1
|
Curien G. A Practical Guide to the Representation of Protein Regulation in the Web Application ChloroKB. Methods Mol Biol 2024; 2776:305-320. [PMID: 38502513 DOI: 10.1007/978-1-0716-3726-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
ChloroKB ( http://chlorokb.fr ) is a knowledge base providing synoptic representations of the metabolism of the model plant Arabidopsis thaliana and its regulation. Initially focused on plastid metabolism, ChloroKB now accounts for the metabolism throughout the cell. ChloroKB is based on the CellDesigner formalism. CellDesigner supports graphical notation and listing of the corresponding symbols based on the Systems Biology Graphical Notation. Thus, this formalism allows biologists to represent detailed biochemical processes in a way that can be easily understood and shared, facilitating communication between researchers. In this chapter, we will focus on a specificity of ChloroKB, the representation of multilayered regulation of protein activity. Information on regulation of protein activity is indeed central to understanding the plant response to fluctuating environmental conditions. However, the intrinsic diversity of the regulatory modes and the abundance of detail may hamper comprehension of the regulatory processes described in ChloroKB. With this chapter, ChloroKB users will be guided through the representation of these sophisticated biological processes of prime importance to understanding metabolism or for applied purposes. The descriptions provided, which summarize years of work and a broad bibliography in a few pages, can help speed up the integration of regulatory processes in kinetic models of plant metabolism.
Collapse
Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble Cedex 9, France.
| |
Collapse
|
2
|
Selma S, Ntelkis N, Nguyen TH, Goossens A. Engineering the plant metabolic system by exploiting metabolic regulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1149-1163. [PMID: 36799285 DOI: 10.1111/tpj.16157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 05/31/2023]
Abstract
Plants are the most sophisticated biofactories and sources of food and biofuels present in nature. By engineering plant metabolism, the production of desired compounds can be increased and the nutritional or commercial value of the plant species can be improved. However, this can be challenging because of the complexity of the regulation of multiple genes and the involvement of different protein interactions. To improve metabolic engineering (ME) capabilities, different tools and strategies for rerouting the metabolic pathways have been developed, including genome editing and transcriptional regulation approaches. In addition, cutting-edge technologies have provided new methods for understanding uncharacterized biosynthetic pathways, protein degradation mechanisms, protein-protein interactions, or allosteric feedback, enabling the design of novel ME approaches.
Collapse
Affiliation(s)
- Sara Selma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nikolaos Ntelkis
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Trang Hieu Nguyen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| |
Collapse
|
3
|
Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement. Metabolites 2022; 12:metabo12060511. [PMID: 35736444 PMCID: PMC9228725 DOI: 10.3390/metabo12060511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.
Collapse
|
4
|
Pérez L, Alves R, Perez-Fons L, Albacete A, Farré G, Soto E, Vilaprinyó E, Martínez-Andújar C, Basallo O, Fraser PD, Medina V, Zhu C, Capell T, Christou P. Multilevel interactions between native and ectopic isoprenoid pathways affect global metabolism in rice. Transgenic Res 2022; 31:249-268. [PMID: 35201538 PMCID: PMC8993735 DOI: 10.1007/s11248-022-00299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/28/2022] [Indexed: 11/29/2022]
Abstract
Isoprenoids are natural products derived from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In plants, these precursors are synthesized via the cytosolic mevalonate (MVA) and plastidial methylerythritol phosphate (MEP) pathways. The regulation of these pathways must therefore be understood in detail to develop effective strategies for isoprenoid metabolic engineering. We hypothesized that the strict regulation of the native MVA pathway could be circumvented by expressing an ectopic plastidial MVA pathway that increases the accumulation of IPP and DMAPP in plastids. We therefore introduced genes encoding the plastid-targeted enzymes HMGS, tHMGR, MK, PMK and MVD and the nuclear-targeted transcription factor WR1 into rice and evaluated the impact of their endosperm-specific expression on (1) endogenous metabolism at the transcriptomic and metabolomic levels, (2) the synthesis of phytohormones, carbohydrates and fatty acids, and (3) the macroscopic phenotype including seed morphology. We found that the ectopic plastidial MVA pathway enhanced the expression of endogenous cytosolic MVA pathway genes while suppressing the native plastidial MEP pathway, increasing the production of certain sterols and tocopherols. Plants carrying the ectopic MVA pathway only survived if WR1 was also expressed to replenish the plastid acetyl-CoA pool. The transgenic plants produced higher levels of fatty acids, abscisic acid, gibberellins and lutein, reflecting crosstalk between phytohormones and secondary metabolism.
