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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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2
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Kiseleva AA, Bragina MK, Muterko AF, Salina EA. Functional characterization of genes with daily expression patterns in common wheat. PLANT MOLECULAR BIOLOGY 2022; 109:135-146. [PMID: 35316425 DOI: 10.1007/s11103-022-01262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Our findings suggest most wheat biological processes are under the control of the daily expressed genes. Plant circadian rhythms represent daily changes in the activity of various processes, which are based on changes in the levels of gene expression and protein synthesis. In wheat, some key components of plant circadian clock have been identified, but there is little data on the daily expression and interactions of these genes. To study the common wheat daily transcriptome, RNA sequencing was performed. Using these data, genes expressed in daily pattern and the metabolic pathways controlled by them were identified: responses to stimuli and nutrients, transport, photoperiodism, photomorphogenesis, synthesis and degradation of different metabolites, and regulation of the processes of RNA synthesis. It was shown that a significant part of the transcriptome can vary greatly daily. Five expression patterns were identified. They were characterized by peaks at different time points and described the genes underlying these patterns. The analysis of the enrichment of gene ontology terms with various patterns allowed us to describe the main metabolic pathways in each group. Wheat homologs of the genes related to circadian clock in Arabidopsis were identified. Most of them were represented by three homoeologous genes expressed uniformly. Comparison of their expression patterns demonstrated a shift in the expression peaks for some core and accessory genes; the majority of wheat circadian genes were expressed in accordance with Arabidopsis homologs. This may indicate a similar functional role of these genes in wheat.
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Affiliation(s)
- Antonina A Kiseleva
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090.
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090.
| | - Mariya K Bragina
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
| | - Aleksandr F Muterko
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
| | - Elena A Salina
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
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3
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Kramer MC, Kim HJ, Palos KR, Garcia BA, Lyons E, Beilstein MA, Nelson ADL, Gregory BD. A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development. FRONTIERS IN PLANT SCIENCE 2022; 13:906603. [PMID: 35693169 PMCID: PMC9175010 DOI: 10.3389/fpls.2022.906603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 05/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED IN BRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system. However, we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and propose a novel mechanism of lincRNA action in which it may act as a scaffold with the RACK1A protein to regulate germination and development, possibly through a role in ribosome biogenesis.
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Affiliation(s)
- Marianne C. Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Kyle R. Palos
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- CyVerse Inc., Tucson, AZ, United States
| | - Mark A. Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | | | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Brian D. Gregory,
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4
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Peska V, Fajkus P, Bubeník M, Brázda V, Bohálová N, Dvořáček V, Fajkus J, Garcia S. Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae. Sci Rep 2021; 11:12784. [PMID: 34140564 PMCID: PMC8211666 DOI: 10.1038/s41598-021-92126-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023] Open
Abstract
Telomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remained uncharacterised in the template region. Here we show that this is mainly due to high variability in telomere sequence. We predicted the telomere sequences using Tandem Repeats Finder and then we identified corresponding putative template regions in TR candidates. Remarkably long telomere units and the corresponding putative TRs were found in Tetrapisispora species. Notably, variable lengths of the annealing sequence of the template region (1–10 nt) were found. Consequently, species with the same telomere sequence may not harbour identical TR templates. Thus, TR sequence alone can be used to predict a template region and telomere sequence, but not to determine these exactly. A conserved feature of telomere sequences, tracts of adjacent Gs, led us to test the propensity of individual telomere sequences to form G4. The results show highly diverse values of G4-propensity, indicating the lack of ubiquitous conservation of this feature across Saccharomycetaceae.
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Affiliation(s)
- Vratislav Peska
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.
| | - Petr Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Michal Bubeník
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Vojtěch Dvořáček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic
| | - Jiří Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain.
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5
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Jacob P, Brisou G, Dalmais M, Thévenin J, van der Wal F, Latrasse D, Suresh Devani R, Benhamed M, Dubreucq B, Boualem A, Lepiniec L, Immink RGH, Hirt H, Bendahmane A. The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis. Genes (Basel) 2021; 12:genes12050746. [PMID: 34063415 PMCID: PMC8156827 DOI: 10.3390/genes12050746] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of these genes. In a yeast 1-hybrid screen with the SIIE, we identified the closely related R2R3-MYB transcription factors TT2 and MYB5. We found overexpression of MYB5 or TT2 rendered plants heat stress tolerant. In contrast, tt2, myb5, and tt2/myb5 loss of function mutants showed heat stress hypersensitivity. Transient expression assays confirmed that MYB5 and TT2 can regulate the HSFA2 promoter together with the other members of the MBW complex, TT8 and TRANSPARENT TESTA GLABRA 1 (TTG1) and that the SIIE was involved in this regulation. Transcriptomic analysis revealed that TT2/MYB5 target promoters were enriched in SIIE. Overall, we report a new function of TT2 and MYB5 in stress resistance and a role in SIIE-mediated HSFA2 regulation.
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Affiliation(s)
- Pierre Jacob
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Gwilherm Brisou
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Marion Dalmais
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Johanne Thévenin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (J.T.); (B.D.); (L.L.)
| | - Froukje van der Wal
- Bioscience and Laboratory of Molecular Biology, Wageningen University and Research, 6708PB Wageningen, The Netherlands; (F.v.d.W.); (R.G.H.I.)
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Ravi Suresh Devani
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (J.T.); (B.D.); (L.L.)
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Loic Lepiniec
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (J.T.); (B.D.); (L.L.)
| | - Richard G. H. Immink
- Bioscience and Laboratory of Molecular Biology, Wageningen University and Research, 6708PB Wageningen, The Netherlands; (F.v.d.W.); (R.G.H.I.)
| | - Heribert Hirt
- Darwin21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
- Correspondence:
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Molitor L, Bacher S, Burczyk S, Niessing D. The Molecular Function of PURA and Its Implications in Neurological Diseases. Front Genet 2021; 12:638217. [PMID: 33777106 PMCID: PMC7990775 DOI: 10.3389/fgene.2021.638217] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
In recent years, genome-wide analyses of patients have resulted in the identification of a number of neurodevelopmental disorders. Several of them are caused by mutations in genes that encode for RNA-binding proteins. One of these genes is PURA, for which in 2014 mutations have been shown to cause the neurodevelopmental disorder PURA syndrome. Besides intellectual disability (ID), patients develop a variety of symptoms, including hypotonia, metabolic abnormalities as well as epileptic seizures. This review aims to provide a comprehensive assessment of research of the last 30 years on PURA and its recently discovered involvement in neuropathological abnormalities. Being a DNA- and RNA-binding protein, PURA has been implicated in transcriptional control as well as in cytoplasmic RNA localization. Molecular interactions are described and rated according to their validation state as physiological targets. This information will be put into perspective with available structural and biophysical insights on PURA’s molecular functions. Two different knock-out mouse models have been reported with partially contradicting observations. They are compared and put into context with cell biological observations and patient-derived information. In addition to PURA syndrome, the PURA protein has been found in pathological, RNA-containing foci of patients with the RNA-repeat expansion diseases such as fragile X-associated tremor ataxia syndrome (FXTAS) and amyotrophic lateral sclerosis (ALS)/fronto-temporal dementia (FTD) spectrum disorder. We discuss the potential role of PURA in these neurodegenerative disorders and existing evidence that PURA might act as a neuroprotective factor. In summary, this review aims at informing researchers as well as clinicians on our current knowledge of PURA’s molecular and cellular functions as well as its implications in very different neuronal disorders.
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Affiliation(s)
- Lena Molitor
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabrina Bacher
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
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Identification of a consensus DNA-binding site for the TCP domain transcription factor TCP2 and its important roles in the growth and development of Arabidopsis. Mol Biol Rep 2021; 48:2223-2233. [PMID: 33689093 DOI: 10.1007/s11033-021-06233-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 02/12/2021] [Indexed: 02/02/2023]
Abstract
TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1 (TCP) transcription factors control multiple aspects of growth and development in various plant species. However, few genes were reported to be directly targeted and regulated by them through their specific binding sites, and then uncover their functions in plants. A consensus DNA-binding site motif of TCP2 was identified by random binding site selection (RBSS). DNA recognized by TCP2 contained the motif G(G/T)GGNCC(A/C), which showed high consistency with motifs bound by other TCP domain proteins. Consequently, this motif was regarded as the specific DNA-binding sites of TCP2. Circadian clock associated 1 (CCA1) and EARLY FLOWERING 3 (ELF3) were subsequently considered as potential target genes owing to the containing of the similar TCP2 binding sites or core binding sites GGNCC and found to be positively regulated by TCP2 via DNA binding. Phenotype analysis results showed that mutation and over-expression of TCP2 resulted in variations in leaf morphogenesis, especially the double or triple mutations of TCP2, 4 and 10. Mutations in TCPs caused late flowering. Finally, TCP2 was shown to influence hypocotyl elongation by mediating the jasmonate signaling pathway. Overall, these results provide a basis for future studies aimed at distinguishing the target genes of TCP2 and elucidating the important roles of TCP2 in plant growth and development.
