1
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Moss BL. AuxSynBio: synthetic biology tools to understand and engineer auxin. Curr Opin Biotechnol 2024; 90:103194. [PMID: 39255527 DOI: 10.1016/j.copbio.2024.103194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 09/12/2024]
Abstract
The plant hormone auxin is a crucial coordinator of nearly all plant growth and development processes. Because of its centrality to plant physiology and the modular nature of the signaling pathway, auxin has played a critical role at the forefront of plant synthetic biology. This review will highlight how auxin is both a subject and an object of synthetic biology. Engineering biology approaches are deepening our understanding of how auxin pathways are wired and tuned, particularly through the creative use of signaling pathway recapitulation in yeast and engineered orthogonal auxin-receptor pairs. Auxin biology has also been mined for parts by synthetic biologists, with components being used for inducible protein degradation systems (auxin-inducible degron), auxin biosensors, synthetic cell-cell communication, and plant engineering.
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Affiliation(s)
- Britney L Moss
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA.
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2
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de Roij M, Borst JW, Weijers D. Protein degradation in auxin response. THE PLANT CELL 2024; 36:3025-3035. [PMID: 38652687 PMCID: PMC11371164 DOI: 10.1093/plcell/koae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/14/2024] [Accepted: 03/01/2024] [Indexed: 04/25/2024]
Abstract
The signaling molecule auxin sits at the nexus of plant biology where it coordinates essentially all growth and developmental processes. Auxin molecules are transported throughout plant tissues and are capable of evoking highly specific physiological responses by inducing various molecular pathways. In many of these pathways, proteolysis plays a crucial role for correct physiological responses. This review provides a chronology of the discovery and characterization of the auxin receptor, which is a fascinating example of separate research trajectories ultimately converging on the discovery of a core auxin signaling hub that relies on degradation of a family of transcriptional inhibitor proteins-the Aux/IAAs. Beyond describing the "classical" proteolysis-driven auxin response system, we explore more recent examples of the interconnection of proteolytic systems, which target a range of other auxin signaling proteins, and auxin response. By highlighting these emerging concepts, we provide potential future directions to further investigate the role of protein degradation within the framework of auxin response.
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Affiliation(s)
- Martijn de Roij
- Laboratory of Biochemistry, Wageningen University, Wageningen 6708WE, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University, Wageningen 6708WE, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen 6708WE, The Netherlands
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3
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Chaisupa P, Rahman MM, Hildreth SB, Moseley S, Gatling C, Bryant MR, Helm RF, Wright RC. Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast. ACS Synth Biol 2024. [PMID: 39197086 DOI: 10.1021/acssynbio.4c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, and animals. Many microbes synthesize and perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), the most prevalent natural auxin, which influences their ability to colonize plants and animals. Understanding auxin biosynthesis and signaling in fungi may allow us to better control interkingdom relationships and microbiomes from agricultural soils to the human gut. Despite this importance, a biological tool for measuring auxin with high spatial and temporal resolution has not been engineered in fungi. In this study, we present a suite of genetically encoded, ratiometric, protein-based auxin biosensors designed for the model yeast Saccharomyces cerevisiae. Inspired by auxin signaling in plants, the ratiometric nature of these biosensors enhances the precision of auxin concentration measurements by minimizing clonal and growth phase variation. We used these biosensors to measure auxin production across diverse growth conditions and phases in yeast cultures and calibrated their responses to physiologically relevant levels of auxin. Future work will aim to improve the fold change and reversibility of these biosensors. These genetically encoded auxin biosensors are valuable tools for investigating auxin biosynthesis and signaling in S. cerevisiae and potentially other yeast and fungi and will also advance quantitative functional studies of the plant auxin perception machinery, from which they are built.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Md Mahbubur Rahman
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sherry B Hildreth
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Saede Moseley
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chauncey Gatling
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Matthew R Bryant
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Richard F Helm
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
- The Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, Virginia 24061, United States
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4
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Morffy N, Van den Broeck L, Miller C, Emenecker RJ, Bryant JA, Lee TM, Sageman-Furnas K, Wilkinson EG, Pathak S, Kotha SR, Lam A, Mahatma S, Pande V, Waoo A, Wright RC, Holehouse AS, Staller MV, Sozzani R, Strader LC. Identification of plant transcriptional activation domains. Nature 2024; 632:166-173. [PMID: 39020176 DOI: 10.1038/s41586-024-07707-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
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Affiliation(s)
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Caelan Miller
- Department of Biology, Duke University, Durham, NC, USA
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - John A Bryant
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Tyler M Lee
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | - Sunita Pathak
- Department of Biology, Duke University, Durham, NC, USA
| | - Sanjana R Kotha
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Angelica Lam
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Saloni Mahatma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Vikram Pande
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Aman Waoo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - R Clay Wright
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Max V Staller
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
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5
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Ferreira Neres D, Wright RC. Pleiotropy, a feature or a bug? Toward co-ordinating plant growth, development, and environmental responses through engineering plant hormone signaling. Curr Opin Biotechnol 2024; 88:103151. [PMID: 38823314 PMCID: PMC11316663 DOI: 10.1016/j.copbio.2024.103151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/03/2024]
Abstract
The advent of gene editing technologies such as CRISPR has simplified co-ordinating trait development. However, identifying candidate genes remains a challenge due to complex gene networks and pathways. These networks exhibit pleiotropy, complicating the determination of specific gene and pathway functions. In this review, we explore how systems biology and single-cell sequencing technologies can aid in identifying candidate genes for co-ordinating specifics of plant growth and development within specific temporal and tissue contexts. Exploring sequence-function space of these candidate genes and pathway modules with synthetic biology allows us to test hypotheses and define genotype-phenotype relationships through reductionist approaches. Collectively, these techniques hold the potential to advance breeding and genetic engineering strategies while also addressing genetic diversity issues critical for adaptation and trait development.
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Affiliation(s)
- Deisiany Ferreira Neres
- Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blackburg, Virginia, United States; Translational Plant Science Center, Virginia Polytechnic Institute and State University, Blackburg, Virginia, United States
| | - R Clay Wright
- Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blackburg, Virginia, United States; Translational Plant Science Center, Virginia Polytechnic Institute and State University, Blackburg, Virginia, United States.
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6
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Cole J, Schulman R. Limiting the Broadcast Range of a Secreting Cell during Intercellular Signaling Using Protease-Mediated Degradation. ACS Synth Biol 2024; 13:2019-2028. [PMID: 38885472 DOI: 10.1021/acssynbio.4c00042] [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: 06/20/2024]
Abstract
Synthetic biology is revolutionizing our approaches to biocomputing, diagnostics, and environmental monitoring through the use of designed genetic circuits that perform a function within a single cell. More complex functions can be performed by multiple cells that coordinate as they perform different subtasks. Cell-cell communication using molecular signals is particularly suited for aiding in this communication, but the number of molecules that can be used in different communication channels is limited. Here we investigate how proteases can limit the broadcast range of communicating cells. We find that adding barrierpepsin to Saccharomyces cerevisiae cells in two-dimensional multicellular networks that use α-factor signaling prevents cells beyond a specific radius from responding to α-factor signals. Such limiting of the broadcast range of cells could allow multiple cells to use the same signaling molecules to direct different communication processes and functions, provided that they are far enough from one another. These results suggest a means by which complex synthetic cellular networks using only a few signals for communication could be created by structuring a community of cells to create distinct broadcast environments.
