems of sweet sorghum function as carbon sinks and accumulate large amounts of sugars and lignocellulosic biomass and considerable amounts of starch, therefore providing a model of carbon allocation and accumulation for other bioenergy crops. While omics data sets for sugar accumulation have been reported in different genotypes, the common features of primary metabolism in sweet genotypes remain unclear. To obtain a cohesive and comparative picture of carbohydrate metabolism between sorghum genotypes, we compared the phenotypes and transcriptome dynamics of sugar-accumulating internodes among three different sweet genotypes (Della, Rio, and SIL-05) and two non-sweet genotypes (BTx406 and R9188). RESULTS Field experiments showed that Della and Rio had similar dynamics and internode patterns of sugar concentration, albeit distinct other phenotypes. Interestingly, cellulose synthases for primary cell wall and key genes in starch synthesis and degradation were coordinately upregulated in sweet genotypes. Sweet sorghums maintained active monolignol biosynthesis compared to the non-sweet genotypes. Comparative RNA-seq results support the role of candidate Tonoplast Sugar Transporter gene (TST), but not the Sugars Will Eventually be Exported Transporter genes (SWEETs) in the different sugar accumulations between sweet and non-sweet genotypes. CONCLUSIONS Comparisons of the expression dynamics of carbon metabolic genes across the RNA-seq data sets identify several candidate genes with contrasting expression patterns between sweet and non-sweet sorghum lines, including genes required for cellulose and monolignol synthesis (CesA, PTAL, and CCR), starch metabolism (AGPase, SS, SBE, and G6P-translocator SbGPT2), and sucrose metabolism and transport (TPP and TST2). The common transcriptome features of primary metabolism identified here suggest the metabolic networks contributing to carbon sink strength in sorghum internodes, prioritize the candidate genes for manipulating carbon allocation with bioenergy purposes, and provide a comparative and cohesive picture of the complexity of carbon sink strength in sorghum stem.
Collapse
Affiliation(s)
- Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Min Tu
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Wenqing Wang
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dong Chuan Road, Shanghai, 200240 China
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| |
Collapse
|
27
|
Lande NV, Barua P, Gayen D, Kumar S, Chakraborty S, Chakraborty N. Proteomic dissection of the chloroplast: Moving beyond photosynthesis. J Proteomics 2019; 212:103542. [PMID: 31704367 DOI: 10.1016/j.jprot.2019.103542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/15/2019] [Accepted: 10/03/2019] [Indexed: 01/28/2023]
Abstract
Chloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO2 and H2O. It also serves as a major production site of multivariate pro-defense molecules, and coordinate with other organelles for cell defense. Chloroplast harbors 30-50% of total cellular proteins, out of which 80% are membrane residents and are difficult to solubilize. While proteome profiling has illuminated vast areas of biological protein space, a great deal of effort must be invested to understand the proteomic landscape of the chloroplast, which plays central role in photosynthesis, energy metabolism and stress-adaptation. Therefore, characterization of chloroplast proteome would not only provide the foundation for future investigation of expression and function of chloroplast proteins, but would open up new avenues for modulation of plant productivity through synchronizing chloroplastic key components. In this review, we summarize the progress that has been made to build new understanding of the chloroplast proteome and implications of chloroplast dynamicsing generate metabolic energy and modulating stress adaptation.
Collapse
Affiliation(s)
- Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dipak Gayen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India.
| |
Collapse
|
28
|
Zhang Y, Zhou Y, Sun Q, Deng D, Liu H, Chen S, Yin Z. Genetic determinants controlling maize rubisco activase gene expression and a comparison with rice counterparts. BMC PLANT BIOLOGY 2019; 19:351. [PMID: 31412785 PMCID: PMC6692957 DOI: 10.1186/s12870-019-1965-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/08/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Rubisco activase (RCA) regulates the activity of Rubisco and is a key enzyme of photosynthesis. RCA expression was widely reported to affect plant photosynthesis and crop yield, but the molecular basis of natural variation in RCA expression in a wide range of maize materials has not been fully elucidated. RESULTS In this study, correlation analysis in approximately 200 maize inbred lines revealed a significantly positive correlation between the expression of maize RCA gene ZmRCAβ and grain yield. A genome-wide association study revealed both cis-expression quantitative trait loci (cis-eQTLs) and trans-eQTLs underlying the expression of ZmRCAβ, with the latter playing a more important role. Further allele mining and genetic transformation analysis showed that a 2-bp insertion and a 14-bp insertion in the promoter of ZmRCAβ conferred increased gene expression. Because rice is reported to have higher RCA gene expression than does maize, we subsequently compared the genetic factors underlying RCA gene expression between maize and rice. The promoter activity of the rice RCA gene was shown to be stronger than that of the maize RCA gene, suggesting that replacing the maize RCA gene promoter with that of the rice RCA gene would improve the expression of RCA in maize. CONCLUSION Our results revealed two DNA polymorphisms regulating maize RCA gene ZmRCAβ expression, and the RCA gene promoter activity of rice was stronger than that of maize. This work increased understanding of the genetic mechanism that underlies RCA gene expression and identify new targets for both genetic engineering and selection for maize yield improvement.
