@article{DurgudGuptaIvanovetal.2018,
  author    = {Durgud, Meriem and Gupta, Saurabh and Ivanov, Ivan and Omidbakhshfard, Mohammad Amin and Benina, Maria and Alseekh, Saleh and Staykov, Nikola and Hauenstein, Mareike and Dijkwel, Paul P. and Hortensteiner, Stefan and Toneva, Valentina and Brotman, Yariv and Fernie, Alisdair R. and M{\"u}ller-R{\"o}ber, Bernd and Gechev, Tsanko S.},
  title     = {Molecular Mechanisms Preventing Senescence in Response to Prolonged Darkness in a Desiccation-Tolerant Plant},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {177},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.18.00055},
  pages     = {1319 -- 1338},
  year      = {2018},
  abstract  = {The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress-and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast-and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis-and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.},
  language  = {en}
}
@article{HochreinMitchellSchulzetal.2018,
  author    = {Hochrein, Lena and Mitchell, Leslie A. and Schulz, Karina and Messerschmidt, Katrin and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast},
  series = {Nature Communications},
  volume    = {9},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-017-02208-6},
  pages     = {10},
  year      = {2018},
  abstract  = {The synthetic yeast genome constructed by the International Synthetic Yeast Sc2.0 consortium adds thousands of loxPsym recombination sites to all 16 redesigned chromosomes, allowing the shuffling of Sc2.0 chromosome parts by the Cre-loxP recombination system thereby enabling genome evolution experiments. Here, we present L-SCRaMbLE, a lightcontrolled Cre recombinase for use in the yeast Saccharomyces cerevisiae. L-SCRaMbLE allows tight regulation of recombinase activity with up to 179-fold induction upon exposure to red light. The extent of recombination depends on induction time and concentration of the chromophore phycocyanobilin (PCB), which can be easily adjusted. The tool presented here provides improved recombination control over the previously reported estradiol-dependent SCRaMbLE induction system, mediating a larger variety of possible recombination events in SCRaMbLE-ing a reporter plasmid. Thereby, L-SCRaMbLE boosts the potential for further customization and provides a facile application for use in the S. cerevisiae genome reengineering project Sc2.0 or in other recombination-based systems.},
  language  = {en}
}
@article{NaseriBehrendRieperetal.2019,
  author    = {Naseri, Gita and Behrend, Jessica and Rieper, Lisa and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors},
  series = {Nature Communications},
  volume    = {10},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-019-10224-x},
  pages     = {18},
  year      = {2019},
  abstract  = {Balanced expression of multiple genes is central for establishing new biosynthetic pathways or multiprotein cellular complexes. Methods for efficient combinatorial assembly of regulatory sequences (promoters) and protein coding sequences are therefore highly wanted. Here, we report a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, COMPASS is equipped with multi-locus CRISPR/Cas9-mediated modification capacity. We demonstrate the application of COMPASS by generating cell libraries producing n-carotene and co-producing p-ionone and biosensor-responsive naringenin. COMPASS will have many applications in synthetic biology projects that require gene expression balancing.},
  language  = {en}
}
@article{YangPerreraSaplaouraetal.2019,
  author    = {Yang, Lei and Perrera, Valentina and Saplaoura, Eleftheria and Apelt, Federico and Bahin, Mathieu and Kramdi, Amira and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Sokolowska, Ewelina and Zhang, Wenna and Li, Runsheng and Pitzalis, Nicolas and Heinlein, Manfred and Zhang, Shoudong and Genovesio, Auguste and Colot, Vincent and Kragler, Friedrich},
  title     = {m(5)C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants},
  series = {Current biology},
  volume    = {29},
  journal   = {Current biology},
  number    = {15},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0960-9822},
  doi       = {10.1016/j.cub.2019.06.042},
  pages     = {2465 -- 2476.e5},
  year      = {2019},