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Affiliation(s)
- Joshua Cole
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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7
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Cohen JD, Strader LC. An auxin research odyssey: 1989-2023. THE PLANT CELL 2024; 36:1410-1428. [PMID: 38382088 PMCID: PMC11062468 DOI: 10.1093/plcell/koae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The phytohormone auxin is at times called the master regulator of plant processes and has been shown to be a central player in embryo development, the establishment of the polar axis, early aspects of seedling growth, as well as growth and organ formation during later stages of plant development. The Plant Cell has been key, since the inception of the journal, to developing an understanding of auxin biology. Auxin-regulated plant growth control is accomplished by both changes in the levels of active hormones and the sensitivity of plant tissues to these concentration changes. In this historical review, we chart auxin research as it has progressed in key areas and highlight the role The Plant Cell played in these scientific developments. We focus on understanding auxin-responsive genes, transcription factors, reporter constructs, perception, and signal transduction processes. Auxin metabolism is discussed from the development of tryptophan auxotrophic mutants, the molecular biology of conjugate formation and hydrolysis, indole-3-butyric acid metabolism and transport, and key steps in indole-3-acetic acid biosynthesis, catabolism, and transport. This progress leads to an expectation of a more comprehensive understanding of the systems biology of auxin and the spatial and temporal regulation of cellular growth and development.
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Affiliation(s)
- Jerry D Cohen
- Department of Horticultural Science and the Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27008, USA
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8
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Leydon AR, Downing B, Sanchez JS, Loll-Krippleber R, Belliveau NM, Rodriguez-Mias RA, Bauer A, Watson IJ, Bae L, Villén J, Brown GW, Nemhauser JL. A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587599. [PMID: 38617365 PMCID: PMC11014602 DOI: 10.1101/2024.04.01.587599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast model Saccharomyces cerevisiae to localize repressive function to two distinct domains. Here, we employed two unbiased whole genome approaches to map the physical and genetic interactions of TPL at a repressed locus. We identified SPT4, SPT5 and SPT6 as necessary for repression with the SPT4 subunit acting as a bridge connecting TPL to SPT5 and SPT6. We also discovered the association of multiple additional constituents of the transcriptional preinitiation complex at TPL-repressed promoters, specifically those involved in early transcription initiation events. These findings were validated in yeast and plants through multiple assays, including a novel method to analyze conditional loss of function of essential genes in plants. Our findings support a model where TPL nucleates preassembly of the transcription activation machinery to facilitate rapid onset of transcription once repression is relieved.
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Affiliation(s)
| | - Benjamin Downing
- Department of Biology, University of Washington, Seattle, 98195, USA
| | | | | | | | | | - Andrew Bauer
- Department of Biology, University of Washington, Seattle, 98195, USA
| | | | - Lena Bae
- Department of Biology, University of Washington, Seattle, 98195, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, 98195, USA
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, CA
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9
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Rademacher DJ, Bello AI, May JP. CASC3 Biomolecular Condensates Restrict Turnip Crinkle Virus by Limiting Host Factor Availability. J Mol Biol 2023; 435:167956. [PMID: 36642157 PMCID: PMC10338645 DOI: 10.1016/j.jmb.2023.167956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/15/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
The exon-junction complex (EJC) plays a role in post-transcriptional gene regulation and exerts antiviral activity towards several positive-strand RNA viruses. However, the spectrum of RNA viruses that are targeted by the EJC or the underlying mechanisms are not well understood. EJC components from Arabidopsis thaliana were screened for antiviral activity towards Turnip crinkle virus (TCV, Tombusviridae). Overexpression of the accessory EJC component CASC3 inhibited TCV accumulation > 10-fold in Nicotiana benthamiana while knock-down of endogenous CASC3 resulted in a > 4-fold increase in TCV accumulation. CASC3 forms cytoplasmic condensates and deletion of the conserved SELOR domain reduced condensate size 7-fold and significantly decreased antiviral activity towards TCV. Mass spectrometry of CASC3 complexes did not identify endogenous stress granule or P-body markers and CASC3 failed to co-localize with an aggresome-specific dye suggesting that CASC3 condensates are distinct from well-established membraneless compartments. Mass spectrometry and bimolecular fluorescence complementation assays revealed that CASC3 sequesters Heat shock protein 70 (Hsp70-1) and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), two host factors with roles in tombusvirus replication. Overexpression of Hsp70-1 or GAPDH reduced the antiviral activity of CASC3 2.1-fold and 2.8-fold, respectively, and suggests that CASC3 inhibits TCV by limiting host factor availability. Unrelated Tobacco mosaic virus (TMV) also depends on Hsp70-1 and CASC3 overexpression restricted TMV accumulation 4-fold and demonstrates that CASC3 antiviral activity is not TCV-specific. Like CASC3, Auxin response factor 19 (ARF19) forms poorly dynamic condensates but ARF19 overexpression failed to inhibit TCV accumulation and suggests that CASC3 has antiviral activities that are not ubiquitous among cytoplasmic condensates.
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Affiliation(s)
- Dana J Rademacher
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, 5009 Rockhill Road, Kansas City, MO 64110, USA
| | - Abudu I Bello
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, 5009 Rockhill Road, Kansas City, MO 64110, USA
| | - Jared P May
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, 5009 Rockhill Road, Kansas City, MO 64110, USA.
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10
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Jing H, Yang X, Emenecker RJ, Feng J, Zhang J, Figueiredo MRAD, Chaisupa P, Wright RC, Holehouse AS, Strader LC, Zuo J. Nitric oxide-mediated S-nitrosylation of IAA17 protein in intrinsically disordered region represses auxin signaling. J Genet Genomics 2023; 50:473-485. [PMID: 37187411 PMCID: PMC11070147 DOI: 10.1016/j.jgg.2023.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/17/2023]
Abstract
The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. Auxin signaling is activated through the phytohormone-induced proteasomal degradation of the Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) family of transcriptional repressors. Notably, many auxin-modulated physiological processes are also regulated by nitric oxide (NO) that executes its biological effects predominantly through protein S-nitrosylation at specific cysteine residues. However, little is known about the molecular mechanisms in regulating the interactive NO and auxin networks. Here, we show that NO represses auxin signaling by inhibiting IAA17 protein degradation. NO induces the S-nitrosylation of Cys-70 located in the intrinsically disordered region of IAA17, which inhibits the TIR1-IAA17 interaction and consequently the proteasomal degradation of IAA17. The accumulation of a higher level of IAA17 attenuates auxin response. Moreover, an IAA17C70W nitrosomimetic mutation renders the accumulation of a higher level of the mutated protein, thereby causing partial resistance to auxin and defective lateral root development. Taken together, these results suggest that S-nitrosylation of IAA17 at Cys-70 inhibits its interaction with TIR1, thereby negatively regulating auxin signaling. This study provides unique molecular insights into the redox-based auxin signaling in regulating plant growth and development.
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Affiliation(s)
- Hongwei Jing
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biology, Duke University, Durham, NC 27008, USA.
| | - Xiaolu Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jian Feng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA; The Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27008, USA
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China.
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11
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Caumon H, Vernoux T. A matter of time: auxin signaling dynamics and the regulation of auxin responses during plant development. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad132. [PMID: 37042516 DOI: 10.1093/jxb/erad132] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 06/19/2023]
Abstract
As auxin is a major regulator of plant development, studying the signaling mechanisms by which auxin influences cellular activities is of primary importance. In this review, we describe the current knowledge on the different modalities of signaling, from the well-characterized canonical nuclear auxin pathway, to the more recently discovered or re-discovered non-canonical modes of auxin signaling. In particular, we discuss how both the modularity of the nuclear auxin pathway and the dynamic regulation of its core components allow to trigger specific transcriptomic responses. We highlight the fact that the diversity of modes of auxin signaling allows for a wide range of timescales of auxin responses, from second-scale cytoplasmic responses to minute/hour-scale modifications of gene expression. Finally, we question the extent to which the temporality of auxin signaling and responses contributes to development in both the shoot and the root meristems. We conclude by stressing the fact that future investigations should allow to build an integrative view not only of the spatial control, but also of the temporality of auxin-mediated regulation of plant development, from the cell to the whole organism.
