The Experts below are selected from a list of 26298 Experts worldwide ranked by ideXlab platform
Tobias Dörr - One of the best experts on this subject based on the ideXlab platform.
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endopeptidase regulation as a novel function of the zur dependent zinc Starvation Response
Mbio, 2019Co-Authors: Shannon G. Murphy, Laura Alvarez, Myfanwy C. Adams, Shuning Liu, Joshua S. Chappie, Felipe Cava, Tobias DörrAbstract:The cell wall is a strong, yet flexible, meshwork of peptidoglycan (PG) that gives a bacterium structural integrity. To accommodate a growing cell, the wall is remodeled by both PG synthesis and de ...
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Endopeptidase regulation as a novel function of the Zur-dependent zinc Starvation Response
2018Co-Authors: Shannon G. Murphy, Laura Alvarez, Myfanwy C. Adams, Shuning Liu, Joshua S. Chappie, Felipe Cava, Tobias DörrAbstract:Abstract The cell wall is a strong, yet flexible, meshwork of peptidoglycan (PG) that gives a bacterium structural integrity. To accommodate a growing cell, the wall is remodeled by both PG synthesis and degradation. Vibrio cholerae encodes a group of three nearly identical zinc-dependent endopeptidases (EPs) that hydrolyze PG to facilitate cell growth. Two of these (shyA and shyC) are housekeeping genes and form a synthetic lethal pair, while the third (shyB) is not expressed under standard laboratory conditions. To investigate the role of ShyB, we conducted a transposon screen to identify mutations that activate shyB transcription. We found that shyB is induced as part of the Zur-mediated zinc Starvation Response, a mode of regulation not previously reported for cell wall lytic enzymes. In vivo, ShyB alone was sufficient to sustain cell growth in low-zinc environments. In vitro, ShyB retained its D,D-endopeptidase activity against purified sacculi in the presence of the metal chelator EDTA at a concentration that inhibits ShyA and ShyC. This suggests that ShyB can substitute for the other EPs during zinc Starvation, a condition that pathogens encounter while infecting a human host. Our survey of transcriptomic data from diverse bacteria identified other candidate Zur-regulated endopeptidases, suggesting that this adaptation to zinc Starvation is conserved in other Gram-negative bacteria. Importance The human host sequesters zinc and other essential metals in order to restrict growth of potentially harmful bacteria. In Response, invading bacteria express a set of genes enabling them to cope with zinc Starvation. In Vibrio cholerae, the causative agent of the diarrheal disease cholera, we have identified a novel member of this zinc Starvation Response: a cell wall hydrolase that retains function in low-zinc environments and is conditionally essential for cell growth. Other human pathogens contain homologs that appear to be under similar regulatory control. These findings are significant because they represent, to our knowledge, the first evidence that zinc homeostasis influences cell wall turnover. Anti-infective therapies commonly target the bacterial cell wall and, therefore, an improved understanding of how the cell wall adapts to host-induced zinc Starvation could lead to new antibiotic development. Such therapeutic interventions are required to combat the rising threat of drug resistant infections.
Vera Meyer - One of the best experts on this subject based on the ideXlab platform.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome
BMC genomics, 2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera Meyer, Arthur F. J. RamAbstract:Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening Starvation conditions, carbon from endogenous resources becomes mobilized to fuel maintenance and self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal Starvation Responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon Starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon Starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential gene expression during at least one of the Starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. This study is the first system-wide analysis of the carbon Starvation Response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome
BMC Genomics, 2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera MeyerAbstract:Background Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening Starvation conditions, carbon from endogenous resources becomes mobilized to fuel maintenance and self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal Starvation Responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. Results This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon Starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger . Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon Starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential gene expression during at least one of the Starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. Conclusions This study is the first system-wide analysis of the carbon Starvation Response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation
2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera Meyer, Arthur F. J. RamAbstract:Published by BioMed Central Nitsche, Benjamin M. ; Jorgensen, Thomas R. ; Akeroyd, Michiel ; Meyer, Vera ; Ram, Arthur F.J. : The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome. - In: BMC Genomics. - ISSN 1471-2164 (online). - 13 (2012), art. 380. - doi:10.1186/1471-2164-13-380.
Benjamin M. Nitsche - One of the best experts on this subject based on the ideXlab platform.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome
BMC genomics, 2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera Meyer, Arthur F. J. RamAbstract:Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening Starvation conditions, carbon from endogenous resources becomes mobilized to fuel maintenance and self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal Starvation Responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon Starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon Starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential gene expression during at least one of the Starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. This study is the first system-wide analysis of the carbon Starvation Response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome
BMC Genomics, 2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera MeyerAbstract:Background Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening Starvation conditions, carbon from endogenous resources becomes mobilized to fuel maintenance and self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal Starvation Responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. Results This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon Starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger . Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon Starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential gene expression during at least one of the Starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. Conclusions This study is the first system-wide analysis of the carbon Starvation Response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation
2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera Meyer, Arthur F. J. RamAbstract:Published by BioMed Central Nitsche, Benjamin M. ; Jorgensen, Thomas R. ; Akeroyd, Michiel ; Meyer, Vera ; Ram, Arthur F.J. : The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome. - In: BMC Genomics. - ISSN 1471-2164 (online). - 13 (2012), art. 380. - doi:10.1186/1471-2164-13-380.
Frédéric Gaymard - One of the best experts on this subject based on the ideXlab platform.
