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Wu Q, Yin J, Jiang M, Zhang J, Sui Z. Identification, characterization and expression profiles of E2 and E3 gene superfamilies during the development of tetrasporophytes in Gracilariopsis lemaneiformis (Rhodophyta). BMC Genomics 2023; 24:549. [PMID: 37723489 PMCID: PMC10506303 DOI: 10.1186/s12864-023-09639-0] [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] [Received: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
E2 ubiquitin conjugating enzymes and E3 ubiquitin ligases play important roles in the growth and development of plants and animals. To date, the systematic analysis of E2 and E3 genes in Rhodophyta is limited. In this study, 14 E2 genes and 51 E3 genes were identified in Gracilariopsis lemaneiformis, an economically important red alga. E2 genes were classified into four classes according to the structure of the conserved domain, UBC. E3 genes were classified into 12 subfamilies according to individual conserved domains. A phylogenetic tree of seven algae species showed that functional differentiation of RING-type E3s was the highest, and the similarity between orthologous genes was high except in Chlamydomonas reinhardtii and Chara braunii. RNA-seq data analysis showed significant differential expression levels of E2 and E3 genes under the life stages of tetraspore formation and release, especially GlUBCN and GlAPC3. According to GO and KEGG analysis of two transcriptomes, GlUBCN and GlAPC3 were involved in ubiquitin-mediated proteolysis, and other subunits of the anaphase promoting complex or cyclosome (APC/C) and its activators GlCDC20 and GlCDH1 were also enriched into this process. The CDH1 and CDC20 in 981 were down-regulated during tetraspores formation and release, with the down-regulation of CDH1 being particularly significant; CDH1 and CDC20 in WLP-1, ZC, and WT were up-regulated during tetraspores formation and release, with CDC20 being more significantly up-regulated. Therefore, GlCDH1, rather than GlCDC20, in '981' might play the leading role in the activation of the APC/C, and GlCDC20 might play the leading role rather than GlCDH1 in strains WLP-1, ZC and wild type. The low fertility of cultivar 981 might be highly correlated with the inactivity of activators CDH1 and CDC20. This study provided a basic and comprehensive understanding of characteristic of E2 and E3 genes in Gp. lemaneiformis and set a foundation for further understanding of E2 ubiquitin conjugating enzymes and E3 ubiquitin ligase in regulating tetrasporophytes development of Gp. lemaneiformis.
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Affiliation(s)
- Qiong Wu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Jingru Yin
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Min Jiang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Jingyu Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China.
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2
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Shaaban M, Clapperton JA, Ding S, Kunzelmann S, Mäeots ME, Maslen SL, Skehel JM, Enchev RI. Structural and mechanistic insights into the CAND1-mediated SCF substrate receptor exchange. Mol Cell 2023:S1097-2765(23)00418-5. [PMID: 37339624 DOI: 10.1016/j.molcel.2023.05.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/22/2023]
Abstract
Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment and subsequent proteasomal degradation. CAND proteins are essential for the efficient and timely exchange of SRs. To gain structural understanding of the underlying molecular mechanism, we reconstituted a human CAND1-driven exchange reaction of substrate-bound SCF alongside its co-E3 ligase DCNL1 and visualized it by cryo-EM. We describe high-resolution structural intermediates, including a ternary CAND1-SCF complex, as well as conformational and compositional intermediates representing SR- or CAND1-dissociation. We describe in molecular detail how CAND1-induced conformational changes in CUL1/RBX1 provide an optimized DCNL1-binding site and reveal an unexpected dual role for DCNL1 in CAND1-SCF dynamics. Moreover, a partially dissociated CAND1-SCF conformation accommodates cullin neddylation, leading to CAND1 displacement. Our structural findings, together with functional biochemical assays, help formulate a detailed model for CAND-SCF regulation.
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Affiliation(s)
- Mohammed Shaaban
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Julie A Clapperton
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Shan Ding
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Märt-Erik Mäeots
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Sarah L Maslen
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - J Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Radoslav I Enchev
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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3
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Vu QT, Song K, Park S, Xu L, Nam HG, Hong S. An auxin-mediated ultradian rhythm positively influences root regeneration via EAR1/EUR1 in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1136445. [PMID: 37351216 PMCID: PMC10282773 DOI: 10.3389/fpls.2023.1136445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/04/2023] [Indexed: 06/24/2023]
Abstract
Ultradian rhythms have been proved to be critical for diverse biological processes. However, comprehensive understanding of the short-period rhythms remains limited. Here, we discover that leaf excision triggers a gene expression rhythm with ~3-h periodicity, named as the excision ultradian rhythm (UR), which is regulated by the plant hormone auxin. Promoter-luciferase analyses showed that the spatiotemporal patterns of the excision UR were positively associated with de novo root regeneration (DNRR), a post-embryonic developmental process. Transcriptomic analysis indicated more than 4,000 genes including DNRR-associated genes were reprogramed toward ultradian oscillation. Genetic studies showed that EXCISION ULTRADIAN RHYTHM 1 (EUR1) encoding ENHANCER OF ABSCISIC ACID CO-RECEPTOR1 (EAR1), an abscisic acid signaling regulator, was required to generate the excision ultradian rhythm and enhance root regeneration. The eur1 mutant exhibited the absence of auxin-induced excision UR generation and partial failure during rescuing root regeneration. Our results demonstrate a link between the excision UR and adventitious root formation via EAR1/EUR1, implying an additional regulatory layer in plant regeneration.
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Affiliation(s)
- Quy Thi Vu
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Kitae Song
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Sungjin Park
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Sunghyun Hong
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
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4
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Li L, Wang K, Zhou Y, Liu X. Review: A silent concert in developing plants: Dynamic assembly of cullin-RING ubiquitin ligases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111662. [PMID: 36822503 PMCID: PMC10065934 DOI: 10.1016/j.plantsci.2023.111662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Plants appear quiet: quietly, they break the ground, expand leaves, search for resources, alert each other to invaders, and heal their own wounds. In contrast to the stationary appearance, the inside world of a plant is full of movements: cells divide to increase the body mass and form new organs; signaling molecules migrate among cells and tissues to drive transcriptional cascades and developmental programs; macromolecules, such as RNAs and proteins, collaborate with different partners to maintain optimal organismal function under changing cellular and environmental conditions. All these activities require a dynamic yet appropriately controlled molecular network in plant cells. In this short review, we used the regulation of cullin-RING ubiquitin ligases (CRLs) as an example to discuss how dynamic biochemical processes contribute to plant development. CRLs comprise a large family of modular multi-unit enzymes that determine the activity and stability of diverse regulatory proteins playing crucial roles in plant growth and development. The mechanism governing the dynamic assembly of CRLs is essential for CRL activity and biological function, and it may provide insights and implications for the regulation of other dynamic multi-unit complexes involved in fundamental processes such as transcription, translation, and protein sorting in plants.
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Affiliation(s)
- Lihong Li
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Kankan Wang
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States.
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Baek K, Scott DC, Henneberg LT, King MT, Mann M, Schulman BA. Systemwide disassembly and assembly of SCF ubiquitin ligase complexes. Cell 2023; 186:1895-1911.e21. [PMID: 37028429 PMCID: PMC10156175 DOI: 10.1016/j.cell.2023.02.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 04/09/2023]
Abstract
Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much protein degradation, require CAND1 to distribute the limiting CUL1 subunit across the family of ∼70 different F box proteins. Yet, how a single factor coordinately assembles numerous distinct multiprotein complexes remains unknown. We obtained cryo-EM structures of CAND1-bound SCF complexes in multiple states and correlated mutational effects on structures, biochemistry, and cellular assays. The data suggest that CAND1 clasps idling catalytic domains of an inactive SCF, rolls around, and allosterically rocks and destabilizes the SCF. New SCF production proceeds in reverse, through SKP1-F box allosterically destabilizing CAND1. The CAND1-SCF conformational ensemble recycles CUL1 from inactive complexes, fueling mixing and matching of SCF parts for E3 activation in response to substrate availability. Our data reveal biogenesis of a predominant family of E3 ligases, and the molecular basis for systemwide multiprotein complex assembly.
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Affiliation(s)
- Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Moeko T King
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Li L, Garsamo M, Yuan J, Wang X, Lam SH, Varala K, Boavida LC, Zhou Y, Liu X. CAND1 is required for pollen viability in Arabidopsis thaliana-a test of the adaptive exchange hypothesis. FRONTIERS IN PLANT SCIENCE 2022; 13:866086. [PMID: 35968124 PMCID: PMC9366119 DOI: 10.3389/fpls.2022.866086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/04/2022] [Indexed: 05/11/2023]
Abstract
The dynamic assembly of SKP1•CUL1•F-box protein (SCF) ubiquitin ligases is important for protein ubiquitination and degradation. This process is enabled by CAND1, which exchanges F-box proteins associated with the common CUL1 scaffold, and thereby, recycles the limited CUL1 core and allows diverse F-box proteins to assemble active SCFs. Previous human cell biological and computational studies have led to the adaptive exchange hypothesis, which suggests that the CAND1-mediated exchange confers plasticity on the SCF system, allowing cells to tolerate large variations in F-box protein expression. Here, we tested this hypothesis using Arabidopsis thaliana, a multicellular organism expressing hundreds of F-box protein genes at variable levels in different tissues. The cand1 null mutant in Arabidopsis is viable but produce almost no seeds. Bioinformatic, cell biological, and developmental analyses revealed that the low fertility in the cand1 mutant is associated with cell death in pollen, where the net expression of F-box protein genes is significantly higher than any other Arabidopsis tissue. In addition, we show that the transmission efficiency of the cand1 null allele was reduced through the male but not the female gametophyte. Our results suggest that CAND1 activity is essential in cells or tissues expressing high levels of F-box proteins. This finding is consistent with the proposed adaptive exchange hypothesis, demonstrating the necessity of the evolutionarily conserved CAND1-mediated exchange system in the development of a multicellular organism.