Collapse
Affiliation(s)
- Yu Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009 China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009 China
| | - Qian Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009 China
| | - Dexiang Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009 China
| | - Huanhuan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009 China
| | - Saihua Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009 China
| | - Zhitong Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009 China
| |
Collapse
|
29
|
Zhang Y, Lu C. The Enigmatic Roles of PPR-SMR Proteins in Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900361. [PMID: 31380188 PMCID: PMC6662315 DOI: 10.1002/advs.201900361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/03/2019] [Indexed: 05/21/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C-terminal small MutS-related (SMR) domain. Although there are relatively few PPR-SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid-to-nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR-SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR-SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.
Collapse
Affiliation(s)
- Yi Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
| | - Congming Lu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
| |
Collapse
|
30
|
Bellasio C, Farquhar GD. A leaf-level biochemical model simulating the introduction of C 2 and C 4 photosynthesis in C 3 rice: gains, losses and metabolite fluxes. THE NEW PHYTOLOGIST 2019; 223:150-166. [PMID: 30859576 DOI: 10.1111/nph.15787] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/03/2019] [Indexed: 05/21/2023]
Abstract
This work aims at developing an adequate theoretical basis for comparing assimilation of the ancestral C3 pathway with CO2 concentrating mechanisms (CCM) that have evolved to reduce photorespiratory yield losses. We present a novel model for C3 , C2 , C2 + C4 and C4 photosynthesis simulating assimilatory metabolism, energetics and metabolite traffic at the leaf level. It integrates a mechanistic description of light reactions to simulate ATP and NADPH production, and a variable engagement of cyclic electron flow. The analytical solutions are compact and thus suitable for larger scale simulations. Inputs were derived with a comprehensive gas-exchange experiment. We show trade-offs in the operation of C4 that are in line with ecophysiological data. C4 has the potential to increase assimilation over C3 at high temperatures and light intensities, but this benefit is reversed under low temperatures and light. We apply the model to simulate the introduction of progressively complex levels of CCM into C3 rice, which feeds > 3.5 billion people. Increasing assimilation will require considerable modifications such as expressing the NAD(P)H Dehydrogenase-like complex and upregulating cyclic electron flow, enlarging the bundle sheath, and expressing suitable transporters to allow adequate metabolite traffic. The simpler C2 rice may be a desirable alternative.
Collapse
Affiliation(s)
- Chandra Bellasio
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
- University of the Balearic Islands, Palma, Illes Balears, 07122, Spain
- Trees and Timber Institute, National Research Council of Italy, Sesto Fiorentino, Florence, 50019, Italy
| | - Graham D Farquhar
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
| |
Collapse
|
31
|
Li H, Thrash A, Tang JD, He L, Yan J, Warburton ML. Leveraging GWAS data to identify metabolic pathways and networks involved in maize lipid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:853-863. [PMID: 30742331 PMCID: PMC6850169 DOI: 10.1111/tpj.14282] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 05/21/2023]
Abstract
Maize (Zea mays mays) oil is a rich source of polyunsaturated fatty acids (FAs) and energy, making it a valuable resource for human food, animal feed, and bio-energy. Although this trait has been studied via conventional genome-wide association study (GWAS), the single nucleotide polymorphism (SNP)-trait associations generated by GWAS may miss the underlying associations when traits are based on many genes, each with small effects that can be overshadowed by genetic background and environmental variation. Detecting these SNPs statistically is also limited by the levels set for false discovery rate. A complementary pathways analysis that emphasizes the cumulative aspects of SNP-trait associations, rather than just the significance of single SNPs, was performed to understand the balance of lipid metabolism, conversion, and catabolism in this study. This pathway analysis indicated that acyl-lipid pathways, including biosynthesis of wax esters, sphingolipids, phospholipids and flavonoids, along with FA and triacylglycerol (TAG) biosynthesis, were important for increasing oil and FA content. The allelic variation found among the genes involved in many degradation pathways, and many biosynthesis pathways leading from FAs and carbon partitioning pathways, was critical for determining final FA content, changing FA ratios and, ultimately, to final oil content. The pathways and pathway networks identified in this study, and especially the acyl-lipid associated pathways identified beyond what had been found with GWAS alone, provide a real opportunity to precisely and efficiently manipulate high-oil maize genetic improvement.
Collapse
Affiliation(s)
- Hui Li
- School of Biological Science and TechnologyUniversity of JinanJinan250022China
| | - Adam Thrash
- Institute for Genomics, Biocomputing & BiotechnologyMississippi State UniversityMS39762USA
| | - Juliet D. Tang
- USDA FS Forest Products LaboratoryDurability and Wood ProtectionStarkvilleMS39759USA
| | - Linlin He
- School of Biological Science and TechnologyUniversity of JinanJinan250022China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Marilyn L. Warburton
- USDA ARS Corn Host Plant Resistance Research Unit (CHPRRU)Mississippi StateMS39762USA
| |
Collapse
|
32
|
Nikkanen L, Rintamäki E. Chloroplast thioredoxin systems dynamically regulate photosynthesis in plants. Biochem J 2019; 476:1159-1172. [PMID: 30988137 PMCID: PMC6463390 DOI: 10.1042/bcj20180707] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/18/2022]
Abstract
Photosynthesis is a highly regulated process in photoautotrophic cells. The main goal of the regulation is to keep the basic photosynthetic reactions, i.e. capturing light energy, conversion into chemical energy and production of carbohydrates, in balance. The rationale behind the evolution of strong regulation mechanisms is to keep photosynthesis functional under all conditions encountered by sessile plants during their lifetimes. The regulatory mechanisms may, however, also impair photosynthetic efficiency by overriding the photosynthetic reactions in controlled environments like crop fields or bioreactors, where light energy could be used for production of sugars instead of dissipation as heat and down-regulation of carbon fixation. The plant chloroplast has a high number of regulatory proteins called thioredoxins (TRX), which control the function of chloroplasts from biogenesis and assembly of chloroplast machinery to light and carbon fixation reactions as well as photoprotective mechanisms. Here, we review the current knowledge of regulation of photosynthesis by chloroplast TRXs and assess the prospect of improving plant photosynthetic efficiency by modification of chloroplast thioredoxin systems.
