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Mishra AK, Kocábek T, Nath VS, Khan A, Matoušek J, Hazzouri KM, Sudalaimuthuasari N, Krofta K, Ludwig-Müller J, Amiri KMA. The multifaceted roles of R2R3 transcription factor HlMYB7 in the regulation of flavonoid and bitter acids biosynthesis, development and biotic stress tolerance in hop (Humulus lupulus L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107636. [PMID: 36958151 DOI: 10.1016/j.plaphy.2023.03.013] [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: 12/07/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Hop (Humulus lupulus) biosynthesizes the highly economically valuable secondary metabolites, which include flavonoids, bitter acids, polyphenols and essential oils. These compounds have important pharmacological properties and are widely implicated in the brewing industry owing to bittering flavor, floral aroma and preservative activity. Our previous studies documented that ternary MYB-bHLH-WD40 (MBW) and binary WRKY1-WD40 (WW) protein complexes transcriptionally regulate the accumulation of bitter acid (BA) and prenylflavonoids (PF). In the present study, we investigated the regulatory functions of the R2R3-MYB repressor HlMYB7 transcription factor, which contains a conserved N-terminal domain along with the repressive motif EAR, in regulating the PF- and BA-biosynthetic pathway and their accumulation in hop. Constitutive expression of HlMYB7 resulted in transcriptional repression of structural genes involved in the terminal steps of biosynthesis of PF and BA, as well as stunted growth, delayed flowering, and reduced tolerance to viroid infection in hop. Furthermore, yeast two-hybrid and transient reporter assays revealed that HlMYB7 targets both PF and BA pathway genes and suppresses MBW and WW protein complexes. Heterologous expression of HlMYB7 leads to down-regulation of structural genes of flavonoid pathway in Arabidopsis thaliana, including a decrease in anthocyanin content in Nicotiana tabacum. The combined results from functional and transcriptomic analyses highlight the important role of HlMYB7 in fine-tuning and balancing the accumulation of secondary metabolites at the transcriptional level, thus offer a plausible target for metabolic engineering in hop.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Vishnu Sukumari Nath
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Ahamed Khan
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Khaled M Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Karel Krofta
- Hop Research Institute, Co. Ltd, Kadaňská 2525, 438 46, Žatec, Czech Republic
| | | | - Khaled M A Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
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Scutt CP. Model Species to Investigate the Origin of Flowers. Methods Mol Biol 2023; 2686:83-109. [PMID: 37540355 DOI: 10.1007/978-1-0716-3299-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The angiosperms, or flowering plants, arose at least 135 million years ago (Ma) and rapidly diversified to form over 300,000 species alive today. This group appears, however, to have separated from its closest living relatives, the extant gymnosperms, much earlier: over 300 Ma. Representatives of basally-diverging angiosperm lineages are of key importance to studies aimed at reconstructing the most recent common ancestor of living angiosperms, including its morphological, anatomical, eco-physiological and molecular aspects. Furthermore, evo-devo comparisons of angiosperms with living gymnosperms may help to determine how the many novel aspects of angiosperms, including those of the flower, first came about. This chapter reviews literature on the origin of angiosperms and focusses on basally-diverging angiosperms and gymnosperms that show advantages as potential experimental models, reviewing information and protocols for the use of these species in an evo-devo context. The final section suggests a means by which data from living and fossil groups could be integrated to better elucidate evolutionary events that took place on the long stem-lineage that apparently preceded the radiation of living angiosperms.
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Affiliation(s)
- Charles P Scutt
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon-1, CNRS, INRA, Lyon, France.