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Bao S, Zhang Z, Lian Q, Sun Q, Zhang R. Evolution and expression of genes encoding TCP transcription factors in Solanum tuberosum reveal the involvement of StTCP23 in plant defence. BMC Genet 2019; 20:91. [PMID: 31801457 PMCID: PMC6892148 DOI: 10.1186/s12863-019-0793-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022] Open
Abstract
Background The plant-specific Teosinte branched1/Cycloidea/Proliferating cell factor (TCP) family of transcription factors is involved in the regulation of cell growth and proliferation, performing diverse functions in plant growth and development. In addition, TCP transcription factors have recently been shown to be targets of pathogenic effectors and are likely to play a vital role in plant immunity. No comprehensive analysis of the TCP family members in potato (Solanum tuberosum L.) has been undertaken, however, and whether their functions are conserved in potato remains unknown. Results To assess TCP gene evolution in potato, we identified TCP-like genes in several publicly available databases. A total of 23 non-redundant TCP transcription factor-encoding genes were identified in the potato genome and subsequently subjected to a systematic analysis that included determination of their phylogenetic relationships, gene structures and expression profiles in different potato tissues under basal conditions and after hormone treatments. These assays also confirmed the function of the class I TCP StTCP23 in the regulation of plant growth and defence. Conclusions This is the first genome-wide study including a systematic analysis of the StTCP gene family in potato. Identification of the possible functions of StTCPs in potato growth and defence provides valuable information for our understanding of the classification and functions of the TCP genes in potato.
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Affiliation(s)
- Sarina Bao
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, China
| | - Zhenxin Zhang
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, China
| | - Qun Lian
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, China
| | - Qinghua Sun
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, China
| | - Ruofang Zhang
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, China.
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9
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Shi X, Jiang F, Wen J, Wu Z. Overexpression of Solanum habrochaites microRNA319d (sha-miR319d) confers chilling and heat stress tolerance in tomato (S. lycopersicum). BMC PLANT BIOLOGY 2019; 19:214. [PMID: 31122194 PMCID: PMC6533698 DOI: 10.1186/s12870-019-1823-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/08/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND MicroRNA319 (miR319) acts as an essential regulator of gene expression during plant development and under stress conditions. Although the role of miR319a in regulating leaf development has been well studied in tomato (Solanum lycopersicum), the function of the recently discovered wild tomato Solanum habrochaites miRNA319d (sha-miR319d) remains poorly understood. In this study, we overexpressed sha-miR319d in cultivated tomato 'Micro-Tom' to further investigate its role in tomato temperature stress responses. RESULTS Under chilling or heat stress, sha-miR319d-overexpressing plants showed enhanced stress tolerance, including lower relative electrolyte leakage (REL), malondialdehyde (MDA) concentration, O2- generation and H2O2 concentration and higher chlorophyll contents and Fv/Fm values than wild-type (WT) plants. Overexpression of sha-miR319d enhanced the activities of superoxide dismutase (SOD) and catalase (CAT), with possible correlation with elevated expression levels of the genes FeSOD, CuZnSOD and CAT. Moreover, different expression levels of key genes involved in chilling (MYB83 and CBF1), heat (HsfA1a, HsfA1b and Hsp90), and reactive oxygen species (ROS) (ZAT12 and ZAT10) signaling in transgenic plants and WT were determined, suggesting a role for sha-miR319d in regulating tomato temperature stress via chilling, heat and ROS signaling. Silencing GAMYB-like1 increased tomato chilling tolerance as well as the expression levels of CBF1, CuZnSOD, CAT, APX1, APX2, ZAT12 and ZAT10. Additionally, overexpression of sha-miR319d in tomato caused plant leaf crinkling and reduced height. CONCLUSIONS Overexpression of sha-miR319d confers chilling and heat stress tolerance in tomato. Sha-miR319d regulates tomato chilling tolerance, possibly by inhibiting expression of GAMYB-like1 and further alters chilling, heat and ROS signal transduction. Our research provides insight for further study of the role of sha-miR319d in tomato growth and stress regulation and lays a foundation for the genetic improvement of tomato.
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Affiliation(s)
- Xiaopu Shi
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Junqin Wen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
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10
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Dokládal L, Benková E, Honys D, Dupľáková N, Lee LY, Gelvin SB, Sýkorová E. An armadillo-domain protein participates in a telomerase interaction network. PLANT MOLECULAR BIOLOGY 2018; 97:407-420. [PMID: 29948659 DOI: 10.1007/s11103-018-0747-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein-protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.
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Affiliation(s)
- Ladislav Dokládal
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Eva Benková
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - David Honys
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojova 263, 16502, Prague, Czech Republic
| | - Nikoleta Dupľáková
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojova 263, 16502, Prague, Czech Republic
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907-1392, USA
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907-1392, USA
| | - Eva Sýkorová
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic.
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11
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Song CB, Shan W, Yang YY, Tan XL, Fan ZQ, Chen JY, Lu WJ, Kuang JF. Heterodimerization of MaTCP proteins modulates the transcription of MaXTH10/11 genes during banana fruit ripening. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:613-622. [PMID: 29935343 DOI: 10.1016/j.bbagrm.2018.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022]
Abstract
The biological processes involved in banana fruit ripening are extremely complex and modulated by a number of genes such as transcription factors (TFs). Although TFs like MADS, ERF and NAC are implicated in controlling banana ripening, little is known about other TFs such as TCP in this process. In this work, 25 MaTCPs named MaTCP1 to MaTCP25 were characterized from our previously reported transcriptomes related to banana ripening. Expression analysis revealed that these MaTCPs displayed differential expression patterns during the progression of banana ripening. Particularly, MaTCP5, MaTCP19 and MaTCP20 were ethylene-inducible and nuclear-localized, with MaTCP5 and MaTCP20 acting as transcriptional activators while MaTCP19 being a transcriptional inhibitor. Moreover, MaTCP5 and MaTCP20 promoted the transcription of MaXTH10/11 that may play a role in fruit softening during banana ripening, whereas MaTCP19 repressed their transcription, by directly binding to their promoters. Importantly, protein-protein interaction assays demonstrated that MaTCP20 physically interacts with MaTCP5 and MaTCP19 to form heterodimers in vitro and in vivo, and these protein complexes affects their transcriptional activities in regulating the target genes. Taken together, our results provide an overview of the interactions between MaTCPs in controlling the ripening-associated genes and lay a foundation for further investigation of MaTCP gene family in regulating banana fruit ripening.
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Affiliation(s)
- Chun-Bo Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiao-Li Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Zhong-Qi Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China.
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12
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Telobox motifs recruit CLF/SWN–PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis. Nat Genet 2018; 50:638-644. [DOI: 10.1038/s41588-018-0109-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 03/13/2018] [Indexed: 12/25/2022]
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13
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Sharma N, Dang TM, Singh N, Ruzicic S, Mueller-Roeber B, Baumann U, Heuer S. Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice. RICE (NEW YORK, N.Y.) 2018; 11:2. [PMID: 29313187 PMCID: PMC5758481 DOI: 10.1186/s12284-017-0192-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/12/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. RESULTS Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. CONCLUSION This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.
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Affiliation(s)
- Niharika Sharma
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Trang Minh Dang
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Intrexon Corp, California, USA
| | - Namrata Singh
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia.
- International Rice Research Institute (IRRI), Los Banos, Philippines.
- Rothamsted Research, Plant Science Department, Hertfordshire, Harpenden, AL5 2JQ, UK.
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14
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Yamasaki Y, Gao F, Jordan MC, Ayele BT. Seed maturation associated transcriptional programs and regulatory networks underlying genotypic difference in seed dormancy and size/weight in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:154. [PMID: 28915785 PMCID: PMC5603048 DOI: 10.1186/s12870-017-1104-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 09/08/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Maturation forms one of the critical seed developmental phases and it is characterized mainly by programmed cell death, dormancy and desiccation, however, the transcriptional programs and regulatory networks underlying acquisition of dormancy and deposition of storage reserves during the maturation phase of seed development are poorly understood in wheat. The present study performed comparative spatiotemporal transcriptomic analysis of seed maturation in two wheat genotypes with contrasting seed weight/size and dormancy phenotype. RESULTS The embryo and endosperm tissues of maturing seeds appeared to exhibit genotype-specific temporal shifts in gene expression profile that might contribute to the seed phenotypic variations. Functional annotations of gene clusters suggest that the two tissues exhibit distinct but genotypically overlapping molecular functions. Motif enrichment predicts genotypically distinct abscisic acid (ABA) and gibberellin (GA) regulated transcriptional networks contribute to the contrasting seed weight/size and dormancy phenotypes between the two genotypes. While other ABA responsive element (ABRE) motifs are enriched in both genotypes, the prevalence of G-box-like motif specifically in tissues of the dormant genotype suggests distinct ABA mediated transcriptional mechanisms control the establishment of dormancy during seed maturation. In agreement with this, the bZIP transcription factors that co-express with ABRE enriched embryonic genes differ with genotype. The enrichment of SITEIIATCYTC motif specifically in embryo clusters of maturing seeds irrespective of genotype predicts a tissue specific role for the respective TCP transcription factors with no or minimal contribution to the variations in seed dormancy. CONCLUSION The results of this study advance our understanding of the seed maturation associated molecular mechanisms underlying variation in dormancy and weight/size in wheat seeds, which is a critical step towards the designing of molecular strategies for enhancing seed yield and quality.