Collapse
Affiliation(s)
- Lauri Nikkanen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Eevi Rintamäki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| |
Collapse
|
33
|
Comprehensive Analysis of the Cadmium Tolerance of Abscisic Acid-, Stress- and Ripening-Induced Proteins (ASRs) in Maize. Int J Mol Sci 2019; 20:ijms20010133. [PMID: 30609672 PMCID: PMC6337223 DOI: 10.3390/ijms20010133] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 12/21/2018] [Accepted: 12/25/2018] [Indexed: 01/07/2023] Open
Abstract
In plants, abscisic acid-, stress-, and ripening-induced (ASR) proteins have been shown to impart tolerance to multiple abiotic stresses such as drought and salinity. However, their roles in metal stress tolerance are poorly understood. To screen plant Cd-tolerance genes, the yeast-based gene hunting method which aimed to screen Cd-tolerance colonies from maize leaf cDNA library hosted in yeast was carried out. Here, maize ZmASR1 was identified to be putative Cd-tolerant through this survival screening strategy. In silico analysis of the functional domain organization, phylogenetic classification and tissue-specific expression patterns revealed that maize ASR1 to ASR5 are typical ASRs with considerable expression in leaves. Further, four of them were cloned for testifying Cd tolerance using yeast complementation assay. The results indicated that they all confer Cd tolerance in Cd-sensitive yeast. Then they were transiently expressed in tobacco leaves for subcellular localization analysis and for Cd-challenged lesion assay, continuously. The results demonstrated that all 4 maize ASRs tested are localized to the cell nucleus and cytoplasm in tobacco leaves. Moreover, they were confirmed to be Cd-tolerance genes in planta through lesion analysis in Cd-infiltrated leaves transiently expressing them. Taken together, our results demonstrate that maize ASRs play important roles in Cd tolerance, and they could be used as promising candidate genes for further functional studies toward improving the Cd tolerance in plants.
Collapse
|
34
|
Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
35
|
Salesse-Smith CE, Sharwood RE, Busch FA, Kromdijk J, Bardal V, Stern DB. Overexpression of Rubisco subunits with RAF1 increases Rubisco content in maize. NATURE PLANTS 2018; 4:802-810. [PMID: 30287949 DOI: 10.1038/s41477-018-0252-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/15/2018] [Indexed: 05/21/2023]
Abstract
Rubisco catalyses a rate-limiting step in photosynthesis and has long been a target for improvement due to its slow turnover rate. An alternative to modifying catalytic properties of Rubisco is to increase its abundance within C4 plant chloroplasts, which might increase activity and confer a higher carbon assimilation rate. Here, we overexpress the Rubisco large (LS) and small (SS) subunits with the Rubisco assembly chaperone RUBISCO ASSEMBLY FACTOR 1 (RAF1). While overexpression of LS and/or SS had no discernable impact on Rubisco content, addition of RAF1 overexpression resulted in a >30% increase in Rubisco content. Gas exchange showed a 15% increase in CO2 assimilation (ASAT) in UBI-LSSS-RAF1 transgenic plants, which correlated with increased fresh weight and in vitro Vcmax calculations. The divergence of Rubisco content and assimilation could be accounted for by the Rubisco activation state, which decreased up to 23%, suggesting that Rubisco activase may be limiting Vcmax, and impinging on the realization of photosynthetic potential from increased Rubisco content.
Collapse
Affiliation(s)
| | - Robert E Sharwood
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Florian A Busch
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Johannes Kromdijk
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | | | | |
Collapse
|
36
|
Gao Z, Shen W, Chen G. Uncovering C4-like photosynthesis in C3 vascular cells. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3531-3540. [PMID: 29684188 DOI: 10.1093/jxb/ery155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
In C4 plants, the vascularization of the leaf is extended to include a ring of photosynthetic bundle sheath cells, which have essential and specific functions. In contrast to the substantial knowledge of photosynthesis in C4 plants, relatively little is known about photosynthesis in C3 plant veins, which differs substantially from that in C3 mesophyll cells. In this review we highlight the specific photosynthetic machinery present in C3 vascular cells, which likely evolved prior to the divergence between C3 and C4 plants. The associated primary processes of carbon recapture, nitrogen transport, and antioxidant metabolism are discussed. This review of the basal C4 photosynthesis in C3 plants is significant in the context of promoting the potential for biotechnological development of C4-transgenic rice crops.