Collapse
Affiliation(s)
- Lucía Pérez
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Rui Alves
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway University of London, Egham Hill, UK
| | - Alfonso Albacete
- Departament of Plant Nutrition, Center of Edaphology and Applied Biology of the Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, 30100, Murcia, Espinardo, Spain
- Department of Plant Production and Agrotechnology, Institute for Agri-Food Research and Development of Murcia, Murcia, La Alberca, Spain
| | - Gemma Farré
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Erika Soto
- Department of Chemistry, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Ester Vilaprinyó
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
- IRBLleida, Lleida, Catalunya, Spain
| | - Cristina Martínez-Andújar
- Departament of Plant Nutrition, Center of Edaphology and Applied Biology of the Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, 30100, Murcia, Espinardo, Spain
| | - Oriol Basallo
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham Hill, UK
| | - Vicente Medina
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
| |
Collapse
|
5
|
Engineered Maize Hybrids with Diverse Carotenoid Profiles and Potential Applications in Animal Feeding. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33783733 DOI: 10.1007/978-981-15-7360-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Multi-gene transformation methods need to be able to introduce multiple transgenes into plants in order to reconstitute a transgenic locus where the introduced genes express in a coordinated manner and do not segregate in subsequent generations. This simultaneous multiple gene transfer enables the study and modulation of the entire metabolic pathways and the elucidation of complex genetic control circuits and regulatory hierarchies. We used combinatorial nuclear transformation to produce multiplex-transgenic maize plants. In proof of principle experiments, we co-expressed five carotenogenic genes in maize endosperm. The resulting combinatorial transgenic maize plant population, equivalent to a "mutant series," allowed us to identify and complement rate-limiting steps in the extended endosperm carotenoid pathway and to recover corn plants with extraordinary levels of β-carotene and other nutritionally important carotenoids. We then introgressed the induced (transgenic) carotenoid pathway in a transgenic line accumulating high levels of nutritionally important carotenoids into a wild-type yellow-endosperm variety with a high β:ε ratio. Novel hybrids accumulated zeaxanthin at unprecedented amounts. We introgressed the same pathway into a different yellow corn line with a low β:ε ratio. The resulting hybrids, in this case, had a very different carotenoid profile. The role of genetic background in determining carotenoid profiles in corn was elucidated, and further rate-limiting steps in the pathway were identified and resolved in hybrids. Astaxanthin accumulation was engineered by overexpression of a β-carotene ketolase in maize endosperm. In early experiments, limited astaxanthin accumulation in transgenic maize plants was attributed to a bottleneck in the conversion of adonixanthin (4-ketozeaxanthin) to astaxanthin. More recent experiments showed that a synthetic β-carotene ketolase with a superior β-carotene/zeaxanthin ketolase activity is critical for the high-yield production of astaxanthin in maize endosperm. Engineered lines were used in animal feeding experiments which demonstrated not only the safety of the engineered lines but also their efficacy in a range of different animal production applications.
Collapse
|
6
|
Zhu Q, Liu YG. TransGene Stacking II Vector System for Plant Metabolic Engineering and Synthetic Biology. Methods Mol Biol 2021; 2238:19-35. [PMID: 33471322 DOI: 10.1007/978-1-0716-1068-8_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Efficient stacking of multiple genes is a critical element in metabolic engineering of complex pathways, synthetic biology, and genetic improvement of complex agronomic traits in plants. Here we present a high-efficiency multigene assembly and transformation vector system, TransGene Stacking II (TGS II), for these purposes. The operation process is described in detail, and the successful operation mainly depends on effective reagents, special Escherichia coli strains, and basic molecular biological means without other specific equipments.
Collapse
Affiliation(s)
- Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, South China Agricultural University, Guangzhou, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, South China Agricultural University, Guangzhou, China.
| |
Collapse
|
7
|
Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges. BIOLOGY 2020; 10:biology10010020. [PMID: 33396370 PMCID: PMC7823625 DOI: 10.3390/biology10010020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Simple Summary This review summarizes the status, applications, and challenges of plant metabolomics in the context of crop breeding, food quality and safety, and human nutrition and health. It also highlights the importance of plant metabolomics in elucidating biochemical and genetic bases of traits associated with nutritive and healthy beneficial foods and other plant products to secure food supply, to ensure food quality, to protect humans from malnutrition and other diseases. Meanwhile, this review calls for comprehensive collaborations to accelerate relevant researches and applications in the context of human nutrition and health. Abstract Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.
