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Laosuntisuk K, Vennapusa A, Somayanda IM, Leman AR, Jagadish SK, Doherty CJ. A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1241-1257. [PMID: 38289828 DOI: 10.1111/tpj.16654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3' RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.
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Affiliation(s)
- Kanjana Laosuntisuk
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Amaranatha Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, Delaware, USA
| | - Impa M Somayanda
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA
| | - Adam R Leman
- Department of Science and Technology, The Good Food Institute, Washington, District of Columbia, 20090, USA
| | - Sv Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA
- Department of Agronomy, Kansas State University, Manhattan, Kansas, 66506, USA
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
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2
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Geng R, Pang X, Li X, Shi S, Hedtke B, Grimm B, Bock R, Huang J, Zhou W. PROGRAMMED CELL DEATH8 interacts with tetrapyrrole biosynthesis enzymes and ClpC1 to maintain homeostasis of tetrapyrrole metabolites in Arabidopsis. THE NEW PHYTOLOGIST 2023; 238:2545-2560. [PMID: 36967598 DOI: 10.1111/nph.18906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/19/2023] [Indexed: 05/19/2023]
Abstract
Tetrapyrrole biosynthesis (TBS) is a dynamically and strictly regulated process. Disruptions in tetrapyrrole metabolism influence many aspects of plant physiology, including photosynthesis, programmed cell death (PCD), and retrograde signaling, thus affecting plant growth and development at multiple levels. However, the genetic and molecular basis of TBS is not fully understood. We report here PCD8, a newly identified thylakoid-localized protein encoded by an essential gene in Arabidopsis. PCD8 knockdown causes a necrotic phenotype due to excessive chloroplast damage. A burst of singlet oxygen that results from overaccumulated tetrapyrrole intermediates upon illumination is suggested to be responsible for cell death in the knockdown mutants. Genetic and biochemical analyses revealed that PCD8 interacts with ClpC1 and a number of TBS enzymes, such as HEMC, CHLD, and PORC of TBS. Taken together, our findings uncover the function of chloroplast-localized PCD8 and provide a new perspective to elucidate molecular mechanism of how TBS is finely regulated in plants.
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Affiliation(s)
- Rudan Geng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoqing Pang
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstraße 13, Berlin, 10115, Germany
| | - Xia Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shanshan Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Boris Hedtke
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstraße 13, Berlin, 10115, Germany
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstraße 13, Berlin, 10115, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Rozanova IV, Grigoriev YN, Efimov VM, Igoshin AV, Khlestkina EK. Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley. Biomolecules 2023; 13:909. [PMID: 37371489 DOI: 10.3390/biom13060909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.
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Affiliation(s)
- Irina V Rozanova
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Yuriy N Grigoriev
- Siberian Research Institute of Plant Cultivation and Breeding-Branch of Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Krasnoobsk, 630501 Novosibirsk, Russia
| | - Vadim M Efimov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Alexander V Igoshin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Elena K Khlestkina
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
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4
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Shrestha A, Hernández-Reyes C, Grimm M, Krumwiede J, Stein E, Schenk ST, Schikora A. AHL-Priming Protein 1 mediates N-3-oxo-tetradecanoyl-homoserine lactone priming in Arabidopsis. BMC Biol 2022; 20:268. [PMID: 36464707 PMCID: PMC9721052 DOI: 10.1186/s12915-022-01464-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND N-3-oxo-tetradecanoyl-L-homoserine lactone (oxo-C14-HSL) is one of the N-acyl homoserine lactones (AHL) that mediate quorum sensing in Gram-negative bacteria. In addition to bacterial communication, AHL are involved in interactions with eukaryotes. Short-chain AHL are easily taken up by plants and transported over long distances. They promote root elongation and growth. Plants typically do not uptake hydrophobic long sidechain AHL such as oxo-C14-HSL, although they prime plants for enhanced resistance to biotic and abiotic stress. Many studies have focused on priming effects of oxo-C14-HSL for enhanced plant resistance to stress. However, specific plant factors mediating oxo-C14-HSL responses in plants remain unexplored. Here, we identify the Arabidopsis protein ALI1 as a mediator of oxo-C14-HSL-induced priming in plants. RESULTS We compared oxo-C14-HSL-induced priming between wild-type Arabidopsis Col-0 and an oxo-C14-HSL insensitive mutant ali1. The function of the candidate protein ALI1 was assessed through biochemical, genetic, and physiological approaches to investigate if the loss of the ALI1 gene resulted in subsequent loss of AHL priming. Through different assays, including MAP kinase activity assay, gene expression and transcriptome analysis, and pathogenicity assays, we revealed a loss of AHL priming in ali1. This phenomenon was reverted by the reintroduction of ALI1 into ali1. We also investigated the interaction between ALI1 protein and oxo-C14-HSL using biochemical and biophysical assays. Although biophysical assays did not reveal an interaction between oxo-C14-HSL and ALI1, a pull-down assay and an indirect method employing biosensor E. coli LuxCDABE support such interaction. We expressed fluorescently tagged ALI1 in tobacco leaves to assess the localization of ALI1 and demonstrate that ALI1 colocalizes with the plasma membrane, tonoplast, and endoplasmic reticulum. CONCLUSIONS These results suggest that the candidate protein ALI1 is indispensable for oxo-C14-HSL-dependent priming for enhanced resistance in Arabidopsis and that the ALI1 protein may interact with oxo-C14-HSL. Furthermore, ALI1 protein is localized in the cell periphery. Our findings advance the understanding of interactions between plants and bacteria and provide an avenue to explore desired outcomes such as enhanced stress resistance, which is useful for sustainable crop protection.
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Affiliation(s)
- Abhishek Shrestha
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | | | - Maja Grimm
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Johannes Krumwiede
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Elke Stein
- grid.8664.c0000 0001 2165 8627Justus Liebig University Giessen, Institute for Phytopathology, , Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Sebastian T. Schenk
- grid.5963.9Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Adam Schikora
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
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5
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Kalachova T, Škrabálková E, Pateyron S, Soubigou-Taconnat L, Djafi N, Collin S, Sekereš J, Burketová L, Potocký M, Pejchar P, Ruelland E. DIACYLGLYCEROL KINASE 5 participates in flagellin-induced signaling in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:1978-1996. [PMID: 35900211 PMCID: PMC9614507 DOI: 10.1093/plphys/kiac354] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/18/2022] [Indexed: 05/04/2023]
Abstract
Flagellin perception is a keystone of pattern-triggered immunity in plants. The recognition of this protein by a plasma membrane (PM) receptor complex is the beginning of a signaling cascade that includes protein phosphorylation and the production of reactive oxygen species (ROS). In both Arabidopsis (Arabidopsis thaliana) seedlings and suspension cells, we found that treatment with flg22, a peptide corresponding to the most conserved domain of bacterial flagellin, caused a rapid and transient decrease in the level of phosphatidylinositol (PI) 4,5-bisphosphate along with a parallel increase in phosphatidic acid (PA). In suspension cells, inhibitors of either phosphoinositide-dependent phospholipases C (PLC) or diacylglycerol kinases (DGKs) inhibited flg22-triggered PA production and the oxidative burst. In response to flg22, receptor-like kinase-deficient fls2, bak1, and bik1 mutants (FLAGELLIN SENSITIVE 2, BRASSINOSTEROID INSENSITIVE 1-associated kinase 1, and BOTRYTIS-INDUCED KINASE 1, respectively) produced less PA than wild-type (WT) plants, whereas this response did not differ in NADPH oxidase-deficient rbohD (RESPIRATORY BURST OXIDASE HOMOLOG D) plants. Among the DGK-deficient lines tested, the dgk5.1 mutant produced less PA and less ROS after flg22 treatment compared with WT seedlings. In response to flg22, dgk5.1 plants showed lower callose accumulation and impaired resistance to Pseudomonas syringae pv. tomato DC3000 hrcC-. Transcriptomics revealed that the basal expression of defense-related genes was altered in dgk5.1 seedlings compared with the WT. A GFP-DGK5 fusion protein localized to the PM, where RBOHD and PLC2 (proteins involved in plant immunity) are also located. The role of DGK5 and its enzymatic activity in flagellin signaling and fine-tuning of early immune responses in plant-microbe interactions is discussed.
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Affiliation(s)
- Tetiana Kalachova
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Eliška Škrabálková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
- Department of Experimental Plant Biology, Charles University, Viničná 5, Prague 12844, Czech Republic
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Nabila Djafi
- Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Sorbonne Université, F-75005 Paris, France
| | - Sylvie Collin
- Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Sorbonne Université, F-75005 Paris, France
| | - Juraj Sekereš
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Lenka Burketová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Martin Potocký
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
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Wang P, Liu D, Yang FH, Ge H, Zhao X, Chen HG, Du T. Identification of key gene networks controlling vernalization development characteristics of Isatis indigotica by full-length transcriptomes and gene expression profiles. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2679-2693. [PMID: 34975240 PMCID: PMC8703213 DOI: 10.1007/s12298-021-01110-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Isatis indigotica Fort., as a common Chinese medicinal raw material, will lose its medicinal value if it blooms early, so it is highly valuable to clarify the induction mechanism of the vernalization of I. indigotica at low temperature. In this study, the concentrations of soluble sugar, proline, glutathione and zeatin in two germplasms of I. indigotica with different degrees of low temperature tolerance (Y1 and Y2) were determined at 10 days, 20 days and 30 days of low-temperature treatment, and the full-length transcriptome of 24 samples was sequenced by Nanopore sequencing with Oxford Nanopore Technologies (ONT). After that, the data of transcripts involved in the vernalization of I. indigotica at low temperature were obtained, and these transcripts were identified using weighted gene co-expression network analysis (WGCNA). The results revealed the massive accumulation of soluble sugar and proline in Y1 and Y2 after low temperature induction. A total of 18,385 new transcripts, 6168 transcription factors and 470 lncRNAs were obtained. Differential expression analysis showed that gibberellin, flavonoids, fatty acids and some processes related to low temperature response were significantly enriched. Eight key transcripts were identified by WGCNA, among which ONT.14640.1, ONT.9119.1, ONT.13080.2 and ONT.16007.1 encodes a flavonoid transporter, 9-cis-epoxycarotenoid dioxygenase 3 (NCED3), growth factor gene and L-aspartate oxidase in plants, respectively. It indicated that secondary metabolites such as hormones and flavonoids play an important role in the vernalization of I. indigotica. qRT-PCR proved the reliability of transcriptome results. These results provide important insights on the low-temperature vernalization of I. indigotica, and provide a research basis for analyzing the vernalization mechanism of I. indigotica. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01110-2.
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Affiliation(s)
- Pan Wang
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Dong Liu
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Fu-Hong Yang
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
- Pingliang Academy of Agricultural Sciences, Pingliang, 744000 China
| | - Hui Ge
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Xin Zhao
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Hong-Gang Chen
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Tao Du
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
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MYC2 Transcription Factors TwMYC2a and TwMYC2b Negatively Regulate Triptolide Biosynthesis in Tripterygium wilfordii Hairy Roots. PLANTS 2021; 10:plants10040679. [PMID: 33916111 PMCID: PMC8067133 DOI: 10.3390/plants10040679] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/17/2022]
Abstract
Triptolide, an important bioactive diterpenoid extracted from the plant Tripterygium wilfordii, exhibits many pharmacological activities. MYC2 transcription factor (TF) plays an important role in the regulation of various secondary metabolites in plants. However, whether MYC2 TF could regulate the biosynthesis of triptolide in T. wilfordii is still unknown. In this study, two homologous MYC2 TF genes, TwMYC2a and TwMYC2b, were isolated from T. wilfordii hairy roots and functionally characterized. The analyses of the phylogenetic tree and subcellular localization showed that they were grouped into the IIIe clade of the bHLH superfamily with other functional MYC2 proteins and localized in the nucleus. Furthermore, yeast one-hybrid and GUS transactivation assays suggested that TwMYC2a and TwMYC2b inhibited the promoter activity of the miltiradiene synthase genes, TwTPS27a and TwTPS27b, by binding to the E-box (CACATG) and T/G-box (CACGTT) motifs in their promoters. Transgenic results revealed that RNA interference of TwMYC2a/b significantly enhanced the triptolide accumulation in hairy roots and liquid medium by upregulating the expression of several key biosynthetic genes, including TwMS (TwTPS27a/b), TwCPS (TwTPS7/9), TwDXR, and TwHMGR1. In summary, our findings show that TwMYC2a and TwMYC2b act as two negative regulators of triptolide biosynthesis in T. wilfordii hairy roots and also provide new insights on metabolic engineering of triptolide in the future.
