TY  - JOUR
A1  - Köslin-Findeklee, Fabian
A1  - Rizi, Vajiheh Safavi
A1  - Becker, Martin A.
A1  - Parra-Londono, Sebastian
A1  - Arif, Muhammad
A1  - Balazadeh, Salma
A1  - Müller-Röber, Bernd
A1  - Kunze, Reinhard
A1  - Horst, Walter J.
T1  - Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.)
JF  - Plant science : an international journal of experimental plant biology
N2  - High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1:4, the ureide transporter UPSS, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding. (C) 2015 Elsevier Ireland Ltd. All rights reserved.
KW  - Brassica napus
KW  - Genotypic differences
KW  - Leaf senescence
KW  - Molecular marker
KW  - N efficiency
KW  - Stay-green
Y1  - 2015
U6  - https://doi.org/10.1016/j.plantsci.2014.11.018
SN  - 0168-9452
VL  - 233
SP  - 174
EP  - 185
PB  - Elsevier
CY  - Clare
ER  - 
TY  - JOUR
A1  - Petrov, Veselin
A1  - Hille, Jacques
A1  - Müller-Röber, Bernd
A1  - Gechev, Tsanko S.
T1  - ROS-mediated abiotic stress-induced programmed cell death in plants
JF  - Frontiers in plant science
N2  - During the course of their ontogenesis plants are continuously exposed to a large variety of abiotic stress factors which can damage tissues and jeopardize the survival of the organism unless properly countered. While animals can simply escape and thus evade stressors, plants as sessile organisms have developed complex strategies to withstand them. When the intensity of a detrimental factor is high, one of the defense programs employed by plants is the induction of programmed cell death (PCD). This is an active, genetically controlled process which is initiated to isolate and remove damaged tissues thereby ensuring the survival of the organism. The mechanism of PCD induction usually includes an increase in the levels of reactive oxygen species (ROS) which are utilized as mediators of the stress signal. Abiotic stress-induced PCD is not only a process of fundamental biological importance, but also of considerable interest to agricultural practice as it has the potential to significantly influence crop yield. Therefore, numerous scientific enterprises have focused on elucidating the mechanisms leading to and controlling PCD in response to adverse conditions in plants. This knowledge may help develop novel strategies to obtain more resilient crop varieties with improved tolerance and enhanced productivity. The aim of the present review is to summarize the recent advances in research on ROS-induced PCD related to abiotic stress and the role of the organelles in the process.
KW  - abiotic stress
KW  - programmed cell death
KW  - reactive oxygen species
KW  - signal transduction
KW  - stress adaptation
Y1  - 2015
U6  - https://doi.org/10.3389/fpls.2015.00069
SN  - 1664-462X
VL  - 6
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Proost, Sebastian
A1  - Van Bel, Michiel
A1  - Vaneechoutte, Dries
A1  - Van de Peer, Yves
A1  - Inze, Dirk
A1  - Müller-Röber, Bernd
A1  - Vandepoele, Klaas
T1  - PLAZA 3.0: an access point for plant comparative genomics
JF  - Nucleic acids research
N2  - Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.
Y1  - 2015
U6  - https://doi.org/10.1093/nar/gku986
SN  - 0305-1048
SN  - 1362-4962
VL  - 43
IS  - D1
SP  - D974
EP  - D981
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Omidbakhshfard, Mohammad Amin
A1  - Proost, Sebastian
A1  - Fujikura, Ushio
A1  - Müller-Röber, Bernd
T1  - Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology
JF  - Molecular plant
N2  - Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.
KW  - abiotic stress
KW  - chromatin remodeling
KW  - flower development
KW  - growth regulation
KW  - leaf development
KW  - miRNA
Y1  - 2015
U6  - https://doi.org/10.1016/j.molp.2015.01.013
SN  - 1674-2052
SN  - 1752-9867
VL  - 8
IS  - 7
SP  - 998
EP  - 1010
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Sree, K. Sowjanya
A1  - Keresztes, Aron
A1  - Müller-Röber, Bernd
A1  - Brandt, Ronny
A1  - Eberius, Matthias
A1  - Fischer, Wolfgang
A1  - Appenroth, Klaus-J.