Collapse
|
8
|
Zafar S, Li YL, Li NN, Zhu KM, Tan XL. Recent advances in enhancement of oil content in oilseed crops. J Biotechnol 2019; 301:35-44. [PMID: 31158409 DOI: 10.1016/j.jbiotec.2019.05.307] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 10/26/2022]
Abstract
Plant oils are very valuable agricultural commodity. The manipulation of seed oil composition to deliver enhanced fatty acid compositions, which are appropriate for feed or fuel, has always been a main objective of metabolic engineers. The last two decennary have been noticeable by numerous significant events in genetic engineering for identification of different gene targets to improve oil yield in oilseed crops. Particularly, genetic engineering approaches have presented major breakthrough in elevating oil content in oilseed crops such as Brassica napus and soybean. Additionally, current research efforts to explore the possibilities to modify the genetic expression of key regulators of oil accumulation along with biochemical studies to elucidate lipid biosynthesis will establish protocols to develop transgenic oilseed crops along much improved oil content. In this review, we describe current distinct genetic engineering approaches investigated by researchers for ameliorating oil content and its nutritional quality. Moreover, we will also discuss some auspicious and innovative approaches and challenges for engineering oil content to yield oil at much higher rate in oilseed crops.
Collapse
Affiliation(s)
- Sundus Zafar
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Yu-Long Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Nan-Nan Li
- School of Resource and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ke-Ming Zhu
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Xiao-Li Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China.
| |
Collapse
|
9
|
Christ B, Pluskal T, Aubry S, Weng JK. Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops. TRENDS IN PLANT SCIENCE 2018; 23:1047-1056. [PMID: 30361071 DOI: 10.1016/j.tplants.2018.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/14/2018] [Accepted: 09/24/2018] [Indexed: 05/20/2023]
Abstract
The nutritional value and safety of food crops are ultimately determined by their chemical composition. Recent developments in the field of metabolomics have made it possible to characterize the metabolic profile of crops in a comprehensive and high-throughput manner. Here, we propose that state-of-the-art untargeted metabolomics technology should be leveraged for safety assessment of new crop products. We suggest generally applicable experimental design principles that facilitate the efficient and rigorous identification of both intended and unintended metabolic alterations associated with a newly engineered trait. Our proposition could contribute to increased transparency of the safety assessment process for new biotech crops.
Collapse
Affiliation(s)
- Bastien Christ
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sylvain Aubry
- Federal Office for Agriculture, 3003 Bern, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
10
|
Holland CK, Jez JM. Arabidopsis: the original plant chassis organism. PLANT CELL REPORTS 2018; 37:1359-1366. [PMID: 29663032 DOI: 10.1007/s00299-018-2286-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/11/2018] [Indexed: 05/20/2023]
Abstract
Arabidopsis thaliana (thale cress) has a past, current, and future role in the era of synthetic biology. Arabidopsis is one of the most well-studied plants with a wealth of genomics, genetics, and biochemical resources available for the metabolic engineer and synthetic biologist. Here we discuss the tools and resources that enable the identification of target genes and pathways in Arabidopsis and heterologous expression in this model plant. While there are numerous examples of engineering Arabidopsis for decreased lignin, increased seed oil, increased vitamins, and environmental remediation, this plant has provided biochemical tools for introducing Arabidopsis genes, pathways, and/or regulatory elements into other plants and microorganisms. Arabidopsis is not a vegetative or oilseed crop, but it is as an excellent model chassis for proof-of-concept metabolic engineering and synthetic biology experiments in plants.
Collapse
Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| |
Collapse
|
11
|
Over-accumulation of astaxanthin in Haematococcus pluvialis through chloroplast genetic engineering. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.02.024] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
12
|
Abstract
Photosynthesis is fundamental to biomass production, but is a dynamic process sensitive to environmental constraints. In recent years, approaches to increase biomass and grain yield by altering photosynthetically related processes in the plant have received considerable attention. However, improving biomass yield requires a predictive understanding of the molecular mechanisms that allow photosynthesis to be adjusted. The important roles of metabolic reactions external to those directly involved in photosynthesis are highlighted in this review; however, our major focus is on the routes taken to improve photosynthetic carbon assimilation and to increase photosynthetic efficiency and consequently biomass yield.