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Affiliation(s)
- Hugo Caumon
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
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12
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Meyer RE, Sartin A, Gish M, Harsha J, Wilkie E, Haworth D, LaVictoire R, Alberola I, Chuong HH, Gorbsky GJ, Dawson DS. Polyploid yeast are dependent on elevated levels of Mps1 for successful chromosome segregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523325. [PMID: 36712123 PMCID: PMC9882063 DOI: 10.1101/2023.01.09.523325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tumor cell lines with elevated chromosome numbers frequently have correlated elevations of Mps1 expression and these tumors are more dependent on Mps1 activity for their survival than control cell lines. Mps1 is a conserved kinase involved in controlling aspects of chromosome segregation in mitosis and meiosis. The mechanistic explanation for the Mps1-addiction of aneuploid cells is unknown. To address this question, we explored Mps1-dependence in yeast cells with increased sets of chromosomes. These experiments revealed that in yeast, increasing ploidy leads to delays and failures in orienting chromosomes on the mitotic spindle. Yeast cells with elevated numbers of chromosomes proved vulnerable to reductions of Mps1 activity. Cells with reduced Mps1 activity exhibit an extended prometaphase with longer spindles and delays in orienting the chromosomes. One known role of Mps1 is in recruiting Bub1 to the kinetochore in meiosis. We found that the Mps1-addiction of polyploid yeast cells is due in part to its role in Bub1 recruitment. Together, the experiments presented here demonstrate that increased ploidy renders cells more dependent on Mps1 for orienting chromosomes on the spindle. The phenomenon described here may be relevant in understanding why hyper-diploid cancer cells exhibit elevated reliance on Mps1 expression for successful chromosome segregation.
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Affiliation(s)
- Régis E Meyer
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Ashlea Sartin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Madeline Gish
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Jillian Harsha
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Emily Wilkie
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Dawson Haworth
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Rebecca LaVictoire
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Isabel Alberola
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Hoa H Chuong
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Gary J Gorbsky
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Dean S Dawson
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
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13
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A single helix repression domain is functional across diverse eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2206986119. [PMID: 36191192 PMCID: PMC9564828 DOI: 10.1073/pnas.2206986119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The corepressor TOPLESS (TPL) and its paralogs coordinately regulate a large number of genes critical to plant development and immunity. As in many members of the larger pan-eukaryotic Tup1/TLE/Groucho corepressor family, TPL contains a Lis1 Homology domain (LisH), whose function is not well understood. We have previously found that the LisH in TPL-and specifically the N-terminal 18 amino acid alpha-helical region (TPL-H1)-can act as an autonomous repression domain. We hypothesized that homologous domains across diverse LisH-containing proteins could share the same function. To test that hypothesis, we built a library of H1s that broadly sampled the sequence and evolutionary space of LisH domains, and tested their activity in a synthetic transcriptional repression assay in Saccharomyces cerevisiae. Using this approach, we found that repression activity was highly conserved and likely the ancestral function of this motif. We also identified key residues that contribute to repressive function. We leveraged this new knowledge for two applications. First, we tested the role of mutations found in somatic cancers on repression function in two human LisH-containing proteins. Second, we validated function of many of our repression domains in plants, confirming that these sequences should be of use to synthetic biology applications across many eukaryotes.
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14
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Figueiredo MRAD, Strader LC. Intrinsic and extrinsic regulators of Aux/IAA protein degradation dynamics. Trends Biochem Sci 2022; 47:865-874. [PMID: 35817652 PMCID: PMC9464691 DOI: 10.1016/j.tibs.2022.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 01/03/2023]
Abstract
The plant hormone auxin acts through regulated degradation of Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins to regulate transcriptional events. In this review, we examine the composition and function of each Aux/IAA structural motif. We then focus on recent characterization of Aux/IAA N-terminal disordered regions, formation of secondary structure within these disordered regions, and post-translational modifications (PTMs) that affect Aux/IAA function and stability. We propose how structural variations between Aux/IAA family members may be tuned for differential transcriptional repression and degradation dynamics.
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15
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Cancé C, Martin-Arevalillo R, Boubekeur K, Dumas R. Auxin response factors are keys to the many auxin doors. THE NEW PHYTOLOGIST 2022; 235:402-419. [PMID: 35434800 DOI: 10.1111/nph.18159] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.
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Affiliation(s)
- Coralie Cancé
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Univ. Lyon, Lyon, France
| | - Kenza Boubekeur
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Renaud Dumas
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
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16
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Abstract
Auxin signaling regulates growth and developmental processes in plants. The core of nuclear auxin signaling relies on just three components: TIR1/AFBs, Aux/IAAs, and ARFs. Each component is itself made up of several domains, all of which contribute to the regulation of auxin signaling. Studies of the structural aspects of these three core signaling components have deepened our understanding of auxin signaling dynamics and regulation. In addition to the structured domains of these components, intrinsically disordered regions within the proteins also impact auxin signaling outcomes. New research is beginning to uncover the role intrinsic disorder plays in auxin-regulated degradation and subcellular localization. Structured and intrinsically disordered domains affect auxin perception, protein degradation dynamics, and DNA binding. Taken together, subtle differences within the domains and motifs of each class of auxin signaling component affect signaling outcomes and specificity.
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Affiliation(s)
- Nicholas Morffy
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, Missouri 63130, USA
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, Missouri 63130, USA
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17
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Abstract
Auxin biology as a field has been at the forefront of advances in delineating the structures, dynamics, and control of plant growth networks. Advances have been enabled by combining the complementary fields of top-down, holistic systems biology and bottom-up, build-to-understand synthetic biology. Continued collaboration between these approaches will facilitate our understanding of and ability to engineer auxin's control of plant growth, development, and physiology. There is a need for the application of similar complementary approaches to improving equity and justice through analysis and redesign of the human systems in which this research is undertaken.
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Affiliation(s)
- R Clay Wright
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia 24061, USA
| | - Britney L Moss
- Department of Biology, Whitman College, Walla Walla, Washington 99362, USA
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18
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Wu T, Kerbler SM, Fernie AR, Zhang Y. Plant cell cultures as heterologous bio-factories for secondary metabolite production. PLANT COMMUNICATIONS 2021; 2:100235. [PMID: 34746764 PMCID: PMC8554037 DOI: 10.1016/j.xplc.2021.100235] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/27/2021] [Accepted: 08/19/2021] [Indexed: 05/06/2023]
Abstract
Synthetic biology has been developing rapidly in the last decade and is attracting increasing attention from many plant biologists. The production of high-value plant-specific secondary metabolites is, however, limited mostly to microbes. This is potentially problematic because of incorrect post-translational modification of proteins and differences in protein micro-compartmentalization, substrate availability, chaperone availability, product toxicity, and cytochrome p450 reductase enzymes. Unlike other heterologous systems, plant cells may be a promising alternative for the production of high-value metabolites. Several commercial plant suspension cell cultures from different plant species have been used successfully to produce valuable metabolites in a safe, low cost, and environmentally friendly manner. However, few metabolites are currently being biosynthesized using plant platforms, with the exception of the natural pigment anthocyanin. Both Arabidopsis thaliana and Nicotiana tabacum cell cultures can be developed by multiple gene transformations and CRISPR-Cas9 genome editing. Given that the introduction of heterologous biosynthetic pathways into Arabidopsis and N. tabacum is not widely used, the biosynthesis of foreign metabolites is currently limited; however, therein lies great potential. Here, we discuss the exemplary use of plant cell cultures and prospects for using A. thaliana and N. tabacum cell cultures to produce valuable plant-specific metabolites.