T1  - Phytotoxicity of cobalt ions on the duckweed Lemna minor - Morphology, ion uptake, and starch accumulation
JF  - Chemosphere : chemistry, biology and toxicology as related to environmental problems
N2  - Cobalt (Co2+) inhibits vegetative growth of Lemna minor gradually from 1 mu M to 100 mu M. Fronds accumulated up to 21 mg Co2+ g(-1) dry weight at 10 mu M external Co2+ indicating hyperaccumulation. Interestingly, accumulation of Co2+ did not decrease the iron (Fe) content in fronds, highlighting L. minor as a suitable system for studying effects of Co2+ undisturbed by Fe deficiency symptoms unlike most other plants. Digital image analysis revealed the size distribution of fronds after Co2+ treatment and also a reduction in pigmentation of newly formed daughter fronds unlike the mother fronds during the 7-day treatment. Neither chlorophyll nor photosystem II fluorescence changed significantly during the initial 4 d, indicating effective photosynthesis. During the later phase of the 7-day treatment, however, chlorophyll content and photosynthetic efficiency decreased in the Co2+-treated daughter fronds, indicating that Co2+ inhibits the biosynthesis of chlorophyll rather than leading to the destruction of pre-existing pigment molecules. In addition, during the first 4 d of Co2+ treatment starch accumulated in the fronds and led to the transition of chloroplasts to chloro-amyloplasts and amylo-chloroplasts, while starch levels strongly decreased thereafter. (C) 2015 Elsevier Ltd. All rights reserved.
KW  - Chloroplast
KW  - Cobalt
KW  - Lemnaceae
KW  - Lemna minor
KW  - Phytotoxicity
KW  - Starch accumulation
Y1  - 2015
U6  - https://doi.org/10.1016/j.chemosphere.2015.03.008
SN  - 0045-6535
SN  - 1879-1298
VL  - 131
SP  - 149
EP  - 156
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Engqvist, Martin K. M.
A1  - Schmitz, Jessica
A1  - Gertzmann, Anke
A1  - Florian, Alexandra
A1  - Jaspert, Nils
A1  - Arif, Muhammad
A1  - Balazadeh, Salma
A1  - Müller-Röber, Bernd
A1  - Fernie, Alisdair R.
A1  - Maurino, Veronica G.
T1  - GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-of-function and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia.
Y1  - 2015
U6  - https://doi.org/10.1104/pp.15.01003
SN  - 0032-0889
SN  - 1532-2548
VL  - 169
IS  - 2
SP  - 1042
EP  - 1061
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Benina, Maria
A1  - Ribeiro, Dimas Mendes
A1  - Gechev, Tsanko S.
A1  - Müller-Röber, Bernd
A1  - Schippers, Jos H. M.
T1  - A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves
JF  - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology
N2  - Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress.
 The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels.
KW  - Arabidopsis
KW  - gene regulation
KW  - oxidative stress
KW  - tissue-specific
KW  - translation
Y1  - 2015
U6  - https://doi.org/10.1111/pce.12355
SN  - 0140-7791
SN  - 1365-3040
VL  - 38
IS  - 2
SP  - 349
EP  - 363
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
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  - Lotkowska, Magda E.
A1  - Tohge, Takayuki
A1  - Fernie, Alisdair R.
A1  - Xue, Gang-Ping
A1  - Balazadeh, Salma
A1  - Müller-Röber, Bernd
T1  - The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions.
Y1  - 2015
U6  - https://doi.org/10.1104/pp.15.00605
SN  - 0032-0889
SN  - 1532-2548
VL  - 169
IS  - 3
SP  - 1862
EP  - 1880
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Garapati, Prashanth
A1  - Feil, Regina
A1  - Lunn, John Edward
A1  - Van Dijck, Patrick
A1  - Balazadeh, Salma
A1  - Müller-Röber, Bernd
T1  - Transcription Factor Arabidopsis Activating Factor1 Integrates Carbon Starvation Responses with Trehalose Metabolism
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - Plants respond to low carbon supply by massive reprogramming of the transcriptome and metabolome. We show here that the carbon starvation-induced NAC (for NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON) transcription factor Arabidopsis (Arabidopsis thaliana) Transcription Activation Factor1 (ATAF1) plays an important role in this physiological process. We identified TREHALASE1, the only trehalase-encoding gene in Arabidopsis, as a direct downstream target of ATAF1. Overexpression of ATAF1 activates TREHALASE1 expression and leads to reduced trehalose-6-phosphate levels and a sugar starvation metabolome. In accordance with changes in expression of starch biosynthesis-and breakdown-related genes, starch levels are generally reduced in ATAF1 overexpressors but elevated in ataf1 knockout plants. At the global transcriptome level, genes affected by ATAF1 are broadly associated with energy and carbon starvation responses. Furthermore, transcriptional responses triggered by ATAF1 largely overlap with expression patterns observed in plants starved for carbon or energy supply. Collectively, our data highlight the existence of a positively acting feedforward loop between ATAF1 expression, which is induced by carbon starvation, and the depletion of cellular carbon/energy pools that is triggered by the transcriptional regulation of downstream gene regulatory networks by ATAF1.
Y1  - 2015
U6  - https://doi.org/10.1104/pp.15.00917
SN  - 0032-0889
SN  - 1532-2548
VL  - 169
IS  - 1
SP  - 379
EP  - 390
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  -