Laurentius A. C. J. Voesenek

Flooding Stress: Acclimations and Genetic Diversity

Flooding is an environmental stress for many natural and man-made ecosystems worldwide. Genetic diversity in the plant response to flooding includes alterations in architecture, metabolism, and elongation growth associated with a low O(2) escape strategy and an antithetical quiescence scheme that allows endurance of prolonged submergence. Flooding is frequently accompanied with a reduction of cellular O(2) content that is particularly severe when photosynthesis is limited or absent. This necessitates the production of ATP and regeneration of NAD(+) through anaerobic respiration. The examination of gene regulation and function in model systems provides insight into low-O(2)-sensing mechanisms and metabolic adjustments associated with controlled use of carbohydrate and ATP. At the developmental level, plants can escape the low-O(2) stress caused by flooding through multifaceted alterations in cellular and organ structure that promote access to and diffusion of O(2). These processes are driven by phytohormones, including ethylene, gibberellin, and abscisic acid. This exploration of natural variation in strategies that improve O(2) and carbohydrate status during flooding provides valuable resources for the improvement of crop endurance of an environmental adversity that is enhanced by global warming.

Flooding: the survival strategies of plants

Floodplains and wetlands are highly suitable for plant ecological studies, whether for agricultural interests, nature conservation or basic science. Traditional work has entailed a descriptive approach at the community or individual plant level. Nowadays these studies are evolving into physiological research on relationships between flooding stress and vegetation zonation. Current experiments aim to unravel the adaptive mechanisms whereby terrestrial plants cope with the peculiar conditions of the floodplain, from the whole plant down to the cell.

Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization

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.

Making sense of low oxygen sensing

Plant-specific group VII Ethylene Response Factor (ERF) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. In rice (Oryza sativa), these proteins regulate contrasting strategies of flooding survival. Recent studies on Arabidopsis thaliana group VII ERFs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the N-end rule pathway of targeted proteolysis. Oxygen-dependent sequestration at the plasma membrane maintains at least one of these proteins, RAP2.12, under normoxia. Remarkably, SUB1A, the rice group VII ERF that enables prolonged submergence tolerance, appears to evade oxygen-regulated N-end rule degradation. We propose that the turnover of group VII ERFs is of ecological relevance in wetland species and might be manipulated to improve flood tolerance of crops.

Plant hormones regulate fast shoot elongation under water: From genes to communities

Flooding affects the abundance and distribution of plant species worldwide. Many plants are damaged or even killed by flooding events due to the associated oxygen deprivation in cells. Stimulated shoot elongation is an important adaptive mode that can restore contact of leaves with the atmosphere above the water surface. This strongly im- proves inward diffusion of oxygen and the rate of photosynthesis. Fast elongation of sub- merged petioles of the model plant Rumex palustris involves the integrated action of the plant hormones ethylene, auxin, gibberellin, and abscisic acid. The closely related Rumex acetosa is unable to switch on petiole elongation when submerged. In a comparative study of these two Rumex species, we found that the response to the gaseous phytohormone ethylene, which accumulates in plant tissues during submergence, explains their contrasting elongation behavior. In order to study the importance of this shoot elongation response in the distributional patterns of plants in natural floodplains, we quantified the ethylene- induced elongation response of 22 plant species occurring in the Rhine River floodplain. These results were compared with the results of a multivariate analysis based on 84 veg- etation surveys performed in the same area. The species compositions of the surveys were grouped along two environmental gradients: flooding duration and soil dehydration after the floodwater subsided. If we superimpose the ethylene-induced elongation capacity on these vegetation data, it becomes clear that the capacity to elongate upon exposure to ethylene positively correlates with flooding duration and negatively with soil dehydration. Based on this analysis, we conclude that the capacity to elongate is an important selective trait in field distribution patterns of plants in flood-prone environments. Fast shoot elon- gation under water seems to be a favorable trait only in environments with shallow and prolonged flooding events, while costs associated with this response prevent its expression in sites with deep floods, sites with floods short in duration, or in sites in which flood water recedes rapidly. The approach outlined in this paper may be more widely applicable in ecological studies that aim to understand the functional relationship between plant traits and species distributions along environmental gradients.

Nomenclature for members of the expansin superfamily of genes and proteins

Hans Kende*, Kent J. Bradford, David A. Brummell, Hyung-Taeg Cho, Daniel J. Cosgrove, Andrew J. Fleming, Chris Gehring, Yi Lee, Simon McQueen-Mason, Jocelyn K.C. Rose and Laurentius A.C.J. Voesenek MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA (*author for correspondence; e-mail hkende@msu.edu); Seed Biotechnology Center, University of California, Davis CA 95616, USA; Crop and Food Research, Private Bag 11600, Palmerston North, 5301, New Zealand; School of Biosciences and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea; Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA; Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; University of the Western Cape, Department of Biotechnology, Private Bag X17, Bellville 7535, South Africa; Department of Tobacco Science, Chungbuk National University, 48 Gaesin-dong Hungduk-ku, Chongju 361-763, Republic of Korea; Biology Department, University of York, PO Box 373, York, YO10 5YW, UK; Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA; Plant Ecophysiology, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands

Auxin transport through PIN-FORMED 3 (PIN3) controls shade avoidance and fitness during competition

