TY - JOUR A1 - Mettler, Tabea A1 - Mühlhaus, Timo A1 - Hemme, Dorothea A1 - Schöttler, Mark Aurel A1 - Rupprecht, Jens A1 - Idoine, Adam A1 - Veyel, Daniel A1 - Pal, Sunil Kumar A1 - Yaneva-Roder, Liliya A1 - Winck, Flavia Vischi A1 - Sommer, Frederik A1 - Vosloh, Daniel A1 - Seiwert, Bettina A1 - Erban, Alexander A1 - Burgos, Asdrubal A1 - Arvidsson, Samuel Janne A1 - Schoenfelder, Stephanie A1 - Arnold, Anne A1 - Guenther, Manuela A1 - Krause, Ursula A1 - Lohse, Marc A1 - Kopka, Joachim A1 - Nikoloski, Zoran A1 - Müller-Röber, Bernd A1 - Willmitzer, Lothar A1 - Bock, Ralph A1 - Schroda, Michael A1 - Stitt, Mark T1 - Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii JF - The plant cell N2 - We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance. Y1 - 2014 U6 - https://doi.org/10.1105/tpc.114.124537 SN - 1040-4651 SN - 1532-298X VL - 26 IS - 6 SP - 2310 EP - 2350 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Winck, Flavia Vischi A1 - Arvidsson, Samuel Janne A1 - Mauricio Riano-Pachon, Diego A1 - Hempel, Sabrina A1 - Koseska, Aneta A1 - Nikoloski, Zoran A1 - Urbina Gomez, David Alejandro A1 - Rupprecht, Jens A1 - Müller-Röber, Bernd T1 - Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga chlamydomonas reinhardtii under carbon deprivation JF - PLoS one N2 - The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0079909 SN - 1932-6203 VL - 8 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Müller-Röber, Bernd A1 - Arvidsson, Samuel Janne T1 - Fertility control : the role of magnesium transporters in pollen development Y1 - 2009 UR - http://www.nature.com/cr/archive/index.html U6 - https://doi.org/10.1038/Cr.2009.82 SN - 1001-0602 ER - TY - JOUR A1 - Rohrmann, Johannes A1 - Tohge, Takayuki A1 - Alba, Rob A1 - Osorio, Sonia A1 - Caldana, Camila A1 - McQuinn, Ryan A1 - Arvidsson, Samuel Janne A1 - van der Merwe, Margaretha J. A1 - Riano-Pachon, Diego Mauricio A1 - Müller-Röber, Bernd A1 - Fei, Zhangjun A1 - Nesi, Adriano Nunes A1 - Giovannoni, James J. A1 - Fernie, Alisdair R. T1 - Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development JF - The plant journal N2 - Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes. KW - transcription factor KW - Solanum lycopersicum KW - quantitative RT-PCR KW - microarray KW - metabolomics KW - fleshy fruit ripening Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-313X.2011.04750.x SN - 0960-7412 VL - 68 IS - 6 SP - 999 EP - 1013 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Omidbakhshfard, Mohammad Amin A1 - Winck, Flavia Vischi A1 - Arvidsson, Samuel Janne A1 - Riano-Pachon, Diego M. A1 - Müller-Röber, Bernd T1 - A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana JF - Journal of integrative plant biology N2 - The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species. KW - Arabidopsis thaliana KW - chromatin KW - cis-regulatory elements KW - epigenomics KW - FAIRE-qPCR KW - FAIRE-seq KW - gene expression KW - gene regulatory network KW - transcription factor Y1 - 2014 U6 - https://doi.org/10.1111/jipb.12151 SN - 1672-9072 SN - 1744-7909 VL - 56 IS - 6 SP - 527 EP - 538 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Arvidsson, Samuel Janne A1 - Perez-Rodriguez, Paulino A1 - Müller-Röber, Bernd T1 - A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects JF - New phytologist : international journal of plant science N2 - To gain a deeper understanding of the mechanisms behind biomass accumulation, it is important to study plant growth behavior. Manually phenotyping large sets of plants requires important human resources and expertise and is typically not feasible for detection of weak growth phenotypes. Here, we established an automated growth phenotyping pipeline for Arabidopsis thaliana to aid researchers in comparing growth behaviors of different genotypes. The analysis pipeline includes automated image analysis of two-dimensional digital plant images and evaluation of manually annotated information of growth stages. It employs linear mixed-effects models to quantify genotype effects on total rosette area and relative leaf growth rate (RLGR) and ANOVAs to quantify effects on developmental times. Using the system, a single researcher can phenotype up to 7000 plants d(-1). Technical variance is very low (typically < 2%). We show quantitative results for the growth-impaired starch-excessmutant sex4-3 and the growth-enhancedmutant grf9. We show that recordings of environmental and developmental variables reduce noise levels in the phenotyping datasets significantly and that careful examination of predictor variables (such as d after sowing or germination) is crucial to avoid exaggerations of recorded phenotypes and thus biased conclusions. KW - development KW - growth KW - leaf area KW - modeling KW - phenotyping Y1 - 2011 U6 - https://doi.org/10.1111/j.1469-8137.2011.03756.x SN - 0028-646X VL - 191 IS - 3 SP - 895 EP - 907 PB - Wiley-Blackwell CY - Malden ER -