152 research outputs found
Novel Regulators in Photosynthetic Redox Control of Plant Metabolism and Gene Expression
No full textDietz K-J, Pfannschmidt T. Novel Regulators in Photosynthetic Redox Control of Plant Metabolism and Gene Expression. Plant Physiology. 2011;155(4):1477-1485
Arabidopsis STN7 Kinase Provides a Link between Short- and Long-Term Photosynthetic Acclimation
No full textFlowering plants control energy allocation to their photosystems in response to light quality changes. This includes the phosphorylation and migration of light-harvesting complex II (LHCII) proteins (state transitions or short-term response) as well as long-term alterations in thylakoid composition (long-term response or LTR). Both responses require the thylakoid protein kinase STN7. Here, we show that the signaling pathways triggering state transitions and LTR diverge at, or immediately downstream from, STN7. Both responses require STN7 activity that can be regulated according to the plastoquinone pool redox state. However, LTR signaling does not involve LHCII phosphorylation or any other state transition step. State transitions appear to play a prominent role in flowering plants, and the ability to perform state transitions becomes critical for photosynthesis in Arabidopsis thaliana mutants that are impaired in thylakoid electron transport but retain a functional LTR. Our data imply that STN7-dependent phosphorylation of an as yet unknown thylakoid protein triggers LTR signaling events, whereby an involvement of the TSP9 protein in the signaling pathway could be excluded. The LTR signaling events then ultimately regulate in chloroplasts the expression of photosynthesis-related genes on the transcript level, whereas expression of nuclear-encoded proteins is regulated at multiple levels, as indicated by transcript and protein profiling in LTR mutants
Retrograde signals from endosymbiotic organelles: a common control principle in eukaryotic cells
No full textEndosymbiotic organelles of eukaryotic cells, the plastids, including chloroplasts and mitochondria, are highly integrated into cellular signalling networks. In both heterotrophic and autotrophic organisms, plastids and/or mitochondria require extensive organelle-to-nucleus communication in order to establish a coordinated expression of their own genomes with the nuclear genome, which encodes the majority of the components of these organelles. This goal is achieved by the use of a variety of signals that inform the cell nucleus about the number and developmental status of the organelles and their reaction to changing external environments. Such signals have been identified in both photosynthetic and non-photosynthetic eukaryotes (known as retrograde signalling and retrograde response, respectively) and, therefore, appear to be universal mechanisms acting in eukaryotes of all kingdoms. In particular, chloroplasts and mitochondria both harbour crucial redox reactions that are the basis of eukaryotic life and are, therefore, especially susceptible to stress from the environment, which they signal to the rest of the cell. These signals are crucial for cell survival, lifespan and environmental adjustment, and regulate quality control and targeted degradation of dysfunctional organelles, metabolic adjustments, and developmental signalling, as well as induction of apoptosis. The functional similarities between retrograde signalling pathways in autotrophic and non-autotrophic organisms are striking, suggesting the existence of common principles in signalling mechanisms or similarities in their evolution. Here, we provide a survey for the newcomers to this field of research and discuss the importance of retrograde signalling in the context of eukaryotic evolution. Furthermore, we discuss commonalities and differences in retrograde signalling mechanisms and propose retrograde signalling as a general signalling mechanism in eukaryotic cells that will be also of interest for the specialist. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.</p
Feature Relevance Bounds for Ordinal Regression
No full textPfannschmidt L, Jakob J, Biehl M, Tino P, Hammer B. Feature Relevance Bounds for Ordinal Regression. In: Verleysen M, ed. Proceedings of the 27th European Symposium on Artificial Neural Networks (ESANN 2019). Louvain-la-Neuve: i6doc; 2019.The increasing occurrence of ordinal data, mainly sociodemographic, led to a
renewed research interest in ordinal regression, i.e. the prediction of ordered
classes. Besides model accuracy, the interpretation of these models itself is
of high relevance, and existing approaches therefore enforce e.g. model
sparsity. For high dimensional or highly correlated data, however, this might
be misleading due to strong variable dependencies. In this contribution, we aim
for an identification of feature relevance bounds which - besides identifying
all relevant features - explicitly differentiates between strongly and weakly
relevant features
Reactive oxygen species modulate HIF-1 mediated PAI-1 expression: involvement of the GTPase Rac1
No full textThe hypoxia-inducible transcription factor HIF-1 mediates upregulation of plasminogen activator inhibitor-1 (PAI-1) expression under hypoxia. Reactive oxygen species (ROS) have also been implicated in PAI-1 gene expression. However, the role of ROS in HIF-1-mediated regulation of PAI-1 is not clear. We therefore investigated the role of the GTPase Rac1 which modulates ROS production in the pathway leading to HIF-1 and PAI-1 induction. . Overexpression of constitutively activated (RacG12V) or dominant-negative (RacT17N) Rac1 increased or decreased, respectively, ROS production. In RacG12V-expressing cells, PAI-1 mRNA levels as well as HIF-1alpha nuclear presence were reduced under normoxia and hypoxia whereas expression of RacT17N resulted in opposite effects. Treatment with the antioxidant pyrrolidinedithiocarbamate or coexpression of the redox factor-1 restored HIF-1 and PAI-1 promoter activity in RacG12V-cells. In contrast, NFkappaB activation was enhanced in RacG12V-cells, but abolished by RacT17N. Thus, these findings suggest a mechanism explaining modified fibrinolysis and tissue remodeling in an oxidized environment
