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  • Omidbakhshfard, Mohammad Amin (6)
  • Brotman, Yariv (3)
  • Fernie, Alisdair R. (3)
  • Gechev, Tsanko S. (3)
  • Gupta, Saurabh (3)
  • Müller-Röber, Bernd (3)
  • Guinan, Kieran J. (2)
  • Mueller-Roeber, Bernd (2)
  • Nikoloski, Zoran (2)
  • Omranian, Nooshin (2)
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  • 2020 (2)
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  • Arabidopsis thaliana (3)
  • Ascophyllum nodosum (2)
  • biostimulant (2)
  • oxidative stress tolerance (2)
  • paraquat (2)
  • priming (2)
  • reactive oxygen species (2)
  • FAIRE-qPCR (1)
  • FAIRE-seq (1)
  • abiotic stress (1)
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  • Institut für Biochemie und Biologie (3)
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Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology (2015)
Omidbakhshfard, Mohammad Amin ; Proost, Sebastian ; Fujikura, Ushio ; Müller-Röber, Bernd
Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.
A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana (2014)
Omidbakhshfard, Mohammad Amin ; Winck, Flavia Vischi ; Arvidsson, Samuel Janne ; Riano-Pachon, Diego M. ; Müller-Röber, Bernd
The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.
Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana (2014)
Omidbakhshfard, Mohammad Amin
Molecular mechanisms preventing senescence in response to prolonged darkness in a desiccation-tolerant plant (2018)
Durgud, Meriem ; Gupta, Saurabh ; Ivanov, Ivan ; Omidbakhshfard, Mohammad Amin ; Benina, Maria ; Alseekh, Saleh ; Staykov, Nikola ; Hauenstein, Mareike ; Dijkwel, Paul P. ; Hortensteiner, Stefan ; Toneva, Valentina ; Brotman, Yariv ; Fernie, Alisdair R. ; Müller-Röber, Bernd ; Gechev, Tsanko S.
The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress-and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast-and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis-and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.
A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress (2020)
Omidbakhshfard, Mohammad Amin ; Sujeeth, Neerakkal ; Gupta, Saurabh ; Omranian, Nooshin ; Guinan, Kieran J. ; Brotman, Yariv ; Nikoloski, Zoran ; Fernie, Alisdair R. ; Mueller-Roeber, Bernd ; Gechev, Tsanko S.
Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.
A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress (2020)
Omidbakhshfard, Mohammad Amin ; Sujeeth, Neerakkal ; Gupta, Saurabh ; Omranian, Nooshin ; Guinan, Kieran J. ; Brotman, Yariv ; Nikoloski, Zoran ; Fernie, Alisdair R. ; Mueller-Roeber, Bernd ; Gechev, Tsanko S.
Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.
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