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8
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Tu T, Zheng S, Ren P, Meng X, Zhao J, Chen Q, Li C. Coordinated cytokinin signaling and auxin biosynthesis mediates arsenate-induced root growth inhibition. PLANT PHYSIOLOGY 2021; 185:1166-1181. [PMID: 33793921 PMCID: PMC8133639 DOI: 10.1093/plphys/kiaa072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/24/2020] [Indexed: 05/05/2023]
Abstract
Interactions between plant hormones and environmental signals are important for the maintenance of root growth plasticity under ever-changing environmental conditions. Here, we demonstrate that arsenate (AsV), the most prevalent form of arsenic (As) in nature, restrains elongation of the primary root through transcriptional regulation of local auxin biosynthesis genes in the root tips of Arabidopsis (Arabidopsis thaliana) plants. The ANTHRANILATE SYNTHASE ALPHA SUBUNIT 1 (ASA1) and BETA SUBUNIT 1 (ASB1) genes encode enzymes that catalyze the conversion of chorismate to anthranilate (ANT) via the tryptophan-dependent auxin biosynthesis pathway. Our results showed that AsV upregulates ASA1 and ASB1 expression in root tips, and ASA1- and ASB1-mediated auxin biosynthesis is involved in AsV-induced root growth inhibition. Further investigation confirmed that AsV activates cytokinin signaling by stabilizing the type-B ARABIDOPSIS RESPONSE REGULATOR1 (ARR1) protein, which directly promotes the transcription of ASA1 and ASB1 genes by binding to their promoters. Genetic analysis revealed that ASA1 and ASB1 are epistatic to ARR1 in the AsV-induced inhibition of primary root elongation. Overall, the results of this study illustrate a molecular framework that explains AsV-induced root growth inhibition via crosstalk between two major plant growth regulators, auxin and cytokinin.
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Affiliation(s)
- Tianli Tu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Shuangshuang Zheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Panrong Ren
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwen Meng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jiuhai Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Qian Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
- Author for communication: (Q.C.), (C.L.)
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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9
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RNA Interference (RNAi) in Tomato Crop Research. Methods Mol Biol 2020. [PMID: 33263909 DOI: 10.1007/978-1-0716-1201-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
RNA interference (RNAi) is a posttranscriptional gene silencing phenomenon induced by double-stranded RNA. It has been widely used as a knockdown technology to analyze gene function in many organisms. In tomato, RNAi technology has widely been used as a reverse genetic tool for functional genomics study. Generally, RNAi is often achieved through transgenes producing hairpin RNA molecules. RNAi lines have the advantage with respect to more modern CRISPR/Cas9 mutants of different levels of downregulation of target gene, and allow the characterization of life-essential genes that cannot be knocked out without killing the organism. Also, RNAi allows to suppress gene expression in multigene families in a regulated manner. In this chapter, an efficient approach to create RNAi stable knockdown-transformed tomato lines is reported. In order, it describes the choice of the target silencing fragment, a highly efficient cloning strategy for the hairpin RNA construct production, a relatively easy procedure to transform and regenerate tomato plants using Agrobacterium tumefaciens and a methodology to test the goodness of the transformation procedure.
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10
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Zhu Y, Ji C, Cao W, Shen J, Zhao Q, Jiang L. Identification and characterization of unconventional membrane protein trafficking regulators in Arabidopsis: A genetic approach. JOURNAL OF PLANT PHYSIOLOGY 2020; 252:153229. [PMID: 32750645 DOI: 10.1016/j.jplph.2020.153229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Proper trafficking and subcellular localization of membrane proteins are essential for plant growth and development. The plant endomembrane system contains several membrane-bound organelles with distinct functions including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN) or early endosome, prevacuolar compartment (PVC) or multivesicular body (MVB) and vacuole. Multiple approaches have been successfully used to identify and study the regulators and components important for signal transduction, growth and development, as well as membrane trafficking in the endomembrane system in plants. These include the homologous characterization of the counterparts in mammals or yeast employing both reverse genetic as well as the forward genetic screen approaches. However, the deletion or mutation of membrane trafficking related proteins usually leads to seedling lethality due to their essential roles in plant development and organelle biogenesis. To overcome the limitation of lethal phenotype of the target proteins, we used DEX-inducible RNAi knock-down lines to study their function in plants. More recently, we developed and used both RNAi knock-down and T-DNA insertional lines as starting materials to screen for mutations that could suppress and rescue the lethal phenotype, or a suppressor screening. Further characterization of the newly identified suppressor mutants has resulted in the identification of novel negative regulators in mediating membrane trafficking and organelle biogenesis in plants. In this review, we summarize the current approaches in studying protein trafficking in the endomembrane system. We then describe three examples of suppressor screening with distinct starting materials (i.e. FREE1, MON1, and SH3P2 that are regulators of MVB, vacuole, and autophagosomes, respectively) to discuss the rationale, procedures, advantages and disadvantages, and possible outcomes of such a suppressor screening. We finally propose that these novel screening approaches will lead to the identification of new unconventional players in regulating protein trafficking and organelle biogenesis in plants and discuss their impact on plant cell biology research.
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Affiliation(s)
- Ying Zhu
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Changyang Ji
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Wenhan Cao
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Qiong Zhao
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; CUHK Shenzhen Research Institute, Shenzhen, China.
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11
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Ahmed F, Senthil-Kumar M, Dai X, Ramu VS, Lee S, Mysore KS, Zhao PX. pssRNAit: A Web Server for Designing Effective and Specific Plant siRNAs with Genome-Wide Off-Target Assessment. PLANT PHYSIOLOGY 2020; 184:65-81. [PMID: 32651189 PMCID: PMC7479913 DOI: 10.1104/pp.20.00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/30/2020] [Indexed: 05/02/2023]
Abstract
We report an advanced web server, the plant-specific small noncoding RNA interference tool pssRNAit, which can be used to design a pool of small interfering RNAs (siRNAs) for highly effective, specific, and nontoxic gene silencing in plants. In developing this tool, we integrated the transcript dataset of plants, several rules governing gene silencing, and a series of computational models of the biological mechanism of the RNA interference (RNAi) pathway. The designed pool of siRNAs can be used to construct a long double-strand RNA and expressed through virus-induced gene silencing (VIGS) or synthetic transacting siRNA vectors for gene silencing. We demonstrated the performance of pssRNAit by designing and expressing the VIGS constructs to silence Phytoene desaturase (PDS) or a ribosomal protein-encoding gene, RPL10 (QM), in Nicotiana benthamiana We analyzed the expression levels of predicted intended-target and off-target genes using reverse transcription quantitative PCR. We further conducted an RNA-sequencing-based transcriptome analysis to assess genome-wide off-target gene silencing triggered by the fragments that were designed by pssRNAit, targeting different homologous regions of the PDS gene. Our analyses confirmed the high accuracy of siRNA constructs designed using pssRNAit The pssRNAit server, freely available at https://plantgrn.noble.org/pssRNAit/, supports the design of highly effective and specific RNAi, VIGS, or synthetic transacting siRNA constructs for high-throughput functional genomics and trait improvement in >160 plant species.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah 21589, Saudi Arabia
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Muthappa Senthil-Kumar
- Noble Research Institute, Ardmore, Oklahoma 73401
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Xinbin Dai
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Vemanna S Ramu
- Noble Research Institute, Ardmore, Oklahoma 73401
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad Haryana 121001, India
| | - Seonghee Lee
- Noble Research Institute, Ardmore, Oklahoma 73401
- Horticultural Science Department, Institute of Food and Agricultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida 33598
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12
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Moutinho AF, Bataillon T, Dutheil JY. Variation of the adaptive substitution rate between species and within genomes. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10026-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AbstractThe importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summarize the current state-of-the-art of these methods and review the factors that affect the molecular rate of adaptation. Several studies have reported extensive cross-species variation in the proportion of adaptive amino-acid substitutions (α) and predicted that species with larger effective population sizes undergo less genetic drift and higher rates of adaptation. Disentangling the rates of positive and negative selection, however, revealed that mutations with deleterious effects are the main driver of this population size effect and that adaptive substitution rates vary comparatively little across species. Conversely, rates of adaptive substitution have been documented to vary substantially within genomes. On a genome-wide scale, gene density, recombination and mutation rate were observed to play a role in shaping molecular rates of adaptation, as predicted under models of linked selection. At the gene level, it has been reported that the gene functional category and the macromolecular structure substantially impact the rate of adaptive mutations. Here, we deliver a comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species.
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13
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Wang P, Pleskot R, Zang J, Winkler J, Wang J, Yperman K, Zhang T, Wang K, Gong J, Guan Y, Richardson C, Duckney P, Vandorpe M, Mylle E, Fiserova J, Van Damme D, Hussey PJ. Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery. Nat Commun 2019; 10:5132. [PMID: 31723129 PMCID: PMC6853982 DOI: 10.1038/s41467-019-12782-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 09/25/2019] [Indexed: 12/16/2022] Open
Abstract
The Arabidopsis EH proteins (AtEH1/Pan1 and AtEH2/Pan1) are components of the endocytic TPLATE complex (TPC) which is essential for endocytosis. Both proteins are homologues of the yeast ARP2/3 complex activator, Pan1p. Here, we show that these proteins are also involved in actin cytoskeleton regulated autophagy. Both AtEH/Pan1 proteins localise to the plasma membrane and autophagosomes. Upon induction of autophagy, AtEH/Pan1 proteins recruit TPC and AP-2 subunits, clathrin, actin and ARP2/3 proteins to autophagosomes. Increased expression of AtEH/Pan1 proteins boosts autophagosome formation, suggesting independent and redundant pathways for actin-mediated autophagy in plants. Moreover, AtEHs/Pan1-regulated autophagosomes associate with ER-PM contact sites (EPCS) where AtEH1/Pan1 interacts with VAP27-1. Knock-down expression of either AtEH1/Pan1 or VAP27-1 makes plants more susceptible to nutrient depleted conditions, indicating that the autophagy pathway is perturbed. In conclusion, we identify the existence of an autophagy-dependent pathway in plants to degrade endocytic components, starting at the EPCS through the interaction among AtEH/Pan1, actin cytoskeleton and the EPCS resident protein VAP27-1. Arabidopsis EH/Pan1 proteins are part of the TPLATE complex (TPC) that is required for endocytosis in plants. Here, the authors show AtEH/Pan1 proteins also act in actin-mediated autophagy, by interacting with VAP27-1 at ER-PM contact sites and recruiting TPLATE and AP-2 complex subunits, clathrin and ARP2/3/ proteins to autophagosomes.