Plants grow in dense vegetations at the risk of being out-competed by neighbors. To increase their competitive power, plants display adaptive responses, such as rapid shoot elongation (shade avoidance) to consolidate light capture. These responses are induced upon detection of proximate neighbors through perception of the reduced ratio between red (R) and far-red (FR) light that is typical for dense vegetations. The plant hormone auxin is a central regulator of plant development and plasticity, but until now it has been unknown how auxin transport is controlled to regulate shade-avoidance responses. Here, we show that low R:FR detection changes the cellular location of the PIN-FORMED 3 (PIN3) protein, a regulator of auxin efflux, in Arabidopsis seedlings. As a result, auxin levels in the elongating hypocotyls are increased under low R:FR. Seedlings of the pin3-3 mutant lack this low R:FR-induced increase of endogenous auxin in the hypocotyl and, accordingly, have no elongation response to low R:FR. We hypothesize that low R:FR-induced stimulation of auxin biosynthesis drives the regulation of PIN3, thus allowing shade avoidance to occur. The adaptive significance of PIN3-mediated control of shade-avoidance is shown in plant competition studies. It was found that pin3 mutants are outcompeted by wild-type neighbors who suppress fitness of pin3-3 by 40%. We conclude that low R:FR modulates the auxin distribution by a change in the cellular location of PIN3, and that this control can be of great importance for plants growing in dense vegetations.

How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results

BackgroundShort oligonucleotide arrays for transcript profiling have been available for several years. Generally, raw data from these arrays are analysed with the aid of the Microarray Analysis Suite or GeneChip Operating Software (MAS or GCOS) from Affymetrix. Recently, more methods to analyse the raw data have become available. Ideally all these methods should come up with more or less the same results. We set out to evaluate the different methods and include work on our own data set, in order to test which method gives the most reliable results.ResultsCalculating gene expression with 6 different algorithms (MAS5, dChip PMMM, dChip PM, RMA, GC-RMA and PDNN) using the same (Arabidopsis) data, results in different calculated gene expression levels. Consequently, depending on the method used, different genes will be identified as differentially regulated. Surprisingly, there was only 27 to 36% overlap between the different methods. Furthermore, 47.5% of the genes/probe sets showed good correlation between the mismatch and perfect match intensities.ConclusionAfter comparing six algorithms, RMA gave the most reproducible results and showed the highest correlation coefficients with Real Time RT-PCR data on genes identified as differentially expressed by all methods. However, we were not able to verify, by Real Time RT-PCR, the microarray results for most genes that were solely calculated by RMA. Furthermore, we conclude that subtraction of the mismatch intensity from the perfect match intensity results most likely in a significant underestimation for at least 47.5% of the expression values. Not one algorithm produced significant expression values for genes present in quantities below 1 pmol. If the only purpose of the microarray experiment is to find new candidate genes, and too many genes are found, then mutual exclusion of the genes predicted by contrasting methods can be used to narrow down the list of new candidate genes by 64 to 73%.

Interactions between Ethylene and Gibberellins in Phytochrome-Mediated Shade Avoidance Responses in Tobacco

Plants respond to proximate neighbors with a suite of responses that comprise the shade avoidance syndrome. These phytochrome-mediated responses include hyponasty (i.e. a more vertical orientation of leaves) and enhanced stem and petiole elongation. We showed recently that ethylene-insensitive tobacco (Nicotiana tabacum) plants (Tetr) have reduced responses to neighbors, showing an important role for this gaseous plant hormone in shade avoidance. Here, we investigate interactions between phytochrome signaling and ethylene action in shade avoidance responses. Furthermore, we investigate if ethylene acts in these responses through an interaction with the GA class of hormones. Low red to far-red light ratios (R:FR) enhanced ethylene production in wild-type tobacco, resulting in shade avoidance responses, whereas ethylene-insensitive plants showed reduced shade avoidance responses. Plants with inhibited GA production showed hardly any shade avoidance responses at all to either a low R:FR or increased ethylene concentrations. Furthermore, low R:FR enhanced the responsiveness of hyponasty and stem elongation in both wild-type and Tetr plants to applied GA3, with the stem elongation process being more responsive to GA3 in the wild type than in Tetr. We conclude that phytochrome-mediated shade avoidance responses involve ethylene action, at least partly by modulating GA action.

Flood adaptive traits and processes: an overview

Unanticipated flooding challenges plant growth and fitness in natural and agricultural ecosystems. Here we describe mechanisms of developmental plasticity and metabolic modulation that underpin adaptive traits and acclimation responses to waterlogging of root systems and submergence of aerial tissues. This includes insights into processes that enhance ventilation of submerged organs. At the intersection between metabolism and growth, submergence survival strategies have evolved involving an ethylene-driven and gibberellin-enhanced module that regulates growth of submerged organs. Opposing regulation of this pathway is facilitated by a subgroup of ethylene-response transcription factors (ERFs), which include members that require low O₂ or low nitric oxide (NO) conditions for their stabilization. These transcription factors control genes encoding enzymes required for anaerobic metabolism as well as proteins that fine-tune their function in transcription and turnover. Other mechanisms that control metabolism and growth at seed, seedling and mature stages under flooding conditions are reviewed, as well as findings demonstrating that true endurance of submergence includes an ability to restore growth following the deluge. Finally, we highlight molecular insights obtained from natural variation of domesticated and wild species that occupy different hydrological niches, emphasizing the value of understanding natural flooding survival strategies in efforts to stabilize crop yields in flood-prone environments.