The link between transcript regulation and de novo protein synthesis in the retrograde high light acclimation response of Arabidopsis thaliana

Background

Efficient light acclimation of photosynthetic cells is a basic and important property of plants. The process of acclimation depends on transformation of retrograde signals in gene expression, transcript accumulation and de novo protein synthesis. While signalling cues, transcriptomes and some involved players have been characterized, an integrated view is only slowly emerging, and information on the translational level is missing. Transfer of low (8 μmol quanta^.m^-2.s^-1) or normal light (80 μmol quanta^.m^-2.s^-1) acclimated 30 d old Arabidopsis thaliana plants to high light (800 μmol quanta^.m^-2.s^-1) triggers retrograde signals. Using this established approach, we sought to link transcriptome data with de novo synthesized proteins by in vivo labelling with ³⁵S methionine and proteome composition.

Results

De novo synthesized protein and proteome patterns could reliably be matched with newly annotated master gels. Each molecular level could be quantified for a set of 41 proteins. Among the proteins preferentially synthesized in plants transferred to high light were enzymes including carbonic anhydrase, fructose-1,6-bisphosphate aldolase, O-acetyl serine thiol lyase, and chaperones, while low rates upon transfer to high light were measured for e.g. dehydroascorbate reductase, glyceraldehyde-3-phosphate dehydrogenase and CuZn superoxide dismutase, and opposite responses between 10-fold and 100-fold light increment for e.g. glutamine synthetase and phosphoglycerate kinase.

Conclusions

The results prove the hypothesis that transcript abundance is poorly linked to de novo protein synthesis due to profound regulation at the level of translation. This vertical systems biology approach enables to quantitatively and kinetically link the molecular levels for scrutinizing signal processing and response generation.

The essential role of sugar metabolism in the acclimation response of Arabidopsis thaliana to high light intensities

Retrograde signals from chloroplasts are thought to control the expression of nuclear genes associated with plastidial processes such as acclimation to varying light conditions. Arabidopsis mutants altered in the day and night path of photoassimilate export from the chloroplasts served as tools to study the involvement of carbohydrates in high light (HL) acclimation. A double mutant impaired in the triose phosphate/phosphate translocator (TPT) and ADP-glucose pyrophosphorylase (AGPase) (adg1-1/tpt-2) exhibits a HL-dependent depletion in endogenous carbohydrates combined with a severe growth and photosynthesis phenotype. The acclimation response of mutant and wild-type plants has been assessed in time series after transfer from low light (LL) to HL by analysing photosynthetic performance, carbohydrates, MgProtoIX (a chlorophyll precursor), and the ascorbate/glutathione redox system, combined with microarray-based transcriptomic and GC-MS-based metabolomic approaches. The data indicate that the accumulation of soluble carbohydrates (predominantly glucose) acts as a short-term response to HL exposure in both mutant and wild-type plants. Only if carbohydrates are depleted in the long term (e.g. after 2 d) is the acclimation response impaired, as observed in the adg1-1/tpt-2 double mutant. Furthermore, meta-analyses conducted with in-house and publicly available microarray data suggest that, in the long term, reactive oxygen species such as H₂O₂ can replace carbohydrates as signals. Moreover, a cross-talk exists between genes associated with the regulation of starch and lipid metabolism. The involvement of genes responding to phytohormones in HL acclimation appears to be less likely. Various candidate genes involved in retrograde control of nuclear gene expression emerged from the analyses of global gene expression.

Kinetics of retrograde signalling initiation in the high light response of Arabidopsis thaliana

High light acclimation depends on retrograde control of nuclear gene expression. Retrograde regulation uses multiple signalling pathways and thus exploits signal patterns. To maximally challenge the acclimation system, Arabidopsis thaliana plants were either adapted to 8 (low light (L-light)) or 80 µmol quanta m(-2) s(-1) (normal light (N-light)) and subsequently exposed to a 100- and 10-fold light intensity increase, respectively, to high light (H-light, 800 µmol quanta m(-2) s(-1)), for up to 6 h. Both L → H- and N → H-light plants efficiently regulated CO2 assimilation to a constant level without apparent damage and inhibition. This experimental set-up was scrutinized for time-dependent regulation and efficiency of adjustment. Transcriptome profiles revealed that N-light and L-light plants differentially accumulated 2119 transcripts. After 6 h in H-light, only 205 remained differently regulated between the L → H- and N → H-light plants, indicating efficient regulation allowing the plants to reach a similar transcriptome state. Time-dependent analysis of transcripts as markers for signalling pathways, and of metabolites and hormones as possibly involved transmitters, suggests that oxylipins such as oxophytodienoic acid and jasmonic acid, metabolites and redox cues predominantly control the acclimation response, whereas abscisic acid, salicylic acid and auxins play an insignificant or minor role.