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Affiliation(s)
- Lihong Li
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Melaku Garsamo
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Jing Yuan
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Xiaojin Wang
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Susan H. Lam
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Kranthi Varala
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Leonor C. Boavida
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- *Correspondence: Xing Liu,
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7
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Fernández H, Grossmann J, Gagliardini V, Feito I, Rivera A, Rodríguez L, Quintanilla LG, Quesada V, Cañal MJ, Grossniklaus U. Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:718932. [PMID: 34868105 PMCID: PMC8633544 DOI: 10.3389/fpls.2021.718932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The gametophyte of ferns reproduces either by sexual or asexual means. In the latter, apogamy represents a peculiar case of apomixis, in which an embryo is formed from somatic cells. A proteomic and physiological approach was applied to the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative D. oreades. The proteomic analysis compared apogamous vs. female gametophytes, whereas the phytohormone study included, in addition to females, three apogamous stages (filamentous, spatulate, and cordate). The proteomic profiles revealed a total of 879 proteins and, after annotation, different regulation was found in 206 proteins of D. affinis and 166 of its sexual counterpart. The proteins upregulated in D. affinis are mostly associated to protein metabolism (including folding, transport, and proteolysis), ribosome biogenesis, gene expression and translation, while in the sexual counterpart, they account largely for starch and sucrose metabolism, generation of energy and photosynthesis. Likewise, ultra-performance liquid chromatography-tandem spectrometry (UHPLC-MS/MS) was used to assess the levels of indol-3-acetic acid (IAA); the cytokinins: 6-benzylaminopurine (BA), trans-Zeatine (Z), trans-Zeatin riboside (ZR), dyhidrozeatine (DHZ), dyhidrozeatin riboside (DHZR), isopentenyl adenine (iP), isopentenyl adenosine (iPR), abscisic acid (ABA), the gibberellins GA3 and GA4, salicylic acid (SA), and the brassinosteroids: brassinolide (BL) and castasterone (CS). IAA, the cytokinins Z, ZR, iPR, the gibberellin GA4, the brassinosteoids castasterone, and ABA accumulated more in the sexual gametophyte than in the apogamous one. When comparing the three apogamous stages, BA and SA peaked in filamentous, GA3 and BL in spatulate and DHRZ in cordate gametophytes. The results point to the existence of large metabolic differences between apogamous and sexual gametophytes, and invite to consider the fern gametophyte as a good experimental system to deepen our understanding of plant reproduction.
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Affiliation(s)
- Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomics Center, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Isabel Feito
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Lucía Rodríguez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Móstoles, Spain
| | - Víctor Quesada
- Department of Biochemistry and Molecular Biology, Institute of Oncology of the Principality of Asturias, Oviedo University, Móstoles, Spain
| | - Mª Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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9
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Li M, Geng L, Xie S, Wu D, Ye L, Zhang G. Genome-Wide Association Study on Total Starch, Amylose and Amylopectin in Barley Grain Reveals Novel Putative Alleles. Int J Mol Sci 2021; 22:ijms22020553. [PMID: 33430526 PMCID: PMC7828029 DOI: 10.3390/ijms22020553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/21/2020] [Accepted: 12/26/2020] [Indexed: 11/18/2022] Open
Abstract
The content and composition of starch in cereal grains are closely related to yield. Few studies have been done on the identification of the genes or loci associated with these traits in barley. This study was conducted to identify the genes or loci controlling starch traits in barley grains, including total starch (TS), amylose (AC) and amylopectin (AP) contents. A large genotypic variation was found in all examined starch traits. GWAS analysis detected 13, 2, 10 QTLs for TS, AC and AP, respectively, and 5 of them were commonly shared by AP and TS content. qTS-3.1, qAC-6.2 and qAP-5.1 may explain the largest variation of TS, AC and AP, respectively. Four putative candidate genes, i.e., HORVU6Hr1G087920, HORVU5Hr1G011230, HORVU5Hr1G011270 and HORVU5Hr1G011280, showed the high expression in the developing barley grains when starch accumulates rapidly. The examined 100 barley accessions could be divided into two groups based on the polymorphism of the marker S5H_29297679, with 93 accessions having allele GG and seven accessions having AA. Moreover, significantly positive correlation was found between the number of favorable alleles of the identified QTLs and TS, AC, AP content. In conclusion, the identified loci or genes in this study could be useful for genetic improvement of grains starch in barley.
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Affiliation(s)
- Mengdi Li
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (M.L.); (L.G.); (S.X.); (D.W.); (G.Z.)
| | - La Geng
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (M.L.); (L.G.); (S.X.); (D.W.); (G.Z.)
| | - Shanggeng Xie
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (M.L.); (L.G.); (S.X.); (D.W.); (G.Z.)
| | - Dezhi Wu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (M.L.); (L.G.); (S.X.); (D.W.); (G.Z.)
| | - Lingzhen Ye
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (M.L.); (L.G.); (S.X.); (D.W.); (G.Z.)
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
- Correspondence:
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (M.L.); (L.G.); (S.X.); (D.W.); (G.Z.)
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
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10
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Cheng W, Yin S, Tu Y, Mei H, Wang Y, Yang Y. SlCAND1, encoding cullin-associated Nedd8-dissociated protein 1, regulates plant height, flowering time, seed germination, and root architecture in tomato. PLANT MOLECULAR BIOLOGY 2020; 102:537-551. [PMID: 31916084 DOI: 10.1007/s11103-020-00963-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
Silencing of SlCAND1 expression resulted in dwarfish, loss of apical dominance, early flowering, suppression of seed germination, and abnormal root architecture in tomato Cullin-RING E3 ligases (CRLs)-dependent ubiquitin proteasome system mediates degradation of numerous proteins that controls a wide range of developmental and physiological processes in eukaryotes. Cullin-associated Nedd8-dissociated protein 1 (CAND1) acts as an exchange factor allowing substrate recognition part exchange and plays a vital role in reactivating CRLs. The present study reports on the identification of SlCAND1, the only one CAND gene in tomato. SlCAND1 expression is ubiquitous and positively regulated by multiple plant hormones. Silencing of SlCAND1 expression using RNAi strategy resulted in a pleiotropic and gibberellin/auxin-associated phenotypes, including dwarf plant with reduced internode length, loss of apical dominance, early flowering, low seed germination percentage, delayed seed germination speed, short primary root, and increased lateral root proliferation and elongation. Moreover, application of exogenous GA3 or IAA could partly rescue some SlCAND1-silenced phenotypes, and the expression levels of gibberellin/auxin-related genes were altered in SlCAND1-RNAi lines. These facts revealed that SlCAND1 is required for gibberellin/auxin-associated regulatory network in tomato. Although SlCAND1 is crucial for multiple developmental processes during vegetative growth stage, SlCAND1-RNAi lines didn't exhibit visible effect on fruit development and ripening. Meanwhile, we discussed that multiple physiological functions of SlCAND1 in tomato are different to previous report of its ortholog in Arabidopsis. Our study adds a new perspective on the functional roles of CAND1 in plants, and strongly supports the hypothesis that CAND1 and its regulated ubiquitin proteasome system are pivotal for plant vegetative growth but possibly have different roles in diverse plant species.
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Affiliation(s)
- Wenjing Cheng
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Shuangqin Yin
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Yun Tu
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Hu Mei
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Yongzhong Wang
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Yingwu Yang
- Bioengineering College, Chongqing University, Chongqing, 400044, China.
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China.
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11
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Wang K, Deshaies RJ, Liu X. Assembly and Regulation of CRL Ubiquitin Ligases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:33-46. [DOI: 10.1007/978-981-15-1025-0_3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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12
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Visser EA, Wegrzyn JL, Steenkamp ET, Myburg AA, Naidoo S. Dual RNA-Seq Analysis of the Pine- Fusarium circinatum Interaction in Resistant ( Pinus tecunumanii) and Susceptible ( Pinus patula) Hosts. Microorganisms 2019; 7:E315. [PMID: 31487786 PMCID: PMC6780516 DOI: 10.3390/microorganisms7090315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022] Open
Abstract
Fusarium circinatum poses a serious threat to many pine species in both commercial and natural pine forests. Knowledge regarding the molecular basis of pine-F. circinatum host-pathogen interactions could assist efforts to produce more resistant planting stock. This study aimed to identify molecular responses underlying resistance against F. circinatum. A dual RNA-seq approach was used to investigate host and pathogen expression in F. circinatum challenged Pinus tecunumanii (resistant) and Pinus patula (susceptible), at three- and seven-days post inoculation. RNA-seq reads were mapped to combined host-pathogen references for both pine species to identify differentially expressed genes (DEGs). F. circinatum genes expressed during infection showed decreased ergosterol biosynthesis in P. tecunumanii relative to P. patula. For P. tecunumanii, enriched gene ontologies and DEGs indicated roles for auxin-, ethylene-, jasmonate- and salicylate-mediated phytohormone signalling. Correspondingly, key phytohormone signaling components were down-regulated in P. patula. Key F. circinatum ergosterol biosynthesis genes were expressed at lower levels during infection of the resistant relative to the susceptible host. This study further suggests that coordination of phytohormone signaling is required for F. circinatum resistance in P. tecunumanii, while a comparatively delayed response and impaired phytohormone signaling contributes to susceptibility in P. patula.