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Affiliation(s)
- Tong Wu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Sandra M. Kerbler
- Leibniz-Institute für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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19
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A Gain-of-Function Mutant of IAA7 Inhibits Stem Elongation by Transcriptional Repression of EXPA5 Genes in Brassica napus. Int J Mol Sci 2021; 22:ijms22169018. [PMID: 34445724 PMCID: PMC8396470 DOI: 10.3390/ijms22169018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/09/2023] Open
Abstract
Plant height is one of the most important agronomic traits of rapeseeds. In this study, we characterized a dwarf Brassica napus mutant, named ndf-2, obtained from fast neutrons and DES mutagenesis. Based on BSA-Seq and genetic properties, we identified causal mutations with a time-saving approach. The ndf-2 mutation was identified on chromosome A03 and can result in an amino acid substitution in the conserved degron motif (GWPPV to EWPPV) of the Auxin/indole-3-acetic acid protein 7 (BnaA03.IAA7) encoded by the causative gene. Aux/IAA protein is one of the core components of the auxin signaling pathway, which regulates many growth and development processes. However, the molecular mechanism of auxin signal regulating plant height is still not well understood. In the following work, we identified that BnaARF6 and BnaARF8 as interactors of BnaA03.IAA7 and BnaEXPA5 as a target of BnaARF6 and BnaARF8. The three genes BnaA03.IAA7, BnaARF6/8 and BnaEXPA5 were highly expressed in stem, suggesting that these genes were involved in stem development. The overexpression of BnaEXPA5 results in larger rosettes leaves and longer inflorescence stems in Arabidopsis thaliana. Our results indicate that BnaA03.IAA7- and BnaARF6/8-dependent auxin signal control stem elongation and plant height by regulating the transcription of BnaEXPA5 gene, which is one of the targets of this signal.
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20
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Khakhar A, Voytas DF. RNA Viral Vectors for Accelerating Plant Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:668580. [PMID: 34249040 PMCID: PMC8261061 DOI: 10.3389/fpls.2021.668580] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/19/2021] [Indexed: 05/03/2023]
Abstract
The tools of synthetic biology have enormous potential to help us uncover the fundamental mechanisms controlling development and metabolism in plants. However, their effective utilization typically requires transgenesis, which is plagued by long timescales and high costs. In this review we explore how transgenesis can be minimized by delivering foreign genetic material to plants with systemically mobile and persistent vectors based on RNA viruses. We examine the progress that has been made thus far and highlight the hurdles that need to be overcome and some potential strategies to do so. We conclude with a discussion of biocontainment mechanisms to ensure these vectors can be used safely as well as how these vectors might expand the accessibility of plant synthetic biology techniques. RNA vectors stand poised to revolutionize plant synthetic biology by making genetic manipulation of plants cheaper and easier to deploy, as well as by accelerating experimental timescales from years to weeks.
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Affiliation(s)
- Arjun Khakhar
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, United States
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, United States
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
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21
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Leydon AR, Wang W, Gala HP, Gilmour S, Juarez-Solis S, Zahler ML, Zemke JE, Zheng N, Nemhauser JL. Repression by the Arabidopsis TOPLESS corepressor requires association with the core mediator complex. eLife 2021; 10:66739. [PMID: 34075876 PMCID: PMC8203292 DOI: 10.7554/elife.66739] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/31/2021] [Indexed: 02/06/2023] Open
Abstract
The plant corepressor TOPLESS (TPL) is recruited to a large number of loci that are selectively induced in response to developmental or environmental cues, yet the mechanisms by which it inhibits expression in the absence of these stimuli are poorly understood. Previously, we had used the N-terminus of Arabidopsis thaliana TPL to enable repression of a synthetic auxin response circuit in Saccharomyces cerevisiae (yeast). Here, we leveraged the yeast system to interrogate the relationship between TPL structure and function, specifically scanning for repression domains. We identified a potent repression domain in Helix 8 located within the CRA domain, which directly interacted with the Mediator middle module subunits Med21 and Med10. Interactions between TPL and Mediator were required to fully repress transcription in both yeast and plants. In contrast, we found that multimer formation, a conserved feature of many corepressors, had minimal influence on the repression strength of TPL.
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Affiliation(s)
| | - Wei Wang
- Department of Pharmacology, Seattle, United States
| | - Hardik P Gala
- Department of Biology, University of Washington, Seattle, United States
| | - Sabrina Gilmour
- Department of Biology, University of Washington, Seattle, United States
| | | | - Mollye L Zahler
- Department of Biology, University of Washington, Seattle, United States
| | - Joseph E Zemke
- Department of Biology, University of Washington, Seattle, United States
| | - Ning Zheng
- Department of Pharmacology, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
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22
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Zhao C, Yaschenko A, Alonso JM, Stepanova AN. Leveraging synthetic biology approaches in plant hormone research. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101998. [PMID: 33476945 DOI: 10.1016/j.pbi.2020.101998] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/20/2020] [Accepted: 12/25/2020] [Indexed: 05/18/2023]
Abstract
The study of plant hormones is critical to understanding development, physiology and interactions of plants with their environment. Synthetic biology holds promise to provide a new perspective and shed fresh light on the molecular mechanisms of plant hormone action and propel the design of novel biotechnologies. With the recent adoption of synthetic biology in plant sciences, exciting first examples of successful tool development and their applications in the area of plant hormone research are emerging, paving the way for new cadres to enter this promising field of science.
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Affiliation(s)
- Chengsong Zhao
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna Yaschenko
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
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23
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Bradley AI, Marsh NM, Borror HR, Mostoller KE, Gama AI, Gardner RG. Acute ethanol stress induces sumoylation of conserved chromatin structural proteins in Saccharomyces cerevisiae. Mol Biol Cell 2021; 32:1121-1133. [PMID: 33788582 PMCID: PMC8351541 DOI: 10.1091/mbc.e20-11-0715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Stress is ubiquitous to life and can irreparably damage essential biomolecules and organelles in cells. To survive, organisms must sense and adapt to stressful conditions. One highly conserved adaptive stress response is through the posttranslational modification of proteins by the small ubiquitin-like modifier (SUMO). Here, we examine the effects of acute ethanol stress on protein sumoylation in the budding yeast Saccharomyces cerevisiae. We found that cells exhibit a transient sumoylation response after acute exposure to ≤7.5% vol/vol ethanol. By contrast, the sumoylation response becomes chronic at 10% ethanol exposure. Mass spectrometry analyses identified 18 proteins that are sumoylated after acute ethanol exposure, with 15 known to associate with chromatin. Upon further analysis, we found that the chromatin structural proteins Smc5 and Smc6 undergo ethanol-induced sumoylation that depends on the activity of the E3 SUMO ligase Mms21. Using cell-cycle arrest assays, we observed that Smc5 and Smc6 ethanol-induced sumoylation occurs during G1 and G2/M phases but not S phase. Acute ethanol exposure also resulted in the formation of Rad52 foci at levels comparable to Rad52 foci formation after exposure to the DNA alkylating agent methyl methanesulfonate (MMS). MMS exposure is known to induce the intra-S-phase DNA damage checkpoint via Rad53 phosphorylation, but ethanol exposure did not induce Rad53 phosphorylation. Ethanol abrogated the effect of MMS on Rad53 phosphorylation when added simultaneously. From these studies, we propose that acute ethanol exposure induces a change in chromatin leading to sumoylation of specific chromatin structural proteins.
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Affiliation(s)
- Amanda I Bradley
- Department of Pharmacology, University of Washington, Seattle, WA 98195.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195
| | - Nicole M Marsh
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Heather R Borror
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | | | - Amber I Gama
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, WA 98195.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195
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24
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Ramos Báez R, Nemhauser JL. Expansion and innovation in auxin signaling: where do we grow from here? Development 2021; 148:dev187120. [PMID: 33712444 PMCID: PMC7970066 DOI: 10.1242/dev.187120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The phytohormone auxin plays a role in almost all growth and developmental responses. The primary mechanism of auxin action involves the regulation of transcription via a core signaling pathway comprising proteins belonging to three classes: receptors, co-receptor/co-repressors and transcription factors. Recent studies have revealed that auxin signaling can be traced back at least as far as the transition to land. Moreover, studies in flowering plants have highlighted how expansion of the gene families encoding auxin components is tied to functional diversification. As we review here, these studies paint a picture of auxin signaling evolution as a driver of innovation.