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Affiliation(s)
- Yuji Yamasaki
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
| | - Feng Gao
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
| | - Mark C. Jordan
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada
| | - Belay T. Ayele
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
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15
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Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol 2017; 18:137. [PMID: 28732548 PMCID: PMC5522596 DOI: 10.1186/s13059-017-1273-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant. Result To predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes. Conclusions Our method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1273-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rurika Oka
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Johan Zicola
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Sarah N Anderson
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Huub C J Hoefsloot
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Franziska Turck
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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16
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Interacting TCP and NLP transcription factors control plant responses to nitrate availability. Proc Natl Acad Sci U S A 2017; 114:2419-2424. [PMID: 28202720 DOI: 10.1073/pnas.1615676114] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants have evolved adaptive strategies that involve transcriptional networks to cope with and survive environmental challenges. Key transcriptional regulators that mediate responses to environmental fluctuations in nitrate have been identified; however, little is known about how these regulators interact to orchestrate nitrogen (N) responses and cell-cycle regulation. Here we report that teosinte branched1/cycloidea/proliferating cell factor1-20 (TCP20) and NIN-like protein (NLP) transcription factors NLP6 and NLP7, which act as activators of nitrate assimilatory genes, bind to adjacent sites in the upstream promoter region of the nitrate reductase gene, NIA1, and physically interact under continuous nitrate and N-starvation conditions. Regions of these proteins necessary for these interactions were found to include the type I/II Phox and Bem1p (PB1) domains of NLP6&7, a protein-interaction module conserved in animals for nutrient signaling, and the histidine- and glutamine-rich domain of TCP20, which is conserved across plant species. Under N starvation, TCP20-NLP6&7 heterodimers accumulate in the nucleus, and this coincides with TCP20 and NLP6&7-dependent up-regulation of nitrate assimilation and signaling genes and down-regulation of the G2/M cell-cycle marker gene, CYCB1;1 TCP20 and NLP6&7 also support root meristem growth under N starvation. These findings provide insights into how plants coordinate responses to nitrate availability, linking nitrate assimilation and signaling with cell-cycle progression.
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17
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Krishnan A, Gupta C, Ambavaram MMR, Pereira A. RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response. FRONTIERS IN PLANT SCIENCE 2017; 8:1640. [PMID: 28979289 PMCID: PMC5611544 DOI: 10.3389/fpls.2017.01640] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 09/06/2017] [Indexed: 05/22/2023]
Abstract
Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 abiotic stress-specific gene modules covering 28,421 rice genes (>72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.
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Affiliation(s)
- Arjun Krishnan
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
| | - Chirag Gupta
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
| | | | - Andy Pereira
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
- *Correspondence: Andy Pereira,
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18
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Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis. Proc Natl Acad Sci U S A 2016; 113:11967-11972. [PMID: 27708161 DOI: 10.1073/pnas.1614852113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Ribosome production in eukaryotes requires the complex and precise coordination of several hundred assembly factors, including many small nucleolar RNAs (snoRNAs). However, at present, the distinct role of key snoRNAs in ribosome biogenesis remains poorly understood in higher plants. Here we report that a previously uncharacterized C (RUGAUGA)/D (CUGA) type snoRNA, HIDDEN TREASURE 2 (HID2), acts as an important regulator of ribosome biogenesis through a snoRNA-rRNA interaction. Nucleolus-localized HID2 is actively expressed in Arabidopsis proliferative tissues, whereas defects in HID2 cause a series of developmental defects reminiscent of ribosomal protein mutants. HID2 associates with the precursor 45S rRNA and promotes the efficiency and accuracy of pre-rRNA processing. Intriguingly, disrupting HID2 in Arabidopsis appears to impair the integrity of 27SB, a key pre-rRNA intermediate that generates 25S and 5.8S rRNA and is known to be vital for the synthesis of the 60S large ribosomal subunit and also produces an imbalanced ribosome profile. Finally, we demonstrate that the antisense-box of HID2 is both functionally essential and highly conserved in eukaryotes. Overall, our study reveals the vital and possibly conserved role of a snoRNA in monitoring the efficiency of pre-rRNA processing during ribosome biogenesis.
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19
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Bouché F, D’Aloia M, Tocquin P, Lobet G, Detry N, Périlleux C. Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana. Sci Rep 2016; 6:29042. [PMID: 27352932 PMCID: PMC4926122 DOI: 10.1038/srep29042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/10/2016] [Indexed: 11/21/2022] Open
Abstract
Molecular data concerning the involvement of roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of the root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutations are reported to alter flowering time are expressed in the roots (i.e. were detected in more than 50% of the microarrays). However, only a few flowering integrator genes passed the analysis cutoff. Comparison of root transcriptome in short days and during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories, and cis-regulatory elements converged towards sugar signaling. We concluded that roots are integrated in systemic signaling, whereby carbon supply coordinates growth at the whole plant level during the induction of flowering. This coordination could involve the root circadian clock and cytokinin biosynthesis as a feed forward loop towards the shoot.
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Affiliation(s)
- Frédéric Bouché
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Maria D’Aloia
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Pierre Tocquin
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Guillaume Lobet
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Nathalie Detry
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Claire Périlleux
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
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Garg R, Aggarwal J, Thakkar B. Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants. Sci Rep 2016; 6:28211. [PMID: 27324275 PMCID: PMC4914980 DOI: 10.1038/srep28211] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/18/2016] [Indexed: 11/22/2022] Open
Abstract
DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as G-quadruplexes. These structures have been implicated in several cellular processes in animals. In this study, we identified different types of G-quadruplex forming sequences (GQSes) in 15 sequenced plants and analyzed their distribution in various genomic features, including gene body, coding, intergenic and promoter regions. G2-type GQSes were most abundant in all the plant species analyzed. A strong association of G3-type GQSes with intergenic, promoter and intronic regions was found. However, G2-type GQSes were enriched in genic, CDS, exonic and untranslated regions. Further, we identified GQSes present in the conserved genes among monocots and dicots. The genes involved in development, cell growth and size, transmembrane transporter, and regulation of gene expression were found to be significantly enriched. In the promoter region, we detected strong co-occurrence of Telobox, ERF, MYB, RAV1B and E2F motifs with GQSes. Further, we validated the structure formation of several plant GQSes, demonstrated their effect on stalling in-vitro replication and revealed their interaction with plant nuclear proteins. Our data provide insights into the prevalence of GQSes in plants, establish their association with different genomic features and functional relevance.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Jyoti Aggarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Bijal Thakkar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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21
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Wang H, Liu C, Cheng J, Liu J, Zhang L, He C, Shen WH, Jin H, Xu L, Zhang Y. Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements. PLoS Genet 2016; 12:e1005771. [PMID: 26760036 PMCID: PMC4711971 DOI: 10.1371/journal.pgen.1005771] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 12/04/2015] [Indexed: 11/19/2022] Open
Abstract
Polycomb repressive complexes (PRCs) play crucial roles in transcriptional repression and developmental regulation in both plants and animals. In plants, depletion of different members of PRCs causes both overlapping and unique phenotypic defects. However, the underlying molecular mechanism determining the target specificity and functional diversity is not sufficiently characterized. Here, we quantitatively compared changes of tri-methylation at H3K27 in Arabidopsis mutants deprived of various key PRC components. We show that CURLY LEAF (CLF), a major catalytic subunit of PRC2, coordinates with different members of PRC1 in suppression of distinct plant developmental programs. We found that expression of flower development genes is repressed in seedlings preferentially via non-redundant role of CLF, which specifically associated with LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In contrast, expression of embryo development genes is repressed by PRC1-catalytic core subunits AtBMI1 and AtRING1 in common with PRC2-catalytic enzymes CLF or SWINGER (SWN). This context-dependent role of CLF corresponds well with the change in H3K27me3 profiles, and is remarkably associated with differential co-occupancy of binding motifs of transcription factors (TFs), including MADS box and ABA-related factors. We propose that different combinations of PRC members distinctively regulate different developmental programs, and their target specificity is modulated by specific TFs. Polycomb group proteins (PcGs) are essential for development in both animals and plants. Studies in plants are advantageous for elucidation of specific effects of PcGs during development, since most PcG mutants are viable in plants but not in animals. Previous efforts in genetic study of plant PcGs revealed that different PcGs have both common and unique effects on plant development, but the mechanisms underlying the specific regulation of different developmental programs by PcGs are still far from clear. In this study, we quantitatively compared the change in H3K27me3 and gene expression profiles between mutants of key PcG members on a genome-wide scale in Arabidopsis seedlings, and successfully unraveled different developmental programs that are specifically regulated by different combinations of PcGs. This context specific effect of PcGs is closely associated with different sets of transcription factor binding motifs. Together, we revealed on a genome-wide scale that different combinations of PcGs, as well as their association with the binding sites of different TFs, serve to explain the specific regulation of different developmental programs by PcGs.
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Affiliation(s)
- Hua Wang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunmei Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingfei Cheng
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Chongsheng He
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Hong Jin
- Department of Chemistry, Fudan University, Shanghai, China
- Institute of Biomedical Science, Fudan University, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
| | - Lin Xu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
| | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
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Schrumpfová PP, Vychodilová I, Hapala J, Schořová Š, Dvořáček V, Fajkus J. Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo. PLANT MOLECULAR BIOLOGY 2016; 90:189-206. [PMID: 26597966 DOI: 10.1007/s11103-015-0409-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/16/2015] [Indexed: 05/24/2023]
Abstract
Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically to telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human shelterin proteins TRF1 or TRF2, also possess a histone-like domain which is involved in protein-protein interactions e.g., with POT1b. Here we set out to investigate the genome-wide localization pattern of TRB1 to reveal its preferential sites of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Our results demonstrate that TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis, in addition to its roles at telomeres. This preference coincides with the frequent occurrence of telobox motifs in the upstream regions of genes in this category, but it is not restricted to the presence of a telobox. We conclude that TRB1 shows a specific genome-wide distribution pattern which suggests its role in regulation of genes involved in biogenesis of the translational machinery, in addition to its preferential telomeric localization.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Ivona Vychodilová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jan Hapala
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Šárka Schořová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Vojtěch Dvořáček
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 61265, Brno, Czech Republic.
