TY - JOUR A1 - Wang, Ting A1 - Tohge, Takayuki A1 - Ivakov, Alexander A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Mutwil, Marek A1 - Schippers, Jos H. M. A1 - Persson, Staffan T1 - Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00962 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 2 SP - 1027 EP - + PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Ruprecht, Colin A1 - Lohaus, Rolf A1 - Vanneste, Kevin A1 - Mutwil, Marek A1 - Nikoloski, Zoran A1 - Van de Peer, Yves A1 - Persson, Staffan T1 - Revisiting ancestral polyploidy in plants JF - Science Advances N2 - Whole-genome duplications (WGDs) or polyploidy events have been studied extensively in plants. In a now widely cited paper, Jiao et al. presented evidence for two ancient, ancestral plant WGDs predating the origin of flowering and seed plants, respectively. This finding was based primarily on a bimodal age distribution of gene duplication events obtained from molecular dating of almost 800 phylogenetic gene trees. We reanalyzed the phylogenomic data of Jiao et al. and found that the strong bimodality of the age distribution may be the result of technical and methodological issues and may hence not be a "true" signal of two WGD events. By using a state-of-the-art molecular dating algorithm, we demonstrate that the reported bimodal age distribution is not robust and should be interpreted with caution. Thus, there exists little evidence for two ancient WGDs in plants from phylogenomic dating. Y1 - 2017 U6 - https://doi.org/10.1126/sciadv.1603195 SN - 2375-2548 VL - 3 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Ruprecht, Colin A1 - Mutwil, Marek A1 - Saxe, Friederike A1 - Eder, Michaela A1 - Nikoloski, Zoran A1 - Persson, Staffan T1 - Large-scale co-expression approach to dissect secondary cell wall formation across plant species JF - Frontiers in plant science N2 - Plant cell walls are complex composites largely consisting of carbohydrate-based polymers, and are generally divided into primary and secondary walls based on content and characteristics. Cellulose microfibrils constitute a major component of both primary and secondary cell walls and are synthesized at the plasma membrane by cellulose synthase (CESA) complexes. Several studies in Arabidopsis have demonstrated the power of co-expression analyses to identify new genes associated with secondary wall cellulose biosynthesis. However, across-species comparative co-expression analyses remain largely unexplored. Here, we compared co-expressed gene vicinity networks of primary and secondary wall CESAsin Arabidopsis, barley, rice, poplar, soybean, Medicago, and wheat, and identified gene families that are consistently co-regulated with cellulose biosynthesis. In addition to the expected polysaccharide acting enzymes, we also found many gene families associated with cytoskeleton, signaling, transcriptional regulation, oxidation, and protein degradation. Based on these analyses, we selected and biochemically analyzed T-DNA insertion lines corresponding to approximately twenty genes from gene families that re-occur in the co-expressed gene vicinity networks of secondary wall CESAs across the seven species. We developed a statistical pipeline using principal component analysis and optimal clustering based on silhouette width to analyze sugar profiles. One of the mutants, corresponding to a pinoresinol reductase gene, displayed disturbed xylem morphology and held lower levels of lignin molecules. We propose that this type of large-scale co-expression approach, coupled with statistical analysis of the cell wall contents, will be useful to facilitate rapid knowledge transfer across plant species. KW - secondary cell wall KW - comparative co-expression analysis KW - Arabidopsis KW - cellulose Y1 - 2011 U6 - https://doi.org/10.3389/fpls.2011.00023 SN - 1664-462X VL - 2 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Ferrari, Camilla A1 - Proost, Sebastian A1 - Janowski, Marcin Andrzej A1 - Becker, Jörg A1 - Nikoloski, Zoran A1 - Bhattacharya, Debashish A1 - Price, Dana A1 - Tohge, Takayuki A1 - Bar-Even, Arren A1 - Fernie, Alisdair R. A1 - Stitt, Mark A1 - Mutwil, Marek T1 - Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida JF - Nature Communications N2 - Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-08703-2 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Mutwil, Marek T1 - Integrative transcriptomic approaches to analyzing plant co-expression networks T1 - Integrative Ansätze zur Analyse von Koexpressionsnetzwerken in Pflanzen N2 - It is well documented that transcriptionally coordinated genes tend to be functionally related, and that such relationships may be conserved across different species, and even kingdoms. (Ihmels et al., 2004). Such relationships was initially utilized to reveal functional gene modules in yeast and mammals (Ihmels et al., 2004), and to explore