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Affiliation(s)
- Román Ramos Báez
- University of Washington, Department of Biology, Seattle, WA 98105-1800, USA
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25
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Yang X, Liu J, Zhang J, Shen Y, Qi Q, Bao X, Hou J. Quorum sensing-mediated protein degradation for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metab Eng 2021; 64:85-94. [PMID: 33545357 DOI: 10.1016/j.ymben.2021.01.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Dynamic regulation has been widely applied to optimize metabolic flux distribution. However, compared with prokaryotes, quorum sensing-mediated pathway control is still very limited in Saccharomyces cerevisiae. In this study, we designed quorum sensing-regulated protein degradation circuits for dynamic metabolic pathway control in S. cerevisiae. The synthetic quorum sensing circuits were developed by integration of a plant hormone cytokinin system with the endogenous yeast Ypd1-Skn7 signal transduction pathway and the positive feedback circuits were optimized by promoter engineering. We then constructed an auxin-inducible protein degradation system and used quorum sensing circuits to regulate auxin synthesis to achieve dynamic control of protein degradation. As a demonstration, the circuits were applied to control Erg9 degradation to produce α-farnesene and the titer of α-farnesene increased by 80%. The population-regulated protein degradation system developed here extends dynamic regulation to the protein level in S. cerevisiae and is a promising approach for metabolic pathway control.
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Affiliation(s)
- Xiaoyu Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Jianhui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Jin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China; State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qi Lu University of Technology, Jinan, 250353, PR China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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26
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Israeli A, Reed JW, Ori N. Genetic dissection of the auxin response network. NATURE PLANTS 2020; 6:1082-1090. [PMID: 32807951 DOI: 10.1038/s41477-020-0739-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/06/2020] [Indexed: 05/24/2023]
Abstract
The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.
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Affiliation(s)
- Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, Rehovot, Israel
| | - Jason W Reed
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, Rehovot, Israel.
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27
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Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu LD, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite JM, Rigal A, Ramans Harborough S, Persiau G, Vanneste S, Kirschner GK, Vandermarliere E, Martens L, Stahl Y, Audenaert D, Friml J, Felix G, Simon R, Bennett MJ, Bishopp A, De Jaeger G, Ljung K, Kepinski S, Robert S, Nemhauser J, Hwang I, Gevaert K, Beeckman T, De Smet I. The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis. Mol Cell Proteomics 2020; 19:1248-1262. [PMID: 32404488 PMCID: PMC8011570 DOI: 10.1074/mcp.ra119.001826] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/02/2020] [Indexed: 01/20/2023] Open
Abstract
Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-TERMINALLY ENCODED PEPTIDE 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical, and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.
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Affiliation(s)
- Stephanie Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Shanshuo Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lisa Joos
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ianto Roberts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Natalia Nikonorova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Antoine Larrieu
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Wei Xuan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Benjamin Goodall
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Brigitte van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jessic Marie Waite
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Adeline Rigal
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sigurd Ramans Harborough
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Gwendolyn K Kirschner
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Elien Vandermarliere
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Dominique Audenaert
- Screening Core, Gent, Belgium; Expertise Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Jirí Friml
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University (MU), Brno, Czech Republic; Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Georg Felix
- Zentrum für Molekularbiologie der Pflanzen, Plant Biochemistry, University Tübingen, Tübingen, Germany
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Malcolm J Bennett
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom; Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Stephanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom; Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom.
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Ramos Báez R, Buckley Y, Yu H, Chen Z, Gallavotti A, Nemhauser JL, Moss BL. A Synthetic Approach Allows Rapid Characterization of the Maize Nuclear Auxin Response Circuit. PLANT PHYSIOLOGY 2020; 182:1713-1722. [PMID: 32123041 PMCID: PMC7140906 DOI: 10.1104/pp.19.01475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/22/2020] [Indexed: 05/20/2023]
Abstract
Auxin plays a key role across all land plants in growth and developmental processes. Although auxin signaling function has diverged and expanded, differences in the molecular functions of signaling components have largely been characterized in Arabidopsis (Arabidopsis thaliana). Here, we used the nuclear Auxin Response Circuit recapitulated in yeast (Saccharomyces cerevisiae) system to functionally annotate maize (Zea mays) auxin signaling components, focusing on genes expressed during the development of ear and tassel inflorescences. All 16 maize auxin/indole-3-acetic acid repressor proteins were degraded in response to auxin with rates that depended on both receptor and repressor identities. When fused to the maize TOPLESS homolog RAMOSA1 ENHANCER LOCUS2, maize auxin/indole-3-acetic acids were able to repress AUXIN RESPONSE FACTOR transcriptional activity. A complete auxin response circuit comprising all maize components, including the ZmAFB2/3 b1 maize AUXIN SIGNALING F-BOX (AFB) receptor, was fully functional. The ZmAFB2/3 b1 auxin receptor was more sensitive to hormone than AtAFB2 and allowed for rapid circuit activation upon auxin addition. These results validate the conserved role of predicted auxin response genes in maize as well as provide evidence that a synthetic approach can facilitate broader comparative studies across the wide range of species with sequenced genomes.
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Affiliation(s)
- Román Ramos Báez
- University of Washington, Department of Biology, Seattle, Washington 98105
| | - Yuli Buckley
- Whitman College, Department of Biology, Walla Walla, Washington 99362
| | - Han Yu
- Whitman College, Department of Biology, Walla Walla, Washington 99362
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901
| | | | - Britney L Moss
- Whitman College, Department of Biology, Walla Walla, Washington 99362
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29
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Powers SK, Strader LC. Regulation of auxin transcriptional responses. Dev Dyn 2019; 249:483-495. [PMID: 31774605 PMCID: PMC7187202 DOI: 10.1002/dvdy.139] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/17/2019] [Accepted: 11/22/2019] [Indexed: 01/27/2023] Open
Abstract
The plant hormone auxin acts as a signaling molecule to regulate a vast number of developmental responses throughout all stages of plant growth. Tight control and coordination of auxin signaling is required for the generation of specific auxin‐response outputs. The nuclear auxin signaling pathway controls auxin‐responsive gene transcription through the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F‐BOX pathway. Recent work has uncovered important details into how regulation of auxin signaling components can generate unique and specific responses to determine auxin outputs. In this review, we discuss what is known about the core auxin signaling components and explore mechanisms important for regulating auxin response specificity. A review of recent updates to our understanding of auxin signaling.
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Affiliation(s)
- Samantha K Powers
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri
| | - Lucia C Strader
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri.,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri.,Center for Engineering MechanoBiology, Washington University in St. Louis, St. Louis, Missouri
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30
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Lakehal A, Chaabouni S, Cavel E, Le Hir R, Ranjan A, Raneshan Z, Novák O, Păcurar DI, Perrone I, Jobert F, Gutierrez L, Bakò L, Bellini C. A Molecular Framework for the Control of Adventitious Rooting by TIR1/AFB2-Aux/IAA-Dependent Auxin Signaling in Arabidopsis. MOLECULAR PLANT 2019; 12:1499-1514. [PMID: 31520787 DOI: 10.1016/j.molp.2019.09.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/20/2019] [Accepted: 09/03/2019] [Indexed: 05/13/2023]
Abstract
In Arabidopsis thaliana, canonical auxin-dependent gene regulation is mediated by 23 transcription factors from the AUXIN RESPONSE FACTOR (ARF) family that interact with auxin/indole acetic acid repressors (Aux/IAAs), which themselves form co-receptor complexes with one of six TRANSPORT INHIBITOR1/AUXIN-SIGNALLING F-BOX (TIR1/AFB) proteins. Different combinations of co-receptors drive specific sensing outputs, allowing auxin to control a myriad of processes. ARF6 and ARF8 are positive regulators of adventitious root initiation upstream of jasmonate, but the exact auxin co-receptor complexes controlling the transcriptional activity of these proteins has remained unknown. Here, using loss-of-function mutants we show that three Aux/IAA genes, IAA6, IAA9, and IAA17, act additively in the control of adventitious root (AR) initiation. These three IAA proteins interact with ARF6 and/or ARF8 and likely repress their activity in AR development. We show that TIR1 and AFB2 are positive regulators of AR formation and TIR1 plays a dual role in the control of jasmonic acid (JA) biosynthesis and conjugation, as several JA biosynthesis genes are up-regulated in the tir1-1 mutant. These results lead us to propose that in the presence of auxin, TIR1 and AFB2 form specific sensing complexes with IAA6, IAA9, and/or IAA17 to modulate JA homeostasis and control AR initiation.