The involvement of the mitochondrial peroxiredoxin PRXIIF in defining physiological differences between orthodox and recalcitrant seeds of two Acer species

Norway maple (Acer platanoides L., orthodox) and sycamore (Acer pseudoplatanus L., recalcitrant) belong to the same genus and grow under similar climatic conditions, but their seeds differ in their tolerance to desiccation. The initial water content (WC) of the seeds used in this study was 50%, and they were dried to 40, 20 and 7%. The mitochondrial peroxiredoxin IIF (PRXIIF) was identified in seeds of both species by immunoblotting. Semiquantitative RT-PCR analyses indicated that the transcript level of PRXIIF in both types of seeds increased during different stages of desiccation and was higher in seeds of Norway maple than in sycamore. General proteome analyses showed important differences between orthodox and recalcitrant seeds. In sycamore seeds that had been desiccated to a 7% WC, the number of protein spots and the levels of those spots were lower than in desiccation-tolerant Norway maple seeds. Post-translational modifications of PRXIIF in seeds at a 50% WC were detected via 2D electrophoresis and subsequent western blot analysis. The detected shift in the pI values (± 0.3) in A. pseudoplatanus was possibly caused by phosphorylation because several potential phosphorylation sites were predicted in silico for that protein. The gene and amino acid sequences were obtained and aligned with known sequences of other plant PRXIIF genes and proteins. High values of sequence identity were noted between the PRXIIF protein sequences of Acer species, Populus trichocarpa Torr. & A. Gray and Arabidopsis thaliana (L.) Heynh. The involvement of PRXIIF in defining the physiological differences between desiccation-tolerant and desiccation-sensitive Acer seeds is discussed in the context of its role in mitochondrial redox homeostasis.

Multiple strategies to prevent oxidative stress in Arabidopsis plants lacking the malate valve enzyme NADP-malate dehydrogenase

The nuclear-encoded chloroplast NADP-dependent malate dehydrogenase (NADP-MDH) is a key enzyme controlling the malate valve, to allow the indirect export of reducing equivalents. Arabidopsis thaliana (L.) Heynh. T-DNA insertion mutants of NADP-MDH were used to assess the role of the light-activated NADP-MDH in a typical C(3) plant. Surprisingly, even when exposed to high-light conditions in short days, nadp-mdh knockout mutants were phenotypically indistinguishable from the wild type. The photosynthetic performance and typical antioxidative systems, such as the Beck-Halliwell-Asada pathway, were barely affected in the mutants in response to high-light treatment. The reactive oxygen species levels remained low, indicating the apparent absence of oxidative stress, in the mutants. Further analysis revealed a novel combination of compensatory mechanisms in order to maintain redox homeostasis in the nadp-mdh plants under high-light conditions, particularly an increase in the NTRC/2-Cys peroxiredoxin (Prx) system in chloroplasts. There were indications of adjustments in extra-chloroplastic components of photorespiration and proline levels, which all could dissipate excess reducing equivalents, sustain photosynthesis, and prevent photoinhibition in nadp-mdh knockout plants. Such metabolic flexibility suggests that the malate valve acts in concert with other NADPH-consuming reactions to maintain a balanced redox state during photosynthesis under high-light stress in wild-type plants.