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Affiliation(s)
- Erik A Visser
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
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13
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Zeng W, Dai X, Sun J, Hou Y, Ma X, Cao X, Zhao Y, Cheng Y. Modulation of Auxin Signaling and Development by Polyadenylation Machinery. PLANT PHYSIOLOGY 2019; 179:686-699. [PMID: 30487141 PMCID: PMC6426405 DOI: 10.1104/pp.18.00782] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/18/2018] [Indexed: 05/25/2023]
Abstract
Polyadenylation influences gene expression by affecting mRNA stability, transport, and translatability. Here, we report that Cleavage stimulation Factor 77 (AtCstF77), a component of the pre-mRNA 3'-end polyadenylation machinery, affects polyadenylation site (PAS) selection in transcripts of some auxin signaling genes in Arabidopsis (Arabidopsis thaliana). Disruption of AtCstF77 reduced auxin sensitivity and decreased the expression of the auxin reporter DR5-GFP Null mutations of cstf77 caused severe developmental defects, but were not lethal as previously reported. cstf77-2 genetically interacted with transport inhibitor response 1 auxin signaling f-box 2 auxin receptor double mutants, further supporting that polyadenylation affects auxin signaling. AtCstF77 was ubiquitously expressed in embryos, seedlings, and adult plants. The AtCstF77 protein was localized in the nucleus, which is consistent with its function in pre-mRNA processing. We observed that PASs in transcripts from approximately 2,400 genes were shifted in the cstf77-2 mutant. Moreover, most of the PAS shifts were from proximal to distal sites. Auxin treatment also caused PAS shifts in transcripts from a small number of genes. Several auxin signaling or homeostasis genes had different PASs in their transcripts in the cstf77-2 mutant. The expression levels of AUXIN RESISTANT 2/INDOLE-3-ACETIC ACID 7 were significantly increased in the cstf77-2 mutant, which can partially account for the auxin resistance phenotype of this mutant. Our results demonstrate that AtCstF77 plays pleiotropic and critical roles in Arabidopsis development. Moreover, disruption of AtCstF64, another component of the polyadenylation machinery, led to developmental defects and reduced auxin response, similar to those of the cstf77-2 mutant. We conclude that AtCstF77 affects auxin responses, likely by controlling PAS selection of transcripts of some auxin signaling components.
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Affiliation(s)
- Wei Zeng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinhua Dai
- Section of Cell and Developmental Biology, University of California, San Diego, California 92093-0116
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifeng Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuan Ma
- College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Xiaofeng Cao
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California, San Diego, California 92093-0116
| | - Youfa Cheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Liu X, Reitsma JM, Mamrosh JL, Zhang Y, Straube R, Deshaies RJ. Cand1-Mediated Adaptive Exchange Mechanism Enables Variation in F-Box Protein Expression. Mol Cell 2019; 69:773-786.e6. [PMID: 29499133 DOI: 10.1016/j.molcel.2018.01.038] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/08/2018] [Accepted: 01/29/2018] [Indexed: 11/16/2022]
Abstract
Skp1⋅Cul1⋅F-box (SCF) ubiquitin ligase assembly is regulated by the interplay of substrate binding, reversible Nedd8 conjugation on Cul1, and the F-box protein (FBP) exchange factors Cand1 and Cand2. Detailed investigations into SCF assembly and function in reconstituted systems and Cand1/2 knockout cells informed the development of a mathematical model for how dynamical assembly of SCF complexes is controlled and how this cycle is coupled to degradation of an SCF substrate. Simulations predicted an unanticipated hypersensitivity of Cand1/2-deficient cells to FBP expression levels, which was experimentally validated. Together, these and prior observations lead us to propose the adaptive exchange hypothesis, which posits that regulation of the koff of an FBP from SCF by the actions of substrate, Nedd8, and Cand1 molds the cellular repertoire of SCF complexes and that the plasticity afforded by this exchange mechanism may enable large variations in FBP expression during development and in FBP gene number during evolution.
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Affiliation(s)
- Xing Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Justin M Reitsma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer L Mamrosh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yaru Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ronny Straube
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany.
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA; Amgen, One Amgen Center Way, Thousand Oaks, CA 91320, USA.
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15
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Li W, Li H, Xu P, Xie Z, Ye Y, Li L, Li D, Zhang Y, Li L, Zhao Y. Identification of Auxin Activity Like 1, a chemical with weak functions in auxin signaling pathway. PLANT MOLECULAR BIOLOGY 2018; 98:275-287. [PMID: 30311174 DOI: 10.1007/s11103-018-0779-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/17/2018] [Indexed: 05/05/2023]
Abstract
A new synthetic auxin AAL1 with new structure was identified. Different from known auxins, it has weak effects. By AAL1, we found specific amino acids could restore the effects of auxin with similar structure. Auxin, one of the most important phytohormones, plays crucial roles in plant growth, development and environmental response. Although many critical regulators have been identified in auxin signaling pathway, some factors, especially those with weak fine-tuning roles, are still yet to be discovered. Through chemical genetic screenings, we identified a small molecule, Auxin Activity Like 1 (AAL1), which can effectively inhibit dark-grown Arabidopsis thaliana seedlings. Genetic screening identified AAL1 resistant mutants are also hyposensitive to indole-3-acetic acid (IAA) and 2,4-dichlorophenoxyacetic acid (2,4-D). AAL1 resistant mutants such as shy2-3c and ecr1-2 are well characterized as mutants in auxin signaling pathway. Genetic studies showed that AAL1 functions through auxin receptor Transport Inhibitor Response1 (TIR1) and its functions depend on auxin influx and efflux carriers. Compared with known auxins, AAL1 exhibits relatively weak effects on plant growth, with 20 µM and 50 µM IC50 (half growth inhibition chemical concentration) in root and hypocotyl growth respectively. Interestingly, we found the inhibitory effects of AAL1 and IAA could be partially restored by tyrosine and tryptophan respectively, suggesting some amino acids can also affect auxin signaling pathway in a moderate manner. Taken together, our results demonstrate that AAL1 acts through auxin signaling pathway, and AAL1, as a weak auxin activity analog, provides us a tool to study weak genetic interactions in auxin pathway.
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Affiliation(s)
- Wenbo Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Haimin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Peng Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhi Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yajin Ye
- University of Chinese Academy of Sciences, Shanghai, 200032, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lingting Li
- University of Chinese Academy of Sciences, Shanghai, 200032, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Deqiang Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Zhao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 68 Wenchang Road, Yunnan, 650000, China.
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16
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Christians MJ, Rottier A, Wiersma C. Light Regulates the RUBylation Levels of Individual Cullin Proteins in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY REPORTER 2018; 36:123-134. [PMID: 29568157 PMCID: PMC5847140 DOI: 10.1007/s11105-017-1064-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In plants, the small protein related to ubiquitin (RUB) modifies cullin (CUL) proteins in ubiquitin E3 ligases to allow for efficient transfer of ubiquitin to substrate proteins for degradation by the 26S proteasome. At the molecular level, the conjugation of RUB to individual CUL proteins is transient in nature, which aids in the stability of the cullins and adaptor proteins. Many changes in cellular processes occur within the plant upon exposure to light, including well-documented changes in the stability of individual proteins. However, overall activity of E3 ligases between dark- and light-grown seedlings has not been assessed in plants. In order to understand more about the activity of the protein degradation pathway, overall levels of RUB-modified CULs were measured in Arabidopsis thaliana seedlings growing in different light conditions. We found that light influenced the global levels of RUBylation on CULs, but not uniformly. Blue light had little effect on both Cul1 and Cul3 RUBylation levels. However, red light directed the increase in Cul3 RUBylation levels, but not Cul1. This red-light regulation of Cul3 was at least partially dependent on the activation of the phytochrome B signaling pathway. The results indicate that the RUBylation levels on individual CULs change in response to different light conditions, which enable plants to fine-tune their growth and development to the various light environments.
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Affiliation(s)
- Matthew J. Christians
- Department of Cell and Molecular Biology, Grand Valley State University, 3300A Douglas Kindschi Hall of Science, Allendale, MI 49401 USA
| | - Aron Rottier
- Department of Cell and Molecular Biology, Grand Valley State University, 3300A Douglas Kindschi Hall of Science, Allendale, MI 49401 USA
| | - Carly Wiersma
- Department of Cell and Molecular Biology, Grand Valley State University, 3300A Douglas Kindschi Hall of Science, Allendale, MI 49401 USA
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17
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Stewart JJ, Polutchko SK, Demmig-Adams B, Adams WW. Arabidopsis thaliana Ei-5: Minor Vein Architecture Adjustment Compensates for Low Vein Density in Support of Photosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:693. [PMID: 29910820 DOI: 10.3389/fpls.2018.00693/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/07/2018] [Indexed: 05/21/2023]
Abstract
An Arabidopsis thaliana accession with naturally low vein density, Eifel-5 (Ei-5), was compared to Columbia-0 (Col-0) with respect to rosette growth, foliar vein architecture, photosynthesis, and transpiration. In addition to having to a lower vein density, Ei-5 grew more slowly, with significantly lower rates of rosette expansion, but had similar capacities for photosynthetic oxygen evolution on a leaf area basis compared to Col-0. The individual foliar minor veins were larger in Ei-5, with a greater number of vascular cells per vein, compared to Col-0. This compensation for low vein density resulted in similar values for the product of vein density × phloem cell number per minor vein in Ei-5 and Col-0, which suggests a similar capacity for foliar sugar export to support similar photosynthetic capacities per unit leaf area. In contrast, the product of vein density × xylem cell number per minor vein was significantly greater in Ei-5 compared to Col-0, and was associated not only with a higher ratio of water-transporting tracheary elements versus sugar-transporting sieve elements but also significantly higher foliar transpiration rates per leaf area in Ei-5. In contrast, previous studies in other systems had reported higher ratios of tracheary to sieve elements and higher transpiration rate to be associated with higher - rather than lower - vein densities. The Ei-5 accession thus further underscores the plasticity of the foliar vasculature by illustrating an example where a higher ratio of tracheary to sieve elements is associated with a lower vein density. Establishment of the Ei-5 accession, with a low vein density but an apparent overcapacity for water flux through the foliar xylem network, may have been facilitated by a higher level of precipitation in its habitat of origin compared to that of the Col-0 accession.