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Danisman S. TCP Transcription Factors at the Interface between Environmental Challenges and the Plant's Growth Responses. FRONTIERS IN PLANT SCIENCE 2016; 7:1930. [PMID: 28066483 PMCID: PMC5174091 DOI: 10.3389/fpls.2016.01930] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/05/2016] [Indexed: 05/04/2023]
Abstract
Plants are sessile and as such their reactions to environmental challenges differ from those of mobile organisms. Many adaptions involve growth responses and hence, growth regulation is one of the most crucial biological processes for plant survival and fitness. The plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) transcription factor family is involved in plant development from cradle to grave, i.e., from seed germination throughout vegetative development until the formation of flowers and fruits. TCP transcription factors have an evolutionary conserved role as regulators in a variety of plant species, including orchids, tomatoes, peas, poplar, cotton, rice and the model plant Arabidopsis. Early TCP research focused on the regulatory functions of TCPs in the development of diverse organs via the cell cycle. Later research uncovered that TCP transcription factors are not static developmental regulators but crucial growth regulators that translate diverse endogenous and environmental signals into growth responses best fitted to ensure plant fitness and health. I will recapitulate the research on TCPs in this review focusing on two topics: the discovery of TCPs and the elucidation of their evolutionarily conserved roles across the plant kingdom, and the variety of signals, both endogenous (circadian clock, plant hormones) and environmental (pathogens, light, nutrients), TCPs respond to in the course of their developmental roles.
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Min L, Hu Q, Li Y, Xu J, Ma Y, Zhu L, Yang X, Zhang X. LEAFY COTYLEDON1-CASEIN KINASE I-TCP15-PHYTOCHROME INTERACTING FACTOR4 Network Regulates Somatic Embryogenesis by Regulating Auxin Homeostasis. PLANT PHYSIOLOGY 2015; 169:2805-21. [PMID: 26491146 PMCID: PMC4677921 DOI: 10.1104/pp.15.01480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/21/2015] [Indexed: 05/19/2023]
Abstract
Somatic embryogenesis (SE) is an efficient tool for the propagation of plant species and also, a useful model for studying the regulatory networks in embryo development. However, the regulatory networks underlying the transition from nonembryogenic callus to somatic embryos during SE remain poorly understood. Here, we describe an upland cotton (Gossypium hirsutum) CASEIN KINASE I gene, GhCKI, which is a unique key regulatory factor that strongly affects SE. Overexpressing GhCKI halted the formation of embryoids and plant regeneration because of a block in the transition from nonembryogenic callus to somatic embryos. In contrast, defective GhCKI in plants facilitated SE. To better understand the mechanism by which GhCKI regulates SE, the regulatory network was analyzed. A direct upstream negative regulator protein, cotton LEAFY COTYLEDON1, was identified to be targeted to a cis-element, CTTTTC, in the promoter of GhCKI. Moreover, GhCKI interacted with and phosphorylated cotton CINCINNATA-like TEOSINTE BRANCHED1-CYCLOIDEA-PCF transcription factor15 by coordinately regulating the expression of cotton PHYTOCHROME INTERACTING FACTOR4, finally disrupting auxin homeostasis, which led to increased cell proliferation and aborted somatic embryo formation in GhCKI-overexpressing somatic cells. Our results show a complex process of SE that is negatively regulated by GhCKI through a complex regulatory network.
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Affiliation(s)
- Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yaoyao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jiao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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25
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Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A, Szweykowska-Kulinska Z, Echeverria M, Karlowski WM. Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. BMC Genomics 2015; 16:1009. [PMID: 26607788 PMCID: PMC4660826 DOI: 10.1186/s12864-015-2221-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/16/2015] [Indexed: 11/18/2022] Open
Abstract
Background In the past few decades, non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression in eukaryotes. Most studies of ncRNAs in plants have focused on the identification of silencing microRNAs (miRNAs) and small interfering RNAs (siRNAs). Another important family of ncRNAs that has been well characterized in plants is the small nucleolar RNAs (snoRNAs) and the related small Cajal body-specific RNAs (scaRNAs). Both target chemical modifications of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In plants, the snoRNA genes are organized in clusters, transcribed by RNA Pol II from a common promoter and subsequently processed into mature molecules. The promoter regions of snoRNA polycistronic genes in plants are highly enriched in two conserved cis-regulatory elements (CREs), Telo-box and Site II, which coordinate the expression of snoRNAs and ribosomal protein coding genes throughout the cell cycle. Results In order to identify novel ncRNA genes, we have used the snoRNA Telo-box/Site II motifs combination as a functional promoter indicator to screen the Arabidopsis genome. The predictions generated by this process were tested by detailed exploration of available RNA-Seq and expression data sets and experimental validation. As a result, we have identified several snoRNAs, scaRNAs and 'orphan' snoRNAs. We also show evidence for 16 novel ncRNAs that lack similarity to any reported RNA family. Finally, we have identified two dicistronic genes encoding precursors that are processed to mature snoRNA and miRNA molecules. We discuss the evolutionary consequences of this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes. Conclusions We present an alternative computational approach for non-coding RNA detection. Instead of depending on sequence or structure similarity in the whole genome screenings, we have explored the properties of promoter regions of well-characterized ncRNAs. Interestingly, besides expected ncRNAs predictions we were also able to recover single precursor arrangement for snoRNA-miRNA. Accompanied by analyses performed on rice sequences, we conclude that such arrangement might have interesting functional and evolutionary consequences and discuss this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2221-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ge Qu
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Patrycja Plewka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Shu-Yi Yang
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd. Sec. 2, Taipei, 115, Taiwan.
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd. Sec. 2, Taipei, 115, Taiwan.
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland.
| | - Manuel Echeverria
- Faculté des Sciences, Université de Perpignan via Domitia, 52, Av Paul Alduy, Perpignan, 66860, France.
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
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26
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Blackmore T, Thomas I, McMahon R, Powell W, Hegarty M. Genetic-geographic correlation revealed across a broad European ecotypic sample of perennial ryegrass (Lolium perenne) using array-based SNP genotyping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1917-1932. [PMID: 26093611 PMCID: PMC4572065 DOI: 10.1007/s00122-015-2556-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 06/05/2015] [Indexed: 05/29/2023]
Abstract
Publically available SNP array increases the marker density for genotyping of forage crop, Lolium perenne. Applied to 90 European ecotypes composed of 716 individuals identifies a significant genetic-geographic correlation. Grassland ecosystems are ubiquitous across temperate and tropical regions, totalling 37% of the terrestrial land cover of the planet, and thus represent a global resource for understanding local adaptations to environment. However, genomic resources for grass species (outside cereals) are relatively poor. The advent of next-generation DNA sequencing and high-density SNP genotyping platforms enables the development of dense marker assays for population genetics analyses and genome-wide association studies. A high-density SNP marker resource (Illumina Infinium assay) for perennial ryegrass (Lolium perenne) was created and validated in a broad ecotype collection of 716 individuals sampled from 90 sites across Europe. Genetic diversity within and between populations was assessed. A strong correlation of geographic origin to genetic structure was found using principal component analysis, with significant correlation to longitude and latitude (P < 0.001). The potential of this array as a resource for studies of germplasm diversity and identifying traits underpinning adaptive variation is highlighted.
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Affiliation(s)
- T Blackmore
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK.
| | - I Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK
| | - R McMahon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK
| | - W Powell
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK
| | - M Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK.
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Baloglu MC, Ulu F, Altunoglu YC, Pekol S, Alagoz G, Ese O. Identification, molecular characterization and expression analysis ofRPL24genes in three Cucurbitaceae family members: cucumber, melon and watermelon. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1079144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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28
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Spatial Regulation of Root Growth: Placing the Plant TOR Pathway in a Developmental Perspective. Int J Mol Sci 2015; 16:19671-97. [PMID: 26295391 PMCID: PMC4581319 DOI: 10.3390/ijms160819671] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/11/2015] [Accepted: 08/11/2015] [Indexed: 12/30/2022] Open
Abstract
Plant cells contain specialized structures, such as a cell wall and a large vacuole, which play a major role in cell growth. Roots follow an organized pattern of development, making them the organs of choice for studying the spatio-temporal regulation of cell proliferation and growth in plants. During root growth, cells originate from the initials surrounding the quiescent center, proliferate in the division zone of the meristem, and then increase in length in the elongation zone, reaching their final size and differentiation stage in the mature zone. Phytohormones, especially auxins and cytokinins, control the dynamic balance between cell division and differentiation and therefore organ size. Plant growth is also regulated by metabolites and nutrients, such as the sugars produced by photosynthesis or nitrate assimilated from the soil. Recent literature has shown that the conserved eukaryotic TOR (target of rapamycin) kinase pathway plays an important role in orchestrating plant growth. We will summarize how the regulation of cell proliferation and cell expansion by phytohormones are at the heart of root growth and then discuss recent data indicating that the TOR pathway integrates hormonal and nutritive signals to orchestrate root growth.
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29
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Lermontova I, Sandmann M, Mascher M, Schmit AC, Chabouté ME. Centromeric chromatin and its dynamics in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:4-17. [PMID: 25976696 DOI: 10.1111/tpj.12875] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 05/22/2023]
Abstract
Centromeres are chromatin structures that are required for proper separation of chromosomes during mitosis and meiosis. The centromere is composed of centromeric DNA, often enriched in satellite repeats, and kinetochore complex proteins. To date, over 100 kinetochore components have been identified in various eukaryotes. Kinetochore assembly begins with incorporation of centromeric histone H3 variant CENH3 into centromeric nucleosomes. Protein components of the kinetochore are either present at centromeres throughout the cell cycle or localize to centromeres transiently, prior to attachment of microtubules to each kinetochore in prometaphase of mitotic cells. This is the case for the spindle assembly checkpoint (SAC) proteins in animal cells. The SAC complex ensures equal separation of chromosomes between daughter nuclei by preventing anaphase onset before metaphase is complete, i.e. the sister kinetochores of all chromosomes are attached to spindle fibers from opposite poles. In this review, we focus on the organization of centromeric DNA and the kinetochore assembly in plants. We summarize recent advances regarding loading of CENH3 into the centromere, and the subcellular localization and protein-protein interactions of Arabidopsis thaliana proteins involved in kinetochore assembly and function. We describe the transcriptional activity of corresponding genes based on in silico analysis of their promoters and cell cycle-dependent expression. Additionally, barley homologs of all selected A. thaliana proteins have been identified in silico, and their sequences and domain structures are presented.
