Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis

Reactive oxygen species ( ROS) are key players in the regulation of plant development, stress responses, and programmed cell death. Previous studies indicated that depending on the type of ROS ( hydrogen peroxide, superoxide, or singlet oxygen) or its subcellular production site ( plastidic, cytosolic, peroxisomal, or apoplastic), a different physiological, biochemical, and molecular response is provoked. We used transcriptome data generated from ROS-related microarray experiments to assess the specificity of ROS-driven transcript expression. Data sets obtained by exogenous application of oxidative stress-causing agents ( methyl viologen, Alternaria alternata toxin, 3-aminotriazole, and ozone) and from a mutant ( fluorescent) and transgenic plants, in which the activity of an individual antioxidant enzyme was perturbed ( catalase, cytosolic ascorbate peroxidase, and copper/zinc superoxide dismutase), were compared. In total, the abundance of nearly 26,000 transcripts of Arabidopsis ( Arabidopsis thaliana) was monitored in response to different ROS. Overall, 8,056, 5,312, and 3,925 transcripts showed at least a 3-, 4-, or 5- fold change in expression, respectively. In addition to marker transcripts that were specifically regulated by hydrogen peroxide, superoxide, or singlet oxygen, several transcripts were identified as general oxidative stress response markers because their steady-state levels were at least 5- fold elevated in most experiments. We also assessed the expression characteristics of all annotated transcription factors and inferred new candidate regulatory transcripts that could be responsible for orchestrating the specific transcriptomic signatures triggered by different ROS. Our analysis provides a framework that will assist future efforts to address the impact of ROS signals within environmental stress conditions and elucidate the molecular mechanisms of the oxidative stress response in plants

Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism

Companion cells and sieve elements play an essential role in vascular plants, and yet the details of the metabolism that underpins their function remain largely unknown. Here, we construct a tissue-scale flux balance analysis (FBA) model to describe the metabolism of phloem loading in a mature Arabidopsis (Arabidopsis thaliana) leaf. We explore the potential metabolic interactions between mesophyll cells, companion cells, and sieve elements based on the current understanding of the physiology of phloem tissue and through the use of cell type–specific transcriptome data as a weighting in our model. We find that companion cell chloroplasts likely play a very different role to mesophyll chloroplasts. Our model suggests that, rather than carbon capture, the most crucial function of companion cell chloroplasts is to provide photosynthetically generated ATP to the cytosol. Additionally, our model predicts that the metabolites imported into the companion cell are not necessarily the same metabolites that are exported in phloem sap; phloem loading is more efficient if certain amino acids are synthesized in the phloem tissue. Surprisingly, in our model predictions, the proton-pumping pyrophosphatase (H+-PPiase) is a more efficient contributor to the energization of the companion cell plasma membrane than the H+-ATPase

Unraveling hydrogen peroxide signaling in Arabidopsis thaliana

Reactive oxygen species (ROS) are toxic molecules that, at high concentrations, result in non-controlled oxidation of a variety of cellular structures, which ultimately lead to disruption of metabolism and destruction of cellular structures. Because plant cells are continuously generating ROS as products of normal aerobic metabolism, it is not surprising that plants also possess a range of antioxidant mechanisms to prevent ROS from reaching destructive levels. However, ROS are far more important to plant biology than simply as toxic by-products and agents of cellular damage. At low concentrations, they are key signaling molecules that regulate growth and development and coordinate responses to biotic and abiotic stress. At the beginning of my PhD, evidence on the importance of ROS as cellular regulators was starting to emerge and the primary objective of the work presented here was to extend this knowledge by means of large-scale identification of H2O2-responsive transcripts in catalase-deficient Arabidopsis thaliana. Similar to catalase-deficient tobacco plants, these plants are an ideal tool to modulate H2O2 levels in planta. Not only were these large-scale transcriptome analyses designed to provide a comprehensive inventory, but also to reveal specific biological processes in which H2O2 is involved. Moreover, they aimed to elucidate interesting candidates for further molecular-genetic characterization