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Affiliation(s)
- Pengwei Wang
- Department of Biosciences, Durham University, South road, Durham, DH1 3LE, UK.,Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, PR China
| | - Roman Pleskot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Jingze Zang
- Department of Biosciences, Durham University, South road, Durham, DH1 3LE, UK.,Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, PR China
| | - Joanna Winkler
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Tong Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, PR China
| | - Kun Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, PR China
| | - Jinli Gong
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, PR China
| | - Yajie Guan
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, PR China
| | | | - Patrick Duckney
- Department of Biosciences, Durham University, South road, Durham, DH1 3LE, UK
| | - Michael Vandorpe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Jindriska Fiserova
- Department of Biosciences, Durham University, South road, Durham, DH1 3LE, UK.,Department of Biology of the Cell Nucleus, Institute of Molecular Genetics CAS, v.v.i., Vídeňská 1083, Prague, 14200, Czech Republic
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
| | - Patrick J Hussey
- Department of Biosciences, Durham University, South road, Durham, DH1 3LE, UK.
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14
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Terry MI, Pérez-Sanz F, Díaz-Galián MV, Pérez de Los Cobos F, Navarro PJ, Egea-Cortines M, Weiss J. The Petunia CHANEL Gene is a ZEITLUPE Ortholog Coordinating Growth and Scent Profiles. Cells 2019; 8:cells8040343. [PMID: 30979023 PMCID: PMC6523265 DOI: 10.3390/cells8040343] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 01/05/2023] Open
Abstract
The floral perianth, comprising sepals and petals, conceals the sexual organs and attracts pollinators. The coordination of growth and scent emission is not fully understood. We have analyzed the effect of knocking down CHANEL (PhCHL), the ZEITLUPE ortholog in petunia (PhCHL) by hairpin RNAs. Plants with low PhCHL mRNA had overall decreased size. Growth evaluation using time lapse image analysis showed that early leaf movement was not affected by RNAi:PhCHL, but flower angle movement was modified, moving earlier during the day in knockdown plants than in wild types. Despite differences in stem length, growth rate was not significantly affected by loss of PhCHL. In contrast, petal growth displayed lower growth rate in RNAi:PhCHL. Decreased levels of PhCHL caused strongly modified scent profiles, including changes in composition and timing of emission resulting in volatile profiles highly divergent from the wild type. Our results show a role of PhCHL in controlling growth and development of vegetative and reproductive organs in petunia. The different effects of PhCHL on organ development indicate an organ-specific interpretation of the down regulation of PhCHL. Through the control of both timing and quantitative volatile emissions, PhCHL appears to be a major coordinator of scent profiles.
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Affiliation(s)
- Marta I Terry
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain.
| | - Fernando Pérez-Sanz
- Biomedical Informatic and Bioinformatic Platform, Biomedical Research Institute of Murcia, University Clinical Hospital 'Virgen de la Arrixaca', University of Murcia, 30120 Murcia, Spain.
| | - M Victoria Díaz-Galián
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain.
| | - Felipe Pérez de Los Cobos
- Plant Breeding Department, Center of Edafology and Applied Biology of Segura-High Council for Scientific Research (CEBAS-CSIC), Espinardo University Campus, Espinardo, 30100 Murcia, Spain.
| | - Pedro J Navarro
- Escuela Técnica Superior de Ingeniería de Telecomunicación (DSIE), Campus Muralla del Mar, s/n., Universidad Politécnica de Cartagena, 30202 Cartagena, Spain.
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain.
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain.
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15
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de Oliveira MVV, Jin X, Chen X, Griffith D, Batchu S, Maeda HA. Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:901-922. [PMID: 30457178 DOI: 10.1111/tpj.14169] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
l-Tyrosine is an essential aromatic amino acid required for the synthesis of proteins and a diverse array of plant natural products; however, little is known on how the levels of tyrosine are controlled in planta and linked to overall growth and development. Most plants synthesize tyrosine by TyrA arogenate dehydrogenases, which are strongly feedback-inhibited by tyrosine and encoded by TyrA1 and TyrA2 genes in Arabidopsis thaliana. While TyrA enzymes have been extensively characterized at biochemical levels, their in planta functions remain uncertain. Here we found that TyrA1 suppression reduces seed yield due to impaired anther dehiscence, whereas TyrA2 knockout leads to slow growth with reticulate leaves. The tyra2 mutant phenotypes were exacerbated by TyrA1 suppression and rescued by the expression of TyrA2, TyrA1 or tyrosine feeding. Low-light conditions synchronized the tyra2 and wild-type growth, and ameliorated the tyra2 leaf reticulation. After shifting to normal light, tyra2 transiently decreased tyrosine and subsequently increased aspartate before the appearance of the leaf phenotypes. Overexpression of the deregulated TyrA enzymes led to hyper-accumulation of tyrosine, which was also accompanied by elevated aspartate and reticulate leaves. These results revealed that TyrA1 and TyrA2 have distinct and overlapping functions in flower and leaf development, respectively, and that imbalance of tyrosine, caused by altered TyrA activity and regulation, impacts growth and development of Arabidopsis. The findings provide critical bases for improving the production of tyrosine and its derived natural products, and further elucidating the coordinated metabolic and physiological processes to maintain tyrosine levels in plants.
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Affiliation(s)
- Marcos V V de Oliveira
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Xing Jin
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Xuan Chen
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Daniel Griffith
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Sai Batchu
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
- Department of Biology, The College of New Jersey, Biology Building, 2000 Pennington Road, Ewing, NJ, 08628, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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16
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Gully K, Pelletier S, Guillou MC, Ferrand M, Aligon S, Pokotylo I, Perrin A, Vergne E, Fagard M, Ruelland E, Grappin P, Bucher E, Renou JP, Aubourg S. The SCOOP12 peptide regulates defense response and root elongation in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1349-1365. [PMID: 30715439 PMCID: PMC6382344 DOI: 10.1093/jxb/ery454] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/12/2018] [Indexed: 05/20/2023]
Abstract
Small secreted peptides are important players in plant development and stress response. Using a targeted in silico approach, we identified a family of 14 Arabidopsis genes encoding precursors of serine-rich endogenous peptides (PROSCOOP). Transcriptomic analyses revealed that one member of this family, PROSCOOP12, is involved in processes linked to biotic and oxidative stress as well as root growth. Plants defective in this gene were less susceptible to Erwinia amylovora infection and showed an enhanced root growth phenotype. In PROSCOOP12 we identified a conserved motif potentially coding for a small secreted peptide. Exogenous application of synthetic SCOOP12 peptide induces various defense responses in Arabidopsis. Our findings show that SCOOP12 has numerous properties of phytocytokines, activates the phospholipid signaling pathway, regulates reactive oxygen species response, and is perceived in a BAK1 co-receptor-dependent manner.
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Affiliation(s)
- Kay Gully
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Sandra Pelletier
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Marie-Charlotte Guillou
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Marina Ferrand
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Sophie Aligon
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Igor Pokotylo
- iEES-Paris (Interaction Plantes-Environnement Institut d’Ecologie et des Sciences de l’Environnement de Paris), UMR CNRS 7618, Université Paris Est Créteil, 61 avenue du général de Gaulle, Créteil, France
| | - Adrien Perrin
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Emilie Vergne
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Mathilde Fagard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Eric Ruelland
- iEES-Paris (Interaction Plantes-Environnement Institut d’Ecologie et des Sciences de l’Environnement de Paris), UMR CNRS 7618, Université Paris Est Créteil, 61 avenue du général de Gaulle, Créteil, France
| | - Philippe Grappin
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Etienne Bucher
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Jean-Pierre Renou
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
- Correspondence: or
| | - Sébastien Aubourg
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
- Correspondence: or
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17
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Vaishak KP, Yadukrishnan P, Bakshi S, Kushwaha AK, Ramachandran H, Job N, Babu D, Datta S. The B-box bridge between light and hormones in plants. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 191:164-174. [PMID: 30640143 DOI: 10.1016/j.jphotobiol.2018.12.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/23/2018] [Accepted: 12/27/2018] [Indexed: 11/29/2022]
Abstract
Plant development is meticulously modulated by interactions between the surrounding environment and the endogenous phytohormones. Light, as an external signal coordinates with the extensive networks of hormones inside the plant to execute its effects on growth and development. Several proteins in plants have been identified for their crucial roles in mediating light regulated development. Among these are the B-box (BBX) family of transcription factors characterized by the presence of zinc-finger B-box domain in their N-terminal region. In Arabidopsis there are 32 BBX proteins that are divided into five structural groups on the basis of the domains present. Several BBX proteins play important roles in seedling photomorphogenesis, neighbourhood detection and photoperiodic regulation of flowering. There is increasing evidence that besides light signaling BBX proteins also play integral roles in several hormone signaling pathways in plants. Here we attempt to comprehensively integrate the roles of multiple BBX proteins in various light and hormone signaling pathways. We further discuss the role of the BBX proteins in mediating crosstalk between the two signaling pathways to harmonize plant growth and development. Finally, we try to analyse the conservation of BBX genes across species and discuss the role of BBX proteins in regulating economically important traits in crop plants.
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Affiliation(s)
- K P Vaishak
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India; School of Biological Sciences, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, India
| | - Premachandran Yadukrishnan
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Souvika Bakshi
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Amit Kumar Kushwaha
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Harshil Ramachandran
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Nikhil Job
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Dion Babu
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Sourav Datta
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India.
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18
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Lichocka M, Rymaszewski W, Morgiewicz K, Barymow-Filoniuk I, Chlebowski A, Sobczak M, Samuel MA, Schmelzer E, Krzymowska M, Hennig J. Nucleus- and plastid-targeted annexin 5 promotes reproductive development in Arabidopsis and is essential for pollen and embryo formation. BMC PLANT BIOLOGY 2018; 18:183. [PMID: 30189843 PMCID: PMC6127919 DOI: 10.1186/s12870-018-1405-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/30/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Pollen development is a strictly controlled post-meiotic process during which microspores differentiate into microgametophytes and profound structural and functional changes occur in organelles. Annexin 5 is a calcium- and lipid-binding protein that is highly expressed in pollen grains and regulates pollen development and physiology. To gain further insights into the role of ANN5 in Arabidopsis development, we performed detailed phenotypic characterization of Arabidopsis plants with modified ANN5 levels. In addition, interaction partners and subcellular localization of ANN5 were analyzed to investigate potential functions of ANN5 at cellular level. RESULTS Here, we report that RNAi-mediated suppression of ANN5 results in formation of smaller pollen grains, enhanced pollen lethality, and delayed pollen tube growth. ANN5 RNAi knockdown plants also displayed aberrant development during the transition from the vegetative to generative phase and during embryogenesis, reflected by delayed bolting time and reduced embryo size, respectively. At the subcellular level, ANN5 was delivered to the nucleus, nucleolus, and cytoplasm, and was frequently localized in plastid nucleoids, suggesting a likely role in interorganellar communication. Furthermore, ANN5-YFP co-immunoprecipitated with RABE1b, a putative GTPase, and interaction in planta was confirmed in plastidial nucleoids using FLIM-FRET analysis. CONCLUSIONS Our findings let us to propose that ANN5 influences basal cell homeostasis via modulation of plastid activity during pollen maturation. We hypothesize that the role of ANN5 is to orchestrate the plastidial and nuclear genome activities via protein-protein interactions however not only in maturing pollen but also during the transition from the vegetative to the generative growth and seed development.
