Modeling the reactive oxygen species (ROS) wave in Chlamydomonas reinhardtii colonies.

Reactive oxygen species (ROS) play a crucial role as signaling molecules in both plant and animal cells, enabling rapid responses to various stimuli. Among the many cellular mechanisms used to generate and transduce ROS signals, ROS-induced-ROS release (RIRR) is emerging as an important pathway involved in the responses of various multicellular and unicellular organisms to environmental stresses. In RIRR, one cellular compartment, organelle, or cell generates or releases ROS, triggering an increased ROS production and release by another compartment, organelle, or cell, thereby giving rise to a fast propagating ROS wave. This RIRR-based signal relay has been demonstrated to facilitate mitochondria-to-mitochondria communication in animal cells and long-distance systemic signaling in plants in response to biotic and abiotic stresses. More recently, it has been discovered that different unicellular microorganism communities also exhibit a RIRR cell-to-cell signaling process triggered by a localized stress treatment. However, the precise mechanism underlying the propagation of the ROS signal among cells within these unicellular communities remained elusive. In this study, we employed a reaction-diffusion model incorporating the RIRR mechanism to analyze the propagation of ROS-mediated signals. By effectively balancing production and scavenging processes, our model successfully reproduces the experimental ROS signal velocities observed in unicellular green algae (Chlamydomonas reinhardtii) colonies grown on agar plates, furthering our understanding of intercellular ROS communication.

CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance.

Mitochondria play a central role in muscle metabolism and function. A unique family of iron-sulfur proteins, termed CDGSH Iron Sulfur Domain-containing (CISD/NEET) proteins, support mitochondrial function in skeletal muscles. The abundance of these proteins declines during aging leading to muscle degeneration. Although the function of the outer mitochondrial CISD/NEET proteins, CISD1/mitoNEET and CISD2/NAF-1, has been defined in skeletal muscle cells, the role of the inner mitochondrial CISD protein, CISD3/MiNT, is currently unknown. Here, we show that CISD3 deficiency in mice results in muscle atrophy that shares proteomic features with Duchenne muscular dystrophy. We further reveal that CISD3 deficiency impairs the function and structure of skeletal muscles, as well as their mitochondria, and that CISD3 interacts with, and donates its [2Fe-2S] clusters to, complex I respiratory chain subunit NADH Ubiquinone Oxidoreductase Core Subunit V2 (NDUFV2). Using coevolutionary and structural computational tools, we model a CISD3-NDUFV2 complex with proximal coevolving residue interactions conducive of [2Fe-2S] cluster transfer reactions, placing the clusters of the two proteins 10 to 16 Å apart. Taken together, our findings reveal that CISD3/MiNT is important for supporting the biogenesis and function of complex I, essential for muscle maintenance and function. Interventions that target CISD3 could therefore impact different muscle degeneration syndromes, aging, and related conditions.

ROS are universal cell-to-cell stress signals.

The interplay between reactive oxygen species (ROS) and the redox state of cells is deeply rooted in the biology of almost all organisms, regulating development, growth, and responses to the environment. Recent studies revealed that the ROS levels and redox state of one cell can be transmitted, as an information 'state' or 'currency', to other cells and spread by cell-to-cell communication within an entire community of cells or an organism. Here, we discuss the different pathways that mediate cell-to-cell signaling in plants, their hierarchy, and the different mechanisms that transmit ROS/redox signaling between different cells. We further hypothesize that ROS/redox signaling between different organisms could play a key role within the 'one world' principle, impacting human health and our future.

Higher Intensity of Salt Stress Accompanied by Heat Inhibits Stomatal Conductance and Induces ROS Accumulation in Tomato Plants.

Under natural conditions, abiotic stresses that limit plant growth and development tend to occur simultaneously, rather than individually. Due to global warming and climate change, the frequency and intensity of heat and salt stresses are becoming more frequent. Our aim is to determine the response mechanisms of tomato to different intensities of combined heat and salt stresses. The physiological and morphological responses and photosynthesis/reactive oxygen species (ROS)-related genes of tomato plants were compared under a control, heat stress, salt stress (50/100/200/400 mM NaCl), and a combination of salt and heat stresses. The stomatal conductance (gs) of tomato leaves significantly increased at a heat + 50 mM NaCl treatment on day 4, but significantly decreased at heat + 100/200/400 mM NaCl treatments, compared with the control on days 4 and 8. The O2·- production rate of tomato plants was significantly higher at heat + 100/200/400 mM NaCl than the control, which showed no significant difference between heat + 50 mM NaCl treatment and the control on days 4 and 8. Ascorbate peroxidase 2 was significantly upregulated by heat + 100/200/400 mM NaCl treatment as compared with heat + 50 mM NaCl treatment on days 4 and 8. This study demonstrated that the dominant effect ratio of combined heat and salt stress on tomato plants can shift from heat to salt, when the intensity of salt stress increased from 50 mM to 100 mM or above. This study provides important information for tomato tolerance improvement at combined heat and salt stresses.

Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using the Arabidopsis thaliana Genome.

The utmost goal of selecting an RNA-Seq alignment software is to perform accurate alignments with a robust algorithm, which is capable of detecting the various intricacies underlying read-mapping procedures and beyond. Most alignment software tools are typically pre-tuned with human or prokaryotic data, and therefore may not be suitable for applications to other organisms, such as plants. The rapidly growing plant RNA-Seq databases call for the assessment of the alignment tools on curated plant data, which will aid the calibration of these tools for applications to plant transcriptomic data. We therefore focused here on benchmarking RNA-Seq read alignment tools, using simulated data derived from the model organism Arabidopsis thaliana. We assessed the performance of five popular RNA-Seq alignment tools that are currently available, based on their usage (citation count). By introducing annotated single nucleotide polymorphisms (SNPs) from The Arabidopsis Information Resource (TAIR), we recorded alignment accuracy at both base-level and junction base-level resolutions for each alignment tool. In addition to assessing the performance of the alignment tools at their default settings, accuracies were also recorded by varying the values of numerous parameters, including the confidence threshold and the level of SNP introduction. The performances of the aligners were found consistent under various testing conditions at the base-level accuracy; however, the junction base-level assessment produced varying results depending upon the applied algorithm. At the read base-level assessment, the overall performance of the aligner STAR was superior to other aligners, with the overall accuracy reaching over 90% under different test conditions. On the other hand, at the junction base-level assessment, SubRead emerged as the most promising aligner, with an overall accuracy over 80% under most test conditions.

Propagation of a rapid cell-to-cell H2O2 signal over long distances in a monolayer of cardiomyocyte cells.

Cell-to-cell communication plays a cardinal role in the biology of multicellular organisms. H2O2 is an important cell-to-cell signaling molecule involved in the response of mammalian cells to wounding and other stimuli. We previously identified a signaling pathway that transmits wound-induced cell-to-cell H2O2 signals within minutes over long distances, measured in centimeters, in a monolayer of cardiomyocytes. Here we report that this long-distance H2O2 signaling pathway is accompanied by enhanced accumulation of cytosolic H2O2 and altered redox state in cells along its path. We further show that it requires the production of superoxide, as well as the function of gap junctions, and that it is accompanied by changes in the abundance of hundreds of proteins in cells along its path. Our findings highlight the existence of a unique and rapid long-distance H2O2 signaling pathway that could play an important role in different inflammatory responses, wound responses/healing, cardiovascular disease, and/or other conditions.

WRKY48 negatively regulates plant acclimation to a combination of high light and heat stress.

Plants growing under natural conditions experience high light (HL) intensities that are often accompanied by elevated temperatures. These conditions could affect photosynthesis, reduce yield, and negatively impact agricultural productivity. The combination of different abiotic challenges creates a new type of stress for plants by generating complex environmental conditions that often exceed the impact of their individual parts. Transcription factors (TFs) play a key role in integrating the different molecular signals generated by multiple stress conditions, orchestrating the acclimation response of plants to stress. In this study, we show that the TF WRKY48 negatively controls the acclimation of Arabidopsis thaliana plants to a combination of HL and heat stress (HL + HS), and its expression is attenuated by jasmonic acid under HL + HS conditions. Using comparative physiological and transcriptomic analyses between wild-type and wrky48 mutants, we further demonstrate that under control conditions, WRKY48 represses the expression of a set of transcripts that are specifically required for the acclimation of plants to HL + HS, hence its suppression during the HL + HS stress combination contributes to plant survival under these conditions. Accordingly, mutants that lack WRKY48 are more resistant to HL + HS, and transgenic plants that overexpress WRKY48 are more sensitive to it. Taken together, our findings reveal that WRKY48 is a negative regulator of the transcriptomic response of Arabidopsis to HL + HS and provide new insights into the complex regulatory networks of plant acclimation to stress combination.