Collapse
|
13
|
Kotopka BJ, Li Y, Smolke CD. Synthetic biology strategies toward heterologous phytochemical production. Nat Prod Rep 2018; 35:902-920. [DOI: 10.1039/c8np00028j] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
This review summarizes the recent progress in heterologous phytochemical biosynthetic pathway reconstitution in plant, bacteria, and yeast, with a focus on the synthetic biology strategies applied in these engineering efforts.
Collapse
Affiliation(s)
| | - Yanran Li
- Department of Chemical and Environmental Engineering
- Riverside
- USA
| | - Christina D. Smolke
- Department of Bioengineering
- Stanford University
- Stanford
- USA
- Chan Zuckerberg Biohub
| |
Collapse
|
14
|
Tuberosa R, Frascaroli E, Salvi S. Leveraging plant genomics for better and healthier food. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
15
|
A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens. Nat Genet 2017; 49:1364-1372. [PMID: 28740263 DOI: 10.1038/ng.3919] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022]
Abstract
Alleles that confer multiple disease resistance (MDR) are valuable in crop improvement, although the molecular mechanisms underlying their functions remain largely unknown. A quantitative trait locus, qMdr9.02, associated with resistance to three important foliar maize diseases-southern leaf blight, gray leaf spot and northern leaf blight-has been identified on maize chromosome 9. Through fine-mapping, association analysis, expression analysis, insertional mutagenesis and transgenic validation, we demonstrate that ZmCCoAOMT2, which encodes a caffeoyl-CoA O-methyltransferase associated with the phenylpropanoid pathway and lignin production, is the gene within qMdr9.02 conferring quantitative resistance to both southern leaf blight and gray leaf spot. We suggest that resistance might be caused by allelic variation at the level of both gene expression and amino acid sequence, thus resulting in differences in levels of lignin and other metabolites of the phenylpropanoid pathway and regulation of programmed cell death.
Collapse
|
16
|
Cao HX, Wang W, Le HTT, Vu GTH. The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding. Int J Genomics 2016; 2016:5078796. [PMID: 28097123 PMCID: PMC5206445 DOI: 10.1155/2016/5078796] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/17/2016] [Accepted: 11/01/2016] [Indexed: 12/26/2022] Open
Abstract
Genome editing with engineered nucleases enabling site-directed sequence modifications bears a great potential for advanced plant breeding and crop protection. Remarkably, the RNA-guided endonuclease technology (RGEN) based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) is an extremely powerful and easy tool that revolutionizes both basic research and plant breeding. Here, we review the major technical advances and recent applications of the CRISPR-Cas9 system for manipulation of model and crop plant genomes. We also discuss the future prospects of this technology in molecular plant breeding.
Collapse
Affiliation(s)
- Hieu X. Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466 Stadt Seeland, Germany
| | - Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Hien T. T. Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi, Vietnam
| | - Giang T. H. Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466 Stadt Seeland, Germany
| |
Collapse
|
17
|
Moreno JA, Díaz-Gómez J, Nogareda C, Angulo E, Sandmann G, Portero-Otin M, Serrano JCE, Twyman RM, Capell T, Zhu C, Christou P. The distribution of carotenoids in hens fed on biofortified maize is influenced by feed composition, absorption, resource allocation and storage. Sci Rep 2016; 6:35346. [PMID: 27739479 PMCID: PMC5064355 DOI: 10.1038/srep35346] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/28/2016] [Indexed: 11/08/2022] Open
Abstract
Carotenoids are important dietary nutrients with health-promoting effects. The biofortification of staple foods with carotenoids provides an efficient delivery strategy but little is known about the fate and distribution of carotenoids supplied in this manner. The chicken provides a good model of human carotenoid metabolism so we supplemented the diets of laying hens using two biofortified maize varieties with distinct carotenoid profiles and compared the fate of the different carotenoids in terms of distribution in the feed, the hen's livers and the eggs. We found that after a period of depletion, pro-vitamin A (PVA) carotenoids were preferentially diverted to the liver and relatively depleted in the eggs, whereas other carotenoids were transported to the eggs even when the liver remained depleted. When retinol was included in the diet, it accumulated more in the eggs than the livers, whereas PVA carotenoids showed the opposite profile. Our data suggest that a transport nexus from the intestinal lumen to the eggs introduces bottlenecks that cause chemically-distinct classes of carotenoids to be partitioned in different ways. This nexus model will allow us to optimize animal feed and human diets to ensure that the health benefits of carotenoids are delivered in the most effective manner.