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Delaux PM, Hetherington AJ, Coudert Y, Delwiche C, Dunand C, Gould S, Kenrick P, Li FW, Philippe H, Rensing SA, Rich M, Strullu-Derrien C, de Vries J. Reconstructing trait evolution in plant evo-devo studies. Curr Biol 2020; 29:R1110-R1118. [PMID: 31689391 DOI: 10.1016/j.cub.2019.09.044] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our planet is teeming with an astounding diversity of plants. In a mere single group of closely related species, tremendous diversity can be observed in their form and function - the colour of petals in flowering plants, the shape of the fronds in ferns, and the branching pattern of the gametophyte in mosses. Diversity can also be found in subtler traits, such as the resistance to pathogens or the ability to recruit symbiotic microbes from the environment. Plant traits can also be highly conserved - at the cellular and metabolic levels, entire biosynthetic pathways are present in all plant groups, and morphological characteristics such as vascular tissues have been conserved for hundreds of millions of years. The research community that seeks to understand these traits - both the diverse and the conserved - by taking an evolutionary point-of-view on plant biology is growing. Here, we summarize a subset of the different aspects of plant evolutionary biology, provide a guide for structuring comparative biology approaches and discuss the pitfalls that (plant) researchers should avoid when embarking on such studies.
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Affiliation(s)
- Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France.
| | | | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, CNRS, INRA, Université Claude Bernard Lyon 1, INRIA, 46 Allée d'Italie, Lyon, 69007, France
| | | | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Sven Gould
- Institute for Molecular Evolution, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA; Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Hervé Philippe
- Centre de Théorisation et de Modélisation de la Biodiversité, Station d'Écologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France; Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University Freiburg, Germany; SYNMIKRO Research Center, University of Marburg, 35043 Marburg, Germany
| | - Mélanie Rich
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Christine Strullu-Derrien
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK; Institut de Systématique, Évolution, Biodiversité, UMR 7205, Muséum National d'Histoire Naturelle, Paris, France
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Institute of Microbiology, Technische Universitaet Braunschweig, 38106 Braunschweig, Germany; Institute for Microbiology and Genetics, Bioinformatics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
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Wu CC, Li FW, Kramer EM. Large-scale phylogenomic analysis suggests three ancient superclades of the WUSCHEL-RELATED HOMEOBOX transcription factor family in plants. PLoS One 2019; 14:e0223521. [PMID: 31603924 PMCID: PMC6788696 DOI: 10.1371/journal.pone.0223521] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/23/2019] [Indexed: 02/07/2023] Open
Abstract
The adaptation of plants to land required multiple morphological innovations. Among these include a variety of lateral organs that are initiated from apical meristems, in which the mantainance of undifferentiated stem cells is regulated by the homeodomain WUSCHEL-RELATED (WOX) transcription factors. Expansion of the WOX gene family has been associated with whole genome duplication (WGD) events and postulated to have been pivotal to the evolution of morphological complexity in land plants. Previous studies have classified the WOX gene family into three superclades (e.g., the ancient clade, the intermediate clade, and the modern clade). In order to improve our understanding of the evolution of the WOX gene family, we surveyed the WOX gene sequences from 38 genomes and 440 transcriptomes spanning the Viridiplantae and Rhodophyta. The WOX phylogeny inferred from 1039 WOX proteins drawn from 267 species with improved support along the backbone of the phylogeny suggests that the plant-specific WOX family contains three ancient superclades, which we term Type 1 (T1WOX, the WOX10/13/14 clade), Type 2 (T2WOX, the WOX8/9 and WOX11/12 clades), and Type 3 (T3WOX, the WUS, WOX1/6, WOX2, WOX3, WOX4 and WOX5/7 clades). Divergence of the T1WOX and T2WOX superclades may predate the diversification of vascular plants. Synteny analysis suggests contribution of WGD to expansion of the WOX family. Promoter analysis finds that the capacity of the WOX genes to be regulated by the auxin and cytokinin signaling pathways may be deeply conserved in the Viridiplantae. This study improves our phylogenetic context for elucidating functional evolution of the WOX gene family, which has likely contributed to the morphological complexity of land plants.