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Affiliation(s)
- Jared J Stewart
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Stephanie K Polutchko
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Barbara Demmig-Adams
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - William W Adams
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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18
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Stewart JJ, Polutchko SK, Demmig-Adams B, Adams WW. Arabidopsis thaliana Ei-5: Minor Vein Architecture Adjustment Compensates for Low Vein Density in Support of Photosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:693. [PMID: 29910820 PMCID: PMC5992485 DOI: 10.3389/fpls.2018.00693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/07/2018] [Indexed: 05/05/2023]
Abstract
An Arabidopsis thaliana accession with naturally low vein density, Eifel-5 (Ei-5), was compared to Columbia-0 (Col-0) with respect to rosette growth, foliar vein architecture, photosynthesis, and transpiration. In addition to having to a lower vein density, Ei-5 grew more slowly, with significantly lower rates of rosette expansion, but had similar capacities for photosynthetic oxygen evolution on a leaf area basis compared to Col-0. The individual foliar minor veins were larger in Ei-5, with a greater number of vascular cells per vein, compared to Col-0. This compensation for low vein density resulted in similar values for the product of vein density × phloem cell number per minor vein in Ei-5 and Col-0, which suggests a similar capacity for foliar sugar export to support similar photosynthetic capacities per unit leaf area. In contrast, the product of vein density × xylem cell number per minor vein was significantly greater in Ei-5 compared to Col-0, and was associated not only with a higher ratio of water-transporting tracheary elements versus sugar-transporting sieve elements but also significantly higher foliar transpiration rates per leaf area in Ei-5. In contrast, previous studies in other systems had reported higher ratios of tracheary to sieve elements and higher transpiration rate to be associated with higher - rather than lower - vein densities. The Ei-5 accession thus further underscores the plasticity of the foliar vasculature by illustrating an example where a higher ratio of tracheary to sieve elements is associated with a lower vein density. Establishment of the Ei-5 accession, with a low vein density but an apparent overcapacity for water flux through the foliar xylem network, may have been facilitated by a higher level of precipitation in its habitat of origin compared to that of the Col-0 accession.
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19
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Sirtinol, a Sir2 protein inhibitor, affects stem cell maintenance and root development in Arabidopsis thaliana by modulating auxin-cytokinin signaling components. Sci Rep 2017; 7:42450. [PMID: 28195159 PMCID: PMC5307962 DOI: 10.1038/srep42450] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/09/2017] [Indexed: 11/08/2022] Open
Abstract
In Arabidopsis thaliana, besides several key transcription factors and chromatin modifiers, phytohormones auxin and cytokinin play pivotal role in shoot and root meristem maintenance, and lateral root (LR) development. Sirtinol, a chemical inhibitor of Sir2 proteins, is known to promote some auxin induced phenotypes in Arabidopsis. However, its effect on plant stem cell maintenance or organ formation remained unaddressed. Here we show that sirtinol affects meristem maintenance by altering the expression of key stem cell regulators, cell division and differentiation by modulating both auxin and cytokinin signaling in Arabidopsis thaliana. The expression of shoot stem cell niche related genes WUSCHEL (WUS) and CLAVATA3 (CLV3) was upregulated, whereas SHOOT MERISTEMLESS (STM) was downregulated in sirtinol treated seedlings. The expression level and domain of key root stem cell regulators PLETHORA (PLTs) and WUS-Related Homeobox 5 (WOX5) were altered in sirtinol treated roots. Sirtinol affects LR development by disturbing proper auxin transport and maxima formation, similar to 2,4-dichlorophenoxyacetic acid (2,4-D). Sirtinol also affects LR formation by altering cytokinin biosynthesis and signaling genes in roots. Therefore, sirtinol affects shoot and root growth, meristem maintenance and LR development by altering the expression of cytokinin-auxin signaling components, and regulators of stem cells, meristems, and LRs.
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20
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Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level. PLoS One 2015; 10:e0141398. [PMID: 26536247 PMCID: PMC4633283 DOI: 10.1371/journal.pone.0141398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022] Open
Abstract
In addition to the micronutrient inadequacy of staple crops for optimal human nutrition, a global downtrend in crop-quality has emerged from intensive breeding for yield. This trend will be aggravated by elevated levels of the greenhouse gas carbon dioxide. Therefore, crop biofortification is inevitable to ensure a sustainable supply of minerals to the large part of human population who is dietary dependent on staple crops. This requires a thorough understanding of plant-mineral interactions due to the complexity of mineral homeostasis. Employing RNA sequencing, we here communicate transfer cell specific effects of excess iron and zinc during grain filling in our model crop plant barley. Responding to alterations in mineral contents, we found a long range of different genes and transcripts. Among them, it is worth to highlight the auxin and ethylene signaling factors Arfs, Abcbs, Cand1, Hps4, Hac1, Ecr1, and Ctr1, diurnal fluctuation components Sdg2, Imb1, Lip1, and PhyC, retroelements, sulfur homeostasis components Amp1, Hmt3, Eil3, and Vip1, mineral trafficking components Med16, Cnnm4, Aha2, Clpc1, and Pcbps, and vacuole organization factors Ymr155W, RabG3F, Vps4, and Cbl3. Our analysis introduces new interactors and signifies a broad spectrum of regulatory levels from chromatin remodeling to intracellular protein sorting mechanisms active in the plant mineral homeostasis. The results highlight the importance of storage proteins in metal ion toxicity-resistance and chelation. Interestingly, the protein sorting and recycling factors Exoc7, Cdc1, Sec23A, and Rab11A contributed to the response as well as the polar distributors of metal-transporters ensuring the directional flow of minerals. Alternative isoform switching was found important for plant adaptation and occurred among transcripts coding for identical proteins as well as transcripts coding for protein isoforms. We also identified differences in the alternative-isoform preference between the treatments, indicating metal-affinity shifts among isoforms of metal transporters. Most important, we found the zinc treatment to impair both photosynthesis and respiration. A wide range of transcriptional changes including stress-related genes and negative feedback loops emphasize the importance to withhold mineral contents below certain cellular levels which otherwise might lead to agronomical impeding side-effects. By illustrating new mechanisms, genes, and transcripts, this report provides a solid platform towards understanding the complex network of plant mineral homeostasis.
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Fierro AC, Leroux O, De Coninck B, Cammue BPA, Marchal K, Prinsen E, Van Der Straeten D, Vandenbussche F. Ultraviolet-B radiation stimulates downward leaf curling in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 93:9-17. [PMID: 25542780 DOI: 10.1016/j.plaphy.2014.12.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/10/2014] [Indexed: 05/15/2023]
Abstract
Plants are very well adapted to growth in ultraviolet-B (UV-B) containing light. In Arabidopsis thaliana, many of these adaptations are mediated by the UV-B receptor UV resistance locus 8 (UVR8). Using small amounts of supplementary UV-B light, we observed changes in the shape of rosette leaf blades. Wild type plants show more pronounced epinasty of the blade edges, while this is not the case in uvr8 mutant plants. The UVR8 effect thus mimics the effect of phytochrome (phy) B in red light. In addition, a meta-analysis of transcriptome data indicates that the UVR8 and phyB signaling pathways have over 70% of gene regulation in common. Moreover, in low levels of supplementary UV-B light, mutant analysis revealed that phyB signaling is necessary for epinasty of the blade edges. Analysis of auxin levels and the auxin signal reporter DR5::GUS suggest that the epinasty relies on altered auxin distribution, keeping auxin at the leaf blade edges in the presence of UV-B. Together, our results suggest a co-action of phyB and UVR8 signaling, with auxin as a downstream factor.
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Affiliation(s)
- Ana Carolina Fierro
- Department of Information Technology, IMinds, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium.
| | - Olivier Leroux
- Department of Biology, Ghent University, KL Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Kathleen Marchal
- Department of Information Technology, IMinds, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium; Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium; Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium.
| | - Els Prinsen
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Physiology, Ghent University, KL Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Filip Vandenbussche
- Laboratory of Functional Plant Biology, Department of Physiology, Ghent University, KL Ledeganckstraat 35, B-9000 Ghent, Belgium.
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22
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Di DW, Zhang C, Guo GQ. Involvement of secondary messengers and small organic molecules in auxin perception and signaling. PLANT CELL REPORTS 2015; 34:895-904. [PMID: 25693494 DOI: 10.1007/s00299-015-1767-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 05/26/2023]
Abstract
Auxin is a major phytohormone involved in most aspects of plant growth and development. Generally, auxin is perceived by three distinct receptors: TRANSPORT INHIBITOR RESISTANT1-Auxin/INDOLE ACETIC ACID, S-Phase Kinase-Associated Protein 2A and AUXIN-BINDING PROTEIN1. The auxin perception is regulated by a variety of secondary messenger molecules, including nitric oxide, reactive oxygen species, calcium, cyclic GMP, cyclic AMP, inositol triphosphate, diacylglycerol and by physiological pH. In addition, some small organic molecules, including inositol hexakisphosphate, yokonolide B, p-chlorophenoxyisobutyric acid, toyocamycin and terfestatin A, are involved in auxin signaling. In this review, we summarize and discuss the recent progress in understanding the functions of these secondary messengers and small organic molecules, which are now thoroughly demonstrated to be pervasive and important in auxin perception and signal transduction.