Collapse
Affiliation(s)
- Jose Antonio Moreno
- Department of Animal Science, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Joana Díaz-Gómez
- Department of Animal Science, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
- Department of Food Technology, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Carmina Nogareda
- Department of Animal Science, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Eduardo Angulo
- Department of Animal Science, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Gerhard Sandmann
- Biosynthesis Group, Department of Molecular Biosciences, J. W. Goethe University, Max-v-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Manuel Portero-Otin
- Department of Experimental Medicine, Faculty of Medicine, University of Lleida–Institut de Recerca Biomèdica de Lleida (IRBLleida), Av. Rovira Roure 80, 25198 Lleida, Spain
| | - José C. E. Serrano
- Department of Experimental Medicine, Faculty of Medicine, University of Lleida–Institut de Recerca Biomèdica de Lleida (IRBLleida), Av. Rovira Roure 80, 25198 Lleida, Spain
| | | | - Teresa Capell
- Department of Plant Production and Forestry Science, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, ETSEA, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
18
|
Yogendra KN, Kushalappa AC. Integrated transcriptomics and metabolomics reveal induction of hierarchies of resistance genes in potato against late blight. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:766-782. [PMID: 32480502 DOI: 10.1071/fp16028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/15/2016] [Indexed: 05/11/2023]
Abstract
Late blight caused by Phytophthora infestans is a devastating disease affecting potato production worldwide. The quantitative resistance is durable, but the underlying molecular and biochemical mechanisms are poorly understood, limiting its application in breeding. Integrated transcriptomics and metabolomics approach was used for the first time to study the hierarchies of molecular events occurring, following inoculation of resistant and susceptible potato genotypes with P. infestans. RNA sequencing revealed a total of 4216 genes that were differentially expressed in the resistant than in the susceptible genotype. Genes that were highly expressed and associated with their biosynthetic metabolites that were highly accumulated, through metabolic pathway regulation, were selected. Quantitative real-time PCR was performed to confirm the RNA-seq expression levels. The induced leucine-rich repeat receptor-like kinases (LRR-RLKs) are considered to be involved in pathogen recognition. These receptor genes are considered to trigger downstream oxidative burst, phytohormone signalling-related genes, and transcription factors that regulated the resistance genes to produce resistance related metabolites to suppress the pathogen infection. It was noted that several resistance genes in metabolic pathways related to phenylpropanoids, flavonoids, alkaloids and terpenoid biosynthesis were strongly induced in the resistant genotypes. The pathway specific gene induction provided key insights into the metabolic reprogramming of induced defence responses in resistant genotypes.
Collapse
Affiliation(s)
| | - Ajjamada C Kushalappa
- Department of Plant Science, McGill University, Ste. Anne de Bellevue, Québec, Canada
| |
Collapse
|
19
|
Hong J, Yang L, Zhang D, Shi J. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci 2016; 17:ijms17060767. [PMID: 27258266 PMCID: PMC4926328 DOI: 10.3390/ijms17060767] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.
Collapse
Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Litao Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
20
|
Nemhauser JL, Torii KU. Plant synthetic biology for molecular engineering of signalling and development. NATURE PLANTS 2016; 2:16010. [PMID: 27249346 PMCID: PMC5164986 DOI: 10.1038/nplants.2016.10] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.