Collapse
Affiliation(s)
- Zhiping Gao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Weijun Shen
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guoxiang Chen
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| |
Collapse
|
37
|
Yin X, Struik PC. The energy budget in C 4 photosynthesis: insights from a cell-type-specific electron transport model. THE NEW PHYTOLOGIST 2018; 218:986-998. [PMID: 29520959 PMCID: PMC5947737 DOI: 10.1111/nph.15051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/16/2018] [Indexed: 05/18/2023]
Abstract
Extra ATP required in C4 photosynthesis for the CO2 -concentrating mechanism probably comes from cyclic electron transport (CET). As metabolic ATP : NADPH requirements in mesophyll (M) and bundle-sheath (BS) cells differ among C4 subtypes, the subtypes may differ in the extent to which CET operates in these cells. We present an analytical model for cell-type-specific CET and linear electron transport. Modelled NADPH and ATP production were compared with requirements. For malic-enzyme (ME) subtypes, c. 50% of electron flux is CET, occurring predominantly in BS cells for standard NADP-ME species, but in a ratio of c. 6 : 4 in BS : M cells for NAD-ME species. Some C4 acids follow a secondary decarboxylation route, which is obligatory, in the form of 'aspartate-malate', for the NADP-ME subtype, but facultative, in the form of phosphoenolpyruvate-carboxykinase (PEP-CK), for the NAD-ME subtype. The percentage for secondary decarboxylation is c. 25% and that for 3-phosphoglycerate reduction in BS cells is c. 40%; but these values vary with species. The 'pure' PEP-CK type is unrealistic because its is impossible to fulfil ATP : NADPH requirements in BS cells. The standard PEP-CK subtype requires negligible CET, and thus has the highest intrinsic quantum yields and deserves further studies in the context of improving canopy productivity.
Collapse
Affiliation(s)
- Xinyou Yin
- Department of Plant SciencesCentre for Crop Systems AnalysisWageningen University & ResearchPO Box 4306700 AKWageningenthe Netherlands
| | - Paul C. Struik
- Department of Plant SciencesCentre for Crop Systems AnalysisWageningen University & ResearchPO Box 4306700 AKWageningenthe Netherlands
| |
Collapse
|
38
|
Vitlin Gruber A, Feiz L. Rubisco Assembly in the Chloroplast. Front Mol Biosci 2018; 5:24. [PMID: 29594130 PMCID: PMC5859369 DOI: 10.3389/fmolb.2018.00024] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/27/2018] [Indexed: 01/13/2023] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step in the Calvin-Benson cycle, which transforms atmospheric carbon into a biologically useful carbon source. The slow catalytic rate of Rubisco and low substrate specificity necessitate the production of high levels of this enzyme. In order to engineer a more efficient plant Rubisco, we need to better understand its folding and assembly process. Form I Rubisco, found in green algae and vascular plants, is a hexadecamer composed of 8 large subunits (RbcL), encoded by the chloroplast genome and 8 small, nuclear-encoded subunits (RbcS). Unlike its cyanobacterial homolog, which can be reconstituted in vitro or in E. coli, assisted by bacterial chaperonins (GroEL-GroES) and the RbcX chaperone, biogenesis of functional chloroplast Rubisco requires Cpn60-Cpn20, the chloroplast homologs of GroEL-GroES, and additional auxiliary factors, including Rubisco accumulation factor 1 (Raf1), Rubisco accumulation factor 2 (Raf2) and Bundle sheath defective 2 (Bsd2). The discovery and characterization of these factors paved the way for Arabidopsis Rubisco assembly in E. coli. In the present review, we discuss the uniqueness of hetero-oligomeric chaperonin complex for RbcL folding, as well as the sequential or concurrent actions of the post-chaperonin chaperones in holoenzyme assembly. The exact stages at which each assembly factor functions are yet to be determined. Expression of Arabidopsis Rubisco in E. coli provided some insight regarding the potential roles for Raf1 and RbcX in facilitating RbcL oligomerization, for Bsd2 in stabilizing the oligomeric core prior to holoenzyme assembly, and for Raf2 in interacting with both RbcL and RbcS. In the long term, functional characterization of each known factor along with the potential discovery and characterization of additional factors will set the stage for designing more efficient plants, with a greater biomass, for use in biofuels and sustenance.
Collapse
Affiliation(s)
- Anna Vitlin Gruber
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Leila Feiz
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| |
Collapse
|
39
|
Non-photosynthetic plastids as hosts for metabolic engineering. Essays Biochem 2018; 62:41-50. [DOI: 10.1042/ebc20170047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/13/2018] [Accepted: 01/22/2018] [Indexed: 01/11/2023]
Abstract
Using plants as hosts for production of complex, high-value compounds and therapeutic proteins has gained increasing momentum over the past decade. Recent advances in metabolic engineering techniques using synthetic biology have set the stage for production yields to become economically attractive, but more refined design strategies are required to increase product yields without compromising development and growth of the host system. The ability of plant cells to differentiate into various tissues in combination with a high level of cellular compartmentalization represents so far the most unexploited plant-specific resource. Plant cells contain organelles called plastids that retain their own genome, harbour unique biosynthetic pathways and differentiate into distinct plastid types upon environmental and developmental cues. Chloroplasts, the plastid type hosting the photosynthetic processes in green tissues, have proven to be suitable for high yield protein and bio-compound production. Unfortunately, chloroplast manipulation often affects photosynthetic efficiency and therefore plant fitness. In this respect, plastids of non-photosynthetic tissues, which have focused metabolisms for synthesis and storage of particular classes of compounds, might prove more suitable for engineering the production and storage of non-native metabolites without affecting plant fitness. This review provides the current state of knowledge on the molecular mechanisms involved in plastid differentiation and focuses on non-photosynthetic plastids as alternative biotechnological platforms for metabolic engineering.