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Affiliation(s)
- Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Wojciech Rymaszewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Karolina Morgiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Izabela Barymow-Filoniuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Miroslaw Sobczak
- Department of Botany, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Marcus A. Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - Elmon Schmelzer
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Magdalena Krzymowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Jacek Hennig
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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19
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Hoang NV, Furtado A, Thirugnanasambandam PP, Botha FC, Henry RJ. De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts. Heliyon 2018; 4:e00583. [PMID: 29862346 PMCID: PMC5968133 DOI: 10.1016/j.heliyon.2018.e00583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/02/2018] [Accepted: 03/16/2018] [Indexed: 12/31/2022] Open
Abstract
Sugarcane biomass has been used for sugar, bioenergy and biomaterial production. The majority of the sugarcane biomass comes from the culm, which makes it important to understand the genetic control of biomass production in this part of the plant. A meta-transcriptome of the culm was obtained in an earlier study by using about one billion paired-end (150 bp) reads of deep RNA sequencing of samples from 20 diverse sugarcane genotypes and combining de novo assemblies from different assemblers and different settings. Although many genes could be recovered, this resulted in a large combined assembly which created the need for clustering to reduce transcript redundancy while maintaining gene content. Here, we present a comprehensive analysis of the effect of different assembly settings and clustering methods on de novo assembly, annotation and transcript profiling focusing especially on the coding transcripts from the highly polyploid sugarcane genome. The new coding sequence-based transcript clustering resulted in a better representation of transcripts compared to the earlier approach, having 121,987 contigs, which included 78,052 main and 43,935 alternative transcripts. About 73%, 67%, 61% and 10% of the transcriptome was annotated against the NCBI NR protein database, GO terms, orthologous groups and KEGG orthologies, respectively. Using this set for a differential gene expression analysis between the young and mature sugarcane culm tissues, a total of 822 transcripts were found to be differentially expressed, including key transcripts involved in sugar/fiber accumulation in sugarcane. In the context of the lack of a whole genome sequence for sugarcane, the availability of a well annotated culm-derived meta-transcriptome through deep sequencing provides useful information on coding genes specific to the sugarcane culm and will certainly contribute to understanding the process of carbon partitioning, and biomass accumulation in the sugarcane culm.
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Affiliation(s)
- Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Prathima P. Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- Sugar Research Australia, Indooroopilly, Queensland, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
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Phua SY, Pornsiriwong W, Chan KX, Estavillo GM, Pogson BJ. Development of strategies for genetic manipulation and fine-tuning of a chloroplast retrograde signal 3'-phosphoadenosine 5'-phosphate. PLANT DIRECT 2018; 2:e00031. [PMID: 31245680 PMCID: PMC6508504 DOI: 10.1002/pld3.31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/09/2017] [Accepted: 12/07/2017] [Indexed: 05/22/2023]
Abstract
Homeostasis of metabolism and regulation of stress-signaling pathways are important for plant growth. The metabolite 3'-phosphoadenosine-5'-phosphate (PAP) plays dual roles as a chloroplast retrograde signal during drought and high light stress, as well as a toxic by-product of secondary sulfur metabolism, and thus, its levels are regulated by the chloroplastic phosphatase, SAL1. Constitutive PAP accumulation in sal1 mutants improves drought tolerance but can impair growth and alter rosette morphology. Therefore, it is of interest to derive strategies to enable controlled and targeted PAP manipulation that could enhance drought tolerance while minimizing the negative effects on plant growth. We systematically tested the potential and efficiency of multiple established transgenic manipulation tools in altering PAP levels in Arabidopsis. Dexamethasone (dex)-inducible silencing of SAL1 via hpRNAi [pOpOff:SAL1hpRNAi] yielded reduction in SAL1 transcript and protein levels, yet failed to significantly induce PAP accumulation. Surprisingly, this was not due to insufficient silencing of the inducible system, as constitutive silencing using a strong promoter to drive hpRNAi and amiRNA targeting the SAL1 transcript also failed to increase PAP content or induce a sal1-like plant morphology despite significantly reducing the SAL1 transcript levels. In contrast, using dex-inducible expression of SAL1 cDNA to complement an Arabidopsis sal1 mutant successfully modulated PAP levels and restored rosette growth in a dosage-dependent manner. Results from this inducible complementation system indicate that plants with intermediate PAP levels could have improved rosette growth without compromising its drought tolerance. Additionally, preliminary evidence suggests that SAL1 cDNA driven by promoters of genes expressed specifically during early developmental stages such as ABA-Insensitive 3 (ABI3) could be another potential strategy for studying and optimizing PAP levels and drought tolerance while alleviating the negative impact of PAP on plant growth in sal1. Thus, we have identified ways that can allow future dissection into multiple aspects of stress and developmental regulation mediated by this chloroplast signal.
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Affiliation(s)
- Su Yin Phua
- ARC Centre of Excellence in Plant Energy BiologyResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Wannarat Pornsiriwong
- ARC Centre of Excellence in Plant Energy BiologyResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
- Department of BiochemistryFaculty of ScienceKasetsart UniversityBangkokThailand
| | - Kai Xun Chan
- ARC Centre of Excellence in Plant Energy BiologyResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Gonzalo M. Estavillo
- ARC Centre of Excellence in Plant Energy BiologyResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
- CSIRO Agriculture & Food, Black MountainCanberraACTAustralia
| | - Barry J. Pogson
- ARC Centre of Excellence in Plant Energy BiologyResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
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21
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Hwang HH, Yu M, Lai EM. Agrobacterium-mediated plant transformation: biology and applications. THE ARABIDOPSIS BOOK 2017; 15:e0186. [PMID: 31068763 PMCID: PMC6501860 DOI: 10.1199/tab.0186] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant genetic transformation heavily relies on the bacterial pathogen Agrobacterium tumefaciens as a powerful tool to deliver genes of interest into a host plant. Inside the plant nucleus, the transferred DNA is capable of integrating into the plant genome for inheritance to the next generation (i.e. stable transformation). Alternatively, the foreign DNA can transiently remain in the nucleus without integrating into the genome but still be transcribed to produce desirable gene products (i.e. transient transformation). From the discovery of A. tumefaciens to its wide application in plant biotechnology, numerous aspects of the interaction between A. tumefaciens and plants have been elucidated. This article aims to provide a comprehensive review of the biology and the applications of Agrobacterium-mediated plant transformation, which may be useful for both microbiologists and plant biologists who desire a better understanding of plant transformation, protein expression in plants, and plant-microbe interaction.
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Affiliation(s)
- Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, 402
| | - Manda Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, 115
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, 115
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Voxeur A, Soubigou-Taconnat L, Legée F, Sakai K, Antelme S, Durand-Tardif M, Lapierre C, Sibout R. Altered lignification in mur1-1 a mutant deficient in GDP-L-fucose synthesis with reduced RG-II cross linking. PLoS One 2017; 12:e0184820. [PMID: 28961242 PMCID: PMC5621668 DOI: 10.1371/journal.pone.0184820] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 08/31/2017] [Indexed: 12/31/2022] Open
Abstract
In the plant cell wall, boron links two pectic domain rhamnogalacturonan II (RG-II) chains together to form a dimer and thus contributes to the reinforcement of cell adhesion. We studied the mur1-1 mutant of Arabidopsis thaliana which has lost the ability to form GDP-fucose in the shoots and show that the extent of RG-II cross-linking is reduced in the lignified stem of this mutant. Surprisingly, MUR1 mutation induced an enrichment of resistant interunit bonds in lignin and triggered the overexpression of many genes involved in lignified tissue formation and in jasmonic acid signaling. The defect in GDP-fucose synthesis induced a loss of cell adhesion at the interface between stele and cortex, as well as between interfascicular fibers. This led to the formation of regenerative xylem, where tissue detachment occurred, and underlined a loss of resistance to mechanical forces. Similar observations were also made on bor1-3 mutant stems which are altered in boron xylem loading, leading us to suggest that diminished RG-II dimerization is responsible for regenerative xylem formation.
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Affiliation(s)
- Aline Voxeur
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment, Orsay, France
| | - Frédéric Legée
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Kaori Sakai
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Sébastien Antelme
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Mylène Durand-Tardif
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Catherine Lapierre
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- * E-mail:
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Bonnet C, Lassueur S, Ponzio C, Gols R, Dicke M, Reymond P. Combined biotic stresses trigger similar transcriptomic responses but contrasting resistance against a chewing herbivore in Brassica nigra. BMC PLANT BIOLOGY 2017; 17:127. [PMID: 28716054 PMCID: PMC5513356 DOI: 10.1186/s12870-017-1074-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/10/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND In nature, plants are frequently exposed to simultaneous biotic stresses that activate distinct and often antagonistic defense signaling pathways. How plants integrate this information and whether they prioritize one stress over the other is not well understood. RESULTS We investigated the transcriptome signature of the wild annual crucifer, Brassica nigra, in response to eggs and caterpillars of Pieris brassicae butterflies, Brevicoryne brassicae aphids and the bacterial phytopathogen Xanthomonas campestris pv. raphani (Xcr). Pretreatment with egg extract, aphids, or Xcr had a weak impact on the subsequent transcriptome profile of plants challenged with caterpillars, suggesting that the second stress dominates the transcriptional response. Nevertheless, P. brassicae larval performance was strongly affected by egg extract or Xcr pretreatment and depended on the site where the initial stress was applied. Although egg extract and Xcr pretreatments inhibited insect-induced defense gene expression, suggesting salicylic acid (SA)/jasmonic acid (JA) pathway cross talk, this was not strictly correlated with larval performance. CONCLUSION These results emphasize the need to better integrate plant responses at different levels of biological organization and to consider localized effects in order to predict the consequence of multiple stresses on plant resistance.
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Affiliation(s)
- Christelle Bonnet
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Steve Lassueur
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Camille Ponzio
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Rieta Gols
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.
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RNAi-based reverse genetics in the chelicerate model Tetranychus urticae: A comparative analysis of five methods for gene silencing. PLoS One 2017; 12:e0180654. [PMID: 28704448 PMCID: PMC5507529 DOI: 10.1371/journal.pone.0180654] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/19/2017] [Indexed: 12/22/2022] Open
Abstract
RNA interference (RNAi) can be used for the protection against agricultural pests through the silencing of genes required for pest fitness. To assess the potential of RNAi approaches in the two-spotted spider mite, Tetranychus urticae, we compared 5 methods for the delivery of double-stranded RNA (dsRNA). These methods include mite feeding on either (i) leaves floating on a dsRNA solution, (ii) dsRNA-expressing plants, (iii) artificial diet supplemented with dsRNA, or (iv) dsRNA-coated leaves, and (v) mite soaking in a dsRNA solution. In all cases, the gene targeted for method validation was the Vacuolar-type H+-ATPase (TuVATPase), encoding a constitutively expressed ATP-driven proton pump located in the membrane. Down-regulation of TuVATPase increased mortality and/or reduced fecundity in all methods, but with variable efficiency. The most efficient methods for dsRNA delivery were direct soaking of mites in the dsRNA solution and mite feeding on dsRNA-coated leaves that mimics dsRNA application as a sprayable pesticide. Both resulted in a dark-body phenotype not observed in mites treated with a control dsRNA. Although with lower efficiency, dsRNA designed for TuVATPase silencing and expressed in transgenic Arabidopsis plants impacted the fitness of mites feeding on these plants. RNAi may thus be a valuable strategy to control spider mite populations, either as a sprayable pesticide or through transgenic crops. This comparative methodological study focusing on the induction of RNAi-based gene silencing in T. urticae paves the way for reverse genetics approaches in this model chelicerate system and prepares large-scale systematic RNAi screens as a first step towards the development of specific RNA-based pesticides. Such alternative molecules may help control spider mites that cause significant damages to crops and ornamental plant species, as well as other chelicerates detrimental to agriculture and health.