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Affiliation(s)
- Dong-Wei Di
- Institute of Cell Biology, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China,
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23
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Mai CD, Phung NTP, To HTM, Gonin M, Hoang GT, Nguyen KL, Do VN, Courtois B, Gantet P. Genes controlling root development in rice. RICE (NEW YORK, N.Y.) 2014; 7:30. [PMID: 26224559 PMCID: PMC4884052 DOI: 10.1186/s12284-014-0030-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/30/2014] [Indexed: 05/20/2023]
Abstract
In this review, we report on the recent developments made using both genetics and functional genomics approaches in the discovery of genes controlling root development in rice. QTL detection in classical biparental mapping populations initially enabled the identification of a very large number of large chromosomal segments carrying root genes. Two segments with large effects have been positionally cloned, allowing the identification of two major genes. One of these genes conferred a tolerance to low phosphate content in soil, while the other conferred a tolerance to drought by controlling root gravitropism, resulting in root system expansion deep in the soil. Findings based on the higher-resolution QTL detection offered by the development of association mapping are discussed. In parallel with genetics approaches, efforts have been made to screen mutant libraries for lines presenting alterations in root development, allowing for the identification of several genes that control different steps of root development, such as crown root and lateral root initiation and emergence, meristem patterning, and the control of root growth. Some of these genes are closely phylogenetically related to Arabidopsis genes involved in the control of lateral root initiation. This close relationship stresses the conservation among plant species of an auxin responsive core gene regulatory network involved in the control of post-embryonic root initiation. In addition, we report on several genetic regulatory pathways that have been described only in rice. The complementarities and the expected convergence of the direct and reverse genetic approaches used to decipher the genetic determinants of root development in rice are discussed in regards to the high diversity characterizing this species and to the adaptations of rice root system architecture to different edaphic environments.
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Affiliation(s)
- Chung D Mai
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | - Nhung TP Phung
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
- />IRD, UMR DIADE, LMI RICE, Hanoi, Vietnam
- />CIRAD, UMR AGAP, Montpellier, France
| | - Huong TM To
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | | | - Giang T Hoang
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | - Khanh L Nguyen
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
- />IRD, UMR DIADE, LMI RICE, Hanoi, Vietnam
| | - Vinh N Do
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
| | | | - Pascal Gantet
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
- />IRD, UMR DIADE, LMI RICE, Hanoi, Vietnam
- />Université Montpellier 2, UMR DIADE, Montpellier, France
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Mergner J, Schwechheimer C. The NEDD8 modification pathway in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:103. [PMID: 24711811 PMCID: PMC3968751 DOI: 10.3389/fpls.2014.00103] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 03/03/2014] [Indexed: 05/19/2023]
Abstract
NEDD8, in plants and yeasts also known as RELATED TO UBIQUITIN (RUB), is an evolutionarily conserved 76 amino acid protein highly related to ubiquitin. Like ubiquitin, NEDD8 can be conjugated to and deconjugated from target proteins, but unlike ubiquitin, NEDD8 has not been reported to form chains similar to the different polymeric ubiquitin chains that have a role in a diverse set of cellular processes. NEDD8-modification is best known as a post-translational modification of the cullin subunits of cullin-RING E3 ubiquitin ligases. In this context, structural analyses have revealed that neddylation induces a conformation change of the cullin that brings the ubiquitylation substrates into proximity of the interacting E2 conjugating enzyme. In turn, NEDD8 deconjugation destabilizes the cullin RING ligase complex allowing for the exchange of substrate recognition subunits via the exchange factor CAND1. In plants, components of the neddylation and deneddylation pathway were identified based on mutants with defects in auxin and light responses and the characterization of these mutants has been instrumental for the elucidation of the neddylation pathway. More recently, there has been evidence from animal and plant systems that NEDD8 conjugation may also regulate the behavior or fate of non-cullin substrates in a number of ways. Here, the current knowledge on NEDD8 processing, conjugation and deconjugation is presented, where applicable, in the context of specific signaling pathways from plants.
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Affiliation(s)
| | - Claus Schwechheimer
- *Correspondence: Claus Schwechheimer, Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany e-mail:
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25
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Choi CM, Gray WM, Mooney S, Hellmann H. Composition, roles, and regulation of cullin-based ubiquitin e3 ligases. THE ARABIDOPSIS BOOK 2014; 12:e0175. [PMID: 25505853 PMCID: PMC4262284 DOI: 10.1199/tab.0175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Due to their sessile nature, plants depend on flexible regulatory systems that allow them to adequately regulate developmental and physiological processes in context with environmental cues. The ubiquitin proteasome pathway, which targets a great number of proteins for degradation, is cellular tool that provides the necessary flexibility to accomplish this task. Ubiquitin E3 ligases provide the needed specificity to the pathway by selectively binding to particular substrates and facilitating their ubiquitylation. The largest group of E3 ligases known in plants is represented by CULLIN-REALLY INTERESTING NEW GENE (RING) E3 ligases (CRLs). In recent years, a great amount of knowledge has been generated to reveal the critical roles of these enzymes across all aspects of plant life. This review provides an overview of the different classes of CRLs in plants, their specific complex compositions, the variety of biological processes they control, and the regulatory steps that can affect their activities.
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Affiliation(s)
| | | | | | - Hanjo Hellmann
- Washington State University, Pullman, Washington
- Address correspondence to
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26
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Zemla A, Thomas Y, Kedziora S, Knebel A, Wood NT, Rabut G, Kurz T. CSN- and CAND1-dependent remodelling of the budding yeast SCF complex. Nat Commun 2013; 4:1641. [PMID: 23535662 DOI: 10.1038/ncomms2628] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/20/2013] [Indexed: 01/10/2023] Open
Abstract
Cullin-RING ligases (CRLs) are ubiquitin E3 enzymes with variable substrate-adaptor and -receptor subunits. All CRLs are activated by modification of the cullin subunit with the ubiquitin-like protein Nedd8 (neddylation). The protein CAND1 (Cullin-associated-Nedd8-dissociated-1) also promotes CRL activity, even though it only interacts with inactive ligase complexes. The molecular mechanism underlying this behaviour remains largely unclear. Here, we find that yeast SCF (Skp1-Cdc53-F-box) Cullin-RING complexes are remodelled in a CAND1-dependent manner, when cells are switched from growth in fermentable to non-fermentable carbon sources. Mechanistically, CAND1 promotes substrate adaptor release following SCF deneddylation by the COP9 signalosome (CSN). CSN- or CAND1-mutant cells fail to release substrate adaptors. This delays the formation of new complexes during SCF reactivation and results in substrate degradation defects. Our results shed light on how CAND1 regulates CRL activity and demonstrate that the cullin neddylation-deneddylation cycle is not only required to activate CRLs, but also to regulate substrate specificity through dynamic substrate adaptor exchange.
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Affiliation(s)
- Aleksandra Zemla
- Scottish Institute for Cell Signalling, Protein Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, Scotland, UK
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27
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Sinha D, Gupta MK, Patel HK, Ranjan A, Sonti RV. Cell wall degrading enzyme induced rice innate immune responses are suppressed by the type 3 secretion system effectors XopN, XopQ, XopX and XopZ of Xanthomonas oryzae pv. oryzae. PLoS One 2013; 8:e75867. [PMID: 24086651 PMCID: PMC3784402 DOI: 10.1371/journal.pone.0075867] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/16/2013] [Indexed: 12/12/2022] Open
Abstract
Innate immune responses are induced in plants and animals through perception of Damage Associated Molecular Patterns. These immune responses are suppressed by pathogens during infection. A number of studies have focussed on identifying functions of plant pathogenic bacteria that are involved in suppression of Pathogen Associated Molecular Pattern induced immune responses. In comparison, there is very little information on functions used by plant pathogens to suppress Damage Associated Molecular Pattern induced immune responses. Xanthomonasoryzae pv. oryzae, a gram negative bacterial pathogen of rice, secretes hydrolytic enzymes such as LipA (Lipase/Esterase) that damage rice cell walls and induce innate immune responses. Here, we show that Agrobacterium mediated transient transfer of the gene for XopN, a X. oryzae pv. oryzae type 3 secretion (T3S) system effector, results in suppression of rice innate immune responses induced by LipA. A xopN- mutant of X. oryzae pv. oryzae retains the ability to suppress these innate immune responses indicating the presence of other functionally redundant proteins. In transient transfer assays, we have assessed the ability of 15 other X. oryzae pv. oryzae T3S secreted effectors to suppress rice innate immune responses. Amongst these proteins, XopQ, XopX and XopZ are suppressors of LipA induced innate immune responses. A mutation in any one of the xopN, xopQ, xopX or xopZ genes causes partial virulence deficiency while a xopN- xopX- double mutant exhibits a greater virulence deficiency. A xopN- xopQ- xopX- xopZ- quadruple mutant of X. oryzae pv. oryzae induces callose deposition, an innate immune response, similar to a X. oryzae pv. oryzae T3S- mutant in rice leaves. Overall, these results indicate that multiple T3S secreted proteins of X. oryzae pv. oryzae can suppress cell wall damage induced rice innate immune responses.
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Affiliation(s)
- Dipanwita Sinha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Mahesh Kumar Gupta
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Hitendra Kumar Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Ashish Ranjan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Ramesh V. Sonti
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
- * E-mail:
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28
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Pierre-Jerome E, Moss BL, Nemhauser JL. Tuning the auxin transcriptional response. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2557-63. [PMID: 23630231 DOI: 10.1093/jxb/ert100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
How does auxin provoke such a diverse array of responses? This long-standing question is further complicated by a remarkably short nuclear auxin signalling pathway. To crack the auxin code, several potential sources of specificity need to be evaluated. These include: specificity of interactions among the core auxin response components, specificity resulting from higher order complex dynamics, and specificity in interactions with global factors controlling protein turnover and transcriptional repression. Here, we review recent progress towards characterizing and quantifying these interactions and highlight key gaps that remain.