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HRS1/HHOs GARP transcription factors and reactive oxygen species are regulators of Arabidopsis nitrogen Starvation Response. Affiliation
2018Co-Authors: Alaeddine Safi, Frédéric Gaymard, Anna Medici, Wojciech Szponarski, Benoît Lacombe, Sandrine Ruffel, Amy Marshall-colon, Gloria M. Coruzzi, Gabriel KroukAbstract:Plants need to cope with strong variations in the nitrogen content of the soil solution. Although many molecular actors are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of Nitrogen. Indeed, following N removal plants activate their Nitrogen Starvation Response (NSR) being characterized in particular by the activation of very high affinity nitrate transport systems (NRT2.4, NRT2.5) and other sentinel genes such as GDH3. Here we show using a combination of functional genomics (via TF perturbation) and molecular physiology studies, that the GARP Transcription Factors (TFs) belonging the HHO sub-family are important regulators of the NSR through two potential mechanisms. First, HHOs directly repress NRT2.4 and NRT2.5 high-affinity nitrate transporters. Genotypes affected in HHO genes (mutants and overexpressors) display modified high-affinity nitrate transport activities opening interesting perspectives in biotechnology applications. Second, we show that Reactive Oxygen Species (ROS) are important to control NSR in wild type plants and that HRS1 and HHO1 overexpressors are affected in their ROS content, defining a potential feedforward branch of the signaling pathway. Taken together our results define two new classes of molecular actors in the control of NSR including ROS and the first transcription factors to date. This work (i) opens perspectives on a poorly understood nutrient related signaling pathway, and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.
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Integration of P, S, Fe, and Zn nutrition signals in Arabidopsis thaliana: potential involvement of PHOSPHATE Starvation Response 1 (PHR1).
Frontiers in plant science, 2015Co-Authors: Jean-françois Briat, Frédéric Gaymard, Nicolas Tissot, Hatem Rouached, Christian DubosAbstract:Phosphate and sulfate are essential macro-elements for plant growth and development, and deficiencies in these mineral elements alter many metabolic functions. Nutritional constraints are not restricted to macro-elements. Essential metals such as zinc and iron have their homeostasis strictly genetically controlled, and deficiency or excess of these micro-elements can generate major physiological disorders, also impacting plant growth and development. Phosphate and sulfate on one hand, and zinc and iron on the other hand, are known to interact. These interactions have been partly described at the molecular and physiological levels, and are reviewed here. Furthermore the two macro-elements phosphate and sulfate not only interact between themselves but also influence zinc and iron nutrition. These intricated nutritional cross-talks are presented. The Responses of plants to phosphorus, sulfur, zinc, or iron deficiencies have been widely studied considering each element separately, and some molecular actors of these regulations have been characterized in detail. Although some scarce reports have started to examine the interaction of these mineral elements two by two, a more complex analysis of the interactions and cross-talks between the signaling pathways integrating the homeostasis of these various elements is still lacking. However, a MYB-like transcription factor, PHOSPHATE Starvation Response 1, emerges as a common regulator of phosphate, sulfate, zinc, and iron homeostasis, and its role as a potential general integrator for the control of mineral nutrition is discussed.
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Arabidopsis Ferritin 1 (AtFer1) Gene Regulation by the Phosphate Starvation Response 1 (AtPHR1) Transcription Factor Reveals a Direct Molecular Link between Iron and Phosphate Homeostasis.
Journal of Biological Chemistry, 2013Co-Authors: Marc Bournier, Jean-françois Briat, Jossia Boucherez, Nicolas Tissot, Stéphane Mari, Eric Lacombe, Frédéric GaymardAbstract:A yeast one-hybrid screening allowed the selection of PHR1 as a factor that interacted with the AtFer1 ferritin gene promoter. In mobility shift assays, PHR1 and its close homologue PHL1 (PHR1-like 1) interact with Element 2 of the AtFer1 promoter, containing a P1BS (PHR1 binding site). In a loss of function mutant for genes encoding PHR1 and PHL1 (phr1 phl1 mutant), the Response of AtFer1 to phosphate Starvation was completely lost, showing that the two transcription factors regulate AtFer1 expression upon phosphate Starvation. This regulation does not involve the IDRS (iron-dependent regulatory sequence) present in the AtFer1 promoter and involved in the iron-dependent regulation. The phosphate Starvation Response of AtFer1 is not linked to the iron status of plants and is specifically initiated by phosphate deficiency. Histochemical localization of iron, visualized by Perls DAB staining, was strongly altered in a phr1 phl1 mutant, revealing that both PHR1 and PHL1 are major factors involved in the regulation of iron homeostasis.
Arthur F. J. Ram - One of the best experts on this subject based on the ideXlab platform.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome
BMC genomics, 2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera Meyer, Arthur F. J. RamAbstract:Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening Starvation conditions, carbon from endogenous resources becomes mobilized to fuel maintenance and self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal Starvation Responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon Starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon Starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential gene expression during at least one of the Starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. This study is the first system-wide analysis of the carbon Starvation Response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.
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The carbon Starvation Response of Aspergillus niger during submerged cultivation
2012Co-Authors: Benjamin M. Nitsche, Thomas R. Jørgensen, Michiel Akeroyd, Vera Meyer, Arthur F. J. RamAbstract:Published by BioMed Central Nitsche, Benjamin M. ; Jorgensen, Thomas R. ; Akeroyd, Michiel ; Meyer, Vera ; Ram, Arthur F.J. : The carbon Starvation Response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome. - In: BMC Genomics. - ISSN 1471-2164 (online). - 13 (2012), art. 380. - doi:10.1186/1471-2164-13-380.