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Affiliation(s)
- Abdellah Lakehal
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Salma Chaabouni
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Emilie Cavel
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Rozenn Le Hir
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Alok Ranjan
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Zahra Raneshan
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden; Department of Biology, Faculty of Science, Shahid Bahonar University, Kerman, Iran
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, 78371 Olomouc, Czech Republic; Umeå Plant Science Centre, Department of Forest Genetics and Physiology, Swedish Agriculture University, 90183 Umeå, Sweden
| | - Daniel I Păcurar
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Irene Perrone
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - François Jobert
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne, 80039 Amiens, France
| | - Laurent Gutierrez
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne, 80039 Amiens, France
| | - Laszlo Bakò
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden
| | - Catherine Bellini
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90736 Umeå, Sweden; Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
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Hamm MO, Moss BL, Leydon AR, Gala HP, Lanctot A, Ramos R, Klaeser H, Lemmex AC, Zahler ML, Nemhauser JL, Wright RC. Accelerating structure-function mapping using the ViVa webtool to mine natural variation. PLANT DIRECT 2019; 3:e00147. [PMID: 31372596 PMCID: PMC6658840 DOI: 10.1002/pld3.147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/20/2019] [Accepted: 04/29/2019] [Indexed: 05/13/2023]
Abstract
Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well-studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less-studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/).
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Affiliation(s)
- Morgan O. Hamm
- Department of BiologyUniversity of WashingtonSeattleWashington
| | | | | | - Hardik P. Gala
- Department of BiologyUniversity of WashingtonSeattleWashington
| | - Amy Lanctot
- Department of BiologyUniversity of WashingtonSeattleWashington
| | - Román Ramos
- Department of BiologyUniversity of WashingtonSeattleWashington
| | - Hannah Klaeser
- Department of BiologyWhitman CollegeWalla WallaWashington
| | | | | | | | - R. Clay Wright
- Biological Systems EngineeringVirginia TechBlacksburgVirginia
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Abstract
Engineered systems that control cellular differentiation and pattern formation are essential for applications like tissue engineering, biomaterial fabrication, and synthetic ecosystems. Synthetic circuits that can take on multiple states have been made to engineer multicellular systems. However, how to use these states to drive interesting cellular behavior remains challenging. Here, we present a cellular differentiation program involving a novel synthetic bistable switch coupled to an antibiotic resistance gene that affects growth in yeast ( S. cerevisiae). The switch is composed of a positive feedback loop involving a novel transcription factor and can be switched ON and OFF via two different transient inducer inputs. By further coupling the bistable switch with an antibiotic resistance gene, we obtained a growth differentiation circuit, where yeast cells can be switched to stable HIGH or LOW growth rate states via transient inducer inputs. This work demonstrates a rationally designed and experimentally validated cellular differentiation behavior in yeast.
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Affiliation(s)
- Yaoyu Yang
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jennifer L. Nemhauser
- Department of Biology, University of Washington, Seattle, Washington 98195, United States
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, United States
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Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development. Proc Natl Acad Sci U S A 2019; 116:6463-6472. [PMID: 30850516 PMCID: PMC6442611 DOI: 10.1073/pnas.1809037116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCFTIR1/AFB functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.
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34
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Matthes MS, Best NB, Robil JM, Malcomber S, Gallavotti A, McSteen P. Auxin EvoDevo: Conservation and Diversification of Genes Regulating Auxin Biosynthesis, Transport, and Signaling. MOLECULAR PLANT 2019; 12:298-320. [PMID: 30590136 DOI: 10.1016/j.molp.2018.12.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/02/2018] [Accepted: 12/16/2018] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin has been shown to be of pivotal importance in growth and development of land plants. The underlying molecular players involved in auxin biosynthesis, transport, and signaling are quite well understood in Arabidopsis. However, functional characterizations of auxin-related genes in economically important crops, specifically maize and rice, are still limited. In this article, we comprehensively review recent functional studies on auxin-related genes in both maize and rice, compared with what is known in Arabidopsis, and highlight conservation and diversification of their functions. Our analysis is illustrated by phylogenetic analysis and publicly available gene expression data for each gene family, which will aid in the identification of auxin-related genes for future research. Current challenges and future directions for auxin research in maize and rice are discussed. Developments in gene editing techniques provide powerful tools for overcoming the issue of redundancy in these gene families and will undoubtedly advance auxin research in crops.
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Affiliation(s)
- Michaela Sylvia Matthes
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Norman Bradley Best
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Janlo M Robil
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Simon Malcomber
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020, USA; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA.
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35
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Jayasinghege CPA, Ozga JA, Nadeau CD, Kaur H, Reinecke DM. TIR1 auxin receptors are implicated in the differential response to 4-Cl-IAA and IAA in developing pea fruit. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1239-1253. [PMID: 30715391 PMCID: PMC6382345 DOI: 10.1093/jxb/ery456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/07/2019] [Indexed: 05/24/2023]
Abstract
The auxins indole-3-acetic acid (IAA) and 4-chloroindole-3-acetic acid (4-Cl-IAA) occur naturally in pea (Pisum sativum); however, only 4-Cl-IAA mimics the presence of seeds in stimulating pericarp growth. To examine if this differential auxin effect is mediated through TIR1/AFB auxin receptors, pea TIR1 and AFB2 homologs were functionally characterized in Arabidopsis, and receptor expression, and auxin distribution and action were profiled in developing pea fruits. PsTIR1a, PsTIR1b, and PsAFB2 restored the auxin-sensitive root growth response to the mutant Arabidopsis seedlings Attir1-10 and/or Attir1-10 afb2-3. Expression of PsTIR1 or AtTIR1 in Attir1-10 afb2-3 mutants also restored the greater root inhibitory response of 4-Cl-IAA compared to that of IAA, implicating TIR1 receptors in this response. The ability of 4-Cl-IAA to stimulate a stronger DR5::GUS auxin response than IAA at the same concentration in pea pericarps was associated with its ability to enrich the auxin-receptor transcript pool with PsTIR1a and PsAFB2 by decreasing the transcript abundance of PsTIR1b (mimicking results in pericarps with developing seeds). Therefore, the markedly different effect of IAA and 4-Cl-IAA on pea fruit growth may at least partially involve TIR1/AFB receptors and the differential modulation of their population, resulting in specific Aux/IAA protein degradation that leads to an auxin-specific tissue response.
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Affiliation(s)
- Charitha P A Jayasinghege
- Plant BioSystems, Department of Agricultural, Food and Nutritional Science University of Alberta, Edmonton, Alberta, Canada
| | - Jocelyn A Ozga
- Plant BioSystems, Department of Agricultural, Food and Nutritional Science University of Alberta, Edmonton, Alberta, Canada
| | - Courtney D Nadeau
- Plant BioSystems, Department of Agricultural, Food and Nutritional Science University of Alberta, Edmonton, Alberta, Canada
| | - Harleen Kaur
- Plant BioSystems, Department of Agricultural, Food and Nutritional Science University of Alberta, Edmonton, Alberta, Canada
| | - Dennis M Reinecke
- Plant BioSystems, Department of Agricultural, Food and Nutritional Science University of Alberta, Edmonton, Alberta, Canada
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37
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Torii KU, Hagihara S, Uchida N, Takahashi K. Harnessing synthetic chemistry to probe and hijack auxin signaling. THE NEW PHYTOLOGIST 2018; 220:417-424. [PMID: 30088268 DOI: 10.1111/nph.15337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 417 I. Introduction 417 II. Auxin analogs 1: Plant growth regulators 418 III. Auxin analogs 2: Molecular genetics and chemical biology 418 IV. Auxin analogs 3: Structure-guided chemical design 418 V. Auxin analogs 4: Synthetic orthogonal auxin-TIR1 pair 420 VI. Conclusions and future perspectives 422 Acknowledgements 422 References 423 SUMMARY: Plant biologists have been fascinated by auxin - a small chemical hormone so simple in structure yet so powerful - which regulates virtually every aspect of plant growth, development and behavior. Synthetic chemistry has played a major role in unraveling the physiological effects of auxin and the application of synthetic analogs has had a dramatic effect on tissue culture, horticulture and the agriculture of economically relevant plant species. Chemical genetics of the model plant, Arabidopsis thaliana, has helped to elucidate the nuclear auxin signaling pathway mediated by the receptor, TIR1, and opened the door to structure-guided, rational designs of auxin agonists and antagonists. Further improvement and tuning of such analogs has been achieved through derivatization and screening. Finally, by harnessing synthetic chemistry and receptor engineering, an orthogonal auxin-TIR1 pair has been created and developed, enabling spatiotemporal control of auxin perception and response. This synergism of chemistry, biology and engineering sparks new ideas and directions to delineate, uncover and manipulate auxin signaling.