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29
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Hu Y, Yang L, Na X, You J, Hu W, Liang X, Liu J, Mao L, Wang X, Wang H, Bi Y. Narciclasine inhibits the responses of Arabidopsis roots to auxin. PLANTA 2012; 236:597-612. [PMID: 22476291 DOI: 10.1007/s00425-012-1632-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/22/2012] [Indexed: 05/31/2023]
Abstract
The plant hormone auxin plays a central role in the regulation of plant growth and development, as well as in responses to environmental stimuli. Narciclasine (NCS, an Amaryllidaceae alkaloid) isolated from Narcissus tazetta bulbs has a broad range of inhibitory effects on plants. In this study, the role of NCS in responses to auxin in Arabidopsis thaliana roots was investigated. We demonstrated the inhibitory effects of NCS on auxin-inducible lateral root formation, root hair formation, primary root growth, and the expression of primary auxin-inducible genes in Arabidopsis roots using DR5::GUS reporter gene, native auxin promoters (IAA12::GUS, IAA13::GUS), and quantitative reverse transcription PCR analysis. Results also showed that NCS did not affect the expression of cytokinin-inducible ARR5::GUS reporter gene. NCS relieved the auxin-enhanced degradation of the Aux/IAA repressor modulated by the SCFTIR1 ubiquitin-proteasome pathway. In addition, NCS did not alter the auxin-stimulated interaction between IAA7/AXR2 (Aux/IAA proteins) and the F-box protein TIR1 activity of the proteasome. Taken together, these results suggest that NCS acts on the auxin signaling pathway upstream of TIR1, which modulates Aux/IAA protein degradation, and thereby affects the auxin-mediated responses in Arabidopsis roots.
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Affiliation(s)
- Yanfeng Hu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
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30
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Hayashi KI. The interaction and integration of auxin signaling components. PLANT & CELL PHYSIOLOGY 2012; 53:965-75. [PMID: 22433459 DOI: 10.1093/pcp/pcs035] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
IAA, a naturally occurring auxin, is a simple signaling molecule that regulates many diverse steps of plant development. Auxin essentially coordinates plant development through transcriptional regulation. Auxin binds to TIR1/AFB nuclear receptors, which are F-box subunits of the SCF ubiquitin ligase complex. The auxin signal is then modulated by the quantitative and qualitative responses of the Aux/IAA repressors and the auxin response factor (ARF) transcription factors. The specificity of the auxin-regulated gene expression profile is defined by several factors, such as the expression of these regulatory proteins, their post-transcriptional regulation, their stability and the affinity between these regulatory proteins. Auxin-binding protein 1 (ABP1) is a candidate protein for an auxin receptor that is implicated in non-transcriptional auxin signaling. ABP1 also affects TIR1/AFB-mediated auxin-responsive gene expression, implying that both the ABP1 and TIR1/AFB signaling machineries coordinately control auxin-mediated physiological events. Systematic approaches using the comprehensive mapping of the expression and interaction of signaling modules and computational modeling would be valuable for integrating our knowledge of auxin signals and responses.
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Affiliation(s)
- Ken-ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, Okayama, 700-0005 Japan.
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Neddylation and CAND1 independently stimulate SCF ubiquitin ligase activity in Candida albicans. EUKARYOTIC CELL 2011; 11:42-52. [PMID: 22080453 DOI: 10.1128/ec.05250-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SCF (Skp1-cullin/Cdc53-F-box protein) ubiquitin ligases bind substrates via the variable F-box protein and, in conjunction with the RING domain protein Rbx1 and the ubiquitin-conjugating enzyme Ubc3/Cdc34, catalyze substrate ubiquitination. The cullin subunit can be modified covalently by conjugation of the ubiquitin-like protein Rub1/NEDD8 (neddylation) or bound noncovalently by the protein CAND1 (cullin-associated, neddylation-dissociated). Expression of the Candida albicans CAND1 gene homolog CaTIP120 in Saccharomyces cerevisiae is toxic only in the presence of CaCdc53, consistent with a specific interaction between CaTip120 and CaCdc53. To genetically analyze this system in C. albicans, we deleted the homologs of RUB1/NEDD8, TIP120/CAND1, and the deneddylase gene JAB1, and we also generated a temperature-sensitive allele of the essential CaCDC53 gene by knock-in site-directed mutagenesis. Deletion of CaRUB1 and CaTIP120 caused morphological, growth, and protein degradation phenotypes consistent with a reduction in SCF ubiquitin ligase activity. Furthermore, the double Carub1(-/-) Catip120(-/-) mutant was more defective in SCF activity than either individual deletion mutant. These results indicate that CAND1 stimulates SCF ubiquitin ligase activity and that it does so independently of neddylation. Our data do not support a role for CAND1 in the protection of either the F-box protein or cullin from degradation but are consistent with the suggested role of CAND1 in SCF complex remodeling.
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Alternating temperature breaks dormancy in leafy spurge seeds and impacts signaling networks associated with HY5. Funct Integr Genomics 2011; 11:637-49. [PMID: 21947436 DOI: 10.1007/s10142-011-0253-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 09/10/2011] [Accepted: 09/13/2011] [Indexed: 01/28/2023]
Abstract
Non-after-ripened seeds of the herbaceous perennial weed leafy spurge do not germinate when imbibed at a constant temperature (C), but transfer to an alternating temperature (A) induced germination. Changes in the transcriptome of seeds during 1 and 3 days of alternating temperature and germinated seeds were compared with seeds incubated at constant temperature. Statistical analysis revealed that 597, 1,491, and 1,329 genes were differentially expressed (P < 0.05) for the comparisons of 21-day C vs. 21-day C + 1-day A, 21-day C vs. 21-day C + 3-day A, and 21-day C vs. 21-day C + Germ (germination), respectively. Functional classifications based on gene set and sub-network enrichment analysis were performed to identify pathways and gene sub-networks that underlie transcriptome changes in the seeds as they germinate. Sugars, plant hormones, photomorphogenesis, and reactive oxygen species were overrepresented at 21-day C + 1-day A. At 21-day C + 3-day A, an increase in cellular activities was observed as the number of overrepresented pathways greatly increased. Many of the metabolic pathways were involved in the biosynthesis of amino acids, macromolecules, and energy and carbon skeleton production for subsequent germination. The 21-day C + 3-day A and 21-day C + Germ pathways and sub-networks were similar and included an overrepresentation of the amino acid biosynthetic pathways; however, 21-day C + Germ seeds have an even wider array of cellular activities such as translation-related pathways, which are most likely for seedling growth. RT-qPCR analysis indicated that the up- and down-regulation of HISTONE H3, GASA2, DREBIII-1, CHS, AOS, PIF3, PLD α1, and LEA may be germination-related since their expression was dramatically changed only in the 21-day C + Germ seeds. Finally, both short-term alternating temperature and short-term light exposure up-regulated the expression targets of the central hub HY5 in leafy spurge and Arabidopsis, respectively, indicating that a signaling network involving HY5 is important for germination.
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Wang XF, He FF, Ma XX, Mao CZ, Hodgman C, Lu CG, Wu P. OsCAND1 is required for crown root emergence in rice. MOLECULAR PLANT 2011; 4:289-99. [PMID: 20978084 DOI: 10.1093/mp/ssq068] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Crown roots are main components of the fibrous root system and important for crops to anchor and absorb water and nutrition. To understand the molecular mechanisms of crown root formation, we isolated a rice mutant defective in crown root emergence designated as Oscand1 (named after the Arabidopsis homologous gene AtCAND1). The defect of visible crown root in the Oscand1 mutant is the result of cessation of the G2/M cell cycle transition in the crown root meristem. Map-based cloning revealed that OsCAND1 is a homolog of Arabidopsis CAND1. During crown root primordium development, the expression of OsCAND1 is confined to the root cap after the establishment of fundamental organization. The transgenic plants harboring DR5::GUS showed that auxin signaling in crown root tip is abnormal in the mutant. Exogenous auxin application can partially rescue the defect of crown root development in Oscand1. Taken together, these data show that OsCAND1 is involved in auxin signaling to maintain the G2/M cell cycle transition in crown root meristem and, consequently, the emergence of crown root. Our findings provide new information about the molecular regulation of the emergence of crown root in rice.
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Affiliation(s)
- Xiao-Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, P.R. China
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Regulation of cullin RING E3 ubiquitin ligases by CAND1 in vivo. PLoS One 2011; 6:e16071. [PMID: 21249194 PMCID: PMC3020946 DOI: 10.1371/journal.pone.0016071] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 12/04/2010] [Indexed: 11/20/2022] Open
Abstract
Cullin RING ligases are multi-subunit complexes consisting of a cullin protein which forms a scaffold onto which the RING protein Rbx1/2 and substrate receptor subunits assemble. CAND1, which binds to cullins that are not conjugated with Nedd8 and not associated with substrate receptors, has been shown to function as a positive regulator of Cullin ligases in vivo. Two models have been proposed to explain this requirement: (i) CAND1 sequesters cullin proteins and thus prevents autoubiquitination of substrate receptors, and (ii) CAND1 is required to promote the exchange of bound substrate receptors. Using mammalian cells, we show that CAND1 is predominantly cytoplasmically localized and that cullins are the major CAND1 interacting proteins. However, only small amounts of CAND1 bind to Cul1 in cells, despite low basal levels of Cul1 neddylation and approximately equal cytoplasmic endogenous protein concentrations of CAND1 and Cul1. Compared to F-box protein substrate receptors, binding of CAND1 to Cul1 in vivo is weak. Furthermore, preventing binding of F-box substrate receptors to Cul1 does not increase CAND1 binding. In conclusion, our study suggests that CAND1 does not function by sequestering cullins in vivo to prevent substrate receptor autoubiquitination and is likely to regulate cullin RING ligase activity via alternative mechanisms.