Efficient acclimation of the chloroplast antioxidant defence of Arabidopsis thaliana leaves in response to a 10- or 100-fold light increment and the possible involvement of retrograde signals

Chloroplasts are equipped with a nuclear-encoded antioxidant defence system the components of which are usually expressed at high transcript and activity levels. To significantly challenge the chloroplast antioxidant system, Arabidopsis thaliana plants, acclimated to extremely low light slightly above the light compensation point or to normal growth chamber light, were moved to high light corresponding to a 100- and 10-fold light jump, for 6 h and 24 h in order to observe the responses of the water-water cycle at the transcript, protein, enzyme activity, and metabolite levels. The plants coped efficiently with the high light regime and the photoinhibition was fully reversible. Reactive oxygen species (ROS), glutathione and ascorbate levels as well as redox states, respectively, revealed no particular oxidative stress in low-light-acclimated plants transferred to 100-fold excess light. Strong regulation of the water-water cycle enzymes at the transcript level was only partly reflected at the protein and activity levels. In general, low light plants had higher stromal (sAPX) and thylakoid ascorbate peroxidase (tAPX), dehydroascorbate reductase (DHAR), and CuZn superoxide dismutase (CuZnSOD) protein contents than normal light-grown plants. Mutants defective in components relevant for retrograde signalling, namely stn7, ex1, tpt1, and a mutant expressing E .coli catalase in the chloroplast showed unaltered transcriptional responses of water-water cycle enzymes. These findings, together with the response of marker transcripts, indicate that abscisic acid is not involved and that the plastoquinone redox state and reactive oxygen species do not play a major role in regulating the transcriptional response at t=6 h, while other marker transcripts suggest a major role for reductive power, metabolites, and lipids as signals for the response of the water-water cycle.

Ultrasonic attenuation estimation of the pregnant cervix: a preliminary report

OBJECTIVE

Estimates of ultrasonic attenuation (the loss of energy as an ultrasonic wave propagates through tissue) have been used to evaluate the structure and function of tissues in health and disease. The purpose of this research was to develop a method to estimate ultrasonic cervical attenuation during human pregnancy using a clinical ultrasound system.

METHODS

Forty women underwent a cervical scan once during pregnancy with the Zonare z.one clinical ultrasound system using a 4-9-MHz endovaginal transducer. This ultrasound system provides access to radiofrequency (RF) image data for processing and analysis. In addition, a scan of a tissue-mimicking phantom with a known attenuation coefficient was acquired and used as a reference. The same settings and transducer used in the clinical scan were used in the reference scan. Digital data of the beam-formed image were saved in Digital Imaging and Communications in Medicine (DICOM) format on a flash drive and converted to RF data on a personal computer using a Matlab program supplied by Zonare. Attenuation estimates were obtained using an algorithm that was independently validated using tissue-mimicking ultrasonic phantoms.

RESULTS

RF data were acquired and analyzed to estimate attenuation of the human pregnant cervix. Regression analysis revealed that attenuation was: a predictor of the interval from ultrasound examination to delivery (beta = 0.43, P = 0.01); not a predictor of gestational age at time of examination (beta = - 0.23, P = 0.15); and not a predictor of cervical length (beta = 0.077, P = 0.65).

CONCLUSIONS

Ultrasonic attenuation estimates have the potential to be an early and objective non-invasive method to detect interval between examination and delivery. We hypothesize that a larger sample size and a longitudinal study design will be needed to detect gestational age-associated changes in cervical attenuation.

Mg protoporphyrin monomethylester cyclase deficiency and effects on tetrapyrrole metabolism in different light conditions

Mg protoporphyrin monomethylester (MgProtoME) cyclase catalyzes isocyclic ring formation to form divinyl protochlorophyllide. The CHL27 protein is part of the cyclase complex. Deficiency of CHL27 has been previously reported to compromise photosynthesis and nuclear gene expression. In a comprehensive analysis of different CHL27 antisense tobacco lines grown under different light conditions, the physiological consequences of gradually reduced CHL27 expression on the tetrapyrrole biosynthetic pathway were explored. Excessive amounts of MgProtoME, the substrate of the cyclase reaction, accumulated in response to the reduced CHL27 content. Moreover, 5-aminolevulinic acid (ALA) synthesis, Mg chelatase and Mg protoporphyrin methyltransferase activities were reduced in transgenic plants. Compared with growth under continuous light exposure, the CHL27-deficient plants showed a stronger reduction in Chl content, cell death and leaf necrosis during diurnal light/dark cycles. This photooxidative phenotype correlated with a rapidly increasing MgProtoME steady-state level at the beginning of each light period. In contrast, the same transformants grown under continuous light exposure possessed a permanently elevated amount of MgProtoME. Its lower phototoxicity correlated with increased activities of ascorbate peroxidase and catalase, and a higher amount of reduced ascorbate. It is proposed that improved stress acclimation during continuous light in comparison with light-dark growth increases the capacity to prevent photooxidation by excess tetrapyrrole precursors and lowers the susceptibility to secondary photodynamic damage.