Hydrogen peroxide-responsive genes in stress acclimation and cell death

Reactive oxygen species (ROS) are key signalling molecules that regulate growth and development and coordinate responses to biotic and abiotic stresses. ROS homeostasis is controlled through a complex network of ROS production and scavenging enzymes. Recently, the first genes involved in ROS perception and signal transduction have been identified and, currently, we are facing the challenge to uncover the other players within the ROS regulatory gene network. The specificity of ensuing cellular responses depends on the type of ROS and their subcellular production sites. Various experimental systems, including catalase-deficient plants, in combination with genome-wide expression studies demonstrated that increased hydrogen peroxide (H2O2) levels significantly affect the transcriptome of plants and are capable of launching both defence responses and cell death events. A comparative analysis between H2O2-induced transcriptional changes and those provoked by different environmental stresses, not only consolidated a prominent role for H2O2 signalling in stress acclimation, but also allowed the identification of new candidate regulatory genes within the plant's abiotic stress response

Unraveling regulatory gene networks involving hydrogen peroxide in plants

Reactive oxygen species (ROS) are key signalling molecules that regulate growth and development and coordinate responses to biotic and abiotic stresses. ROS homeostasis is controlled through a complex network of ROS production and scavenging enzymes. Recently, the first genes involved in ROS perception and signal transduction have been identified and, currently, we are facing the challenge to uncover the other players within the ROS regulatory gene network. The specificity of ensuing cellular responses depends on the type of ROS and their subcellular production sites. Various experimental systems, including catalase-deficient plants, in combination with genome-wide expression studies demonstrated that increased hydrogen peroxide (H2O2) levels significantly affect the transcriptome of plants and are capable of launching both defence responses and cell death events. A comparative analysis between H2O2-induced transcriptional changes and those provoked by different environmental stresses, not only consolidated a prominent role for H2O2 signalling in stress acclimation, but also allowed the identification of new candidate regulatory genes within the plant’s abiotic stress response

Reactive oxygen gene network of plants

Reactive oxygen species (ROS) control many different processes in plants. However, being toxic molecules, they are also capable of injuring cells. How this conflict is resolved in plants is largely unknown. Nonetheless, it is clear that the steady-state level of ROS in cells needs to be tightly regulated. In Arabidopsis, a network of at least 152 genes is involved in managing the level of ROS. This network is highly dynamic and redundant, and encodes ROS-scavenging and ROS-producing proteins. Although recent studies have unraveled some of the key players in the network, many questions related to its mode of regulation, its protective roles and its modulation of signaling networks that control growth, development and stress response remain unanswered

Unraveling hydrogen peroxide signaling in Arabidopsis thaliana /

Diss. doct. wetenschappen: biotechnologi

Catalase function in plants: a focus on Arabidopsis mutants as stress-mimic models

Hydrogen peroxide (H2O2) is an important signal molecule involved in plant development and environmental responses. Changes in H2O2 availability can result from increased production or decreased metabolism. While plants contain several types of H2O2-metabolizing proteins, catalases are highly active enzymes that do not require cellular reductants as they primarily catalyse a dismutase reaction. This review provides an update on plant catalase genes, function, and subcellular localization, with a focus on recent information generated from studies on Arabidopsis. Original data are presented on Arabidopsis catalase single and double mutants, and the use of some of these lines as model systems to investigate the outcome of increases in intracellular H2O2 are discussed. Particular attention is paid to interactions with cell thiol-disulphide status; the use of catalase-deficient plants to probe the apparent redundancy of reductive H2O2-metabolizing pathways; the importance of irradiance and growth daylength in determining the outcomes of catalase deficiency; and the induction of pathogenesis-related responses in catalase-deficient lines. Within the context of strategies aimed at understanding and engineering plant stress responses, the review also considers whether changes in catalase activities in wild-type plants are likely to be a significant part of plant responses to changes in environmental conditions or biotic challenge