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Affiliation(s)
- Keiko U Torii
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- RIKEN Center for Sustainable Resource Science (CSRS), Wako, Saitama, 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
| | - Naoyuki Uchida
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Koji Takahashi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
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38
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Tao S, Estelle M. Mutational studies of the Aux/IAA proteins in Physcomitrella reveal novel insights into their function. THE NEW PHYTOLOGIST 2018; 218:1534-1542. [PMID: 29461641 PMCID: PMC6054139 DOI: 10.1111/nph.15039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/09/2018] [Indexed: 05/27/2023]
Abstract
The plant hormone auxin regulates many aspects of plant growth and development. Auxin signaling involves hormone perception by the TRANSPORT INHIBITOR RESPONSE/AUXIN F-BOX (TIR1/AFB)-Aux/IAA co-receptor system, and the subsequent degradation of the Aux/IAA transcriptional repressors by the ubiquitin proteasome pathway. This leads to the activation of downstream gene expression and diverse physiological responses. Here, we investigate how the structural elements in the Aux/IAAs determine their function in Auxin perception and transcriptional repression. We took advantage of the facile genetics of the moss Physcomitrella patens to determine the activity of wild-type and mutant PpIAA1a proteins in a Δaux/iaa null background. In this way, Aux/IAA function was characterized at the molecular and physiological levels without the interference of genetic redundancy. We identified and characterized degron variants in Aux/IAAs that affect their stability and Auxin response. We also demonstrated that neither the Aux/IAA EAR motif nor Aux/IAA oligomerization is essential for the repressive function of Aux/IAA. Our study demonstrates how key elements within the Aux/IAA proteins fine tune stability and repressor activity, as well as the long-term developmental outcome.
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Affiliation(s)
- Sibo Tao
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
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Kelley DR. E3 Ubiquitin Ligases: Key Regulators of Hormone Signaling in Plants. Mol Cell Proteomics 2018; 17:1047-1054. [PMID: 29514858 PMCID: PMC5986243 DOI: 10.1074/mcp.mr117.000476] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/09/2018] [Indexed: 02/05/2023] Open
Abstract
Ubiquitin-mediated control of protein stability is central to most aspects of plant hormone signaling. Attachment of ubiquitin to target proteins occurs via an enzymatic cascade with the final step being catalyzed by a family of enzymes known as E3 ubiquitin ligases, which have been classified based on their protein domains and structures. Although E3 ubiquitin ligases are conserved among eukaryotes, in plants they are well-known to fulfill unique roles as central regulators of phytohormone signaling, including hormone perception and regulation of hormone biosynthesis. This review will highlight up-to-date findings that have refined well-known E3 ligase-substrate interactions and defined novel E3 ligase substrates that mediate numerous hormone signaling pathways. Additionally, examples of how particular E3 ligases may mediate hormone crosstalk will be discussed as an emerging theme. Looking forward, promising experimental approaches and methods that will provide deeper mechanistic insight into the roles of E3 ubiquitin ligases in plants will be considered.
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Affiliation(s)
- Dior R Kelley
- From the ‡Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011
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Nemhauser JL. Back to basics: what is the function of an Aux/IAA in auxin response? THE NEW PHYTOLOGIST 2018; 218:1295-1297. [PMID: 29738089 DOI: 10.1111/nph.15172] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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41
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Lambrus BG, Moyer TC, Holland AJ. Applying the auxin-inducible degradation system for rapid protein depletion in mammalian cells. Methods Cell Biol 2018; 144:107-135. [PMID: 29804665 DOI: 10.1016/bs.mcb.2018.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ability to deplete a protein of interest is critical for dissecting cellular processes. Traditional methods of protein depletion are often slow acting, which can be problematic when characterizing a cellular process that occurs within a short period of time, such as mitosis. Furthermore, these methods are usually not reversible. Recent advances to achieve protein depletion function by inducibly trafficking proteins of interest to an endogenous E3 ubiquitin ligase complex to promote ubiquitination and subsequent degradation by the proteasome. One of these systems, the auxin-inducible degron (AID) system, has been shown to permit rapid and inducible degradation of AID-tagged target proteins in mammalian cells. The AID system can control the abundance of a diverse set of cellular proteins, including those contained within protein complexes, and is active in all phases of the cell cycle. Here we discuss considerations for the successful implementation of the AID system and describe a protocol using CRISPR/Cas9 to achieve biallelic insertion of an AID in human cells. This method can also be adapted to insert other tags, such as fluorescent proteins, at defined genomic locations.
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Affiliation(s)
- Bramwell G Lambrus
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tyler C Moyer
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrew J Holland
- Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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Abstract
Recapitulation of the nuclear auxin response pathway in Saccharomyces cerevisiae (yeast) provides a means to functionally assay the contribution of individual signaling components to response dynamics. Here, we describe a time course assay for characterizing auxin response circuits using flow cytometry. This method allows for quantitative measurements of the dynamic response of up to 12 circuits (strains) at once. We also describe a steady-state assay and how to utilize an R package we developed to facilitate data analysis.
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Ma Q, Grones P, Robert S. Auxin signaling: a big question to be addressed by small molecules. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:313-328. [PMID: 29237069 PMCID: PMC5853230 DOI: 10.1093/jxb/erx375] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/16/2017] [Indexed: 05/20/2023]
Abstract
Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.
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Affiliation(s)
- Qian Ma
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
| | - Peter Grones
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
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Kato H, Nishihama R, Weijers D, Kohchi T. Evolution of nuclear auxin signaling: lessons from genetic studies with basal land plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:291-301. [PMID: 28992186 DOI: 10.1093/jxb/erx267] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Auxin plays critical roles in growth and development through the regulation of cell differentiation, cell expansion, and pattern formation. The auxin signal is mainly conveyed through a so-called nuclear auxin pathway involving the receptor TIR1/AFB, the transcriptional co-repressor AUX/IAA, and the transcription factor ARF with direct DNA-binding ability. Recent progress in sequence information and molecular genetics in basal plants has provided many insights into the evolutionary origin of the nuclear auxin pathway and its pleiotropic roles in land plant development. In this review, we summarize the latest knowledge of the nuclear auxin pathway gained from studies using basal plants, including charophycean green algae and two major model bryophytes, Marchantia polymorpha and Physcomitrella patens. In addition, we discuss the functional implication of the increase in genetic complexity of the nuclear auxin pathway during land plant evolution.