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25
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Hoang NV, Furtado A, Mason PJ, Marquardt A, Kasirajan L, Thirugnanasambandam PP, Botha FC, Henry RJ. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics 2017; 18:395. [PMID: 28532419 PMCID: PMC5440902 DOI: 10.1186/s12864-017-3757-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. RESULTS The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms. A total of 107,598 unique transcript isoforms were obtained, representing about 71% of the total number of predicted sugarcane genes. The majority of this dataset (92%) matched the plant protein database, while just over 2% was novel transcripts, and over 2% was putative long non-coding RNAs. About 56% and 23% of total sequences were annotated against the gene ontology and KEGG pathway databases, respectively. Comparison with de novo contigs from Illumina RNA-Sequencing (RNA-Seq) of the internode samples from the same experiment and public databases showed that the Iso-Seq method recovered more full-length transcript isoforms, had a higher N50 and average length of largest 1,000 proteins; whereas a greater representation of the gene content and RNA diversity was captured in RNA-Seq. Only 62% of PacBio transcript isoforms matched 67% of de novo contigs, while the non-matched proportions were attributed to the inclusion of leaf/root tissues and the normalization in PacBio, and the representation of more gene content and RNA classes in the de novo assembly, respectively. About 69% of PacBio transcript isoforms and 41% of de novo contigs aligned with the sorghum genome, indicating the high conservation of orthologs in the genic regions of the two genomes. CONCLUSIONS The transcriptome dataset should contribute to improved sugarcane gene models and sugarcane protein predictions; and will serve as a reference database for analysis of transcript expression in sugarcane.
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Affiliation(s)
- Nam V Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia
| | - Patrick J Mason
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia
| | - Annelie Marquardt
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,Sugar Research Australia, Indooroopilly, QLD, 4068, Australia
| | - Lakshmi Kasirajan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Prathima P Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,Sugar Research Australia, Indooroopilly, QLD, 4068, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.
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Zarattini M, Launay A, Farjad M, Wénès E, Taconnat L, Boutet S, Bernacchia G, Fagard M. The bile acid deoxycholate elicits defences in Arabidopsis and reduces bacterial infection. MOLECULAR PLANT PATHOLOGY 2017; 18:540-554. [PMID: 27085087 PMCID: PMC6638291 DOI: 10.1111/mpp.12416] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Disease has an effect on crop yields, causing significant losses. As the worldwide demand for agricultural products increases, there is a need to pursue the development of new methods to protect crops from disease. One mechanism of plant protection is through the activation of the plant immune system. By exogenous application, 'plant activator molecules' with elicitor properties can be used to activate the plant immune system. These defence-inducing molecules represent a powerful and often environmentally friendly tool to fight pathogens. We show that the secondary bile acid deoxycholic acid (DCA) induces defence in Arabidopsis and reduces the proliferation of two bacterial phytopathogens: Erwinia amylovora and Pseudomonas syringae pv. tomato. We describe the global defence response triggered by this new plant activator in Arabidopsis at the transcriptional level. Several induced genes were selected for further analysis by quantitative reverse transcription-polymerase chain reaction. We describe the kinetics of their induction and show that abiotic stress, such as moderate drought or nitrogen limitation, does not impede DCA induction of defence. Finally, we investigate the role in the activation of defence by this bile acid of the salicylic acid biosynthesis gene SID2, of the receptor-like kinase family genes WAK1-3 and of the NADPH oxidase-encoding RbohD gene. Altogether, we show that DCA constitutes a promising molecule for plant protection which can induce complementary lines of defence, such as callose deposition, reactive oxygen species accumulation and the jasmonic acid and salicylic acid signalling pathways.
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Affiliation(s)
- Marco Zarattini
- Institut Jean‐Pierre BourginUMR 1318, INRA, AgroParistech, ERL CNRS 3559, U. Paris‐Saclay, RD10VersaillesF‐78026France
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerrara 44121Italy
| | - Alban Launay
- Institut Jean‐Pierre BourginUMR 1318, INRA, AgroParistech, ERL CNRS 3559, U. Paris‐Saclay, RD10VersaillesF‐78026France
- Université Paris‐Sud, U. Paris‐SaclayOrsay91405France
| | - Mahsa Farjad
- Institut Jean‐Pierre BourginUMR 1318, INRA, AgroParistech, ERL CNRS 3559, U. Paris‐Saclay, RD10VersaillesF‐78026France
| | - Estelle Wénès
- Institut Jean‐Pierre BourginUMR 1318, INRA, AgroParistech, ERL CNRS 3559, U. Paris‐Saclay, RD10VersaillesF‐78026France
| | - Ludivine Taconnat
- Institute of Plant Sciences – Paris‐Saclay, INRA, CNRSU. Paris‐Sud, U. Paris‐SaclayOrsay91405France
| | - Stéphanie Boutet
- Institut Jean‐Pierre BourginUMR 1318, INRA, AgroParistech, ERL CNRS 3559, U. Paris‐Saclay, RD10VersaillesF‐78026France
| | - Giovanni Bernacchia
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerrara 44121Italy
| | - Mathilde Fagard
- Institut Jean‐Pierre BourginUMR 1318, INRA, AgroParistech, ERL CNRS 3559, U. Paris‐Saclay, RD10VersaillesF‐78026France
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Pedroza-García JA, Mazubert C, Del Olmo I, Bourge M, Domenichini S, Bounon R, Tariq Z, Delannoy E, Piñeiro M, Jarillo JA, Bergounioux C, Benhamed M, Raynaud C. Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis. PLANT PHYSIOLOGY 2017; 173:1735-1749. [PMID: 28153919 PMCID: PMC5338674 DOI: 10.1104/pp.17.00031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/30/2017] [Indexed: 05/17/2023]
Abstract
Faithful transmission of the genetic information is essential in all living organisms. DNA replication is therefore a critical step of cell proliferation, because of the potential occurrence of replication errors or DNA damage when progression of a replication fork is hampered causing replicative stress. Like other types of DNA damage, replicative stress activates the DNA damage response, a signaling cascade allowing cell cycle arrest and repair of lesions. The replicative DNA polymerase ε (Pol ε) was shown to activate the S-phase checkpoint in yeast in response to replicative stress, but whether this mechanism functions in multicellular eukaryotes remains unclear. Here, we explored the genetic interaction between Pol ε and the main elements of the DNA damage response in Arabidopsis (Arabidopsis thaliana). We found that mutations affecting the polymerase domain of Pol ε trigger ATR-dependent signaling leading to SOG1 activation, WEE1-dependent cell cycle inhibition, and tolerance to replicative stress induced by hydroxyurea, but result in enhanced sensitivity to a wide range of DNA damaging agents. Using knock-down lines, we also provide evidence for the direct role of Pol ε in replicative stress sensing. Together, our results demonstrate that the role of Pol ε in replicative stress sensing is conserved in plants, and provide, to our knowledge, the first genetic dissection of the downstream signaling events in a multicellular eukaryote.
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Affiliation(s)
- José-Antonio Pedroza-García
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Christelle Mazubert
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Ivan Del Olmo
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Mickael Bourge
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Séverine Domenichini
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Rémi Bounon
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Zakia Tariq
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Manuel Piñeiro
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - José A Jarillo
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.);
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.);
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
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Angelovici R, Batushansky A, Deason N, Gonzalez-Jorge S, Gore MA, Fait A, DellaPenna D. Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids. PLANT PHYSIOLOGY 2017; 173:872-886. [PMID: 27872244 PMCID: PMC5210728 DOI: 10.1104/pp.16.01287] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/16/2016] [Indexed: 05/18/2023]
Abstract
Amino acids are essential for proper growth and development in plants. Amino acids serve as building blocks for proteins but also are important for responses to stress and the biosynthesis of numerous essential compounds. In seed, the pool of free amino acids (FAAs) also contributes to alternative energy, desiccation, and seed vigor; thus, manipulating FAA levels can significantly impact a seed's nutritional qualities. While genome-wide association studies (GWAS) on branched-chain amino acids have identified some regulatory genes controlling seed FAAs, the genetic regulation of FAA levels, composition, and homeostasis in seeds remains mostly unresolved. Hence, we performed GWAS on 18 FAAs from a 313-ecotype Arabidopsis (Arabidopsis thaliana) association panel. Specifically, GWAS was performed on 98 traits derived from known amino acid metabolic pathways (approach 1) and then on 92 traits generated from an unbiased correlation-based metabolic network analysis (approach 2), and the results were compared. The latter approach facilitated the discovery of additional novel metabolic interactions and single-nucleotide polymorphism-trait associations not identified by the former approach. The most prominent network-guided GWAS signal was for a histidine (His)-related trait in a region containing two genes: a cationic amino acid transporter (CAT4) and a polynucleotide phosphorylase resistant to inhibition with fosmidomycin. A reverse genetics approach confirmed CAT4 to be responsible for the natural variation of His-related traits across the association panel. Given that His is a semiessential amino acid and a potent metal chelator, CAT4 orthologs could be considered as candidate genes for seed quality biofortification in crop plants.
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Affiliation(s)
- Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.);
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.);
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.);
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Albert Batushansky
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Nicholas Deason
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Sabrina Gonzalez-Jorge
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Michael A Gore
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Aaron Fait
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Dean DellaPenna
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
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Lv Q, Lan Y, Shi Y, Wang H, Pan X, Li P, Shi T. AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. Nucleic Acids Res 2016; 45:D1060-D1063. [PMID: 27899679 PMCID: PMC5210528 DOI: 10.1093/nar/gkw1029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/16/2016] [Accepted: 11/08/2016] [Indexed: 01/01/2023] Open
Abstract
AtPID (Arabidopsis thalianaProtein Interactome Database, available at http://www.megabionet.org/atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3919 genes. After integrated these genotype–phenotype associations with the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4457 novel high confidence gene-PO pairs with 1369 genes as the complement. Along with the accumulated novel data for protein interaction and functional annotation, and the updated visualization toolkits, we present a genome-scale resource for genotype–phenotype associations for Arabidopsis in AtPID 5.0. In our updated website, all the new genotype–phenotype associations from mutants, protein network, and the protein annotation information can be vividly displayed in a comprehensive network view, which will greatly enhance plant protein function and genotype–phenotype association studies in a systematical way.