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Affiliation(s)
- Cheng-Chiang Wu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, United States of America
- Section of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Elena M. Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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Stanley L, Yuan YW. Transcriptional Regulation of Carotenoid Biosynthesis in Plants: So Many Regulators, So Little Consensus. FRONTIERS IN PLANT SCIENCE 2019; 10:1017. [PMID: 31447877 PMCID: PMC6695471 DOI: 10.3389/fpls.2019.01017] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/22/2019] [Indexed: 05/19/2023]
Abstract
In plants, the carotenoid biosynthesis pathway (CBP) is essential for the production of photosynthetic and protective pigments, plant hormones, and visual/olfactory attractants for animal pollinators and seed dispersers. The regulation of carotenoid biosynthesis at the transcriptional level is vitally important for all of these functions and has been the subject of intensive research. Many putative transcriptional regulators, both direct and indirect, have been identified through conventional mutant analysis, transcriptome profiling, yeast one-hybrid screening, and candidate gene approaches. Despite this progress, our understanding of the transcriptional regulation of carotenoid biosynthesis remains fragmented and incomplete. Frequently, a stimulus or regulator is known, but the mechanism by which it affects transcription has not been elucidated. In other cases, mechanisms have been proposed (such as direct binding of a CBP gene promoter by a transcription factor), but function was tested only in vitro or in heterologous systems, making it unclear whether these proteins actually play a role in carotenoid regulation in their endogenous environments. Even in cases where the mechanism is relatively well understood, regulators are often studied in isolation, either in a single plant species or outside the context of other known regulators. This presents a conundrum: why so many candidate regulators but so little consensus? Here we summarize current knowledge on transcriptional regulation of the CBP, lay out the challenges contributing to this conundrum, identify remaining knowledge gaps, and suggest future research directions to address these challenges and knowledge gaps.
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Affiliation(s)
- Lauren Stanley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
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Marcellini S, González F, Sarrazin AF, Pabón-Mora N, Benítez M, Piñeyro-Nelson A, Rezende GL, Maldonado E, Schneider PN, Grizante MB, Da Fonseca RN, Vergara-Silva F, Suaza-Gaviria V, Zumajo-Cardona C, Zattara EE, Casasa S, Suárez-Baron H, Brown FD. Evolutionary Developmental Biology (Evo-Devo) Research in Latin America. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:5-40. [PMID: 27491339 DOI: 10.1002/jez.b.22687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/29/2022]
Abstract
Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.
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Affiliation(s)
- Sylvain Marcellini
- Laboratorio de Desarrollo y Evolución, Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Favio González
- Facultad de Ciencias, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Andres F Sarrazin
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Xochimilco, Ciudad de México, México
| | - Gustavo L Rezende
- Universidade Estadual do Norte Fluminense, CBB, LQFPP, Campos dos Goytacazes, RJ, Brazil
| | - Ernesto Maldonado
- EvoDevo Lab, Unidad de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, México
| | | | | | - Rodrigo Nunes Da Fonseca
- Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro, Macae, RJ, Brazil
| | | | | | | | | | - Sofia Casasa
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Federico D Brown
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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Byers KJRP, Xu S, Schlüter PM. Molecular mechanisms of adaptation and speciation: why do we need an integrative approach? Mol Ecol 2016; 26:277-290. [DOI: 10.1111/mec.13678] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Kelsey J. R. P. Byers
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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Nikolov LA, Tsiantis M. Interspecies Gene Transfer as a Method for Understanding the Genetic Basis for Evolutionary Change: Progress, Pitfalls, and Prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:1135. [PMID: 26734038 PMCID: PMC4686936 DOI: 10.3389/fpls.2015.01135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/30/2015] [Indexed: 05/29/2023]
Abstract
The recent revolution in high throughput sequencing and associated applications provides excellent opportunities to catalog variation in DNA sequences and gene expression between species. However, understanding the astonishing diversity of the Tree of Life requires understanding the phenotypic consequences of such variation and identification of those rare genetic changes that are causal to diversity. One way to study the genetic basis for trait diversity is to apply a transgenic approach and introduce genes of interest from a donor into a recipient species. Such interspecies gene transfer (IGT) is based on the premise that if a gene is causal to the morphological divergence of the two species, the transfer will endow the recipient with properties of the donor. Extensions of this approach further allow identifying novel loci for the diversification of form and investigating cis- and trans-contributions to morphological evolution. Here we review recent examples from both plant and animal systems that have employed IGT to provide insight into the genetic basis of evolutionary change. We outline the practice of IGT, its methodological strengths and weaknesses, and consider guidelines for its application, emphasizing the importance of phylogenetic distance, character polarity, and life history. We also discuss future perspectives for exploiting IGT in the context of expanding genomic resources in emerging experimental systems and advances in genome editing.
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