Collapse
Affiliation(s)
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| |
Collapse
|
21
|
Ghareeb H, Laukamm S, Lipka V. COLORFUL-Circuit: A Platform for Rapid Multigene Assembly, Delivery, and Expression in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:246. [PMID: 26973687 PMCID: PMC4772762 DOI: 10.3389/fpls.2016.00246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/14/2016] [Indexed: 05/20/2023]
Abstract
Advancing basic and applied plant research requires the continuous innovative development of the available technology toolbox. Essential components of this toolbox are methods that simplify the assembly, delivery, and expression of multiple transgenes of interest. To allow simultaneous and directional multigene assembly on the same plant transformation vector, several strategies based on overlapping sequences or restriction enzymes have recently been developed. However, the assembly of homologous and repetitive DNA sequences can be inefficient and the frequent occurrence of target sequences recognized by commonly used restriction enzymes can be a limiting factor. Here, we noted that recognition sites for the restriction enzyme SfiI are rarely occurring in plant genomes. This fact was exploited to establish a multigene assembly system called "COLORFUL-Circuit." To this end, we developed a set of binary vectors which provide a flexible and cost efficient cloning platform. The gene expression cassettes in our system are flanked with unique SfiI sites, which allow simultaneous multi-gene cassette assembly in a hosting binary vector. We used COLORFUL-Circuit to transiently and stably express up to four fluorescent organelle markers in addition to a selectable marker and analyzed the impact of assembly design on coexpression efficiency. Finally, we demonstrate the utility of our optimized "COLORFUL-Circuit" system in an exemplary case study, in which we monitored simultaneously the subcellular behavior of multiple organelles in a biotrophic plant-microbe interaction by Confocal Laser Scanning Microscopy.
Collapse
Affiliation(s)
- Hassan Ghareeb
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, Georg-August-University of GöttingenGöttingen, Germany
- Department of Plant Biotechnology, National Research CentreCairo, Egypt
- *Correspondence: Hassan Ghareeb
| | - Sabine Laukamm
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, Georg-August-University of GöttingenGöttingen, Germany
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, Georg-August-University of GöttingenGöttingen, Germany
- Volker Lipka
| |
Collapse
|
22
|
Quétier F. The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:65-76. [PMID: 26566825 DOI: 10.1016/j.plantsci.2015.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 05/23/2023]
Abstract
The first period of plant genome editing was based on Agrobacterium; chemical mutagenesis by EMS (ethyl methanesulfonate) and ionizing radiations; each of these technologies led to randomly distributed genome modifications. The second period is associated with the discoveries of homing and meganuclease enzymes during the 80s and 90s, which were then engineered to provide efficient tools for targeted editing. From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology. The latest revolution surfaced in 2013 with the CRISPR-Cas9 system, whose high efficiency and technical ease of use is really impressive; scientists can use in-house kits or commercially available kits; the only two requirements are to carefully choose the location of the DNA double strand breaks to be induced and then to order an oligonucleotide. While this close-to- ultimate toolkit for targeted editing of genomes represents dramatic scientific progress which allows the development of more complex useful agronomic traits through synthetic biology, the social acceptance of genome editing remains regularly questioned by anti-GMO citizens and organizations.
Collapse
Affiliation(s)
- Francis Quétier
- University of Evry Val d'Essonne, Evry 91025, France; Genopole, Evry 91025, France.
| |
Collapse
|
23
|
Rai A, Saito K. Omics data input for metabolic modeling. Curr Opin Biotechnol 2015; 37:127-134. [PMID: 26723010 DOI: 10.1016/j.copbio.2015.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/09/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022]
Abstract
Recent advancements in high-throughput large-scale analytical methods to sequence genomes of organisms, and to quantify gene expression, proteins, lipids and metabolites have changed the paradigm of metabolic modeling. The cost of data generation and analysis has decreased significantly, which has allowed exponential increase in the amount of omics data being generated for an organism in a very short time. Compared to progress made in microbial metabolic modeling, plant metabolic modeling still remains limited due to its complex genomes and compartmentalization of metabolic reactions. Herein, we review and discuss different omics-datasets with potential application in the functional genomics. In particular, this review focuses on the application of omics-datasets towards construction and reconstruction of plant 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.