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Affiliation(s)
- Qi Lv
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.,School of Finance and Statistics, East China Normal University, Shanghai 200241, China
| | - Yiheng Lan
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yan Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Huan Wang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xia Pan
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Peng Li
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
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Dumas AS, Taconnat L, Barbas E, Rigaill G, Catrice O, Bernard D, Benamar A, Macherel D, El Amrani A, Berthomé R. Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure. BMC Genomics 2016; 17:818. [PMID: 27769163 PMCID: PMC5073745 DOI: 10.1186/s12864-016-3133-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/27/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Higher plants have to cope with increasing concentrations of pollutants of both natural and anthropogenic origin. Given their capacity to concentrate and metabolize various compounds including pollutants, plants can be used to treat environmental problems - a process called phytoremediation. However, the molecular mechanisms underlying the stabilization, the extraction, the accumulation and partial or complete degradation of pollutants by plants remain poorly understood. RESULTS Here, we determined the molecular events involved in the early plant response to phenanthrene, used as a model of polycyclic aromatic hydrocarbons. A transcriptomic and a metabolic analysis strongly suggest that energy availability is the crucial limiting factor leading to high and rapid transcriptional reprogramming that can ultimately lead to death. We show that the accumulation of phenanthrene in leaves inhibits electron transfer and photosynthesis within a few minutes, probably disrupting energy transformation. CONCLUSION This kinetic analysis improved the resolution of the transcriptome in the initial plant response to phenanthrene, identifying genes that are involved in primary processes set up to sense and detoxify this pollutant but also in molecular mechanisms used by the plant to cope with such harmful stress. The identification of first events involved in plant response to phenanthrene is a key step in the selection of candidates for further functional characterization, with the prospect of engineering efficient ecological detoxification systems for polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Anne-Sophie Dumas
- Université de Rennes 1, CNRS/OSUR/UMR 6553, Ecosystèmes-Biodiversité-Evolution, campus de Beaulieu, Bâtiment 14A, 35042, Rennes cedex, France
| | - Ludivine Taconnat
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France
| | - Evangelos Barbas
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France
- Present Address: Laboratory of Forest Genetics and Tree Breeding, AUTH, University Campus, 54124, Thessaloniki, Greece
| | - Guillem Rigaill
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France
| | - Olivier Catrice
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR INRA 441/CNRS 2594, CS 52627, 31326, Castanet Tolosan cedex, France
| | - Delphine Bernard
- Université de Rennes 1, CNRS/OSUR/UMR 6553, Ecosystèmes-Biodiversité-Evolution, campus de Beaulieu, Bâtiment 14A, 35042, Rennes cedex, France
- Present Address: Laboratoire de Génétique Moléculaire et de Génétique Epidémiologique, INSERM U1078, 46, rue Felix Le Dantec, CS 51819, 29218, Brest Cedex 2, France
| | - Abdelilah Benamar
- Université d'Angers, UMR 1345, Institut de Recherche en Horticulture et Semences (IRHS), Bat ARES, 16 Boulevard Lavoisier, 49045, Angers cedex, France
| | - David Macherel
- Université d'Angers, UMR 1345, Institut de Recherche en Horticulture et Semences (IRHS), Bat ARES, 16 Boulevard Lavoisier, 49045, Angers cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, CNRS/OSUR/UMR 6553, Ecosystèmes-Biodiversité-Evolution, campus de Beaulieu, Bâtiment 14A, 35042, Rennes cedex, France.
| | - Richard Berthomé
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France.
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR INRA 441/CNRS 2594, CS 52627, 31326, Castanet Tolosan cedex, France.
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31
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Baykal U, Liu H, Chen X, Nguyen HT, Zhang ZJ. Novel constructs for efficient cloning of sRNA-encoding DNA and uniform silencing of plant genes employing artificial trans-acting small interfering RNA. PLANT CELL REPORTS 2016; 35:2137-50. [PMID: 27417696 DOI: 10.1007/s00299-016-2024-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/03/2016] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE TAS atasiRNA-producing region swapping used one-step, high efficiency, and high fidelity directional TC-cloning. Uniform silencing was achieved without lethality using miRNA trigger- TAS overexpression fusion cassettes to generate 21-nt atasiRNA. Plant transgenic technologies are very important for basic plant research and biotechnology. Artificial trans-acting small interfering RNA (atasiRNA) represents an attractive platform with certain advantages over other silencing approaches, such as hairpin RNA, artificial microRNA (amiRNA), and virus-induced gene silencing (VIGS). In this study, we developed two types of constructs for atasiRNA-mediated gene silencing in plants. To functionally validate our constructs, we chose TAS1a as a test model. Type 1 constructs had miR173-precursor sequence fused with TAS1a locus driven by single promoter-terminator cassette, which simplified the expression cassette and resulted in uniform gene silencing. Type 2 constructs contained two separate cassettes for miR173 and TAS1a co-expression. The constructs in each type were further improved by deploying the XcmI-based TC-cloning system for highly efficient directional cloning of short DNA fragments encoding atasiRNAs into TAS1a locus. The effectiveness of the constructs was demonstrated by cloning an atasiRNA DNA into the TC site of engineered TAS1a and silencing of CHLORINA 42 (CH42) gene in Arabidopsis. Our results show that the directional TC-cloning of the atasiRNA DNA into the engineered TAS1a is highly efficient and the miR173-TAS1a fusion system provides an attractive alternative to achieve moderate but more uniform gene silencing without lethality, as compared to conventional two separate cassettes for miR173 and TAS locus co-expression system. The design principles described here should be applicable to other TAS loci such as TAS1b, TAS1c, TAS2, or TAS3, and cloning of amiRNA into amiRNA stem-loop.
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Affiliation(s)
- Ulku Baykal
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
| | - Hua Liu
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
| | - Xinlu Chen
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
- Department of Plant Sciences, University of Tennessee, 347/359 Plant Biotech, Knoxville, TX, 37996, USA
| | - Henry T Nguyen
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
| | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA.
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Ma Y, Ma XH, Meng FY, Zhan ZL, Guo J, Huang LQ. RNA interference targeting CYP76AH1 in hairy roots of Salvia miltiorrhiza reveals its key role in the biosynthetic pathway of tanshinones. Biochem Biophys Res Commun 2016; 477:155-60. [DOI: 10.1016/j.bbrc.2016.06.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 11/17/2022]
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Wang P, Richardson C, Hawkins TJ, Sparkes I, Hawes C, Hussey PJ. Plant VAP27 proteins: domain characterization, intracellular localization and role in plant development. THE NEW PHYTOLOGIST 2016; 210:1311-26. [PMID: 27159525 DOI: 10.1111/nph.13857] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/14/2015] [Indexed: 05/24/2023]
Abstract
The endoplasmic reticulum (ER) is connected to the plasma membrane (PM) through the plant-specific NETWORKED protein, NET3C, and phylogenetically conserved vesicle-associated membrane protein-associated proteins (VAPs). Ten VAP homologues (VAP27-1 to 27-10) can be identified in the Arabidopsis genome and can be divided into three clades. Representative members from each clade were tagged with fluorescent protein and expressed in Nicotiana benthamiana. Proteins from clades I and III localized to the ER as well as to ER/PM contact sites (EPCSs), whereas proteins from clade II were found only at the PM. Some of the VAP27-labelled EPCSs localized to plasmodesmata, and we show that the mobility of VAP27 at EPCSs is influenced by the cell wall. EPCSs closely associate with the cytoskeleton, but their structure is unaffected when the cytoskeleton is removed. VAP27-labelled EPCSs are found in most cell types in Arabidopsis, with the exception of cells in early trichome development. Arabidopsis plants expressing VAP27-GFP fusions exhibit pleiotropic phenotypes, including defects in root hair morphogenesis. A similar effect is also observed in plants expressing VAP27 RNAi. Taken together, these data indicate that VAP27 proteins used at EPCSs are essential for normal ER-cytoskeleton interaction and for plant development.
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Affiliation(s)
- Pengwei Wang
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Christine Richardson
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Timothy J Hawkins
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Imogen Sparkes
- College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Chris Hawes
- Department of Biological and Biomedical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Patrick J Hussey
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
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Lang J, Gonzalez-Mula A, Taconnat L, Clement G, Faure D. The plant GABA signaling downregulates horizontal transfer of the Agrobacterium tumefaciens virulence plasmid. THE NEW PHYTOLOGIST 2016; 210:974-983. [PMID: 26714842 DOI: 10.1111/nph.13813] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/18/2015] [Indexed: 06/05/2023]
Abstract
In the tumor-inducing (Ti) Agrobacterium tumefaciens, quorum sensing activates the horizontal transfer of the virulent Ti plasmid. In pure culture, this process can be impaired by the A. tumefaciens BlcC lactonase, whose expression is induced by gamma-aminobutyrate (GABA). It was therefore hypothesized that host GABA content might modulate quorum sensing and virulence gene dissemination during A. tumefaciens infection. We examined GABA metabolism and transport in Arabidopsis thaliana tumors combining transcriptomic, metabolomic and histological approaches. In addition, using genetically modified plants and bacteria, we evaluated the impact of plant host GABA content on Ti plasmid dissemination. The results showed that GABA and free proline, which acts as an antagonist of GABA uptake in A. tumefaciens, accumulated in wild-type tumors relative to uninfected plant tissues. Moreover, comparisons of tumors induced on Col-0 and her1 plants showed that the increase in the plant GABA : proline ratio was associated with both the upregulated expression of the blcC gene and the decreased dissemination of Ti plasmid in tumor-colonizing A. tumefaciens populations. This work demonstrates experimentally that the variation in the GABA content in plant tumors can interfere with the dissemination of A. tumefaciens Ti plasmids, and therefore highlights plant GABA content as an important trait in the struggle against pathogenic bacteria.
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Affiliation(s)
- Julien Lang
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Almudena Gonzalez-Mula
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Ludivine Taconnat
- POPS Transcriptomic Platform - Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité Université Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Gilles Clement
- Plateforme de Chimie - Métabolisme, INRA Centre de Versailles-Grignon, Route de Saint-Cyr, 78026, Versailles Cedex, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
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Shumbe L, Chevalier A, Legeret B, Taconnat L, Monnet F, Havaux M. Singlet Oxygen-Induced Cell Death in Arabidopsis under High-Light Stress Is Controlled by OXI1 Kinase. PLANT PHYSIOLOGY 2016; 170:1757-71. [PMID: 26747288 PMCID: PMC4775124 DOI: 10.1104/pp.15.01546] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/07/2016] [Indexed: 05/03/2023]
Abstract
Studies of the singlet oxygen ((1)O2)-overproducing flu and chlorina1 (ch1) mutants of Arabidopsis (Arabidopsis thaliana) have shown that (1)O2-induced changes in gene expression can lead to either programmed cell death (PCD) or acclimation. A transcriptomic analysis of the ch1 mutant has allowed the identification of genes whose expression is specifically affected by each phenomenon. One such gene is OXIDATIVE SIGNAL INDUCIBLE1 (OXI1) encoding an AGC kinase that was noticeably induced by excess light energy and (1)O2 stress conditions leading to cell death. Photo-induced oxidative damage and cell death were drastically reduced in the OXI1 null mutant (oxi1) and in the double mutant ch1*oxi1 compared with the wild type and the ch1 single mutant, respectively. This occurred without any changes in the production rate of (1)O2 but was cancelled by exogenous applications of the phytohormone jasmonate. OXI1-mediated (1)O2 signaling appeared to operate through a different pathway from the previously characterized OXI1-dependent response to pathogens and H2O2 and was found to be independent of the EXECUTER proteins. In high-light-stressed plants, the oxi1 mutation was associated with reduced jasmonate levels and with the up-regulation of genes encoding negative regulators of jasmonate signaling and PCD. Our results show that OXI1 is a new regulator of (1)O2-induced PCD, likely acting upstream of jasmonate.
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Affiliation(s)
- Leonard Shumbe
- CEA, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologie, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);Aix-Marseille Université, F-13284 Marseille, France (L.S., A.C., B.L., F.M., M.H.);POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay IPS2, Rue de Noetzlin, 91405 Orsay, France (L.T.); andUniversité Avignon et des Pays de Vaucluse, 84000 Avignon, France (F.M.)
| | - Anne Chevalier
- CEA, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologie, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);Aix-Marseille Université, F-13284 Marseille, France (L.S., A.C., B.L., F.M., M.H.);POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay IPS2, Rue de Noetzlin, 91405 Orsay, France (L.T.); andUniversité Avignon et des Pays de Vaucluse, 84000 Avignon, France (F.M.)
| | - Bertrand Legeret
- CEA, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologie, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);Aix-Marseille Université, F-13284 Marseille, France (L.S., A.C., B.L., F.M., M.H.);POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay IPS2, Rue de Noetzlin, 91405 Orsay, France (L.T.); andUniversité Avignon et des Pays de Vaucluse, 84000 Avignon, France (F.M.)
| | - Ludivine Taconnat
- CEA, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologie, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);Aix-Marseille Université, F-13284 Marseille, France (L.S., A.C., B.L., F.M., M.H.);POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay IPS2, Rue de Noetzlin, 91405 Orsay, France (L.T.); andUniversité Avignon et des Pays de Vaucluse, 84000 Avignon, France (F.M.)
| | - Fabien Monnet
- CEA, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologie, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);Aix-Marseille Université, F-13284 Marseille, France (L.S., A.C., B.L., F.M., M.H.);POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay IPS2, Rue de Noetzlin, 91405 Orsay, France (L.T.); andUniversité Avignon et des Pays de Vaucluse, 84000 Avignon, France (F.M.)
| | - Michel Havaux
- CEA, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologie, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, F-13108 Saint-Paul-lez-Durance, France (L.S., A.C., B.L., F.M., M.H.);Aix-Marseille Université, F-13284 Marseille, France (L.S., A.C., B.L., F.M., M.H.);POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay IPS2, Rue de Noetzlin, 91405 Orsay, France (L.T.); andUniversité Avignon et des Pays de Vaucluse, 84000 Avignon, France (F.M.)