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Affiliation(s)
- Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Michael Sandmann
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Anne-Catherine Schmit
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR 2357, associée à l'Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR 2357, associée à l'Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
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Hedayati V, Mousavi A, Razavi K, Cultrera N, Alagna F, Mariotti R, Hosseini-Mazinani M, Baldoni L. Polymorphisms in the AOX2 gene are associated with the rooting ability of olive cuttings. PLANT CELL REPORTS 2015; 34:1151-64. [PMID: 25749737 DOI: 10.1007/s00299-015-1774-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/11/2015] [Accepted: 02/17/2015] [Indexed: 05/05/2023]
Abstract
Different rooting ability candidate genes were tested on an olive cross progeny. Our results demonstrated that only the AOX2 gene was strongly induced. OeAOX2 was fully characterised and correlated to phenotypical traits. The formation of adventitious roots is a key step in the vegetative propagation of trees crop species, and this ability is under strict genetic control. While numerous studies have been carried out to identify genes controlling adventitious root formation, only a few loci have been characterised. In this work, candidate genes that were putatively involved in rooting ability were identified in olive (Olea europaea L.) by similarity with orthologs identified in other plant species. The mRNA levels of these genes were analysed by real-time PCR during root induction in high- (HR) and low-rooting (LR) individuals. Interestingly, alternative oxidase 2 (AOX2), which was previously reported to be a functional marker for rooting in olive cuttings, showed a strong induction in HR individuals. From the OeAOX2 full-length gene, alleles and effective polymorphisms were distinguished and analysed in the cross progeny, which were segregated based on rooting. The results revealed a possible correlation between two single nucleotide polymorphisms of OeAOX2 gene and rooting ability.
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Affiliation(s)
- Vahideh Hedayati
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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31
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Narsai R, Edwards JM, Roberts TH, Whelan J, Joss GH, Atwell BJ. Mechanisms of growth and patterns of gene expression in oxygen-deprived rice coleoptiles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:25-40. [PMID: 25650041 DOI: 10.1111/tpj.12786] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 01/21/2015] [Accepted: 01/22/2015] [Indexed: 05/04/2023]
Abstract
Coleoptiles of rice (Oryza sativa) seedlings grown under water commonly elongate by up to 1 mm h(-1) to reach the atmosphere. We initially analysed this highly specialized phenomenon by measuring epidermal cell lengths along the coleoptile axis to determine elongation rates. This revealed a cohort of cells in the basal zone that elongated rapidly following emergence from the embryo, reaching 200 μm within 12 h. After filming coleoptiles in vivo for a day, kinematic analysis was applied. Eight time-sliced 'segments' were defined by their emergence from the embryo at four-hourly intervals, revealing a mathematically simple growth model. Each segment entering the coleoptile from the embryo elongated at a constant velocity, resulting in accelerating growth for the entire organ. Consistent with the epidermal cell lengths, relative rates of elongation (mm mm(-1) h(-1)) were tenfold greater in the small, newly emerged basal segments than the older distal tip segments. This steep axial gradient defined two contrasting growth zones (bases versus tips) in which we measured ATP production and protein, RNA and DNA content, and analysed the global transcriptome under steady-state normoxia, hypoxia (3% O2) and anoxia. Determination of the transcriptome revealed tip-specific induction of genes encoding TCP [Teosinte Branched1 (Tb1) of maize, Cycloidea (Cyc), and Proliferating Cell Factor (Pcf)] transcription factors, RNA helicases, ribosomal proteins and proteins involved in protein folding, whilst expression of F-box domain-containing proteins in the ubiquitin E3-SCF complex (Skp, Cullin, F-box containing complex) was induced specifically in bases under low oxygen conditions. We ascribed the sustained elongation under hypoxia to hypoxia-specific responses such as controlled suppression of photosystem components and induction of RNA binding/splicing functions, indicating preferential allocation of energy to cell extension.
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Affiliation(s)
- Reena Narsai
- Department of Botany, School of Life Science, La Trobe University, Melbourne, Victoria, 3086, Australia
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Tokizawa M, Kobayashi Y, Saito T, Kobayashi M, Iuchi S, Nomoto M, Tada Y, Yamamoto YY, Koyama H. SENSITIVE TO PROTON RHIZOTOXICITY1, CALMODULIN BINDING TRANSCRIPTION ACTIVATOR2, and other transcription factors are involved in ALUMINUM-ACTIVATED MALATE TRANSPORTER1 expression. PLANT PHYSIOLOGY 2015; 167:991-1003. [PMID: 25627216 PMCID: PMC4348791 DOI: 10.1104/pp.114.256552] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 01/22/2015] [Indexed: 05/18/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana) the root apex is protected from aluminum (Al) rhizotoxicity by excretion of malate, an Al chelator, by ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (AtALMT1). AtALMT1 expression is fundamentally regulated by the SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) zinc finger protein, but other transcription factors have roles that enable Al-inducible expression with a broad dynamic range. In this study, we characterized multiple cis-elements in the AtALMT1 promoter that interact with transcription factors. In planta complementation assays of AtALMT1 driven by 5' truncated promoters of different lengths showed that the promoter region between -540 and 0 (the first ATG) restored the Al-sensitive phenotype of atalm1 and thus contains cis-elements essential for AtALMT1 expression for Al tolerance. Computation of overrepresented octamers showed that eight regions in this promoter region contained potential cis-elements involved in Al induction and STOP1 regulation. Mutation in a position around -297 from the first ATG completely inactivated AtALMT1 expression and Al response. In vitro binding assays showed that this region contained the STOP1 binding site, which accounted for the recognition by four zinc finger domains of the protein. Other positions were characterized as cis-elements that regulated expression by repressors and activators and a transcription factor that determines root tip expression of AtALMT1. From the consensus of known cis-elements, we identified CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR2 to be an activator of AtALMT1 expression. Al-inducible expression of AtALMT1 changed transcription starting sites, which increased the abundance of transcripts with a shortened 5' untranslated region. The present analyses identified multiple mechanisms that regulate AtALMT1 expression.
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Affiliation(s)
- Mutsutomo Tokizawa
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Yuriko Kobayashi
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Tatsunori Saito
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Masatomo Kobayashi
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Satoshi Iuchi
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Mika Nomoto
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Yasuomi Tada
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Yoshiharu Y Yamamoto
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
| | - Hiroyuki Koyama
- Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan (M.T., Y.K., T.S., Y.Y.Y., H.K.);RIKEN BioResource Center, Ibaraki 305-0074, Japan (M.K., S.I.); andDivision of Biological Science, Graduate School of Science (M.N.), and The Center for Gene Research, Division of Biological Science (Y.T.), Nagoya University, Aichi 464-8602, Japan
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Nelson ADL, Forsythe ES, Gan X, Tsiantis M, Beilstein MA. Extending the model of Arabidopsis telomere length and composition across Brassicaceae. Chromosome Res 2015; 22:153-66. [PMID: 24846723 DOI: 10.1007/s10577-014-9423-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Telomeres are repetitive TG-rich DNA elements essential for maintaining the stability of genomes and replicative capacity of cells in almost all eukaryotes. Most of what is known about telomeres in plants comes from the angiosperm Arabidopsis thaliana, which has become an important comparative model for telomere biology. Arabidopsis tolerates numerous insults to its genome, many of which are catastrophic or lethal in other eukaryotic systems such as yeast and vertebrates. Despite the importance of Arabidopsis in establishing a model for the structure and regulation of plant telomeres, only a handful of studies have used this information to assay components of telomeres from across land plants, or even among the closest relatives of Arabidopsis in the plant family Brassicaceae. Here, we determined how well Arabidopsis represents Brassicaceae by comparing multiple aspects of telomere biology in species that represent major clades in the family tree. Specifically, we determined the telomeric repeat sequence, measured bulk telomere length, and analyzed variation in telomere length on syntenic chromosome arms. In addition, we used a phylogenetic approach to infer the evolutionary history of putative telomere-binding proteins, CTC1, STN1, TEN1 (CST), telomere repeat-binding factor like (TRFL), and single Myb histone (SMH). Our analyses revealed conservation of the telomeric DNA repeat sequence, but considerable variation in telomere length among the sampled species, even in comparisons of syntenic chromosome arms. We also found that the single-stranded and double-stranded telomeric DNA-binding complexes CST and TRFL, respectively, differ in their pattern of gene duplication and loss. The TRFL and SMH gene families have undergone numerous duplication events, and these duplicate copies are often retained in the genome. In contrast, CST components occur as single-copy genes in all sampled genomes, even in species that experienced recent whole genome duplication events. Taken together, our results place the Arabidopsis model in the context of other species in Brassicaceae, making the family the best characterized plant group in regard to telomere architecture.
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Affiliation(s)
- Andrew D L Nelson
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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Liu SJ, Yue QJ, Zhang W. Structural and functional analysis of an asymmetric bidirectional promoter in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:162-170. [PMID: 25370697 DOI: 10.1111/jipb.12308] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
Bidirectional promoters are relatively abundant in eukaryotic genomes, suggesting that they have an important biological significance. As yet, few of these promoters have been characterized in detail. Here, using a promoter::GUS transgene approach has revealed that the intergenic region of Arabidopsis thaliana divergent genes At1g71850 and At1g71860 is an asymmetric bidirectional promoter, which exhibits an orientation-dependent expression profile. The strength of the forward promoter was greater than that of the reverse promoter, and their tissue specificities were not identical. Deletion analyses revealed that this bidirectional promoter could be divided into three functional regions. The basal level and tissue specificity of the promoter in the reverse orientation were regulated positively by region II and negatively by region III, whereas promoter activity in the forward orientation was regulated negatively by region II and positively by region I. Thus the 52-bp stretch of region II had a dual function, enhancing expression in the reverse orientation and suppressing it in the forward orientation. These results demonstrated that the activity of the At1g71850-At1g71860 bidirectional promoter was modulated by complex interactions between both positive and negative cis-acting elements. These findings will enhance our understanding of the regulatory mechanisms of plant bidirectional promoters.
