Center for Biosystems Genomics

Wageningen, Netherlands

Center for Biosystems Genomics

Wageningen, Netherlands
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Bailey-Serres J.,University of California at Riverside | Voesenek L.A.C.J.,University Utrecht | Voesenek L.A.C.J.,Center for Biosystems Genomics
Current Opinion in Plant Biology | Year: 2010

Recent reports on responses to flooding, submergence, and low-oxygen stress have connected components in an essential regulatory network that underlies plasticity in growth and metabolism essential for the survival of distinct flooding regimes. Here, we discuss growth under severe oxygen-limited conditions (anaerobic growth) and less oxygen-deficient underwater conditions (ethylene-driven underwater growth). Low-oxygen stress causes an energy and carbohydrate crisis that must be controlled through regulated consumption of carbohydrates and energy reserves. In rice (Oryza sativa L.), low-oxygen stress, energy homeostasis and growth are connected by a calcineurin B-like interacting binding kinase (CIPK) in seeds germinated under water. In shoots, two opposing adaptive strategies to submergence, elongation (escape) and inhibition of elongation (quiescence), are controlled by related ethylene response factor (ERF) DNA binding proteins that act downstream of ethylene and modulate gibberellin-mediated shoot growth. Increased resolution of the flooding signaling network will require more precise investigation of the interactions between oxygen tension and cellular energy status in regulation of anaerobic metabolism and ethylene-driven growth, both essential to survival in variable flooding environments. © 2010 Elsevier Ltd.


Licausi F.,Max Planck Institute of Molecular Plant Physiology | Licausi F.,PlantLab | Kosmacz M.,Max Planck Institute of Molecular Plant Physiology | Weits D.A.,Max Planck Institute of Molecular Plant Physiology | And 6 more authors.
Nature | Year: 2011

The majority of eukaryotic organisms rely on molecular oxygen for respiratory energy production. When the supply of oxygen is compromised, a variety of acclimation responses are activated to reduce the detrimental effects of energy depletion. Various oxygen-sensing mechanisms have been described that are thought to trigger these responses, but they each seem to be kingdom specific and no sensing mechanism has been identified in plants until now. Here we show that one branch of the ubiquitin-dependent N-end rule pathway for protein degradation, which is active in both mammals and plants, functions as an oxygen-sensing mechanism in Arabidopsis thaliana. We identified a conserved amino-terminal amino acid sequence of the ethylene response factor (ERF)-transcription factor RAP2.12 to be dedicated to an oxygen-dependent sequence of post-translational modifications, which ultimately lead to degradation of RAP2.12 under aerobic conditions. When the oxygen concentration is low-as during flooding-RAP2.12 is released from the plasma membrane and accumulates in the nucleus to activate gene expression for hypoxia acclimation. Our discovery of an oxygen-sensing mechanism opens up new possibilities for improving flooding tolerance in crops. © 2011 Macmillan Publishers Limited. All rights reserved.


Takken F.L.W.,University of Amsterdam | Takken F.L.W.,Center for BioSystems Genomics | Goverse A.,Wageningen University | Goverse A.,Center for BioSystems Genomics
Current Opinion in Plant Biology | Year: 2012

Many plant disease resistance (R) proteins belong to the family of nucleotide-binding-leucine rich repeat (NB-LRR) proteins. NB-LRRs mediate recognition of pathogen-derived effector molecules and subsequently activate host defence. Their multi-domain structure allows these pathogen detectors to simultaneously act as sensor, switch and response factor. Structure-function analyses and the recent elucidation of the 3D structures of subdomains have provided new insight in how these different functions are combined and what the contribution is of the individual subdomains. Besides interdomain contacts, interactions with chaperones, the proteasome and effector baits are required to keep NB-LRRs in a signalling-competent, yet auto-inhibited state. In this review we explore operational models of NB-LRR functioning based on recent advances in understanding their structure. © 2012 Elsevier Ltd.


Stassen J.H.M.,University Utrecht | Van den Ackerveken G.,University Utrecht | Van den Ackerveken G.,Center for BioSystems Genomics
Current Opinion in Plant Biology | Year: 2011

Oomycete genomes have yielded a large number of predicted effector proteins that collectively interfere with plant life in order to create a favourable environment for pathogen infection. Oomycetes secrete effectors that can be active in the host's extracellular environment, for example inhibiting host defence enzymes, or inside host cells where they can interfere with plant processes, in particular suppression of defence. Two classes of effectors are known to be host-translocated: the RXLRs and Crinklers. Many effectors show defence-suppressive activity that is important for pathogen virulence. A striking example is AVR3a of Phytophthora infestans that targets an ubiquitin ligase, the stabilisation of which may prevent host cell death. The quest for other effector targets and mechanisms is in full swing. © 2011 Elsevier Ltd.


Pieterse C.M.J.,University Utrecht | Pieterse C.M.J.,Center for BioSystems Genomics | Van Der Does D.,University Utrecht | Zamioudis C.,University Utrecht | And 2 more authors.
Annual Review of Cell and Developmental Biology | Year: 2012

Plant hormones have pivotal roles in the regulation of plant growth, development, and reproduction. Additionally, they emerged as cellular signal molecules with key functions in the regulation of immune responses to microbial pathogens, insect herbivores, and beneficial microbes. Their signaling pathways are interconnected in a complex network, which provides plants with an enormous regulatory potential to rapidly adapt to their biotic environment and to utilize their limited resources for growth and survival in a cost-efficient manner. Plants activate their immune system to counteract attack by pathogens or herbivorous insects. Intriguingly, successful plant enemies evolved ingenious mechanisms to rewire the plant's hormone signaling circuitry to press or evade host immunity. Evidence is emerging that beneficial root-inhabiting microbes also hijack the hormone-regulated immune signaling network to establish a prolonged mutualistic association, highlighting the central role of plant hormones in the regulation of plant growth and survival. Copyright © 2012 by Annual Reviews. All rights reserved.