orthologous gene functions between different species and kingdoms (Stuart et al., 2003; Bergmann et al., 2004). Model organisms, such as Arabidopsis, are readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer the acquired knowledge from these model organisms to species that are of greater importance to our society. However, due to large gene families in plants, the identification of functional equivalents of well characterized Arabidopsis genes in other plants is a non-trivial task, which often returns erroneous or inconclusive results. In this thesis, concepts of utilizing co-expression networks to help infer (i) gene function, (ii) organization of biological processes and (iii) knowledge transfer between species are introduced. An often overlooked fact by bioinformaticians is that a bioinformatic method is as useful as its accessibility. Therefore, majority of the work presented in this thesis was directed on developing freely available, user-friendly web-tools accessible for any biologist. N2 - Es ist bereits ausgiebig gezeigt worden, dass Gene, deren Expression auf Transkriptionsebene koordiniert ist, häufig auch funktional in verwandten Stoffwechselwegen vorkommen, und dass sich dies wahrscheinlich auch Spezies- und sogar Reichübergreifend sagen lässt (Ihmels et al., 2004). Anfänglich wurden solche Beziehungen verwendet, um sogenannte Genfunktionsmodule in Hefe und Säugern aufzudecken (Ihmels et al., 2004), um dann orthologe Genfunktionen zwischen verschiedene Spezies und Reichen zu entdecken (Stuart et al., 2003; Bergmann et al., 2004). Modellorganismen wie Arabidopsis werden bevorzugt in der Forschung verwendet, weil man durch die schnelle Generationszeit in kurzer Zeit viele Daten erheben kann und aufgrund dessen die Ressourcen- und Informationsvielfalt um ein Vielfaches größer ist. Ein Hauptziel ist der Wissenstransfer von Modellorganismen auf Spezies, die gesellschaftlich von höherer Bedeutung sind wie z.B. Getreidearten oder andere Feldfrüchte. Pflanzen besitzen oft große Genfamilien und die eindeutige Identifizierung von gut charakterisierten Arabidopsisorthologen in besagten Nutzpflanzen ist kein triviales Vorhaben. In der vorliegenden Arbeit werden Konzepte zur Nutzung von Co-expressionsnetzwerken beschrieben, die helfen sollen (i) Genfunktionen zu identifizieren, (ii) die Organisation von biologischen Prozessen aufzuklären und (iii) das erworbene Wissen auf andere Spezies übertragbar zu machen. Ein häufig von Bioinformatikern übersehender Umstand ist, dass bioinformatische Methoden nur so sinnvoll sind wie ihre Zugänglichkeit. Deshalb basiert der Großteil dieser Arbeit auf freiverfügbaren und vor allem für Biologen nutzerfreundlichen Webtools. KW - Koexpression KW - vergleichend KW - Transkriptom KW - co-expression KW - comparative KW - transcriptomics Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-50752 ER - TY - JOUR A1 - Hansen, Bjoern Oest A1 - Meyer, Etienne H. A1 - Ferrari, Camilla A1 - Vaid, Neha A1 - Movahedi, Sara A1 - Vandepoele, Klaas A1 - Nikoloski, Zoran A1 - Mutwil, Marek T1 - Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana JF - New phytologist : international journal of plant science N2 - Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists. KW - Arabidopsis thaliana KW - co-function network KW - complex I KW - ensemble prediction KW - gene function prediction Y1 - 2017 U6 - https://doi.org/10.1111/nph.14921 SN - 0028-646X SN - 1469-8137 VL - 217 IS - 4 SP - 1521 EP - 1534 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Janowski, Marcin Andrzej A1 - Zoschke, Reimo A1 - Scharff, Lars B. A1 - Jaime, Silvia Martinez A1 - Ferrari, Camilla A1 - Proost, Sebastian A1 - Xiong, Jonathan Ng Wei A1 - Omranian, Nooshin A1 - Musialak-Lange, Magdalena A1 - Nikoloski, Zoran A1 - Graf, Alexander A1 - Schoettler, Mark Aurel A1 - Sampathkumar, Arun A1 - Vaid, Neha A1 - Mutwil, Marek T1 - AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome JF - The plant journal N2 - Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function. Significance Statement AtRsgA is an assembly factor necessary for maturation of the small subunit of the chloroplast ribosome. Depletion of AtRsgA leads to dwarfed, chlorotic plants, a decrease of mature 16S rRNA and smaller, but more numerous, chloroplasts. Large-scale transcriptomic and proteomic analysis revealed that chloroplast-encoded and -targeted proteins were less abundant, while the corresponding transcripts were increased in the mutant. We analyze the transcriptional responses of several retrograde signaling pathways to suggest the mechanism underlying this compensatory response. KW - ribosome assembly KW - chloroplast ribosome KW - assembly factor KW - 30S subunit KW - RsgA KW - Arabidopsis thaliana Y1 - 2018 U6 - https://doi.org/10.1111/tpj.14040 SN - 0960-7412 SN - 1365-313X VL - 96 IS - 2 SP - 404 EP - 420 PB - Wiley CY - Hoboken ER -