Collapse
|
40
|
Zhou Y, Zhang B, Stuart-Williams H, Grice K, Hocart CH, Gessler A, Kayler ZE, Farquhar GD. On the contributions of photorespiration and compartmentation to the contrasting intramolecular 2H profiles of C 3 and C 4 plant sugars. PHYTOCHEMISTRY 2018; 145:197-206. [PMID: 29175728 DOI: 10.1016/j.phytochem.2017.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Compartmentation of C4 photosynthetic biochemistry into bundle sheath (BS) and mesophyll (M) cells, and photorespiration in C3 plants is predicted to have hydrogen isotopic consequences for metabolites at both molecular and site-specific levels. Molecular-level evidence was recently reported (Zhou et al., 2016), but evidence at the site-specific level is still lacking. We propose that such evidence exists in the contrasting 2H distribution profiles of glucose samples from naturally grown C3, C4 and CAM plants: photorespiration contributes to the relative 2H enrichment in H5 and relative 2H depletion in H1 & H6 (the average of the two pro-chiral Hs and in particular H6,pro-R) in C3 glucose, while 2H-enriched C3 mesophyll cellular (chloroplastic) water most likely contributes to the enrichment at H4; export of (transferable hydrogen atoms of) NADPH from C4 mesophyll cells to bundle sheath cells (via the malate shuttle) and incorporation of 2H-relatively unenriched BS cellular water contribute to the relative depletion of H4 & H5 respectively; shuttling of triose-phosphates (PGA: phosphoglycerate dand DHAP: dihydroacetone phosphate) between C4 bundle sheath and mesophyll cells contributes to the relative enrichment in H1 & H6 (in particular H6,pro-R) in C4 glucose.
Collapse
Affiliation(s)
- Youping Zhou
- School of Chemistry & Chemical Engineering, Shaanxi University of Science & Technology, Xi'an, China; Institute for Landscape Biogeochemistry, ZALF, Germany; Leibniz Institute for Freshwater Ecology & Inland Fisheries, Germany.
| | - Benli Zhang
- School of Chemistry & Chemical Engineering, Shaanxi University of Science & Technology, Xi'an, China
| | | | - Kliti Grice
- WA-Organic and Isotope Geochemistry Centre, Department of Chemistry, Curtin University, Australia
| | - Charles H Hocart
- School of Chemistry & Chemical Engineering, Shaanxi University of Science & Technology, Xi'an, China; Research School of Biology, Australian National University, Australia
| | - Arthur Gessler
- Institute for Landscape Biogeochemistry, ZALF, Germany; Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Zachary E Kayler
- Institute for Landscape Biogeochemistry, ZALF, Germany; USDA Forest Service, Northern Research Station, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Graham D Farquhar
- Research School of Biology, Australian National University, Australia
| |
Collapse
|
41
|
Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm. Proc Natl Acad Sci U S A 2017; 115:E24-E33. [PMID: 29255019 DOI: 10.1073/pnas.1715668115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maize opaque2 (o2) mutations are beneficial for endosperm nutritional quality but cause negative pleiotropic effects for reasons that are not fully understood. Direct targets of the bZIP transcriptional regulator encoded by o2 include pdk1 and pdk2 that specify pyruvate phosphate dikinase (PPDK). This enzyme reversibly converts AMP, pyrophosphate, and phosphoenolpyruvate to ATP, orthophosphate, and pyruvate and provides diverse functions in plants. This study addressed PPDK function in maize starchy endosperm where it is highly abundant during grain fill. pdk1 and pdk2 were inactivated individually by transposon insertions, and both genes were simultaneously targeted by endosperm-specific RNAi. pdk2 accounts for the large majority of endosperm PPDK, whereas pdk1 specifies the abundant mesophyll form. The pdk1- mutation is seedling-lethal, indicating that C4 photosynthesis is essential in maize. RNAi expression in transgenic endosperm eliminated detectable PPDK protein and enzyme activity. Transgenic kernels weighed the same on average as nontransgenic siblings, with normal endosperm starch and total N contents, indicating that PPDK is not required for net storage compound synthesis. An opaque phenotype resulted from complete PPDK knockout, including loss of vitreous endosperm character similar to the phenotype conditioned by o2-. Concentrations of multiple glycolytic intermediates were elevated in transgenic endosperm, energy charge was altered, and starch granules were more numerous but smaller on average than normal. The data indicate that PPDK modulates endosperm metabolism, potentially through reversible adjustments to energy charge, and reveal that o2- mutations can affect the opaque phenotype through regulation of PPDK in addition to their previously demonstrated effects on storage protein gene expression.