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Affiliation(s)
- Shi-Juan Liu
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education; School of Life Sciences, Shandong University, Jinan, 250100, China; College of Life Science, Qufu Normal University, Qufu, 273165, China
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Li S. The Arabidopsis thaliana TCP transcription factors: A broadening horizon beyond development. PLANT SIGNALING & BEHAVIOR 2015; 10:e1044192. [PMID: 26039357 PMCID: PMC4622585 DOI: 10.1080/15592324.2015.1044192] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/20/2015] [Indexed: 05/18/2023]
Abstract
The TCP family of transcription factors is named after the first 4 characterized members, namely TEOSINTE BRANCHED1 (TB1) from maize (Zea mays), CYCLOIDEA (CYC) from snapdragon (Antirrhinum majus), as well as PROLIFERATING CELL NUCLEAR ANTIGEN FACTOR1 (PCF1) and PCF2 from rice (Oryza sativa). Phylogenic analysis of this plant-specific protein family unveils a conserved bHLH-containing DNA-binding motif known as the TCP domain. In accordance with the structure of this shared domain, TCP proteins are grouped into class I (TCP-P) and class II (TCP-C), which are suggested to antagonistically modulate plant growth and development via competitively binding similar cis-regulatory modules called site II elements. Over the last decades, TCPs across the plant kingdom have been demonstrated to control a plethora of plant processes. Notably, TCPs also regulate plant development and defense responses via stimulating the biosynthetic pathways of bioactive metabolites, such as brassinosteroid (BR), jasmonic acid (JA) and flavonoids. Besides, mutagenesis analysis coupled with biochemical experiments identifies several crucial amino acids located within the TCP domain, which confer the redox sensitivity of class I TCPs and determine the distinct DNA-binding properties of TCPs. In this review, developmental functions of TCPs in various biological pathways are briefly described with an emphasis on their involvement in the synthesis of bioactive substances. Furthermore, novel biochemical aspects of TCPs with respect to redox regulation and DNA-binding preferences are elaborated. In addition, the unexpected participation of TCPs in effector-triggered immunity (ETI) and defense against insects indicates that the widely recognized developmental regulators are capable of fine-tuning defense signaling and thereby enable plants to evade deleterious developmental phenotypes. Altogether, these recent impressive breakthroughs remarkably advance our understanding as to how TCPs integrate internal developmental cues with external environmental stimuli to orchestrate plant development.
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Affiliation(s)
- Shutian Li
- Department of Biology/Chemistry; Osnabrück University; Osnabrück, Germany
- Correspondence to: Shutian Li; ;
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Zografidis A, Kapolas G, Podia V, Beri D, Papadopoulou K, Milioni D, Haralampidis K. Transcriptional regulation and functional involvement of the Arabidopsis pescadillo ortholog AtPES in root development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:53-65. [PMID: 25443833 DOI: 10.1016/j.plantsci.2014.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/21/2014] [Indexed: 05/25/2023]
Abstract
The Pescadillo gene is highly conserved from yeasts to human and has been shown to impact on both the cell cycle and on ribosome biogenesis. However, the biological function and transcriptional regulation of the plant orthologs remain unclear. In the present study, we have implemented a combination of molecular and genetic approaches, in order to characterize the Arabidopsis thaliana pescadillo ortholog (AtPES) and its role in root development. The RNAi transgenic lines displayed severely compromised meristem structures and a reduction of the primary root length of up to 70%. The correct pattern of the cell files is distorted, whereas in the root elongation and differentiation zone the epidermal and cortex cells appear abnormally enlarged. Yeast two hybrid and BiFC experiments confirmed that AtPES interacts physically with AtPEIP1 and AtPEIP2, the orthologs of the murine Bop1 and WDR12. Promoter deletion analysis revealed that AtPES expression depends on a number of transcription factor binding sites, with the TELO-box being a crucial site for regulating its accurate tissue-specific manifestation. Our results indicate that AtPES is firmly regulated at the transcriptional level and that the corresponding protein plays a role in root developmental processes.
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Affiliation(s)
- Aris Zografidis
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Giorgos Kapolas
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Varvara Podia
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Despoina Beri
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Kalliope Papadopoulou
- University of Thessaly, Department of Biochemistry & Biotechnology, 41221 Larissa, Greece.
| | - Dimitra Milioni
- Agricultural University of Athens, Department of Agricultural Biotechnology, 11855 Athens, Greece.
| | - Kosmas Haralampidis
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
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Nitrate foraging by Arabidopsis roots is mediated by the transcription factor TCP20 through the systemic signaling pathway. Proc Natl Acad Sci U S A 2014; 111:15267-72. [PMID: 25288754 DOI: 10.1073/pnas.1411375111] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To compete for nutrients in diverse soil microenvironments, plants proliferate lateral roots preferentially in nutrient-rich zones. For nitrate, root foraging involves local and systemic signaling; however, little is known about the genes that function in the systemic signaling pathway. By using nitrate enhancer DNA to screen a library of Arabidopsis transcription factors in the yeast one-hybrid system, the transcription factor gene TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1-20 (TCP20) was identified. TCP20, which belongs to an ancient, plant-specific gene family that regulates shoot, flower, and embryo development, was implicated in nitrate signaling by its ability to bind DNA in more than 100 nitrate-regulated genes. Analysis of insertion mutants of TCP20 showed that they had normal primary and lateral root growth on homogenous nitrate media but were impaired in preferential lateral root growth (root foraging) on heterogeneous media in split-root plates. Inhibition of preferential lateral root growth was still evident in the mutants even when ammonium was uniformly present in the media, indicating that the TCP20 response was to nitrate. Comparison of tcp20 mutants with those of nlp7 mutants, which are defective in local control of root growth but not in the root-foraging response, indicated that TCP20 function is independent of and distinct from NLP7 function. Further analysis showed that tcp20 mutants lack systemic control of root growth regardless of the local nitrate concentrations. These results indicate that TCP20 plays a key role in the systemic signaling pathway that directs nitrate foraging by Arabidopsis roots.
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Class I TCP-DELLA interactions in inflorescence shoot apex determine plant height. Curr Biol 2014; 24:1923-8. [PMID: 25127215 DOI: 10.1016/j.cub.2014.07.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/07/2014] [Accepted: 07/03/2014] [Indexed: 11/22/2022]
Abstract
Regulation of plant height, one of the most important agronomic traits, is the focus of intensive research for improving crop performance. Stem elongation takes place as a result of repeated cell divisions and subsequent elongation of cells produced by apical and intercalary meristems. The gibberellin (GA) phytohormones have long been known to control stem and internodal elongation by stimulating the degradation of nuclear growth-repressing DELLA proteins; however, the mechanism allowing GA-responsive growth is only slowly emerging. Here, we show that DELLAs directly regulate the activity of the plant-specific class I TCP transcription factor family, key regulators of cell proliferation. Our results demonstrate that class I TCP factors directly bind the promoters of core cell-cycle genes in Arabidopsis inflorescence shoot apices while DELLAs block TCP function by binding to their DNA-recognition domain. GAs antagonize such repression by promoting DELLA destruction and therefore cause a concomitant accumulation of TCP factors on promoters of cell-cycle genes. Consistent with this model, the quadruple mutant tcp8 tcp14 tcp15 tcp22 exhibits severe dwarfism and reduced responsiveness to GA action. Altogether, we conclude that GA-regulated DELLA-TCP interactions in inflorescence shoot apex provide a novel mechanism to control plant height.
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Parapunova V, Busscher M, Busscher-Lange J, Lammers M, Karlova R, Bovy AG, Angenent GC, de Maagd RA. Identification, cloning and characterization of the tomato TCP transcription factor family. BMC PLANT BIOLOGY 2014; 14:157. [PMID: 24903607 PMCID: PMC4070083 DOI: 10.1186/1471-2229-14-157] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/22/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome. RESULTS We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato. CONCLUSIONS The comprehensive analysis we performed, like phylogenetic analysis, expression studies, identification of the upstream regulators and the dimerization specificity of the tomato TCP transcription factor family provides the basis for functional studies to reveal the role of this family in tomato development.