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Abstract
The posttranslational addition of ubiquitin (Ub) helps control the half-life, localization, and action of many intracellular plant proteins. A primary function is the degradation of ubiquitylated proteins by the 26S proteasome, which in turn plays important housekeeping and regulatory roles by removing aberrant polypeptides and various normal short-lived regulators. Strikingly, both genetic and genomic studies reveal that Ub conjugation is extraordinarily complex in plants, with more than 1500 Ub-protein ligases (or E3s) possible that could direct the final transfer of the Ub moiety to an equally large number of targets. The cullin-RING ligases (CRLs) are a highly polymorphic E3 collection composed of a cullin backbone onto which binds carriers of activated Ub and a diverse assortment of adaptors that recruit appropriate substrates for ubiquitylation. Here, we review our current understanding of the organization and structure of CRLs in plants and their dynamics, substrates, potential functions, and evolution. The importance of CRLs is exemplified by their ability to serve as sensors of hormones and light; their essential participation in various signaling pathways; their control of the cell cycle, transcription, the stress response, self-incompatibility, and pathogen defense; and their dramatically divergent evolutionary histories in many plant lineages. Given both their organizational complexities and their critical influences, CRLs likely impact most, if not all, aspects of plant biology.
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Affiliation(s)
- Zhihua Hua
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706-1574, USA.
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Villeneuve NF, Lau A, Zhang DD. Regulation of the Nrf2-Keap1 antioxidant response by the ubiquitin proteasome system: an insight into cullin-ring ubiquitin ligases. Antioxid Redox Signal 2010; 13:1699-712. [PMID: 20486766 PMCID: PMC2966484 DOI: 10.1089/ars.2010.3211] [Citation(s) in RCA: 323] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nrf2 is a transcription factor that has emerged as the cell's main defense mechanism against many harmful environmental toxicants and carcinogens. Nrf2 is negatively regulated by Keap1, a substrate adaptor protein for the Cullin3 (Cul3)-containing E3-ligase complex, which targets Nrf2 for ubiquitination and degradation by the ubiquitin proteasome system (UPS). Recent evidence suggests that constitutive activation of Nrf2, due to mutations in Keap1 or Nrf2, is prominent in many cancer types and contributes to chemoresistance. Regulation of Nrf2 by the Cul3-Keap1-E3 ligase provides strong evidence that tight regulation of Cullin-ring ligases (CRLs) is imperative to maintain cellular homeostasis. There are seven known Cullin proteins that form various CRL complexes. They are regulated by neddylation/deneddylation, ubiquitination/deubiquitination, CAND1-assisted complex assembly/disassembly, and subunit dimerization. In this review, we will discuss the regulation of each CRL using the Cul3-Keap1-E3 ligase complex as the primary focus. The substrates of CRLs are involved in many signaling pathways. Therefore, deregulation of CRLs affects several cellular processes, including cell cycle arrest, DNA repair, cell proliferation, senescence, and death, which may lead to many human diseases, including cancer. This makes CRLs a promising target for novel cancer drug therapies.
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Affiliation(s)
- Nicole F Villeneuve
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, 85721, USA
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Helmstaedt K, Schwier EU, Christmann M, Nahlik K, Westermann M, Harting R, Grond S, Busch S, Braus GH. Recruitment of the inhibitor Cand1 to the cullin substrate adaptor site mediates interaction to the neddylation site. Mol Biol Cell 2010; 22:153-64. [PMID: 21119001 PMCID: PMC3016973 DOI: 10.1091/mbc.e10-08-0732] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cand1 inhibits cullin RING ubiquitin ligases by binding unneddylated cullins. The Cand1 N-terminus blocks the cullin neddylation site, whereas the C-terminus inhibits cullin adaptor interaction. These Cand1 binding sites can be separated into two functional polypeptides which bind sequentially. C-terminal Cand1 can directly bind to unneddylated cullins in the nucleus without blocking the neddylation site. The smaller N-terminal Cand1 cannot bind to the cullin neddylation region without C-terminal Cand1. The separation of a single cand1 into two independent genes represents the in vivo situation of the fungus Aspergillus nidulans, where C-terminal Cand1 recruits smaller N-terminal Cand1 in the cytoplasm. Either deletion results in an identical developmental and secondary metabolism phenotype in fungi, which resembles csn mutants deficient in the COP9 signalosome (CSN) deneddylase. We propose a two-step Cand1 binding to unneddylated cullins which initiates at the adaptor binding site and subsequently blocks the neddylation site after CSN has left.
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Affiliation(s)
- Kerstin Helmstaedt
- Institute of Microbiology and Genetics, Georg-August-Universität, D-37077 Göttingen, Germany
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Bosu DR, Feng H, Min K, Kim Y, Wallenfang MR, Kipreos ET. C. elegans CAND-1 regulates cullin neddylation, cell proliferation and morphogenesis in specific tissues. Dev Biol 2010; 346:113-26. [PMID: 20659444 DOI: 10.1016/j.ydbio.2010.07.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 07/14/2010] [Accepted: 07/18/2010] [Indexed: 11/26/2022]
Abstract
Cullin-RING ubiquitin ligases (CRLs) are critical regulators of multiple developmental and cellular processes in eukaryotes. CAND1 is a biochemical inhibitor of CRLs, yet has been shown to promote CRL activity in plant and mammalian cells. Here we analyze CAND1 function in the context of a developing metazoan organism. Caenorhabditis elegans CAND-1 is capable of binding to all of the cullins, and we show that it physically interacts with CUL-2 and CUL-4 in vivo. The covalent attachment of the ubiquitin-like protein Nedd8 is required for cullin activity in animals and plants. In cand-1 mutants, the levels of the neddylated isoforms of CUL-2 and CUL-4 are increased, indicating that CAND-1 is a negative regulator of cullin neddylation. cand-1 mutants are hypersensitive to the partial loss of cullin activity, suggesting that CAND-1 facilitates CRL functions. cand-1 mutants exhibit impenetrant phenotypes, including developmental arrest, morphological defects of the vulva and tail, and reduced fecundity. cand-1 mutants share with cul-1 and lin-23 mutants the phenotypes of supernumerary seam cell divisions, defective alae formation, and the accumulation of the SCF(LIN-23) target the glutamate receptor GLR-1. The observation that cand-1 mutants have phenotypes associated with the loss of the SCF(LIN-23) complex, but lack phenotypes associated with other specific CRL complexes, suggests that CAND-1 is differentially required for the activity of distinct CRL complexes.
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Affiliation(s)
- Dimple R Bosu
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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Santner A, Estelle M. The ubiquitin-proteasome system regulates plant hormone signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:1029-40. [PMID: 20409276 PMCID: PMC3066055 DOI: 10.1111/j.1365-313x.2010.04112.x] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants utilize the ubiquitin-proteasome system (UPS) to modulate nearly every aspect of growth and development. Ubiquitin is covalently attached to target proteins through the action of three enzymes known as E1, E2, and E3. The ultimate outcome of this post-translational modification depends on the nature of the ubiquitin linkage and the extent of polyubiquitination. In most cases, ubiquitination results in degradation of the target protein in the 26S proteasome. During the last 10 years it has become clear that the UPS plays a prominent regulatory role in hormone biology. E3 ubiquitin ligases in particular actively participate in hormone perception, de-repression of hormone signaling pathways, degradation of hormone specific transcription factors, and regulation of hormone biosynthesis. It is certain that additional functions will be discovered as more of the nearly 1200 potential E3s in plants are elucidated.
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Affiliation(s)
- Aaron Santner
- Molecular Kinetics, Inc., 6201 La Pas Trail, Suite 160, Indianapolis, IN 46268, USA
| | - Mark Estelle
- University of California San Diego, Section of Cell and Developmental Biology, 9500 Gilman Drive, La Jolla, CA 9209, USA
- For correspondence (fax +858 534 7108; )
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O'Malley RC, Ecker JR. Linking genotype to phenotype using the Arabidopsis unimutant collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:928-40. [PMID: 20409268 DOI: 10.1111/j.1365-313x.2010.04119.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The large collections of Arabidopsis thaliana sequence-indexed T-DNA insertion mutants are among the most important resources to emerge from the sequencing of the genome. Several laboratories around the world have used the Arabidopsis reference genome sequence to map T-DNA flanking sequence tags (FST) for over 325,000 T-DNA insertion lines. Over the past decade, phenotypes identified with T-DNA-induced mutants have played a critical role in advancing both basic and applied plant research. These widely used mutants are an invaluable tool for direct interrogation of gene function. However, most lines are hemizygous for the insertion, necessitating a genotyping step to identify homozygous plants for the quantification of phenotypes. This situation has limited the application of these collections for genome-wide screens. Isolating multiple homozygous insert lines for every gene in the genome would make it possible to systematically test the phenotypic consequence of gene loss under a wide variety of conditions. One major obstacle to achieving this goal is that 12% of genes have no insertion and 8% are only represented by a single allele. Generation of additional mutations to achieve full genome coverage has been slow and expensive since each insertion is sequenced one at a time. Recent advances in high-throughput sequencing technology open up a potentially faster and cost-effective means to create new, very large insertion mutant populations for plants or animals. With the combination of new tools for genome-wide studies and emerging phenotyping platforms, these sequence-indexed mutant collections are poised to have a larger impact on our understanding of gene function.
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Affiliation(s)
- Ronan C O'Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92307, USA
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De Rybel B, Audenaert D, Beeckman T, Kepinski S. The past, present, and future of chemical biology in auxin research. ACS Chem Biol 2009; 4:987-98. [PMID: 19736989 DOI: 10.1021/cb9001624] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Research into the plant hormone auxin has always been tightly linked with the use of small molecules. In fact, most of the known players in auxin signaling and transport in the model plant Arabidopsis thaliana were identified by screening for resistance to auxin analogues. The use of high-throughput screening technologies has since yielded many novel molecules, opening the way for the identification of new target proteins to further elucidate known pathways. Here, we give an overview of well-established and novel molecules used in auxin research and highlight the current status and future perspectives of chemical biology approaches to auxin biology.
