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Mutte SK, Kato H, Rothfels C, Melkonian M, Wong GKS, Weijers D. Origin and evolution of the nuclear auxin response system. eLife 2018; 7:33399. [PMID: 29580381 PMCID: PMC5873896 DOI: 10.7554/elife.33399] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/06/2018] [Indexed: 01/22/2023] Open
Abstract
The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal. Across all kingdoms of life, signaling molecules like hormones, for example, control many aspects of the lives of organisms, including how they grow and develop. Cells have dedicated proteins that can recognize the signaling molecules, relay the information, and respond to the signal, for example by switching genes on or off. Such response systems usually consist of multiple components, and, throughout evolution, these response components have regularly been copied such that many species have multiple different versions of each one. Auxin is a plant hormone that controls virtually all growth and developmental processes in plants, including many yield traits in crops. However, no one knows why it is involved in so many processes. This is partly because it is not clear how the response system for this central signaling molecule was first born, or how it has increased in its complexity. To address this, Mutte, Kato et al. explored the genetic information of more than a thousand plant species, including algae, which span more than 700 million years of evolution. Their analysis showed that all auxin response components were assembled from pieces of much older genes, but that they first came together when plants conquered land. Indeed, the auxin response appears to have developed on top of a pre-existing genetic regulator that is still present in modern-day algae. Mutte, Kato et al. then used experiments to show how stepwise increases in the number and types of auxin response components have shaped sophisticated, complex responses in land plants, and to demonstrate how ancient components control auxin response. Together these findings provide a framework for understanding the many functions of auxin in plants, and how this came to be. They also show how complexity can be accomplished in a signal response pathway, and how diversity evolves in gene families. Similar studies on other response systems in plants and beyond are likely to help reveal common principles of hormone response evolution and diversification of gene regulation systems.
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Affiliation(s)
- Sumanth K Mutte
- Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands
| | - Hirotaka Kato
- Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands
| | - Carl Rothfels
- Department of Integrative Biology, University of California, Berkeley, United States
| | - Michael Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Medicine, University of Alberta, Edmonton, Canada.,BGI-Shenzhen, Shenzhen, China
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands
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Bennett T, Brockington SF, Rothfels C, Graham SW, Stevenson D, Kutchan T, Rolf M, Thomas P, Wong GKS, Leyser O, Glover BJ, Harrison CJ. Paralogous radiations of PIN proteins with multiple origins of noncanonical PIN structure. Mol Biol Evol 2014; 31:2042-60. [PMID: 24758777 PMCID: PMC4104312 DOI: 10.1093/molbev/msu147] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The plant hormone auxin is a conserved regulator of development which has been implicated in the generation of morphological novelty. PIN-FORMED1 (PIN) auxin efflux carriers are central to auxin function by regulating its distribution. PIN family members have divergent structures and cellular localizations, but the origin and evolutionary significance of this variation is unresolved. To characterize PIN family evolution, we have undertaken phylogenetic and structural analyses with a massive increase in taxon sampling over previous studies. Our phylogeny shows that following the divergence of the bryophyte and lycophyte lineages, two deep duplication events gave rise to three distinct lineages of PIN proteins in euphyllophytes. Subsequent independent radiations within each of these lineages were taxonomically asymmetric, giving rise to at least 21 clades of PIN proteins, of which 15 are revealed here for the first time. Although most PIN protein clades share a conserved canonical structure with a modular central loop domain, a small number of noncanonical clades dispersed across the phylogeny have highly divergent protein structure. We propose that PIN proteins underwent sub- and neofunctionalization with substantial modification to protein structure throughout plant evolution. Our results have important implications for plant evolution as they suggest that structurally divergent PIN proteins that arose in paralogous radiations contributed to the convergent evolution of organ systems in different land plant lineages.
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Affiliation(s)
- Tom Bennett
- Department of Plant Sciences, University of Cambridge, Cambridge, United KingdomSainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Carl Rothfels
- Department of Zoology, University of British Columbia, Vancouver, British Colombia, Canada
| | - Sean W Graham
- UBC Botanical Garden Campbell Building, Vancouver, British Colombia, Canada
| | | | | | | | - Philip Thomas
- Royal Botanic Gardens Edinburgh, 20A Inverleith Row, Edinburgh, United Kingdom
| | - Gane Ka-Shu Wong
- Department of Medicine, University of Alberta, Edmonton, Alberta, CanadaDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta, CanadaBGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Beverley J Glover
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - C Jill Harrison
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GKS. Data access for the 1,000 Plants (1KP) project. Gigascience 2014; 3:17. [PMID: 25625010 PMCID: PMC4306014 DOI: 10.1186/2047-217x-3-17] [Citation(s) in RCA: 395] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/02/2014] [Indexed: 01/06/2023] Open
Abstract
The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.
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Affiliation(s)
- Naim Matasci
- iPlant Collaborative, Tucson 85721, AZ, USA ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA
| | - Ling-Hong Hung
- Department of Microbiology, University of Washington, Seattle 98109, WA, USA
| | - Zhixiang Yan
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Norman J Wickett
- Chicago Botanic Garden, Glencoe 60022, IL, USA ; Program in Biological Sciences, Northwestern University, Evanston 60208, IL, USA
| | - Siavash Mirarab
- Department of Computer Science, University of Texas, Austin, TX, 78712, USA
| | - Nam Nguyen
- Department of Computer Science, University of Texas, Austin, TX, 78712, USA
| | - Tandy Warnow
- Department of Computer Science, University of Texas, Austin, TX, 78712, USA
| | | | - Michael Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | | | - Eric Wafula
- Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA
| | - Joshua P Der
- Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA
| | - Claude W dePamphilis
- Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA
| | - Béatrice Roure
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada
| | - Hervé Philippe
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada ; CNRS, USR 2936, Station d' Ecologie Expérimentale du CNRS, Moulis 09200, France
| | - Brad R Ruhfel
- Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, MA, 02138, USA
| | - Barbara Surek
- Botanical Institute, Universität zu Köln, Köln D-50674, Germany
| | | | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Gainesville, FL, 32611, USA ; Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Gainesville, FL, 32611, USA ; Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Carl Rothfels
- Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lisa Pokorny
- Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
| | - Jonathan A Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | | | - Juan Carlos Villarreal
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Megan Rolf
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Ram Samudrala
- Department of Microbiology, University of Washington, Seattle 98109, WA, USA
| | - Zhijian Tian
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Xiaolei Wu
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Xiao Sun
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Yong Zhang
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Jun Wang
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China ; Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada ; Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
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