| |
Collapse
|
24
|
Xiao Y, Ji Q, Gao S, Tan H, Chen R, Li Q, Chen J, Yang Y, Zhang L, Wang Z, Chen W, Hu Z. Combined transcriptome and metabolite profiling reveals that IiPLR1 plays an important role in lariciresinol accumulation in Isatis indigotica. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6259-71. [PMID: 26163698 PMCID: PMC7107596 DOI: 10.1093/jxb/erv333] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A lignan, lariciresinol, is an important efficacious compound for the antiviral effect of Isatis indigotica, a widely used herb for the treatment of colds, fever, and influenza. Although some rate-limiting steps of the lariciresinol biosynthetic pathway are well known, the specific roles of gene family members in I. indigotica in regulating lariciresinol production are poorly understood. In the present study, a correlation analysis between the RNA sequencing (RNA-Seq) expression profile and lignan content by using I. indigotica hairy roots treated with methyl jamonate (0.5 μM) at different time points as a source implicated that I. indigotica pinoresinol/lariciresinol reductase 1 (IiPLR1), but not IiPLR2 or IiPLR3, contributed greatly to lariciresinol accumulation. Gene silencing by RNA interference (RNAi) demonstrated that IiPLR1 indeed influenced lariciresinol biosynthesis, whereas suppression of IiPLR2 or IiPLR3 did not change lariciresinol abundance significantly. IiPLR1 was thus further characterized; IiPLR1 was constitutively expressed in roots, stems, leaves, and flowers of I. indigotica, with the highest expression in roots, and it responds to different stress treatments to various degrees. Recombinant IiPLR1 reduces both (±)-pinoresinol and (±)-lariciresinol efficiently, with comparative K cat/K m values. Furthermore, overexpression of IiPLR1 significantly enhanced lariciresinol accumulation in I. indigotica hairy roots, and the best line (ovx-2) produced 353.9 μg g(-1) lariciresinol, which was ~6.3-fold more than the wild type. This study sheds light on how to increase desired metabolites effectively by more accurate or appropriate genetic engineering strategies, and also provides an effective approach for the large-scale commercial production of pharmaceutically valuable lariciresinol by using hairy root culture systems as bioreactors.
Collapse
Affiliation(s)
- Ying Xiao
- The MOE Key Laboratory of Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Qian Ji
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Shouhong Gao
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Hexin Tan
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Qing Li
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Junfeng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Yingbo Yang
- The MOE Key Laboratory of Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Zhengtao Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Zhibi Hu
- The MOE Key Laboratory of Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| |
Collapse
|
25
|
Solovchenko AE. Recent breakthroughs in the biology of astaxanthin accumulation by microalgal cell. PHOTOSYNTHESIS RESEARCH 2015; 125:437-49. [PMID: 25975708 DOI: 10.1007/s11120-015-0156-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/06/2015] [Indexed: 05/09/2023]
Abstract
Massive accumulation of the secondary ketokarotenoid astaxanthin is a characteristic stress response of certain microalgal species with Haematococcus pluvialis as an illustrious example. The carotenogenic response confers these organisms a remarkable ability to survive in extremely unfavorable environments and makes them the richest source of natural astaxanthin. Exerting a plethora of beneficial effects on human and animal health, astaxanthin is among the most important bioproducts from microalgae. Though our understanding of astaxanthin biosynthesis, induction, and regulation is far from complete, this gap is filling rapidly with new knowledge generated predominantly by application of advanced "omics" approaches. This review focuses on the most recent progress in the biology of astaxanthin accumulation in microalgae including the genomic, proteomic, and metabolomics insights into the induction and regulation of secondary carotenogenesis and its role in stress tolerance of the photosynthetic microorganisms. Special attention is paid to the coupling of the carotenoid and lipid biosynthesis as well as deposition of astaxanthin in the algal cell. The place of the carotenogenic response among the stress tolerance mechanisms is revisited, and possible implications of the new findings for biotechnological production of astaxanthin from microalgae are considered. The potential use of the carotenogenic microalgae as a source not only of value-added carotenoids, but also of biofuel precursors is discussed.
Collapse
Affiliation(s)
- Alexei E Solovchenko
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia,
| |
Collapse
|
26
|
Martínez-Esteso MJ, Martínez-Márquez A, Sellés-Marchart S, Morante-Carriel JA, Bru-Martínez R. The role of proteomics in progressing insights into plant secondary metabolism. FRONTIERS IN PLANT SCIENCE 2015; 6:504. [PMID: 26217358 PMCID: PMC4493368 DOI: 10.3389/fpls.2015.00504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 06/23/2015] [Indexed: 05/29/2023]
Abstract
The development of omics has enabled the genome-wide exploration of all kinds of biological processes at the molecular level. Almost every field of plant biology has been analyzed at the genomic, transcriptomic and proteomic level. Here we focus on the particular contribution that proteomic technologies have made in progressing knowledge and characterising plant secondary metabolism (SM) pathways since early expectations were created 15 years ago. We analyzed how three major issues in the proteomic analysis of plant SM have been implemented in various research studies. These issues are: (i) the selection of a suitable plant material rich in secondary metabolites of interest, such as specialized tissues and organs, and in vitro cell cultures; (ii) the proteomic strategy to access target proteins, either a comprehensive or a differential analysis; (iii) the proteomic approach, represented by the hypothesis-free discovery proteomics and the hypothesis-driven targeted proteomics. We also examine to what extent the most-advanced technologies have been incorporated into proteomic research in plant SM and highlight some cutting edge techniques that would strongly benefit the progress made in this field.