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Affiliation(s)
- Hirotaka Kato
- Laboratory of Biochemistry, Wageningen University, The Netherlands
| | | | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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Grigolon S, Bravi B, Martin OC. Responses to auxin signals: an operating principle for dynamical sensitivity yet high resilience. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172098. [PMID: 29410878 PMCID: PMC5792956 DOI: 10.1098/rsos.172098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/08/2017] [Indexed: 05/29/2023]
Abstract
Plants depend on the signalling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signalling network involves a negative feedback on Aux/IAA proteins which mediate the influence of auxin (the signal) on the auxin response factor (ARF) transcription factors (the drivers of the response). To probe the role of this feedback, we consider alternative in silico signalling networks implementing different operating principles. By a comparative analysis, we find that the presence of a negative feedback allows the system to have a far larger sensitivity in its dynamical response to auxin and that this sensitivity does not prevent the system from being highly resilient. Given this insight, we build a new biomolecular signalling model for quantitatively describing such Aux/IAA and ARF responses.
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Affiliation(s)
- S. Grigolon
- LPTMS, Université Paris-Sud XI-Université Paris-Saclay, 15, Rue Georges Clémenceau, 91405 Orsay, France
| | - B. Bravi
- Department of Mathematics, King’s College London, The Strand, London WC2R 2LS, UK
| | - O. C. Martin
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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46
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Abstract
Auxin triggers diverse responses in plants, and this is reflected in quantitative and qualitative diversity in the auxin signaling machinery.
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Affiliation(s)
- Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
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Wright RC, Zahler ML, Gerben SR, Nemhauser JL. Insights into the Evolution and Function of Auxin Signaling F-Box Proteins in Arabidopsis thaliana Through Synthetic Analysis of Natural Variants. Genetics 2017; 207:583-591. [PMID: 28760746 PMCID: PMC5629325 DOI: 10.1534/genetics.117.300092] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/24/2017] [Indexed: 12/20/2022] Open
Abstract
The evolution of complex body plans in land plants has been paralleled by gene duplication and divergence within nuclear auxin-signaling networks. A deep mechanistic understanding of auxin signaling proteins therefore may allow rational engineering of novel plant architectures. Toward that end, we analyzed natural variation in the auxin receptor F-box family of wild accessions of the reference plant Arabidopsis thaliana and used this information to populate a structure/function map. We employed a synthetic assay to identify natural hypermorphic F-box variants and then assayed auxin-associated phenotypes in accessions expressing these variants. To more directly measure the impact of the strongest variant in our synthetic assay on auxin sensitivity, we generated transgenic plants expressing this allele. Together, our findings link evolved sequence variation to altered molecular performance and auxin sensitivity. This approach demonstrates the potential for combining synthetic biology approaches with quantitative phenotypes to harness the wealth of available sequence information and guide future engineering efforts of diverse signaling pathways.
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Affiliation(s)
- R Clay Wright
- Department of Biology, University of Washington, Seattle, Washington 98195-1800
| | - Mollye L Zahler
- Department of Biology, University of Washington, Seattle, Washington 98195-1800
| | - Stacey R Gerben
- Department of Biology, University of Washington, Seattle, Washington 98195-1800
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Abstract
The plant hormone auxin triggers complex growth and developmental processes. Its underlying molecular mechanism of action facilitates rapid switching between transcriptional repression and gene activation through the auxin-dependent degradation of transcriptional repressors. The nuclear auxin signaling pathway consists of a small number of core components. However, in most plants each component is represented by a large gene family. The modular construction of the pathway can thus produce diverse transcriptional outputs depending on the cellular and environmental context. Here, and in the accompanying poster, we outline the current model for TIR1/AFB-dependent auxin signaling with an emphasis on recent studies.
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Affiliation(s)
- Meirav Lavy
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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Xu J, Li J, Cui L, Zhang T, Wu Z, Zhu PY, Meng YJ, Zhang KJ, Yu XQ, Lou QF, Chen JF. New insights into the roles of cucumber TIR1 homologs and miR393 in regulating fruit/seed set development and leaf morphogenesis. BMC PLANT BIOLOGY 2017; 17:130. [PMID: 28747179 PMCID: PMC5530481 DOI: 10.1186/s12870-017-1075-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/13/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND TIR1-like proteins act as auxin receptors and play essential roles in auxin-mediated plant development processes. The number of auxin receptor family members varies among species. While the functions of auxin receptor genes have been widely studied in Arabidopsis, the distinct functions of cucumber (Cucumis sativus L.) auxin receptors remains poorly understood. To further our understanding of their potential role in cucumber development, two TIR1-like genes were identified and designated CsTIR1 and CsAFB2. In the present study, tomato (Sonanum lycopersicum) was used as a model to investigate the phenotypic and molecular changes associated with the overexpression of CsTIR1 and CsAFB2. RESULTS Differences in the subcellular localizations of CsTIR1 and CsAFB2 were identified and both genes were actively expressed in leaf, female flower and young fruit tissues of cucumber. Moreover, CsTIR1- and CsAFB2-overexpressing lines exhibited pleotropic phenotypes ranging from leaf abnormalities to seed germination and parthenocarpic fruit compared with the wild-type plants. To further elucidate the regulation of CsTIR1 and CsAFB2, the role of the miR393/TIR1 module in regulating cucumber fruit set were investigated. Activation of miR393-mediated mRNA cleavage of CsTIR1 and CsAFB2 was revealed by qPCR and semi-qPCR, which highlighted the critical role of the miR393/TIR1 module in mediating fruit set development in cucumber. CONCLUSION Our results provide new insights into the involvement of CsTIR1 and CsAFB2 in regulating various phenotype alterations, and suggest that post-transcriptional regulation of CsTIR1 and CsAFB2 mediated by miR393 is essential for cucumber fruit set initiation. Collectively, these results further clarify the roles of cucumber TIR1 homologs and miR393 in regulating fruit/seed set development and leaf morphogenesis.
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Affiliation(s)
- Jian Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Li Cui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ting Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhe Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Pin-Yu Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yong-Jiao Meng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kai-Jing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xia-Qing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qun-Feng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jin-Feng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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50
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Yamamoto KT, Watahiki MK, Matsuzaki J, Satoh S, Shimizu H. Space-time analysis of gravitropism in etiolated Arabidopsis hypocotyls using bioluminescence imaging of the IAA19 promoter fusion with a destabilized luciferase reporter. JOURNAL OF PLANT RESEARCH 2017; 130:765-777. [PMID: 28396964 PMCID: PMC6105228 DOI: 10.1007/s10265-017-0932-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/14/2017] [Indexed: 05/23/2023]
Abstract
Imaging analysis was carried out during the gravitropic response of etiolated Arabidopsis hypocotyls, using an IAA19 promoter fusion of destabilized luciferase as a probe. From the bright-field images we obtained the local deflection angle to the vertical, A, local curvature, C, and the partial derivative of C with respect to time, [Formula: see text]. These were determined every 19.9 µm along the curvilinear length of the hypocotyl, at ~10 min intervals over a period of ~6 h after turning hypocotyls through 90° to the horizontal. Similarly from the luminescence images we measured the luminescence intensity of the convex and concave flanks of the hypocotyl as well as along the median of the hypocotyl, to determine differential expression of auxin-inducible IAA19. Comparison of these parameters as a function of time and curvilinear length shows that the gravitropic response is composed of three successive elements: the first and second curving responses and a decurving response (autostraightening). The maximum of the first curving response occurs when A is 76° along the entire length of the hypocotyl, suggesting that A is the sole determinant in this response; in contrast, the decurving response is a function of both A and C, as predicted by the newly-proposed graviproprioception model (Bastien et al., Proc Natl Acad Sci USA 110:755-760, 2013). Further, differential expression of IAA19, with higher expression in the convex flank, is observed at A = 44°, and follows the Sachs' sine law. This also suggests that IAA19 is not involved in the first curving response. In summary, the gravitropic response of Arabidopsis hypocotyls consists of multiple elements that are each determined by separate principles.
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Affiliation(s)
- Kotaro T Yamamoto
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Masaaki K Watahiki
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Jun Matsuzaki
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Center for Sustainable Resource Science, RIKEN, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Soichirou Satoh
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Graduate School of Life and Environmental Sciences, Kyoto Prefecture University, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Hisayo Shimizu
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
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