Collapse
|
42
|
Salesse C, Sharwood R, Sakamoto W, Stern D. The Rubisco Chaperone BSD2 May Regulate Chloroplast Coverage in Maize Bundle Sheath Cells. PLANT PHYSIOLOGY 2017; 175:1624-1633. [PMID: 29089394 PMCID: PMC5717744 DOI: 10.1104/pp.17.01346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/27/2017] [Indexed: 05/04/2023]
Abstract
In maize (Zea mays), Bundle Sheath Defective2 (BSD2) plays an essential role in Rubisco biogenesis and is required for correct bundle sheath (BS) cell differentiation. Yet, BSD2 RNA and protein levels are similar in mesophyll (M) and BS chloroplasts, although Rubisco accumulates only in BS chloroplasts. This raises the possibility of additional BSD2 roles in cell development. To test this hypothesis, transgenic lines were created that overexpress and underexpress BSD2 in both BS and M cells, driven by the cell type-specific Rubisco Small Subunit (RBCS) or Phosphoenolpyruvate Carboxylase (PEPC) promoters or the ubiquitin promoter. Genetic crosses showed that each of the transgenes could complement Rubisco deficiency and seedling lethality conferred by the bsd2 mutation. This was unexpected, as RBCS-BSD2 lines lacked BSD2 in M chloroplasts and PEPC-BSD2 lines expressed half the wild-type BSD2 level in BS chloroplasts. We conclude that BSD2 does not play a vital role in M cells and that BS BSD2 is in excess of requirements for Rubisco accumulation. BSD2 levels did affect chloroplast coverage in BS cells. In PEPC-BSD2 lines, chloroplast coverage decreased 30% to 50%, whereas lines with increased BSD2 content exhibited a 25% increase. This suggests that BSD2 has an ancillary role in BS cells related to chloroplast size. Gas exchange showed decreased photosynthetic rates in PEPC-BSD2 lines despite restored Rubisco function, correlating with reduced chloroplast coverage and pointing to CO2 diffusion changes. Conversely, increased chloroplast coverage did not result in increased Rubisco abundance or photosynthetic rates. This suggests another limitation beyond chloroplast volume, most likely Rubisco biogenesis and/or turnover rates.
Collapse
Affiliation(s)
- Coralie Salesse
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
| | - Robert Sharwood
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - David Stern
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
| |
Collapse
|
43
|
Salesse C, Sharwood R, Sakamoto W, Stern D. The Rubisco Chaperone BSD2 May Regulate Chloroplast Coverage in Maize Bundle Sheath Cells. PLANT PHYSIOLOGY 2017. [PMID: 29089394 DOI: 10.1104/pp.17.0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In maize (Zea mays), Bundle Sheath Defective2 (BSD2) plays an essential role in Rubisco biogenesis and is required for correct bundle sheath (BS) cell differentiation. Yet, BSD2 RNA and protein levels are similar in mesophyll (M) and BS chloroplasts, although Rubisco accumulates only in BS chloroplasts. This raises the possibility of additional BSD2 roles in cell development. To test this hypothesis, transgenic lines were created that overexpress and underexpress BSD2 in both BS and M cells, driven by the cell type-specific Rubisco Small Subunit (RBCS) or Phosphoenolpyruvate Carboxylase (PEPC) promoters or the ubiquitin promoter. Genetic crosses showed that each of the transgenes could complement Rubisco deficiency and seedling lethality conferred by the bsd2 mutation. This was unexpected, as RBCS-BSD2 lines lacked BSD2 in M chloroplasts and PEPC-BSD2 lines expressed half the wild-type BSD2 level in BS chloroplasts. We conclude that BSD2 does not play a vital role in M cells and that BS BSD2 is in excess of requirements for Rubisco accumulation. BSD2 levels did affect chloroplast coverage in BS cells. In PEPC-BSD2 lines, chloroplast coverage decreased 30% to 50%, whereas lines with increased BSD2 content exhibited a 25% increase. This suggests that BSD2 has an ancillary role in BS cells related to chloroplast size. Gas exchange showed decreased photosynthetic rates in PEPC-BSD2 lines despite restored Rubisco function, correlating with reduced chloroplast coverage and pointing to CO2 diffusion changes. Conversely, increased chloroplast coverage did not result in increased Rubisco abundance or photosynthetic rates. This suggests another limitation beyond chloroplast volume, most likely Rubisco biogenesis and/or turnover rates.
Collapse
Affiliation(s)
- Coralie Salesse
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
| | - Robert Sharwood
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - David Stern
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
| |
Collapse
|
44
|
Kretschmer M, Croll D, Kronstad JW. Chloroplast-associated metabolic functions influence the susceptibility of maize to Ustilago maydis. MOLECULAR PLANT PATHOLOGY 2017; 18:1210-1221. [PMID: 27564650 PMCID: PMC6638283 DOI: 10.1111/mpp.12485] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/15/2016] [Accepted: 08/25/2016] [Indexed: 05/10/2023]
Abstract
Biotrophic fungal pathogens must evade or suppress plant defence responses to establish a compatible interaction in living host tissue. In addition, metabolic changes during disease reflect both the impact of nutrient acquisition by the fungus to support proliferation and the integration of metabolism with the plant defence response. In this study, we used transcriptome analyses to predict that the chloroplast and associated functions are important for symptom formation by the biotrophic fungus Ustilago maydis on maize. We tested our prediction by examining the impact on disease of a genetic defect (whirly1) in chloroplast function. In addition, we examined whether disease was influenced by inhibition of glutamine synthetase by glufosinate (impacting amino acid biosynthesis) or inhibition of 3-phosphoshikimate 1-carboxyvinyltransferase by glyphosate (influencing secondary metabolism). All of these perturbations increased the severity of disease, thus suggesting a contribution to resistance. Overall, these findings provide a framework for understanding the components of host metabolism that benefit the plant versus the pathogen during a biotrophic interaction. They also reinforce the emerging importance of the chloroplast as a mediator of plant defence.