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Affiliation(s)
- Bert De Rybel
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
- Department Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Dominique Audenaert
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
- Department Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
- Department Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Stefan Kepinski
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, U.K
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Isolation and characterization of cul1-7, a recessive allele of CULLIN1 that disrupts SCF function at the C terminus of CUL1 in Arabidopsis thaliana. Genetics 2008; 181:945-63. [PMID: 19114460 DOI: 10.1534/genetics.108.097675] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many aspects of plant biology depend on the ubiquitin proteasome system for degradation of regulatory proteins. Ubiquitin E3 ligases confer substrate specificity in this pathway, and SCF-type ligases comprise a major class of E3s. SCF ligases have four subunits: SKP1, CUL1, RBX1, and an F-box protein for substrate recognition. The Aux/IAAs are a well-characterized family of SCF substrates in plants. Here, we report characterization of a mutant isolated from a genetic screen in Arabidopsis thaliana designed to identify plants defective in degradation of an Aux/IAA fusion protein, Aux/IAA1-luciferase (IAA1-LUC). This mutant exhibited fourfold slower IAA1-LUC degradation compared with the progenitor line, and seedlings displayed altered auxin responses. Experiments identified the mutant as an allele of CUL1, named cul1-7. The cul1-7 mutation affects the C terminus of the protein, results in reduced cul1-7 levels, and interferes with RBX1 interaction. cul1-7 seedlings are defective in degradation of an endogenous SCF substrate, Repressor of ga1-3 (RGA), and have altered responses to gibberellins. cul1-7 seedlings exhibit slower degradation of the light-labile red/far-red photoreceptor phytochrome A and are photomorphogenic in the dark. This mutation represents the first reported allele of CUL1 to directly affect subunit interactions at the CUL1 C terminus.
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Affiliation(s)
| | - Mark Estelle
- Department of Biology, Indiana University, Bloomington, Indiana 47405; ,
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Christian M, Hannah WB, Lüthen H, Jones AM. Identification of auxins by a chemical genomics approach. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:2757-67. [PMID: 18515827 PMCID: PMC2486469 DOI: 10.1093/jxb/ern133] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 03/31/2008] [Accepted: 04/14/2008] [Indexed: 05/20/2023]
Abstract
Thirteen auxenic compounds were discovered in a screen of 10 000 compounds for auxin-like activity in Arabidopsis roots. One of the most potent substances was 2-(4-chloro-2-methylphenoxy)-N-(4-H-1,2,4-triazol-3-yl)acetamide (WH7) which shares similar structure to the known auxenic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). A selected set of 20 analogues of WH7 was used to provide detailed information about the structure-activity relationship based on their efficacy at inhibiting and stimulating root and shoot growth, respectively, and at induction of gene expression. It was shown that WH7 acts in a genetically defined auxin pathway. These small molecules will extend the arsenal of substances that can be used to define auxin perception site(s) and to dissect subsequent signalling events.
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Affiliation(s)
- May Christian
- Departments of Biology and Pharmacology, The University of North Carolina at Chapel Hill, NC 27599-3280, USA
| | - William B. Hannah
- Departments of Biology and Pharmacology, The University of North Carolina at Chapel Hill, NC 27599-3280, USA
| | - Hartwig Lüthen
- Biozentrum Klein Flottbek und Botanischer Garten, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Alan M. Jones
- Departments of Biology and Pharmacology, The University of North Carolina at Chapel Hill, NC 27599-3280, USA
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Bosu DR, Kipreos ET. Cullin-RING ubiquitin ligases: global regulation and activation cycles. Cell Div 2008; 3:7. [PMID: 18282298 PMCID: PMC2266742 DOI: 10.1186/1747-1028-3-7] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 02/18/2008] [Indexed: 11/29/2022] Open
Abstract
Cullin-RING ubiquitin ligases (CRLs) comprise the largest known category of ubiquitin ligases. CRLs regulate an extensive number of dynamic cellular processes, including multiple aspects of the cell cycle, transcription, signal transduction, and development. CRLs are multisubunit complexes composed of a cullin, RING H2 finger protein, a variable substrate-recognition subunit (SRS), and for most CRLs, an adaptor that links the SRS to the complex. Eukaryotic species contain multiple cullins, with five major types in metazoa. Each cullin forms a distinct class of CRL complex, with distinct adaptors and/or substrate-recognition subunits. Despite this diversity, each of the classes of CRL complexes is subject to similar regulatory mechanisms. This review focuses on the global regulation of CRL complexes, encompassing: neddylation, deneddylation by the COP9 Signalosome (CSN), inhibitory binding by CAND1, and the dimerization of CRL complexes. We also address the role of cycles of activation and inactivation in regulating CRL activity and switching between substrate-recognition subunits.
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Affiliation(s)
- Dimple R Bosu
- Department of Cellular Biology, University of Georgia, 724 Biological Sciences Bldg,, Athens, GA 30602-2607, USA.
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46
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Norambuena L, Zouhar J, Hicks GR, Raikhel NV. Identification of cellular pathways affected by Sortin2, a synthetic compound that affects protein targeting to the vacuole in Saccharomyces cerevisiae. BMC CHEMICAL BIOLOGY 2008; 8:1. [PMID: 18179719 PMCID: PMC2265672 DOI: 10.1186/1472-6769-8-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Accepted: 01/07/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND Sortin2 is a low mass compound that interferes with vacuolar delivery of proteins in plants and yeast. The Sortin2 phenotype was tested in Arabidopsis thaliana and found to be reversible upon drug removal, demonstrating the ability of chemical genomics to induce reversible phenotypes that would be difficult to achieve using conventional genetics 1. However, standard genetic methods can be used to identify drug target pathways in a high-throughput manner. RESULTS In this study, we analyzed structure-function relationships of Sortin2 using structural analogues. The results show the key roles of sulphite substitution and a benzoic acid group. A Sortin 2 hypersensitivity screen for the induced secretion of a vacuolar cargo protein was done utilizing a yeast haploid deletion library. Using bioinformatics approaches, we highlighted functional information about the cellular pathways affected by drug treatment which included protein sorting and other endomembrane system-related processes. CONCLUSION Chemical, genomic and genetics approaches were used to understand the mode of action of Sortin2, a bioactive chemical that affects the delivery of a vacuolar protein. Critical features of Sortin2 structure necessary for bioactivity suggest a binding pocket that may recognize two ends of Sortin2. The genome-wide screen shows that Sortin2 treatment in yeast affects primarily components within the endomembrane system. This approach allowed us to assign putative functions in protein sorting for fifteen genes of previously unknown function.
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Affiliation(s)
- Lorena Norambuena
- Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile.,Center for Plant Cell Biology and Department of Botany and Plant Sciences at University of California. 2109 Batchelor Hall, University of California Riverside, CA 92521 USA
| | - Jan Zouhar
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, E-28049 Madrid, Spain.,Center for Plant Cell Biology and Department of Botany and Plant Sciences at University of California. 2109 Batchelor Hall, University of California Riverside, CA 92521 USA
| | - Glenn R Hicks
- Center for Plant Cell Biology and Department of Botany and Plant Sciences at University of California. 2109 Batchelor Hall, University of California Riverside, CA 92521 USA
| | - Natasha V Raikhel
- Center for Plant Cell Biology and Department of Botany and Plant Sciences at University of California. 2109 Batchelor Hall, University of California Riverside, CA 92521 USA
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Abstract
The ubiquitin/26S proteasome pathway largely mediates selective proteolysis in the nucleus and cytosol. This pathway catalyzes covalent attachment of ubiquitin (UBQ) to substrate proteins in an E1-E2-E3 cascade. Ubiquitin E3 ligases interact with substrates to catalyze UBQ transfer from E2 to substrate. Within the E3 ligase superfamily, cullin RING ligases (CRLs) are significant in plants because they are linked to hormonal signaling, developmental programs, and environmental responses. Thus, knowledge of CRL regulation is required for a complete understanding of these processes. A major mechanism modulating CRL activity is modification of the cullin subunit by RUB (RELATED TO UBIQUITIN), a ubiquitin-like protein, and demodification by the COP9 signalosome (CSN). CULLIN-ASSOCIATED NEDD8-DISSOCIATED 1 (CAND1) interacts with CRLs, affecting both rubylation and derubylation. Described here are the pathways, regulation, and biological function of rubylation and derubylation, as well as future directions and outstanding questions.
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Affiliation(s)
- Sara K Hotton
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA.
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48
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Sungur C, Miller S, Bergholz J, Hoye RC, Brisbois RG, Overvoorde P. The Small Molecule 2-Furylacrylic Acid Inhibits Auxin-Mediated Responses in Arabidopsis thaliana. ACTA ACUST UNITED AC 2007; 48:1693-701. [DOI: 10.1093/pcp/pcm141] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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49
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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50
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Candela H, Alonso-Peral MM, Ponce MR, Micol JL. Role of HEMIVENATA and the Ubiquitin Pathway in Venation Pattern Formation. PLANT SIGNALING & BEHAVIOR 2007; 2:258-9. [PMID: 19704672 PMCID: PMC2634141 DOI: 10.4161/psb.2.4.3869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 01/16/2007] [Indexed: 05/20/2023]
Abstract
Elegant work by others has highlighted the importance of auxin transport in venation patterning, an idea substantiated by the severe effects of auxin polar transport inhibitors and by the mutant phenotype and expression patterns associated with the auxin efflux transporter PIN-FORMED1 (PIN1). It is striking, therefore, that little attention has been paid to the venation patterns of mutants insensitive to this hormone, since both auxin transport and perception are crucial components in theoretical models of vascular patterning. Our finding that HEMIVENATA (HVE) is the same gene as CAND1 confirms the role of ubiquitin-mediated auxin perception in vascular patterning and sets the stage for a re-examination of the leaf venation phenotypes of other auxin-resistant mutants and additional components of the ubiquitin pathway.
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Affiliation(s)
- Héctor Candela
- División de Genética and Instituto de Bioingeniería; Universidad Miguel Hernández; Alicante, Spain
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