Collapse
Affiliation(s)
- María J. Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
| | - Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
- Biotechnology and Molecular Biology Group, Quevedo State Technical University, Quevedo, Ecuador
| | - Jaime A. Morante-Carriel
- Proteomics and Genomics Division, Research Technical Facility, University of Alicante, Alicante, Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
| |
Collapse
|
27
|
Chang S, Berman J, Sheng Y, Wang Y, Capell T, Shi L, Ni X, Sandmann G, Christou P, Zhu C. Cloning and Functional Characterization of the Maize (Zea mays L.) Carotenoid Epsilon Hydroxylase Gene. PLoS One 2015; 10:e0128758. [PMID: 26030746 PMCID: PMC4452274 DOI: 10.1371/journal.pone.0128758] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/15/2015] [Indexed: 01/18/2023] Open
Abstract
The assignment of functions to genes in the carotenoid biosynthesis pathway is necessary to understand how the pathway is regulated and to obtain the basic information required for metabolic engineering. Few carotenoid ε-hydroxylases have been functionally characterized in plants although this would provide insight into the hydroxylation steps in the pathway. We therefore isolated mRNA from the endosperm of maize (Zea mays L., inbred line B73) and cloned a full-length cDNA encoding CYP97C19, a putative heme-containing carotenoid ε hydroxylase and member of the cytochrome P450 family. The corresponding CYP97C19 genomic locus on chromosome 1 was found to comprise a single-copy gene with nine introns. We expressed CYP97C19 cDNA under the control of the constitutive CaMV 35S promoter in the Arabidopsis thaliana lut1 knockout mutant, which lacks a functional CYP97C1 (LUT1) gene. The analysis of carotenoid levels and composition showed that lutein accumulated to high levels in the rosette leaves of the transgenic lines but not in the untransformed lut1 mutants. These results allowed the unambiguous functional annotation of maize CYP97C19 as an enzyme with strong zeinoxanthin ε-ring hydroxylation activity.
Collapse
Affiliation(s)
- Shu Chang
- School of Life Sciences, Changchun Normal University, Changchun, 130032, China
- School of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Judit Berman
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, 25198, Spain
| | - Yanmin Sheng
- School of Life Sciences, Changchun Normal University, Changchun, 130032, China
| | - Yingdian Wang
- School of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Teresa Capell
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, 25198, Spain
| | - Lianxuan Shi
- School of Life Sciences, Northeast Normal University, Changchun, 130024, China
| | - Xiuzhen Ni
- School of Life Sciences, Changchun Normal University, Changchun, 130032, China
| | - Gerhard Sandmann
- Biosynthesis Group, Molecular Biosciences, Goethe University Frankfurt, D-60438, Frankfurt, Germany
| | - Paul Christou
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, 25198, Spain
- Institució Catalana de Recerca i Estudis Avancats, Barcelona, 08010, Spain
| | - Changfu Zhu
- School of Life Sciences, Changchun Normal University, Changchun, 130032, China
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, 25198, Spain
- * E-mail:
| |
Collapse
|
28
|
High-value products from plants: the challenges of process optimization. Curr Opin Biotechnol 2015; 32:156-162. [PMID: 25562816 DOI: 10.1016/j.copbio.2014.12.018] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 11/20/2022]
Abstract
Plants can be used to produce a diverse repertoire of complex small-molecule compounds and recombinant proteins that are valuable as industrial and pharmaceutical products. But as we move from proof-of-principle experiments and begin to consider the realistic prospects of commercial production, the focus must shift from the achievement of target molecule production and move towards quality, purity and yield aspects that determine commercial feasibility. This review describes some of the recent advances that have been implemented to improve the development of integrated production processes for high-value molecules expressed in plants, including the introduction of novel procedures to increase the likelihood of regulatory acceptance.
Collapse
|