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Affiliation(s)
- Violeta Parapunova
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 AJ Wageningen, the Netherlands
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Marco Busscher
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | | | - Michiel Lammers
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Rumyana Karlova
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Arnaud G Bovy
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 AJ Wageningen, the Netherlands
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Ruud A de Maagd
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
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Kim SH, Son GH, Bhattacharjee S, Kim HJ, Nam JC, Nguyen PDT, Hong JC, Gassmann W. The Arabidopsis immune adaptor SRFR1 interacts with TCP transcription factors that redundantly contribute to effector-triggered immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:978-89. [PMID: 24689742 DOI: 10.1111/tpj.12527] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 05/20/2023]
Abstract
The plant immune system must be tightly controlled both positively and negatively to maintain normal plant growth and health. We previously identified SUPPRESSOR OF rps4-RLD1 (SRFR1) as a negative regulator specifically of effector-triggered immunity. SRFR1 is localized in both a cytoplasmic microsomal compartment and in the nucleus. Its TPR domain has sequence similarity to TPR domains of transcriptional repressors in other organisms, suggesting that SRFR1 may negatively regulate effector-triggered immunity via transcriptional control. We show here that excluding SRFR1 from the nucleus prevented complementation of the srfr1 phenotype. To identify transcription factors that interact with SRFR1, we screened an Arabidopsis transcription factor prey library by yeast two-hybrid assay and isolated six class I members of the TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factor family. Specific interactions were verified in planta. Although single or double T-DNA mutant tcp8, tcp14 or tcp15 lines were not more susceptible to bacteria expressing AvrRps4, the triple tcp8 tcp14 tcp15 mutant displayed decreased effector-triggered immunity mediated by the resistance genes RPS2, RPS4, RPS6 and RPM1. In addition, expression of PATHOGENESIS-RELATED PROTEIN2 was attenuated in srfr1-4 tcp8-1 tcp14-5 tcp15-3 plants compared to srfr1-4 plants. To date, TCP transcription factors have been implicated mostly in developmental processes. Our data indicate that one function of a subset of TCP proteins is to regulate defense gene expression in antagonism to SRFR1, and suggest a mechanism for an intimate connection between plant development and immunity.
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Affiliation(s)
- Sang Hee Kim
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211-7310, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211-7310, USA
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Valsecchi I, Guittard-Crilat E, Maldiney R, Habricot Y, Lignon S, Lebrun R, Miginiac E, Ruelland E, Jeannette E, Lebreton S. The intrinsically disordered C-terminal region of Arabidopsis thaliana TCP8 transcription factor acts both as a transactivation and self-assembly domain. MOLECULAR BIOSYSTEMS 2014; 9:2282-95. [PMID: 23760157 DOI: 10.1039/c3mb70128j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
TCPs are plant specific transcription factors with non-canonical basic helix-loop-helix domains. While Arabidopsis thaliana has 24 TCPs involved in cell proliferation and differentiation, their mode of action has not been fully elucidated. Using bioinformatic tools, we demonstrate that TCP transcription factors belong to the intrinsically disordered proteins (IDP) family and that disorder is higher in class I TCPs than in class II TCPs. In particular, using bioinformatic and biochemical approaches, we have characterized TCP8, a class I TCP. TCP8 exhibits three intrinsically disordered regions (IDR) made of more than 50 consecutive residues, in which phosphorylable Ser residues are mainly clustered. Phosphorylation of Ser-211 that belongs to the central IDR was confirmed by mass spectrometry. Yeast two-hybrid assays also showed that the C-terminal IDR corresponds to a transactivation domain. Moreover, biochemical experiments demonstrated that TCP8 tends to oligomerize in dimers, trimers and higher-order multimers. Bimolecular fluorescence complementation (BiFC) experiments carried out on a truncated form of TCP8 lacking the C-terminal IDR indicated that it is effectively required for the pronounced self-assembly of TCP8. These data were reinforced by the prediction of a coiled coil domain in this IDR. The C-terminal IDR acts thus as an oligomerization domain and also a transactivation domain. Moreover, many Molecular Recognition Features (MoRFs) were predicted, indicating that TCP8 could interact with several partners to fulfill a fine regulation of transcription in response to various stimuli.
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Affiliation(s)
- Isabel Valsecchi
- Université Pierre et Marie Curie, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Unité de Recherche 5 - Equipe d'Accueil 7180 du Centre National de la Recherche Scientifique, case 156, 4 place Jussieu, 75252 Paris cedex 05, France
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Shankar A, Srivastava AK, Yadav AK, Sharma M, Pandey A, Raut VV, Das MK, Suprasanna P, Pandey GK. Whole genome transcriptome analysis of rice seedling reveals alterations in Ca(2+) ion signaling and homeostasis in response to Ca(2+) deficiency. Cell Calcium 2014; 55:155-65. [PMID: 24814644 DOI: 10.1016/j.ceca.2014.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 01/18/2014] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
Ca(2+) is an essential inorganic macronutrient, involved in regulating major physiological processes in plants. It has been well established as a second messenger and is predominantly stored in the cell wall, endoplasmic reticulum, mitochondria and vacuoles. In the cytosol, the concentration of this ion is maintained at nano-molar range. Upon requirement, Ca(2+) is released from intra-cellular as well as extracellular compartments such as organelles and cell wall. In this study, we report for the first time, a whole genome transcriptome response to short (5 D) and long (14 D) term Ca(2+) starvation and restoration in rice. Our results manifest that short and long term Ca(2+) starvation involves a very different response in gene expression with respect to both the number and function of genes involved. A larger number of genes were up- or down-regulated after 14 D (5588 genes) than after 5 D (798 genes) of Ca(2+) starvation. The functional classification of these genes indicated their connection with various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. The results obtained here will enable to understand how changes in Ca(2+) concentration or availability are interpreted into adaptive responses in plants.
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Affiliation(s)
- Alka Shankar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Akhilesh K Yadav
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.
| | - Manisha Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.
| | - Amita Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.
| | - Vaibhavi V Raut
- Radioanalytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Mirnal K Das
- Radioanalytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India.
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Juraniec M, Lequeux H, Hermans C, Willems G, Nordborg M, Schneeberger K, Salis P, Vromant M, Lutts S, Verbruggen N. Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2014; 201:810-824. [PMID: 24134393 DOI: 10.1111/nph.12554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/16/2013] [Indexed: 05/23/2023]
Abstract
The exposure of plants to high concentrations of trace metallic elements such as copper involves a remodeling of the root system, characterized by a primary root growth inhibition and an increase in the lateral root density. These characteristics constitute easy and suitable markers for screening mutants altered in their response to copper excess. A forward genetic approach was undertaken in order to discover novel genetic factors involved in the response to copper excess. A Cu(2+) -sensitive mutant named copper modified resistance1 (cmr1) was isolated and a causative mutation in the CMR1 gene was identified by using positional cloning and next-generation sequencing. CMR1 encodes a plant-specific protein of unknown function. The analysis of the cmr1 mutant indicates that the CMR1 protein is required for optimal growth under normal conditions and has an essential role in the stress response. Impairment of the CMR1 activity alters root growth through aberrant activity of the root meristem, and modifies potassium concentration and hormonal balance (ethylene production and auxin accumulation). Our data support a putative role for CMR1 in cell division regulation and meristem maintenance. Research on the role of CMR1 will contribute to the understanding of the plasticity of plants in response to changing environments.
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Affiliation(s)
- Michal Juraniec
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Hélène Lequeux
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Glenda Willems
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Pietrino Salis
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Maud Vromant
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
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Welchen E, García L, Mansilla N, Gonzalez DH. Coordination of plant mitochondrial biogenesis: keeping pace with cellular requirements. FRONTIERS IN PLANT SCIENCE 2014; 4:551. [PMID: 24409193 PMCID: PMC3884152 DOI: 10.3389/fpls.2013.00551] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/23/2013] [Indexed: 05/20/2023]
Abstract
Plant mitochondria are complex organelles that carry out numerous metabolic processes related with the generation of energy for cellular functions and the synthesis and degradation of several compounds. Mitochondria are semiautonomous and dynamic organelles changing in shape, number, and composition depending on tissue or developmental stage. The biogenesis of functional mitochondria requires the coordination of genes present both in the nucleus and the organelle. In addition, due to their central role, all processes held inside mitochondria must be finely coordinated with those in other organelles according to cellular demands. Coordination is achieved by transcriptional control of nuclear genes encoding mitochondrial proteins by specific transcription factors that recognize conserved elements in their promoter regions. In turn, the expression of most of these transcription factors is linked to developmental and environmental cues, according to the availability of nutrients, light-dark cycles, and warning signals generated in response to stress conditions. Among the signals impacting in the expression of nuclear genes, retrograde signals that originate inside mitochondria help to adjust mitochondrial biogenesis to organelle demands. Adding more complexity, several nuclear encoded proteins are dual localized to mitochondria and either chloroplasts or the nucleus. Dual targeting might establish a crosstalk between the nucleus and cell organelles to ensure a fine coordination of cellular activities. In this article, we discuss how the different levels of coordination of mitochondrial biogenesis interconnect to optimize the function of the organelle according to both internal and external demands.
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Affiliation(s)
- Elina Welchen
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
- *Correspondence: Elina Welchen and Daniel H. Gonzalez, Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, CC 242 Paraje El Pozo, 3000 Santa Fe, Argentina e-mail: ;
| | - Lucila García
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
| | - Daniel H. Gonzalez
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
- *Correspondence: Elina Welchen and Daniel H. Gonzalez, Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, CC 242 Paraje El Pozo, 3000 Santa Fe, Argentina e-mail: ;
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Sano S, Aoyama M, Nakai K, Shimotani K, Yamasaki K, Sato MH, Tojo D, Suwastika IN, Nomura H, Shiina T. Light-dependent expression of flg22-induced defense genes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2014; 5:531. [PMID: 25346742 PMCID: PMC4191550 DOI: 10.3389/fpls.2014.00531] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/18/2014] [Indexed: 05/08/2023]
Abstract
Chloroplasts have been reported to generate retrograde immune signals that activate defense gene expression in the nucleus. However, the roles of light and photosynthesis in plant immunity remain largely elusive. In this study, we evaluated the effects of light on the expression of defense genes induced by flg22, a peptide derived from bacterial flagellins which acts as a potent elicitor in plants. Whole-transcriptome analysis of flg22-treated Arabidopsis thaliana seedlings under light and dark conditions for 30 min revealed that a number of (30%) genes strongly induced by flg22 (>4.0) require light for their rapid expression, whereas flg22-repressed genes include a significant number of genes that are down-regulated by light. Furthermore, light is responsible for the flg22-induced accumulation of salicylic acid (SA), indicating that light is indispensable for basal defense responses in plants. To elucidate the role of photosynthesis in defense, we further examined flg22-induced defense gene expression in the presence of specific inhibitors of photosynthetic electron transport: 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-benzoquinone (DBMIB). Light-dependent expression of defense genes was largely suppressed by DBMIB, but only partially suppressed by DCMU. These findings suggest that photosynthetic electron flow plays a role in controlling the light-dependent expression of flg22-inducible defense genes.
