Genome-wide Analysis of Transcript Abundance and Translation in Arabidopsis Seedlings Subjected to Oxygen Deprivation

Abstract

Alterations in transcript abundance and translation contribute to the differential regulation of gene expression in response to oxygen deprivation.

Flooding tolerance: suites of plant traits in variable environments

“…For example, Arabidopsis protoplasts that are not well aerated demonstrate large reductions in accumulation of many gene transcripts, especially those coding for energy consuming processes such as ribosome biogenesis and anabolism (Baena-González et al 2007). Furthermore, in Arabidopsis seedlings a large portion (70%) of cellular mRNA's become poorly translated upon low O 2 stress (Branco-Price et al 2005, 2008. Even in highly-tolerant species with relatively high rates of ethanolic fermentation supporting anoxic shoot elongation (e.g.…”

“…Examples are the use of pyrophosphate (PP i ) over ATP as a high-energy donor (Huang et al 2008) and the preferred use of sucrose synthase (SuSy) and UDPglucose pyrophosphorylase for the degradation of sucrose (Geigenberger 2003). More generally, certain mRNAs circumvent translational repression and/or are transcriptionally upregulated thus selectively ensuring production of a specific set of proteins (Branco-Price et al 2005, 2008. These 'anaerobic Fig.…”

“…The IRRI protocol involves transplanting 14-day-old seedlings into the field, submerge when 28-day-old, de-submerge when 42-day-old, and the photo was taken~3 weeks after de-submergence (A. M. Ismail, pers. comm proteins' are involved in (i) glycolysis, (ii) conversion of pyruvate to fermentation end products, (iii) sucrose degradation, and (iv) controlling reactive oxygen species (ROS) (Sachs et al 1996;Klok et al 2002;Branco-Price et al 2005;Huang et al 2005;Liu et al 2005;Loreti et al 2005;Lasanthi-Kudahettige et al 2007;Igamberdiev and Hill 2009;Kreuzwieser et al 2009;van Dongen et al 2009). There is evidence that protein kinases belonging to the SnRK1 group, such as Arabidopsis KIN10 and KIN11, orchestrate transcriptional networks to globally promote catabolism (cell wall, starch, sucrose, amino acid, lipid and protein degradation) to provide alternative sources of energy and metabolites and suppress anabolism during hypoxiainduced carbohydrate starvation and/or energy deprivation (Baena-González et al 2007).…”

Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog

“…In plants, evidence suggests that r-protein regulation occurs predominantly post-transcriptionally, via partitioning of r-protein transcripts in either the polysomal (actively translated) or RNP (inactive) fractions. For example, in response to sucrose starvation (Nicolai et al 2006), drought (Kawaguchi et al 2004), or hypoxia (Branco-Price et al 2005), r-protein transcripts exhibit a coordinated decrease in polysomal loading. Nevertheless, transcriptional regulation is also important given Wndings that r-protein transcripts from a number of plant species show their greatest accumulation in mitotically active tissues and are coordinately upregulated following wounding and phytohormone treatments (reviewed in McIntosh and Bonham-Smith 2006).…”

Effect of osmotic stress on in vitro translational capacity of polysomes and on the composition of polysome-associated proteins in germinating seeds of pea (Pisum sativum L.)

“…The end products from in vitro translation of polysomes also reflect the activity of mRNAs that respond to stress [43]. Synthesis of most proteins under environmental stresses is reduced but translation of individual mRNA species is differentially regulated [23,[44][45][46]. Kawaguchi et al [45] showed that less than 1% of the stress-induced mRNAs increased significantly in polysome association, what can suggest that proteins encoded by this mRNAs were synthesized at higher levels during stress conditions.…”