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Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. THE NEW PHYTOLOGIST 2016; 209:921-44. [PMID: 26465351 DOI: 10.1111/nph.13687] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 05/14/2023]
Abstract
922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vincent Colot
- Departement de Biologie École Normale Supérieure, Biologie Moleculaire des Organismes Photosynthetiques, F-75230, Paris, France
| | - Sean Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Jeff Dangl
- Department of Biology and Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Joanna D Friesner
- Department of Plant Biology, Agricultural Sustainability Institute, University of California, Davis, CA, 95616, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erich Grotewold
- Center for Applied Plant Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, A-1030, Vienna, Austria
| | - Craig Pikaard
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chris Somerville
- Energy Biosciences Institute, University of California, Berkeley, CA, 94704, USA
| | - Mark Stitt
- Metabolic Networks Department, Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Jamie Waese
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter McCourt
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Czarnecki O, Bryan AC, Jawdy SS, Yang X, Cheng ZM, Chen JG, Tuskan GA. Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana. PLANT METHODS 2016; 12:16. [PMID: 26889205 PMCID: PMC4756541 DOI: 10.1186/s13007-016-0116-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/08/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Genetic engineering of plants that results in successful establishment of new biochemical or regulatory pathways requires stable introduction of one or more genes into the plant genome. It might also be necessary to down-regulate or turn off expression of endogenous genes in order to reduce activity of competing pathways. An established way to knockdown gene expression in plants is expressing a hairpin-RNAi construct, eventually leading to degradation of a specifically targeted mRNA. Knockdown of multiple genes that do not share homologous sequences is still challenging and involves either sophisticated cloning strategies to create vectors with different serial expression constructs or multiple transformation events that is often restricted by a lack of available transformation markers. RESULTS Synthetic RNAi fragments were assembled in yeast carrying homologous sequences to six or seven non-family genes and introduced into pAGRIKOLA. Transformation of Arabidopsis thaliana and subsequent expression analysis of targeted genes proved efficient knockdown of all target genes. CONCLUSIONS We present a simple and cost-effective method to create constructs to simultaneously knockdown multiple non-family genes or genes that do not share sequence homology. The presented method can be applied in plant and animal synthetic biology as well as traditional plant and animal genetic engineering.
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Affiliation(s)
- Olaf Czarnecki
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ; KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Anthony C Bryan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Zong-Ming Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nat Commun 2015; 6:8821. [PMID: 26578065 PMCID: PMC4673502 DOI: 10.1038/ncomms9821] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 10/07/2015] [Indexed: 11/24/2022] Open
Abstract
Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal ‘memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level. Lateral root development is dependent on precise control of the distribution of the plant hormone auxin. Here Chen et al. propose the transcription factors ARF7 and FLP participate in a feed forward motif to mediate expression of the auxin transporter PIN3 and consequently regulate lateral root development.
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El Amrani A, Dumas AS, Wick LY, Yergeau E, Berthomé R. "Omics" Insights into PAH Degradation toward Improved Green Remediation Biotechnologies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11281-91. [PMID: 26352597 DOI: 10.1021/acs.est.5b01740] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This review summarizes recent knowledge of polycyclic aromatic hydrocarbons (PAHs) biotransformation by microorganisms and plants. Whereas most research has focused on PAH degradation either by plants or microorganisms separately, this review specifically addresses the interactions of plants with their rhizosphere microbial communities. Indeed, plant roots release exudates that contain various nutritional and signaling molecules that influence bacterial and fungal populations. The complex interactions of these populations play a pivotal role in the biodegradation of high-molecular-weight PAHs and other complex molecules. Emerging integrative approaches, such as (meta-) genomics, (meta-) transcriptomics, (meta-) metabolomics, and (meta-) proteomics studies are discussed, emphasizing how "omics" approaches bring new insight into decipher molecular mechanisms of PAH degradation both at the single species and community levels. Such knowledge address new pictures on how organic molecules are cometabolically degraded in a complex ecosystem and should help in setting up novel decontamination strategies based on the rhizosphere interactions between plants and their microbial associates.
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Affiliation(s)
- Abdelhak El Amrani
- University of Rennes 1 , CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Anne-Sophie Dumas
- University of Rennes 1 , CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Lukas Y Wick
- UFZ, Department of Environmental Microbiology, Helmholtz Centre for Environmental Research , Permoserstraße 15, D-04318 Leipzig, Germany
| | - Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec Canada
| | - Richard Berthomé
- Plant Genomics Research Unit, UMR INRA 1165 - CNRS 8114 - UEVE , 2, Gaston Crémieux St., CP5708, 91057 Evry Cedex, France
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40
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Applications of comparative evolution to human disease genetics. Curr Opin Genet Dev 2015; 35:16-24. [PMID: 26338499 DOI: 10.1016/j.gde.2015.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 12/15/2022]
Abstract
Direct comparison of human diseases with model phenotypes allows exploration of key areas of human biology which are often inaccessible for practical or ethical reasons. We review recent developments in comparative evolutionary approaches for finding models for genetic disease, including high-throughput generation of gene/phenotype relationship data, the linking of orthologous genes and phenotypes across species, and statistical methods for linking human diseases to model phenotypes.
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41
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Van Hove J, De Jaeger G, De Winne N, Guisez Y, Van Damme EJM. The Arabidopsis lectin EULS3 is involved in stomatal closure. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:312-22. [PMID: 26259197 DOI: 10.1016/j.plantsci.2015.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 05/04/2023]
Abstract
Plants synthesize carbohydrate binding proteins in response to adverse environmental conditions such as drought, heat, pathogen attack, etc. The Arabidopsis EULS3 lectin (referred to as ArathEULS3, encoded by At2g39050) has recently been linked to the drought stress response. In this study, endogenous binding partners for this protein have been investigated. Tandem affinity purifications and mass spectrometry analyses allowed the identification of two putative interacting proteins, Embryo-specific protein 3A (ATS3A, At2g41475) and Embryo-specific protein 3B (ATS3B, At5g62200). Bimolecular fluorescence complementation experiments confirmed the interaction between ArathEULS3 and ATS3B in closed stomata of Nicotiana benthamiana plants. Transgenic lines with reduced ArathEULS3 expression exhibited an aberrant ABA-induced stomatal closure compared to plants overexpressing ArathEULS3 and control plants suggesting a role for ArathEULS3 in ABA-induced stomatal closure. Stomata are known as the major route for Pseudomonas syringae entry into the plant tissues. Bacterial infection of wild type Arabidopsis thaliana plants was accompanied by a 6-fold increase of transcript levels for ArathEULS3. Furthermore, infection experiments with ArathEULS3 overexpression lines resulted in a clear reduction of P. syringae disease symptoms whereas plants with reduced ArathEULS3 expression showed the highest levels of leaf damage at 3 days post infection. These data point towards the physiological importance of ArathEULS3 for stomatal movement.
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Affiliation(s)
- Jonas Van Hove
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium; Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium; Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
| | - Yves Guisez
- Laboratory of Molecular Plant Physiology and Biotechnology, Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; Centre for Proteome Analysis and Mass Spectrometry, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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Mai HJ, Lindermayr C, von Toerne C, Fink-Straube C, Durner J, Bauer P. Iron and FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR-dependent regulation of proteins and genes in Arabidopsis thaliana
roots. Proteomics 2015; 15:3030-47. [DOI: 10.1002/pmic.201400351] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 03/10/2015] [Accepted: 04/30/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Hans-Jörg Mai
- Institute of Botany; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian Lindermayr
- Helmholtz Zentrum München (GmbH); German Research Center for Environmental Health; Institute of Biochemical Plant Pathology (BIOP); Neuherberg Germany
| | - Christine von Toerne
- Research Unit Protein Science; Helmholtz Zentrum München (GmbH); German Research Center for Environmental Health; Neuherberg Germany
| | | | - Jörg Durner
- Helmholtz Zentrum München (GmbH); German Research Center for Environmental Health; Institute of Biochemical Plant Pathology (BIOP); Neuherberg Germany
| | - Petra Bauer
- Institute of Botany; Heinrich Heine University Düsseldorf; Düsseldorf Germany
- CEPLAS Cluster of Excellence on Plant Sciences; Heinrich Heine Universität Düsseldorf; Düsseldorf Germany
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Germline-transmitted genome editing in Arabidopsis thaliana Using TAL-effector-nucleases. PLoS One 2015; 10:e0121056. [PMID: 25822541 PMCID: PMC4378910 DOI: 10.1371/journal.pone.0121056] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/29/2015] [Indexed: 11/19/2022] Open
Abstract
Transcription activator-like effector nucleases (TALENs) are custom-made bi-partite endonucleases that have recently been developed and applied for genome engineering in a wide variety of organisms. However, they have been only scarcely used in plants, especially for germline-modification. Here we report the efficient creation of small, germline-transmitted deletions in Arabidopsis thaliana via TALENs that were delivered by stably integrated transgenes. Using meristem specific promoters to drive expression of two TALEN arms directed at the CLV3 coding sequence, we observed very high phenotype frequencies in the T2 generation. In some instances, full CLV3 loss-of-function was already observed in the T1 generation, suggesting that transgenic delivery of TALENs can cause highly efficient genome modification. In contrast, constitutive TALEN expression in the shoot apical meristem (SAM) did not cause additional phenotypes and genome re-sequencing confirmed little off-target effects, demonstrating exquisite target specificity.
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Zhou W, Karcher D, Fischer A, Maximova E, Walther D, Bock R. Multiple RNA processing defects and impaired chloroplast function in plants deficient in the organellar protein-only RNase P enzyme. PLoS One 2015; 10:e0120533. [PMID: 25793367 PMCID: PMC4368725 DOI: 10.1371/journal.pone.0120533] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/23/2015] [Indexed: 01/22/2023] Open
Abstract
Transfer RNA (tRNA) precursors undergo endoribonucleolytic processing of their 5’ and 3’ ends. 5’ cleavage of the precursor transcript is performed by ribonuclease P (RNase P). While in most organisms RNase P is a ribonucleoprotein that harbors a catalytically active RNA component, human mitochondria and the chloroplasts (plastids) and mitochondria of seed plants possess protein-only RNase P enzymes (PRORPs). The plant organellar PRORP (PRORP1) has been characterized to some extent in vitro and by transient gene silencing, but the molecular, phenotypic and physiological consequences of its down-regulation in stable transgenic plants have not been assessed. Here we have addressed the function of the dually targeted organellar PRORP enzyme in vivo by generating stably transformed Arabidopsis plants in which expression of the PRORP1 gene was suppressed by RNA interference (RNAi). PRORP1 knock-down lines show defects in photosynthesis, while mitochondrial respiration is not appreciably affected. In both plastids and mitochondria, the effects of PRORP1 knock-down on the processing of individual tRNA species are highly variable. The drastic reduction in the levels of mature plastid tRNA-Phe(GAA) and tRNA-Arg(ACG) suggests that these two tRNA species limit plastid gene expression in the PRORP1 mutants and, hence, are causally responsible for the mutant phenotype.