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Affiliation(s)
- Satoshi Sano
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Mayu Aoyama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Kana Nakai
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Koji Shimotani
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Kanako Yamasaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Masa H. Sato
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Daisuke Tojo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | | | - Hironari Nomura
- Department of Health and Nutrition, Gifu Women's UniversityGifu, Japan
| | - Takashi Shiina
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- *Correspondence: Takashi Shiina, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan e-mail:
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Korkuć P, Schippers JH, Walther D. Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. PLANT PHYSIOLOGY 2014; 164:181-200. [PMID: 24204023 PMCID: PMC3875800 DOI: 10.1104/pp.113.229716] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/06/2013] [Indexed: 05/19/2023]
Abstract
Identifying regulatory elements and revealing their role in gene expression regulation remains a central goal of plant genome research. We exploited the detailed genomic sequencing information of a large number of Arabidopsis (Arabidopsis thaliana) accessions to characterize known and to identify novel cis-regulatory elements in gene promoter regions of Arabidopsis by relying on conservation as the hallmark signal of functional relevance. Based on the genomic layout and the obtained density profiles of single-nucleotide polymorphisms (SNPs) in sequence regions upstream of transcription start sites, the average length of promoter regions in Arabidopsis could be established at 500 bp. Genes associated with high degrees of variability of their respective upstream regions are preferentially involved in environmental response and signaling processes, while low levels of promoter SNP density are common among housekeeping genes. Known cis-elements were found to exhibit a decreased SNP density than sequence regions not associated with known motifs. For 15 known cis-element motifs, strong positional preferences relative to the transcription start site were detected based on their promoter SNP density profiles. Five novel candidate cis-element motifs were identified as consensus motifs of 17 sequence hexamers exhibiting increased sequence conservation combined with evidence of positional preferences, annotation information, and functional relevance for inducing correlated gene expression. Our study demonstrates that the currently available resolution of SNP data offers novel ways for the identification of functional genomic elements and the characterization of gene promoter sequences.
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Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genet 2013; 9:e1003840. [PMID: 24098147 PMCID: PMC3789834 DOI: 10.1371/journal.pgen.1003840] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression. A commonly used method for this purpose is a top-down approach based on clustering the network into a range of densely connected segments, treating these segments as expression modules, and extracting promoter motifs from these modules. Here, we describe a novel bottom-up approach to identify gene expression modules driven by known cis-regulatory motifs in the gene promoters. For a specific motif, genes in the co-expression network are ranked according to their probability of belonging to an expression module regulated by that motif. The ranking is conducted via motif enrichment or motif position bias analysis. Our results indicate that motif position bias analysis is an effective tool for genome-wide motif analysis. Sub-networks containing the top ranked genes are extracted and analyzed for inherent gene expression modules. This approach identified novel expression modules for the G-box, W-box, site II, and MYB motifs from an Arabidopsis thaliana gene co-expression network based on the graphical Gaussian model. The novel expression modules include those involved in house-keeping functions, primary and secondary metabolism, and abiotic and biotic stress responses. In addition to confirmation of previously described modules, we identified modules that include new signaling pathways. To associate transcription factors that regulate genes in these co-expression modules, we developed a novel reporter system. Using this approach, we evaluated MYB transcription factor-promoter interactions within MYB motif modules. Gene co-expression networks unite genes with similar expression patterns. From these networks, gene co-expression modules can be identified. A specific family of transcription factor(s) may regulate the genes within a co-expression module. Thus, module identification is important to decipher the gene regulatory network. Previously, module identification relied on clustering the gene network into gene clusters that were then treated as modules. This represents a top-down approach. Here, we introduce a reverse approach aiming at identifying gene co-expression modules regulated by known promoter motifs. For a given promoter motif, we calculated the probability of each gene within the network to belong to a module regulated by that motif via motif enrichment analysis or motif position bias analysis. A sub-network containing the genes with a high probability of belonging to a motif driven module was then extracted from the gene co-expression network. From this sub-network, the modular structure can be identified via visual inspection. Our bottom-up approach recovered many known and novel modules for the G-box, MYB, W-box and site II elements motif, whose expression may be regulated by the transcription factors that bind to these motifs. Additionally, we developed a rapid transcription factor-promoter interaction screening system to validate predicted interactions.
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Noguero M, Atif RM, Ochatt S, Thompson RD. The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 209:32-45. [PMID: 23759101 DOI: 10.1016/j.plantsci.2013.03.016] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 05/18/2023]
Abstract
The DOF (DNA-binding One Zinc Finger) family of transcription factors is involved in many fundamental processes in higher plants, including responses to light and phytohormones as well as roles in seed maturation and germination. DOF transcription factor genes are restricted in their distribution to plants, where they are in many copies in both gymnosperms and angiosperms and also present in lower plants such as the moss Physcomitrella patens and in the alga Chlamydomonas reinhardtii which possesses a single DOF gene. DOF transcription factors bind to their promoter targets at the consensus sequence AAAG. This binding depends upon the presence of the highly conserved DOF domain in the protein. Depending on the target gene, DOF factor binding may activate or repress transcription. DOF factors are expressed in most if not all tissues of higher plants, but frequently appear to be functionally redundant. Recent next-generation sequencing data provide a more comprehensive survey of the distribution of DOF sequence classes among plant species and within tissue types, and clues as to the evolution of functions assumed by this transcription factor family. DOFs do not appear to be implicated in the initial differentiation of the plant body plan into organs via the resolution of meristematic zones, in contrast to MADS-box and homeobox transcription factors, which are found in other non-plant eukaryotes, and this may reflect a more recent evolutionary origin.
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Wang MY, Zhao PM, Cheng HQ, Han LB, Wu XM, Gao P, Wang HY, Yang CL, Zhong NQ, Zuo JR, Xia GX. The cotton transcription factor TCP14 functions in auxin-mediated epidermal cell differentiation and elongation. PLANT PHYSIOLOGY 2013; 162:1669-80. [PMID: 23715527 PMCID: PMC3707559 DOI: 10.1104/pp.113.215673] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/22/2013] [Indexed: 05/17/2023]
Abstract
Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play crucial roles in development, but their functional mechanisms remain largely unknown. Here, we characterized the cellular functions of the class I TCP transcription factor GhTCP14 from upland cotton (Gossypium hirsutum). GhTCP14 is expressed predominantly in fiber cells, especially at the initiation and elongation stages of development, and its expression increased in response to exogenous auxin. Induced heterologous overexpression of GhTCP14 in Arabidopsis (Arabidopsis thaliana) enhanced initiation and elongation of trichomes and root hairs. In addition, root gravitropism was severely affected, similar to mutant of the auxin efflux carrier PIN-FORMED2 (PIN2) gene. Examination of auxin distribution in GhTCP14-expressing Arabidopsis by observation of auxin-responsive reporters revealed substantial alterations in auxin distribution in sepal trichomes and root cortical regions. Consistent with these changes, expression of the auxin uptake carrier AUXIN1 (AUX1) was up-regulated and PIN2 expression was down-regulated in the GhTCP14-expressing plants. The association of GhTCP14 with auxin responses was also evidenced by the enhanced expression of auxin response gene IAA3, a gene in the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) family. Electrophoretic mobility shift assays showed that GhTCP14 bound the promoters of PIN2, IAA3, and AUX1, and transactivation assays indicated that GhTCP14 had transcription activation activity. Taken together, these results demonstrate that GhTCP14 is a dual-function transcription factor able to positively or negatively regulate expression of auxin response and transporter genes, thus potentially acting as a crucial regulator in auxin-mediated differentiation and elongation of cotton fiber cells.
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Viola IL, Güttlein LN, Gonzalez DH. Redox modulation of plant developmental regulators from the class I TCP transcription factor family. PLANT PHYSIOLOGY 2013; 162:1434-47. [PMID: 23686421 PMCID: PMC3707549 DOI: 10.1104/pp.113.216416] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR1 (TCP) transcription factors participate in plant developmental processes associated with cell proliferation and growth. Most members of class I, one of the two classes that compose the family, have a conserved cysteine at position 20 (Cys-20) of the TCP DNA-binding and dimerization domain. We show that Arabidopsis (Arabidopsis thaliana) class I proteins with Cys-20 are sensitive to redox conditions, since their DNA-binding activity is inhibited after incubation with the oxidants diamide, oxidized glutathione, or hydrogen peroxide or with nitric oxide-producing agents. Inhibition can be reversed by treatment with the reductants dithiothreitol or reduced glutathione or by incubation with the thioredoxin/thioredoxin reductase system. Mutation of Cys-20 in the class I protein TCP15 abolished its redox sensitivity. Under oxidizing conditions, covalently linked dimers were formed, suggesting that inactivation is associated with the formation of intermolecular disulfide bonds. Inhibition of class I TCP protein activity was also observed in vivo, in yeast (Saccharomyces cerevisiae) cells expressing TCP proteins and in plants after treatment with redox agents. This inhibition was correlated with modifications in the expression of the downstream CUC1 gene in plants. Modeling studies indicated that Cys-20 is located at the dimer interface near the DNA-binding surface. This places this residue in the correct orientation for intermolecular disulfide bond formation and explains the sensitivity of DNA binding to the oxidation of Cys-20. The redox properties of Cys-20 and the observed effects of cellular redox agents both in vitro and in vivo suggest that class I TCP protein action is under redox control in plants.
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