Discrete Redox Signaling Pathways Regulate Photosynthetic Light-Harvesting and Chloroplast Gene Transcription
No full textThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Piriformospora indica released factors and its role in the molecular interaction with Arabidopsis thaliana
No full textThe interaction between P. indica and A. thaliana results in growth promotion and enhanced seed production. I studied the role of various P. indica-released factors in the interaction and the signalling pathways they activate. We describe the isolation of a growth-promoting factor from the cell wall of P. indica. The cell wall extract (CWE) induces a transient cytosolic Ca2+ elevation in the roots of Arabidopsis and tobacco plants expressing the Ca2+ bioluminescent indicator aequorin. The CWE and the fungus induce a similar set of genes in Arabidopsis roots, among them are genes with Ca2+ signalling-related functions. The CWE does not promote growth of P. indica insensitive lines and the growth promotion is abolished if the Ca2+ inhibitor BAPTA is added. The cellular Ca2+ elevations and are thus crucial for growth promotion, and Ca2+ signalling pathways are activated by incoming fungus. The CWE does not stimulate H2O2 production and the activation of defence gene expression, although it led to phosphorylation of mitogen-activated protein kinases (MAPKs) in a Ca2+-dependent manner. Thus, Ca2+ is likely to be an early signalling component in the mutualistic interaction between P. indica and A. thaliana similar to other interactions like AM symbiosis. P. indica releases isopentenyl-adenine (iP) and cis-Zeatin (cZ)-type cytokinins into axenic cultures, but elevated levels of cis Zeatin (cZ) isomers accumulate in colonized roots. However, our data clearly demonstrate that trans-zeatin (tZ) biosynthesis in Arabidopsis is required for the beneficial interaction as knocking out atipt1 atipt3 atipt5 atipt7 genes required for (tZ) biosynthesis results in no response to the fungus. The double mutant cre1ahk2 shows no growth response to P. indica. The CRE1 AHK2 receptor combination is thus crucial for the response to P. indica
Feature Relevance Determination for Ordinal Regression in the Context of Feature Redundancies and Privileged Information
No full textPfannschmidt L, Jakob J, Hinder F, Biehl M, Tino P, Hammer B. Feature Relevance Determination for Ordinal Regression in the Context of Feature Redundancies and Privileged Information. Neurocomputing. 2020.Advances in machine learning technologies have led to increasingly powerful
models in particular in the context of big data. Yet, many application
scenarios demand for robustly interpretable models rather than optimum model
accuracy; as an example, this is the case if potential biomarkers or causal
factors should be discovered based on a set of given measurements. In this
contribution, we focus on feature selection paradigms, which enable us to
uncover relevant factors of a given regularity based on a sparse model. We
focus on the important specific setting of linear ordinal regression, i.e.
data have to be ranked into one of a finite number of ordered categories by a
linear projection. Unlike previous work, we consider the case that features are
potentially redundant, such that no unique minimum set of relevant features
exists. We aim for an identification of all strongly and all weakly relevant
features as well as their type of relevance (strong or weak); we achieve this
goal by determining feature relevance bounds, which correspond to the minimum
and maximum feature relevance, respectively, if searched over all equivalent
models. In addition, we discuss how this setting enables us to substitute some
of the features, e.g. due to their semantics, and how to extend the framework
of feature relevance intervals to the setting of privileged information, i.e.
potentially relevant information is available for training purposes only, but
cannot be used for the prediction itself
Dynamic plastid redox signals integrate gene expression and metabolism to induce distinct metabolic states in photosynthetic acclimation in Arabidopsis
No full textPlants possess acclimation responses in which structural reconfigurations adapt the photosynthetic apparatus to fluctuating illumination. Long-term acclimation involves changes in plastid and nuclear gene expression and is controlled by redox signals from photosynthesis. The kinetics of these signals and the adjustments of energetic and metabolic demands to the changes in the photosynthetic apparatus are currently poorly understood. Using a redox signaling system that preferentially excites either photosystem I or II, we measured the time-dependent impact of redox signals on the transcriptome and metabolome of Arabidopsis thaliana. We observed rapid and dynamic changes in nuclear transcript accumulation resulting in differential and specific expression patterns for genes associated with photosynthesis and metabolism. Metabolite pools also exhibited dynamic changes and indicate readjustments between distinct metabolic states depending on the respective illumination. These states reflect reallocation of energy resources in a defined and reversible manner, indicating that structural changes in the photosynthetic apparatus during long-term acclimation are additionally supported at the level of metabolism. We propose that photosynthesis can act as an environmental sensor, producing retrograde redox signals that trigger two parallel adjustment loops that coordinate photosynthesis and metabolism to adapt plant primary productivity to the environment
- …