Redox regulation and overreduction control in the photosynthesizing cell: complexity in redox regulatory networks

Regulation of the photosynthetic apparatus between efficient energy conversion at low light and avoidance of overreduction and damage development at excess light resembles dangerous navigating between Scylla and Charybdis. Photosynthesis is a high rate redox metabolic pathway that generates redox intermediates with extreme redox potentials and eventually reactive oxygen species and oxidative stress. Therefore it is not surprising that the states of defined redox reactions in the chloroplast provide the predominant information and thus directly or indirectly the decisive signals for the multilevel control of cell activities in the chloroplast, cytoplasm, mitochondrion and nucleus. This review elaborates on the diversity of photosynthesis-derived redox signals such as the plastoquinone and thiol redox state that regulate and coordinate light use efficiency, electron transport activity, metabolic reactions, gene transcription and translation not only in the chloroplast but through retrograde signaling also essentially in all other cell compartments. The synergistic and antagonistic interrelations between the redox-dependent signaling pathways and their interactions with other signals such as abscisic acid and tetrapyrol intermediates constitute a redundant and probably buffered regulatory network to optimize performance of photosynthesis on the cellular and whole leaf level.

The function of peroxiredoxins in plant organelle redox metabolism

In 1996, cDNA sequences referred to as plant peroxiredoxins (Prx), i.e. a 1-Cys Prx and a 2-Cys Prx, were reported from barley. Ten years of research have advanced our understanding of plant Prx as thiol-based peroxide reductases with a broad substrate specificity, ranging from hydrogen peroxide to alkyl hydroperoxides and peroxinitrite. Prx have several features in common. (i) They are abundant proteins that are routinely detected in proteomics approaches. (ii) They interact with proteins such as glutaredoxins, thioredoxins, and cyclophilins as reductants, but also non-dithiol-disulphide exchange proteins. By work with transgenic plants, their activity was shown to (iii) affect metabolic integrity, (iv) protect DNA from damage in vitro and as shown here in vivo, and (v) modulate intracellular signalling related to reactive oxygen species and reactive nitrogen species. (vi) In all organisms Prx are encoded by small gene families that are of particular complexity in higher plants. A comparison of the Prx gene families in rice and Arabidopsis thaliana supports previous suggestions on Prx function in specific subcellular and metabolic context. (vii) Prx gene expression and activity are subjected to complex regulation realized by an integration of various signalling pathways. 2-Cys Prx expression depends on redox signals, abscisic acid, and protein kinase cascades. Besides these general properties, the chloroplast Prx have acquired specific roles in the context of photosynthesis. The thioredoxin-dependent peroxidase activity can be measured in crude plant extracts and contributes significantly to the overall H(2)O(2) detoxification capacity. Thus organellar Prx proteins enable an alternative water-water cycle for detoxification of photochemically produced H(2)O(2), which acts independently from the ascorbate-dependent Asada-Halliwell-Foyer cycle. 2-Cys Prx and Prx Q associate with thylakoid membrane components. The mitochondrial PrxII F is essential for root growth under stress. Following a more general introduction, the paper summarizes present knowledge on plant organellar Prx, addressing Prx in signalling, and also suggests some lines for future research.

Roughness characterization of porous soil with acoustic backscatter

The use of acoustics to determine the pore properties of soils, such as porosity, permeability, and tortuosity, is well established. A theoretical surface impedance and complex bulk wavenumber was developed by K. Attenborough for porous media that incorporated the soil pore properties as parameters [J. Acoust. Soc. Am. 73, 785-799 (1983)]. Acoustic level difference measurements were used as a noninvasive means of finding the soil pore properties. Acoustic reflection measurements showed that the sound field over porous rough surfaces is modified by the surface impedance and by surface roughness. It is not possible to separate the signal modification due to impedance and the signal modification from roughness scattering in a forward scattering measurement. In order to accurately determine the soil pore properties, the roughness effects must be known independently from the surface impedance. A means of measuring roughness apart from impedance would allow the effects of roughness to be taken out of the level difference measurements. The underwater acoustics community has used acoustic backscatter for many years to examine surface roughness. The feasibility of adapting these acoustic backscatter techniques to outdoor porous soil surfaces is examined.