  abstract  = {In plants, transcripts move to distant body parts to potentially act as systemic signals regulating development and growth. Thousands of messenger RNAs (mRNAs) are transported across graft junctions via the phloem to distinct plant parts. Little is known regarding features, structural motifs, and potential base modifications of transported transcripts and how these may affect their mobility. We identified Arabidopsis thalianam RNAs harboring the modified base 5-methylcytosine (m(5)C) and found that these are significantly enriched in mRNAs previously described as mobile, moving over graft junctions to distinct plant parts. We confirm this finding with graft-mobile methylated mRNAs TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1 (TCTP1) and HEAT SHOCK COGNATE PROTEIN 70.1 (HSC70.1), whose mRNA transport is diminished in mutants deficient in m(5)C mRNA methylation. Together, our results point toward an essential role of cytosine methylation in systemic mRNA mobility in plants and that TCTP1 mRNA mobility is required for its signaling function.},
  language  = {en}
}
@article{DongGuptaSieversetal.2019,
  author    = {Dong, Yanni and Gupta, Saurabh and Sievers, Rixta and Wargent, Jason J. and Wheeler, David and Putterill, Joanna and Macknight, Richard and Gechev, Tsanko S. and M{\"u}ller-R{\"o}ber, Bernd and Dijkwel, Paul P.},
  title     = {Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals environment},
  series = {BMC genomics},
  volume    = {20},
  journal   = {BMC genomics},
  number    = {1},
  publisher = {BMC},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-019-6084-4},
  pages     = {14},
  year      = {2019},
  abstract  = {BackgroundPachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with UV-B stress, we sequenced its genome and compared the UV-B tolerance of two Pachycladon accessions with those of two A. thaliana accessions from different altitudes.ResultsA high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologs. Synteny analysis with genomes from other species of the Brassicaceae family found a close phylogenetic relationship of P. cheesemanii with Boechera stricta from Brassicaceae lineage I. While UV-B radiation caused a greater growth reduction in the A. thaliana accessions than in the P. cheesemanii accessions, growth was not reduced in one P. cheesemanii accession. The homologues of A. thaliana UV-B radiation response genes were duplicated in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii appears to differ from that in A. thaliana.ConclusionAlthough the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies allowing the plant to tolerate relatively high UV-B radiation.},
  language  = {en}
}
@article{NaseriBalazadehMachensetal.2017,
  author    = {Naseri, Gita and Balazadeh, Salma and Machens, Fabian and Kamranfar, Iman and Messerschmidt, Katrin and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Plant-Derived Transcription Factors for Orthologous Regulation of Gene Expression in the Yeast Saccharomyces cerevisiae},
  series = {ACS synthetic biology},
  volume    = {6},
  journal   = {ACS synthetic biology},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {2161-5063},
  doi       = {10.1021/acssynbio.7b00094},
  pages     = {1742 -- 1756},
  year      = {2017},
  abstract  = {Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects for which a tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harboring cognate cis regulatory motifs driving a yEGFP reporter. Transcriptional output of the different driver/reporter combinations varied over a wide spectrum, with EDLL being a considerably stronger transcription activation domain in yeast than the GAL4 activation domain, in particular when fused to Arabidopsis NAC TFs. Notably, the strength of several NAC-EDLL fusions exceeded that of the strong yeast TDH3 promoter by 6- to 10-fold. We furthermore show that plant TFs can be used to build regulatory systems encoded by centromeric or episomal plasmids. Our library of TF-DNA binding site combinations offers an excellent tool for diverse synthetic biology applications in yeast.},
  language  = {en}
}
@article{CzarnockaVanDerKelenWillemsetal.2017,
  author    = {Czarnocka, Weronika and Van Der Kelen, Katrien and Willems, Patrick and Szechynska-Hebda, Magdalena and Shahnejat-Bushehri, Sara and Balazadeh, Salma and Rusaczonek, Anna and M{\"u}ller-R{\"o}ber, Bernd and Van Breusegem, Frank and Karpinski, Stanislaw},
  title     = {The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator},
  series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  volume    = {40},
  journal   = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0140-7791},
  doi       = {10.1111/pce.12994},
  pages     = {2644 -- 2662},
  year      = {2017},
