Treatment of Arabidopsis (Arabidopsis thaliana) alternative oxidase1a (aox1a) mutant plants with moderate light under drought conditions resulted in a phenotypic difference compared with ecotype Columbia (Col-0), as evidenced by a 10-fold increase in the accumulation of anthocyanins in leaves, alterations in photosynthetic efficiency, and increased superoxide radical and reduced root growth at the early stages of seedling growth. Analysis of metabolite profiles revealed significant changes upon treatment in aox1a plants typical of combined stress treatments, and these were less pronounced or absent in Col-0 plants. These changes were accompanied by alteration in the abundance of a variety of transcripts during the stress treatment, providing a molecular fingerprint for the stress-induced phenotype of aox1a plants. Transcripts encoding proteins involved in the synthesis of anthocyanins, transcription factors, chloroplastic and mitochondrial components, cell wall synthesis, and sucrose and starch metabolism changed, indicating that effects were not confined to mitochondria, where the AOX1a protein is located. Microarray and quantitative reverse transcription-polymerase chain reaction analysis revealed that transcripts typically induced upon stress treatment or involved in antioxidant defense systems, especially chloroplast-located antioxidant defense components, had altered basal levels in untreated aox1a plants, suggesting a significant change in the basal equilibrium of signaling pathways that regulate these components. Taken together, these results indicate that aox1a plants have a greatly altered stress response even when mitochondria or the mitochondrial electron transport chain are not the primary target of the stress and that AOX1a plays a broad role in determining the normal redox balance in the cell.

To gain a global view of mRNA decay in Arabidopsis thaliana, suspension cell cultures were treated with a transcriptional inhibitor, and microarrays were used to measure transcript abundance over time. The deduced mRNA half-lives varied widely, from minutes to >24 h. Three features of the transcript displayed a correlation with decay rates: (1) genes possessing at least one intron produce mRNA transcripts significantly more stable than those of intronless genes, and this was not related to overall length, sequence composition, or number of introns; (2) various sequence elements in the 39 untranslated region are enriched among short-and long-lived transcripts, and their multiple occurrence suggests combinatorial control of transcript decay; and (3) transcripts that are microRNA targets generally have short half-lives. The decay rate of transcripts correlated with subcellular localization and function of the encoded proteins. Analysis of transcript decay rates for genes encoding orthologous proteins between Arabidopsis, yeast, and humans indicated that yeast and humans had a higher percentage of transcripts with shorter half-lives and that the relative stability of transcripts from genes encoding proteins involved in cell cycle, transcription, translation, and energy metabolism is conserved. Comparison of decay rates with changes in transcript abundance under a variety of abiotic stresses reveal that a set of transcription factors are downregulated with similar kinetics to decay rates, suggesting that inhibition of their transcription is an important early response to abiotic stress.

The molecular and physiological responses of gray poplar (Populus 3 canescens) following root hypoxia were studied in roots and leaves using transcript and metabolite profiling. The results indicate that there were changes in metabolite levels in both organs, but changes in transcript abundance were restricted to the roots. In roots, starch and sucrose degradation were altered under hypoxia, and concurrently, the availability of carbohydrates was enhanced, concomitant with depletion of sucrose from leaves and elevation of sucrose in the phloem. Consistent with the above, glycolytic flux and ethanolic fermentation were stimulated in roots but not in leaves. Various messenger RNAs encoding components of biosynthetic pathways such as secondary cell wall formation (i.e. cellulose and lignin biosynthesis) and other energy-demanding processes such as transport of nutrients were significantly down-regulated in roots but not in leaves. The reduction of biosynthesis was unexpected, as shoot growth was not affected by root hypoxia, suggesting that the up-regulation of glycolysis yields sufficient energy to maintain growth. Besides carbon metabolism, nitrogen metabolism was severely affected in roots, as seen from numerous changes in the transcriptome and the metabolome related to nitrogen uptake, nitrogen assimilation, and amino acid metabolism. The coordinated physiological and molecular responses in leaves and roots, coupled with the transport of metabolites, reveal important stress adaptations to ensure survival during long periods of root hypoxia.Higher plants are aerobic organisms and depend on the availability of O 2 . A lack of O 2 in the rhizosphere affects the maintenance of numerous pathways and is therefore an important environmental stress for vascular plants (Drew, 1997). Plant adaptations to O 2 deprivation include avoidance strategies at the morphological level and physiological tolerance mechanisms (Bailey-Serres and Voesenek, 2008). One of the major cellular pathways dependent on O 2 is mitochondrial respiration. In order to maintain energy generation under conditions of decreased O 2 availability, plants switch from respiration to fermentative metabolism. Fermentation allows regeneration of NAD + in the absence of respiration, thereby maintaining glycolysis and the generation of ATP under anaerobic conditions. As an initial reaction to O 2 deprivation, many plants activate lactic acid fermentation. As generation of lactic acid causes a decrease in cytosolic pH (Roberts et al., 1984), which reduces the activity of the responsible enzyme, lactate dehydrogenase (LDH; Hanson and Jacobson, 1984), lactic acid fermentation is followed by alcoholic fermentation (Davies et al., 1974;Roberts et al., 1984). The significantly lower energy yield of alcoholic fermentation, compared with mitochondrial respiration, causes an energy crisis in anaerobic tissues (Bailey-Serres and Voesenek, 2008).A high rate of fermentation increases the demand for carbohydrates, leading to the hypothesis that carbohydrate supply becomes c...

As the sun tracks daily through the sky from east to west, different parts of the canopy are exposed to high light (HL). The extent of and mechanisms by which a systemic acquired acclimation (SAA) response might preacclimate shaded leaves that will be subsequently exposed to full sunlight is largely undefined. We investigated the role of an Arabidopsis thaliana zinc finger transcription factor, ZAT10, in SAA. ZAT10 overexpression resulted in enhanced tolerance to photoinhibitory light and exogenous H 2 O 2 , increased expression of antioxidative genes whose products are targeted to multiple subcellular compartments. Partial HL exposure of a leaf or leaves rapidly induced ZAT10 mRNA in distal, shaded photosynthetic tissues, including the floral stem, cauline leaves, and rosette, but not in roots. Fully 86% of fivefold HL-upregulated and 71% of HL-downregulated genes were induced and repressed, respectively, in distal, shaded leaves. Between 15 and 23% of genes whose expression changed in the HL and/or distal tissues were coexpressed in the ZAT10 overexpression plants, implicating ZAT10 in modulating the expression of SAA-regulated genes. The SAA response was detectable in plants with mutations in abscisic acid, methyl jasmonate, or salicylic acid synthesis or perception, and systemic H 2 O 2 diffusion was not detected. Hence, SAA is distinct from pathogen-stimulated systemic acquired resistance and apparently involves a novel signal or combination of signals that preacclimate photosynthetic tissues to HL.