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Affiliation(s)
- Wenbin Zhou
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Axel Fischer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Eugenia Maximova
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Dirk Walther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
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45
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Wounding of Arabidopsis halleri leaves enhances cadmium accumulation that acts as a defense against herbivory. Biometals 2015; 28:521-8. [PMID: 25753945 PMCID: PMC4427619 DOI: 10.1007/s10534-015-9829-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/01/2015] [Indexed: 11/09/2022]
Abstract
Approximately 0.2 % of all angiosperms are classified as metal hyperaccumulators based on their extraordinarily high leaf metal contents, for example >1 % zinc, >0.1 % nickel or >0.01 % cadmium (Cd) in dry biomass. So far, metal hyperaccumulation has been considered to be a taxon-wide, constitutively expressed trait, the extent of which depends solely on available metal concentrations in the soil. Here we show that in the facultative metallophyte Arabidopsis halleri, both insect herbivory and mechanical wounding of leaves trigger an increase specifically in leaf Cd accumulation. Moreover, the Cd concentrations accumulated in leaves can serve as an elemental defense against herbivory by larvae of the Brassicaceae specialist small white (Pieris rapae), thus allowing the plant to take advantage of this non-essential trace element and toxin. Metal homeostasis genes are overrepresented in the systemic transcriptional response of roots to the wounding of leaves in A. halleri, supporting that leaf Cd accumulation is preceded by systemic signaling events. A similar, but quantitatively less pronounced transcriptional response was observed in A. thaliana, suggesting that the systemically regulated modulation of metal homeostasis in response to leaf wounding also occurs in non-hyperaccumulator plants. This is the first report of an environmental stimulus influencing metal hyperaccumulation.
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Abstract
Studies in functional genomics and crop improvement programs often rely on the introduction and expression of transgenes in plants. There are two essential components required for in planta transgene expression, a plasmid vector on which the transgene sequence is carried and a delivery system capable of transferring the vector to the target cells. Agrobacterium-mediated plant transformation and the binary plasmid vector system is the preferred method of transgene delivery. The cloning technologies used for DNA manipulation underpin many of these studies. Increased demand for efficient high-throughput transformation systems is driving forward improvements in gene cloning techniques. This chapter gives an overview of Gateway(®)-compatible binary vectors for use in Agrobacterium-mediated transformation systems. It describes a fast, efficient, and robust cloning protocol for the production of an over-expression binary vector using Gateway(®) recombinational cloning.
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Affiliation(s)
- Mark A Smedley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK,
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47
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Abstract
RNA interference (RNAi) is one of the most popular and effective molecular technologies for knocking down the expression of an individual gene of interest in living organisms. Yet the technology still faces the major issue of nonspecific gene silencing, which can compromise gene functional characterization and the interpretation of phenotypes associated with individual gene knockdown. Designing an effective and target-specific small interfering RNA (siRNA) for induction of RNAi is therefore the major challenge in RNAi-based gene silencing. A 'good' siRNA molecule must possess three key features: (a) the ability to specifically silence an individual gene of interest, (b) little or no effect on the expressions of unintended siRNA gene targets (off-target genes), and (c) no cell toxicity. Although several siRNA design and analysis algorithms have been developed, only a few of them are specifically focused on gene silencing in plants. Furthermore, current algorithms lack a comprehensive consideration of siRNA specificity, efficacy, and nontoxicity in siRNA design, mainly due to lack of integration of all known rules that govern different steps in the RNAi pathway. In this review, we first describe popular RNAi methods that have been used for gene silencing in plants and their serious limitations regarding gene-silencing potency and specificity. We then present novel, rationale-based strategies in combination with computational and experimental approaches to induce potent, specific, and nontoxic gene silencing in plants.
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Affiliation(s)
- Firoz Ahmed
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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48
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Fernández-Calvino L, Osorio S, Hernández ML, Hamada IB, del Toro FJ, Donaire L, Yu A, Bustos R, Fernie AR, Martínez-Rivas JM, Llave C. Virus-induced alterations in primary metabolism modulate susceptibility to Tobacco rattle virus in Arabidopsis. PLANT PHYSIOLOGY 2014; 166:1821-38. [PMID: 25358898 PMCID: PMC4256867 DOI: 10.1104/pp.114.250340] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 10/30/2014] [Indexed: 05/20/2023]
Abstract
During compatible virus infections, plants respond by reprogramming gene expression and metabolite content. While gene expression studies are profuse, our knowledge of the metabolic changes that occur in the presence of the virus is limited. Here, we combine gene expression and metabolite profiling in Arabidopsis (Arabidopsis thaliana) infected with Tobacco rattle virus (TRV) in order to investigate the influence of primary metabolism on virus infection. Our results revealed that primary metabolism is reconfigured in many ways during TRV infection, as reflected by significant changes in the levels of sugars and amino acids. Multivariate data analysis revealed that these alterations were particularly conspicuous at the time points of maximal accumulation of TRV, although infection time was the dominant source of variance during the process. Furthermore, TRV caused changes in lipid and fatty acid composition in infected leaves. We found that several Arabidopsis mutants deficient in branched-chain amino acid catabolism or fatty acid metabolism possessed altered susceptibility to TRV. Finally, we showed that increments in the putrescine content in TRV-infected plants correlated with enhanced tolerance to freezing stress in TRV-infected plants and that impairment of putrescine biosynthesis promoted virus multiplication. Our results thus provide an interesting overview for a better understanding of the relationship between primary metabolism and virus infection.
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Affiliation(s)
- Lourdes Fernández-Calvino
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - Sonia Osorio
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - M Luisa Hernández
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - Ignacio B Hamada
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - Francisco J del Toro
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - Livia Donaire
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - Agnés Yu
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - Regla Bustos
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - Alisdair R Fernie
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - José M Martínez-Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
| | - César Llave
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain (L.F.-C., I.B.H., F.J.d.T., L.D., C.L.);Max Planck Institute for Molecular Plant Physiology, 14476 Postdam-Golm, Germany (S.O., A.R.F.);Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Seville, Spain (M.L.H., J.M.M.-R.);Unité de Recherche en Génomique Végétale, 91057 Evry cedex, France (A.Y.); andCentro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain (R.B.)
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49
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Van Hove J, Stefanowicz K, De Schutter K, Eggermont L, Lannoo N, Al Atalah B, Van Damme EJM. Transcriptional profiling of the lectin ArathEULS3 from Arabidopsis thaliana toward abiotic stresses. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1763-73. [PMID: 25238657 DOI: 10.1016/j.jplph.2014.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 05/04/2023]
Abstract
The family of EUL-related lectins groups all proteins with an Euonymus lectin (EUL) domain, a protein motif which is highly conserved throughout the plant kingdom and occurs as part of many chimeric proteins with different domain architectures. The S3 type EUL lectin from Arabidopsis thaliana (ArathEULS3) has become the model protein within this EUL family. Based on sequence homology to an ABA/NaCl inducible gene from rice and some publicly available high-throughput micro-array data, it was hypothesized that ArathEULS3 is transcriptionally regulated by osmotic stress responses. Here we present a detailed expression analysis of the ArathEULS3 lectin gene. Under normal growth conditions, ArathEULS3 is stably expressed throughout plant development. After ABA, NaCl and methyl jasmonate (MeJA) treatments transcription is upregulated. Furthermore, in silico promoter and co-expression analyses suggested the A. thaliana Homeobox 7 (ATHB-7) as a candidate transcription factor that may regulate ArathEULS3 expression. Taken together, our data confirm that the ArathEULS3 lectin gene indeed shows a stress-inducible expression pattern. We speculate on a role for ArathEULS3 in the plant stress response.
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Affiliation(s)
- J Van Hove
- Ghent University, Dept. Molecular Biotechnology, Lab of Biochemistry and Glycobiology, Coupure Links 653, 9000 Ghent, Belgium
| | - K Stefanowicz
- Ghent University, Dept. Molecular Biotechnology, Lab of Biochemistry and Glycobiology, Coupure Links 653, 9000 Ghent, Belgium
| | - K De Schutter
- Ghent University, Dept. Molecular Biotechnology, Lab of Biochemistry and Glycobiology, Coupure Links 653, 9000 Ghent, Belgium
| | - L Eggermont
- Ghent University, Dept. Molecular Biotechnology, Lab of Biochemistry and Glycobiology, Coupure Links 653, 9000 Ghent, Belgium
| | - N Lannoo
- Ghent University, Dept. Molecular Biotechnology, Lab of Biochemistry and Glycobiology, Coupure Links 653, 9000 Ghent, Belgium
| | - B Al Atalah
- Ghent University, Dept. Molecular Biotechnology, Lab of Biochemistry and Glycobiology, Coupure Links 653, 9000 Ghent, Belgium
| | - E J M Van Damme
- Ghent University, Dept. Molecular Biotechnology, Lab of Biochemistry and Glycobiology, Coupure Links 653, 9000 Ghent, Belgium.
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50
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Arias MC, Pelletier S, Hilliou F, Wattebled F, Renou JP, D'Hulst C. From dusk till dawn: the Arabidopsis thaliana sugar starving responsive network. FRONTIERS IN PLANT SCIENCE 2014; 5:482. [PMID: 25295047 PMCID: PMC4170100 DOI: 10.3389/fpls.2014.00482] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 08/31/2014] [Indexed: 05/28/2023]
Abstract
Plant growth and development are tightly controlled by photosynthetic carbon availability. The understanding of mechanisms governing carbon partitioning in plants will be a valuable tool in order to satisfy the rising global demand for food and biofuel. The goal of this study was to determine if sugar starvation responses were transcriptionally coordinated in Arabidopsis thaliana. A set of sugar-starvation responsive (SSR) genes was selected to perform a co-expression network analysis. Posteriorly, a guided-gene approach was used to identify the SSR-network from public data and to discover candidate regulators of this network. In order to validate the SSR network, a global transcriptome analysis was realized on three A. thaliana starch-deficient mutants. The starch-deficient phenotype in leaves induces sugar starvation syndrome at the end of the night due to the absence of photosynthesis. Promoter sequences of genes belonging to the SSR-network were analyzed in silico reveling over-represented motifs implicated in light, abscisic acid, and sugar responses. A small cluster of protein encoding genes belonging to different metabolic pathways, including three regulatory proteins, a protein kinase, a transcription factor, and a blue light receptor, were identified as the cornerstones of the SSR co-expression network. In summary, a large transcriptionally coordinated SSR network was identified and was validated with transcriptional data from three starch-deficient mutant lines. Candidate master regulators of this network were point out.
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Affiliation(s)
- Maria C. Arias
- Unité Glycobiologie Structurale et Fonctionnelle, UMR 8576-CNRS, Université de Lille 1Villeneuve d'Ascq, France
| | | | - Frédérique Hilliou
- Institut Sophia Agrobiotech, UMR 1355, Institut National de la Recherche AgronomiqueSophia-Antipolis, France
| | - Fabrice Wattebled
- Unité Glycobiologie Structurale et Fonctionnelle, UMR 8576-CNRS, Université de Lille 1Villeneuve d'Ascq, France
| | | | - Christophe D'Hulst
- Unité Glycobiologie Structurale et Fonctionnelle, UMR 8576-CNRS, Université de Lille 1Villeneuve d'Ascq, France
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