Liebrand T.W.H.,Wageningen University | Liebrand T.W.H.,Center for BioSystems Genomics | van den Burg H.A.,University of Amsterdam | Joosten M.H.A.J.,Wageningen University | Joosten M.H.A.J.,Center for BioSystems Genomics
Trends in Plant Science | Year: 2014

Leucine-rich repeat-receptor-like proteins (LRR-RLPs) are ubiquitous cell surface receptors lacking a cytoplasmic signalling domain. For most of these LRR-RLPs, it remained enigmatic how they activate cellular responses upon ligand perception. Recently, the LRR-receptor-like kinase (LRR-RLK) SUPPRESSOR OF BIR1-1 (SOBIR1) was shown to be essential for triggering defence responses by certain LRR-RLPs that act as immune receptors. In addition to SOBIR1, the regulatory LRR-RLK BRI1-ASSOCIATED KINASE-1 (BAK1) is also required for LRR-RLP function. Here, we compare the roles of SOBIR1 and BAK1 as regulatory LRR-RLKs in immunity and development. BAK1 has a general regulatory role in plasma membrane-associated receptor complexes comprising LRR-RLPs and/or LRR-RLKs. By contrast, SOBIR1 appears to be specifically required for the function of receptor complexes containing LRR-RLPs. © 2013 Elsevier Ltd.


Sasidharan R.,University Utrecht | Sasidharan R.,Center for Biosystems Genomics | Mustroph A.,University of Bayreuth
Plant Cell | Year: 2011

Like all aerobic organisms, plants require molecular oxygen for respiratory energy production. In plants, hypoxic conditions can occur during natural events (e.g., flooding), during developmental processes (e.g., seed germination), and in cells of compact tissues with high metabolic rates. Plant acclimation responses to hypoxia involve a modulation of gene expression leading to various biochemical, physiological, and morphological changes that stave off eventual anoxia. In contrast with the animal kingdom, a direct oxygen-sensing mechanism in plants has been elusive so far. However, two recent independent studies show that oxygen sensing in plants operates via posttranslational regulation of key hypoxia response transcription factors by the N-end rule pathway. The N-end rule is an evolutionarily conserved pathway for protein degradation that relates the fate of a protein with the identity of its N-terminal residues. Results from these studies demonstrate that oxygen-dependent modification and targeted proteolysis of members of the ethylene response factor group VII transcription factor family regulate hypoxia-responsive gene expression in Arabidopsis thaliana. The discovery of this plant hypoxia-sensing mechanism sets the stage for further research on plant homeostatic response to oxygen, which could be relevant to understanding plant distributions in flood-prone ecosystems and improving hypoxia tolerance of crops. © 2011 American Society of Plant Biologists.


Zamioudis C.,University Utrecht | Pieterse C.M.J.,University Utrecht | Pieterse C.M.J.,Center for BioSystems Genomics
Molecular Plant-Microbe Interactions | Year: 2012

In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and Rhizobium bacteria that fix atmospheric nitrogen for the plant. Several other types of beneficial soilborne microbes, such as plant-growth-promoting rhizobacteria and fungi with biological control activity, can stimulate plant growth by directly suppressing deleterious soilborne pathogens or by priming aboveground plant parts for enhanced defense against foliar pathogens or insect herbivores. The establishment of beneficial associations requires mutual recognition and substantial coordination of plant and microbial responses. A growing body of evidence suggests that beneficial microbes are initially recognized as potential invaders, after which an immune response is triggered, whereas, at later stages of the interaction, mutualists are able to shortcircuit plant defense responses to enable successful colonization of host roots. Here, we review our current understanding of how symbiotic and nonsymbiotic beneficial soil microbes modulate the plant immune system and discuss the role of local and systemic defense responses in establishing the delicate balance between the two partners. © 2012 The American Phytopathological Society.


Berendsen R.L.,University Utrecht | Pieterse C.M.J.,University Utrecht | Pieterse C.M.J.,Center for BioSystems Genomics | Bakker P.A.H.M.,University Utrecht
Trends in Plant Science | Year: 2012

The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production. © 2012 Elsevier Ltd.


Al-Babili S.,King Abdullah University of Science and Technology | Bouwmeester H.J.,Wageningen University | Bouwmeester H.J.,Center for BioSystems Genomics
Annual Review of Plant Biology | Year: 2015

Strigolactones (SLs) are carotenoid-derived plant hormones and signaling molecules. When released into the soil, SLs indicate the presence of a host to symbiotic fungi and root parasitic plants. In planta, they regulate several developmental processes that adapt plant architecture to nutrient availability. Highly branched/tillered mutants in Arabidopsis, pea, and rice have enabled the identification of four SL biosynthetic enzymes: a cis/trans-carotene isomerase, two carotenoid cleavage dioxygenases, and a cytochrome P450 (MAX1). In vitro and in vivo enzyme assays and analysis of mutants have shown that the pathway involves a combination of new reactions leading to carlactone, which is converted by a rice MAX1 homolog into an SL parent molecule with a tricyclic lactone moiety. In this review, we focus on SL biosynthesis, describe the hormonal and environmental factors that determine this process, and discuss SL transport and downstream signaling as well as the role of SLs in regulating plant development. ©2015 by Annual Reviews. All rights reserved.

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