Collapse
Affiliation(s)
- Matthias Kretschmer
- Michael Smith Laboratories, University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Daniel Croll
- Michael Smith Laboratories, University of British ColumbiaVancouverBCV6T 1Z4Canada
- Present address:
Institute of Integrative BiologyETH Zürich8092 ZürichSwitzerland
| | - James W. Kronstad
- Michael Smith Laboratories, University of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| |
Collapse
|
45
|
Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN. Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome. FRONTIERS IN PLANT SCIENCE 2017; 8:1239. [PMID: 28775726 PMCID: PMC5517461 DOI: 10.3389/fpls.2017.01239] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/30/2017] [Indexed: 05/18/2023]
Abstract
Leaves of Arabidopsis thaliana transferred from low to high light increase their capacity for photosynthesis, a process of dynamic acclimation. A mutant, gpt2, lacking a chloroplast glucose-6-phosphate/phosphate translocator, is deficient in its ability to acclimate to increased light. Here, we have used a label-free proteomics approach, to perform relative quantitation of 1993 proteins from Arabidopsis wild type and gpt2 leaves exposed to increased light. Data are available via ProteomeXchange with identifier PXD006598. Acclimation to light is shown to involve increases in electron transport and carbon metabolism but no change in the abundance of photosynthetic reaction centers. The gpt2 mutant shows a similar increase in total protein content to wild type but differences in the extent of change of certain proteins, including in the relative abundance of the cytochrome b6f complex and plastocyanin, the thylakoid ATPase and selected Benson-Calvin cycle enzymes. Changes in leaf metabolite content as plants acclimate can be explained by changes in the abundance of enzymes involved in metabolism, which were reduced in gpt2 in some cases. Plants of gpt2 invest more in stress-related proteins, suggesting that their reduced ability to acclimate photosynthetic capacity results in increased stress.
Collapse
Affiliation(s)
- Matthew A. E. Miller
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
| | - Ronan O’Cualain
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Julian Selley
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - David Knight
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Mohd F. Karim
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
| | - Simon J. Hubbard
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Giles N. Johnson
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
| |
Collapse
|
46
|
Mwaba I, Rey MEC. Nitric oxide associated protein 1 is associated with chloroplast perturbation and disease symptoms in Nicotiana benthamiana infected with South African cassava mosaic virus. Virus Res 2017; 238:75-83. [PMID: 28577889 DOI: 10.1016/j.virusres.2017.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/22/2017] [Accepted: 05/26/2017] [Indexed: 12/31/2022]
Abstract
Nitric oxide associated 1 (NOA1) in plants is a cyclic GTPase involved in protein translation in the chloroplast and has been indirectly linked to nitric oxide (NO) accumulation and response to biotic stress. The association between NOA1 and NO accumulation in Arabidopsis noa1 mutants has been linked to the inability of noa1 mutants to accumulate carbon reserves such as fumarate, leading to chloroplast dysfunction and a pale green leaf phenotype. To understand the role played by NOA1 in response to South African cassava mosaic virus infection in Nicotiana benthamiana, the expression of NbNOA1 and the accumulation of NO in leaf samples was compared between south african cassava mosaic (SACMV)-infected and mock-infected plants at 14 and 28 dpi. Real-time qPCR was used to measure SACMV viral load which increased significantly by 20% from 14 to 28 dpi as chlorosis and symptom severity progressed. At 14 and 28 dpi, NbNOA1 expression was significantly lower than mock inoculated plants (2-fold lower at 14 dpi, p-value=0.01 and 5-fold lower at 28, p-value=0.00). At 14 dpi, NO accumulation remained unchanged in infected leaf tissue compared to mock inoculated, while at 28 dpi, NO accumulation was 40% lower (p-value=0.01). At 28 dpi, the decrease in NbNOA1 expression and NO accumulation was accompanied by chloroplast dysfunction, evident from the significant reduction in chlorophylls a and b and carotenoids in SACMV-infected leaves. Furthermore, the expression of chloroplast translation factors (chloroplast RNA binding, chloroplast elongation factor G, translation elongation factor Tu, translation initiation factor 3-2, plastid-specific ribosomal protein 6 and plastid ribosome recycling factor) were found to be repressed in infected N. benthamiana. GC-MS analysis showed a decrease in fumarate and an increase in glucose in SACMV-infected N. benthamiana in comparison to mock samples suggesting a decrease in carbon stores. Collectively, these results provide evidence that in response to SACMV infection, a decrease in photopigments and carbon stores, accompanied by an increase in glucose and decrease in fumarate, leads to a decline in NbNOA1expression and NO levels. This is manifested by suppressed translation factors and disruption of chloroplast function, thereby contributing to chlorotic disease symptoms.