  abstract  = {Since its discovery over two decades ago as an important cell death regulator in Arabidopsis thaliana, the role of LESION SIMULATING DISEASE 1 (LSD1) has been studied intensively within both biotic and abiotic stress responses as well as with respect to plant fitness regulation. However, its molecular mode of action remains enigmatic. Here, we demonstrate that nucleo-cytoplasmic LSD1 interacts with a broad range of other proteins that are engaged in various molecular pathways such as ubiquitination, methylation, cell cycle control, gametogenesis, embryo development and cell wall formation. The interaction of LSD1 with these partners is dependent on redox status, as oxidative stress significantly changes the quantity and types of LSD1-formed complexes. Furthermore, we show that LSD1 regulates the number and size of leaf mesophyll cells and affects plant vegetative growth. Importantly, we also reveal that in addition to its function as a scaffold protein, LSD1 acts as a transcriptional regulator. Taken together, our results demonstrate that LSD1 plays a dual role within the cell by acting as a condition-dependent scaffold protein and as a transcription regulator.},
  language  = {en}
}
@article{OmranianEloundouMbebiMuellerRoeberetal.2016,
  author    = {Omranian, Nooshin and Eloundou-Mbebi, Jeanne Marie Onana and M{\"u}ller-R{\"o}ber, Bernd and Nikoloski, Zoran},
  title     = {Gene regulatory network inference using fused LASSO on multiple data sets},
  series = {Scientific reports},
  volume    = {6},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/srep20533},
  pages     = {14},
  year      = {2016},
  abstract  = {Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcription factor coding genes, (2) networks inferred from different data sets should be similar with respect to the type and number of regulatory interactions, and (3) relationships between genes which exhibit similar differential behavior over the considered perturbations should be favored. We demonstrate that these constraints can be transformed in a fused LASSO formulation for the proposed method. The comparative analysis on transcriptomics time-series data from prokaryotic species, Escherichia coli and Mycobacterium tuberculosis, as well as a eukaryotic species, mouse, demonstrated that the proposed method has the advantages of the most recent approaches for regulatory network inference, while obtaining better performance and assigning higher scores to the true regulatory links. The study indicates that the combination of sparse regression techniques with other biologically meaningful constraints is a promising framework for gene regulatory network reconstructions.},
  language  = {en}
}
@article{SedaghatmehrMuellerRoeberBalazadeh2016,
  author    = {Sedaghatmehr, Mastoureh and M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma},
  title     = {The plastid metalloprotease FtsH6 and small heat shock protein HSP21 jointly regulate thermomemory in Arabidopsis},
  series = {Nature Communications},
  volume    = {7},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/ncomms12439},
  pages     = {14},
  year      = {2016},
  abstract  = {Acquired tolerance to heat stress is an increased resistance to elevated temperature following a prior exposure to heat. The maintenance of acquired thermotolerance in the absence of intervening stress is called 'thermomemory' but the mechanistic basis for this memory is not well defined. Here we show that Arabidopsis HSP21, a plastidial small heat shock protein that rapidly accumulates after heat stress and remains abundant during the thermomemory phase, is a crucial component of thermomemory. Sustained memory requires that HSP21 levels remain high. Through pharmacological interrogation and transcriptome profiling, we show that the plastid-localized metalloprotease FtsH6 regulates HSP21 abundance. Lack of a functional FtsH6 protein promotes HSP21 accumulation during the later stages of thermomemory and increases thermomemory capacity. Our results thus reveal the presence of a plastidial FtsH6-HSP21 control module for thermomemory in plants.},
  language  = {en}
}
@article{GuptaDongDijkweletal.2019,
  author    = {Gupta, Saurabh and Dong, Yanni and Dijkwel, Paul P. and M{\"u}ller-R{\"o}ber, Bernd and Gechev, Tsanko S.},
  title     = {Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation},
  series = {International Journal of Molecular Sciences},
  volume    = {20},
  journal   = {International Journal of Molecular Sciences},
  number    = {12},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms20123101},
  pages     = {22},
  year      = {2019},
  abstract  = {Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginella moellendorffi. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress.},
  language  = {en}
}