Collapse
Affiliation(s)
- Imanu Mwaba
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts Avenue, Braamfontein, Johannesburg 2000, South Africa
| | - Marie Emma Christine Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts Avenue, Braamfontein, Johannesburg 2000, South Africa.
| |
Collapse
|
47
|
Kolesinski P, Rydzy M, Szczepaniak A. Is RAF1 protein from Synechocystis sp. PCC 6803 really needed in the cyanobacterial Rubisco assembly process? PHOTOSYNTHESIS RESEARCH 2017; 132:135-148. [PMID: 28108864 PMCID: PMC5387032 DOI: 10.1007/s11120-017-0336-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/02/2017] [Indexed: 05/29/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for carbon dioxide conversion during photosynthesis and, therefore, is the most important protein in biomass generation. Modifications of this biocatalyst toward improvements in its properties are hindered by the complicated and not yet fully understood assembly process required for the formation of active holoenzymes. An entire set of auxiliary factors, including chaperonin GroEL/GroES and assembly chaperones RbcX or Rubisco accumulation factor 1 (RAF1), is involved in the folding and subsequent assembly of Rubisco subunits. Recently, it has been shown that cyanobacterial RAF1 acts during the formation of the large Rubisco subunit (RbcL) dimer. However, both its physiological function and its necessity in the prokaryotic Rubisco formation process remain elusive. Here, we demonstrate that the Synechocystis sp. PCC 6803 strain with raf1 gene disruption shows the same growth rate as wild-type cells under standard conditions. Moreover, the Rubisco biosynthesis process seems to be unperturbed in mutant cells despite the absence of RbcL-RAF1 complexes. However, in the tested environmental conditions, sulfur starvation triggers the degradation of RbcL and subsequent proteolysis of other polypeptides in wild-type but not Δraf1 strains. Pull-down experiments also indicate that, apart from Rubisco, RAF1 co-purifies with phycocyanins. We postulate that RAF1 is not an obligatory factor in cyanobacterial Rubisco assembly, but rather participates in environmentally regulated Rubisco homeostasis.
Collapse
Affiliation(s)
- Piotr Kolesinski
- Laboratory of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383, Wroclaw, Poland.
| | - Malgorzata Rydzy
- Laboratory of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Andrzej Szczepaniak
- Laboratory of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383, Wroclaw, Poland
| |
Collapse
|
48
|
Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
Collapse
Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| |
Collapse
|
49
|
Abstract
Cereals contribute a major part of human nutrition and are considered as an integral source of energy for human diets. With genomic databases already available in cereals such as rice, wheat, barley, and maize, the focus has now moved to proteome analysis. Proteomics studies involve the development of appropriate databases based on developing suitable separation and purification protocols, identification of protein functions, and can confirm their functional networks based on already available data from other sources. Tremendous progress has been made in the past decade in generating huge data-sets for covering interactions among proteins, protein composition of various organs and organelles, quantitative and qualitative analysis of proteins, and to characterize their modulation during plant development, biotic, and abiotic stresses. Proteomics platforms have been used to identify and improve our understanding of various metabolic pathways. This article gives a brief review of efforts made by different research groups on comparative descriptive and functional analysis of proteomics applications achieved in the cereal science so far.
Collapse
Affiliation(s)
- Monika Bansal
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab.,b School of Agriculture , Lovely Professional University , Phagwara 144411 , Punjab
| | - Madhu Sharma
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab
| | - Priyanka Kanwar
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab
| | - Aakash Goyal
- c Biodiversity and Integrated Gene Management Program , International Center for Agriculture Research in the Dry Areas (ICARDA) , P.O.Box 6299, Rabat-Institutes, Rabat , Morocco
| |
Collapse
|
50
|
Salon C, Avice JC, Colombié S, Dieuaide-Noubhani M, Gallardo K, Jeudy C, Ourry A, Prudent M, Voisin AS, Rolin D. Fluxomics links cellular functional analyses to whole-plant phenotyping. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2083-2098. [PMID: 28444347 DOI: 10.1093/jxb/erx126] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping. This review presents and discusses sets of methodologies that have been developed to measure the fluxome. First, the principles of metabolic flux analysis (MFA), its 'short time interval' version Inst-MFA, and of constraints-based methods, such as flux balance analysis and kinetic analysis, are briefly described. The use of these powerful methods for flux characterization at the cellular scale up to the organ (fruits, seeds) and whole-plant level is illustrated. The added value given by fluxomics methods for unravelling how the abiotic environment affects flux, the process, and key metabolic steps are also described. Challenges associated with the development of fluxomics and its integration with 'omics' for thorough plant and organ functional phenotyping are discussed. Taken together, these will ultimately provide crucial clues for identifying appropriate target plant phenotypes for breeding.
Collapse
Affiliation(s)
- Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Jean-Christophe Avice
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Sophie Colombié
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Martine Dieuaide-Noubhani
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Christian Jeudy
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Alain Ourry
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Anne-Sophie Voisin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Dominique Rolin
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| |
Collapse
|