Impact of oxidative stress on the function,abundance, and turnover of the Arabidopsis 80S cytosolic ribosome

Abiotic stress in plants causes accumulation of reactive oxygen species (ROS) leading to the need for new protein synthesis to defend against ROS and to replace existing proteins that are damaged by oxidation. Functional plant ribosomes are critical for these activities, however we know little about the impact of oxidative stress on plant ribosome abundance, turnover, and function. Using Arabidopsis cell culture as a model system, we induced oxidative stress using 1 µm of H₂O₂ or 5 µm menadione to more than halve cell growth rate and limit total protein content. We show that ribosome content on a total cell protein basis decreased in oxidatively stressed cells. However, overall protein synthesis rates on a ribosome abundance basis showed the resident ribosomes retained their function in oxidatively stressed cells. ¹⁵N progressive labelling was used to calculate the rate of ribosome synthesis and degradation to track the fate of 62 r‐proteins. The degradation rates and the synthesis rates of most r‐proteins slowed following oxidative stress leading to an ageing population of ribosomes in stressed cells. However, there were exceptions to this trend; r‐protein RPS14C doubled its degradation rate in both oxidative treatments. Overall, we show that ribosome abundance decreases and their age increases with oxidative stress in line with loss of cell growth rate and total cellular protein amount, but ribosome function of the ageing ribosomes appeared to be maintained concomittently with differences in the turnover rate and abundance of specific ribosomal proteins. Data are available via ProteomeXchange with identifier PXD012840.     

The effect of the dw gene on the muscle protein turnover rate in chickens

Fractional rates (%/day) of muscle protein synthesis and degradation of the genotypes Dw/Dw and dw/dw of male White Plymouth Rock chickens were determined by measuring the output of N-methylhistidine (N-MH) in the excreta at 2, 4, and 8 weeks of age. The fractional growth rate of dw/dw was significantly lower (P<0.05) than that of Dw/Dw at 2 weeks of age but not at 4 and 8 weeks of age. No significant differences in the degradation rate (K _d; %/day) were found at any age. A significant difference (P<0.05) between genotypes in the rate of synthesis (K _s; %/day) was found at 2 weeks of age (Dw/Dw=11.8, dw/dw=9.9) but not at 4 and 8 weeks of age. These results suggest that the dw gene has a depressing effect on the synthesis rate of muscle protein, and the difference between genotypes in the growth rate at the early stage is a reflection of this effect.     

The dynamics of the proteome: strategies for measuring protein turnover on a proteome-wide scale.

Quantitative proteomics captures the steady-state amount of a protein in a cell but does not explain how a change in protein amount is manifest -- whether through a change in synthesis or a change in degradation. If we are to understand the changes in the proteome, we will need to define such processes. In this brief review, strategies for the determination of intracellular protein dynamics on a proteome-wide scale are discussed.     

Bacterial protein meal in diets for pigs and minks: Comparative studies on protein turnover rate and urinary excretion of purine base derivatives

Abstract

The effect of increasing the dietary content of bacterial protein meal (BPM) on protein turnover rate, and on nucleic acid and creatinine metabolism in growing minks and pigs was investigated in two experiments. In each experiment, 16 animals were allocated to four experimental diets. The diets containing no BPM served as controls, i.e. for minks diet M1, for pigs P1; the experimental diets contained increasing levels of BPM to replace fish meal (minks) or soybean meal (pigs), so that up to 17% (P2), 20% (M2), 35% (P3), 40% (M3), 52% (P4), and 60% (M4) of digestible N was BPM derived. Protein turnover rate was measured by means of the end-product method using [¹⁵N]glycine as tracer and urinary nitrogen as end-product. In minks, protein flux, synthesis, and breakdown increased significantly with increasing dietary BPM. In pigs, diet had no observed effect on protein turnover rate. The intake of nucleic acid nitrogen (NAN) increased from 0.15 g/kg W^0.75 on M1 to 0.26 g/kg W^0.75 on M3 and M4 in the mink experiment, and from 0.08 g/kg W^0.75 on P1 to 0.33 g/kg W^0.75 on P4 in the pig experiment. Increased NAN intake led, in both experiments, to increased allantoin excretion. Analysis of species effects showed that minks excreted 1.72 mmol/kg W^0.75 of allantoin, significantly more than the 0.95 mmol/kg W^0.75 excreted by pigs. In minks, approximately 96% of the excreted purine base derivatives consisted of allantoin, whereas in pigs approximately 93% did. Thus, increasing the dietary content of BPM increased protein turnover rate in minks but not in pigs, and allantoin excretion increased with increasing dietary BPM although it seemed that mink decomposed purine bases to their end-product more completely than pigs did. Collectively these data show that BPM is a suitable protein source for pigs and mink, and recorded differences between species were to a large extent due to differences in protein retention capacity and muscle mass.     

The WAG1 and WAG2 protein kinases negatively regulate root waving in Arabidopsis

The WAG1 and WAG2 genes of Arabidopsis thaliana encode protein-serine/threonine kinases that are closely related to PINOID. In order to determine what roles WAG1 and WAG2 play in seedling development, we used a reverse genetics approach to study the wag1, wag2 and wag1/wag2 mutant phenotypes for clues. Although the wag mutants do not contain detectable amounts of the corresponding mRNA, they are wild type in most respects. However, wag1/wag2 double mutants exhibit a pronounced wavy root phenotype when grown vertically on agar plates, a phenotype observed in wild-type plants only on plates inclined to angles less than 90 degrees. The wag1 and wag2 mutants also demonstrate enhanced root waving, but to a lesser extent. Moreover, the double mutant roots are more resistant to the effects of N-1-naphthylphthalamic acid on the inhibition of root curling, raising the possibility that transport of auxin is affected in the wag mutants. Promoter fusions to the gusA reporter gene demonstrate that the WAG promoters are most active in root tips, consistent with the observed phenotypes in the wag mutants.     

Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions

Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (Φ_PSII) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in Φ_PSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in Φ_PSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.     

Photodamaged D1 protein is degraded in Arabidopsis mutants lacking the Deg2 protease

In plants exposed to high irradiances of visible light, the D1 protein in the reaction center of photosystem II is oxidatively damaged and rapidly degraded. Earlier work in our laboratory showed that the serine protease Deg2 performs the primary cleavage of photodamaged D1 protein in vitro. Here, we demonstrate that the rate of D1 protein degradation under light stress conditions in Arabidopsis mutants lacking the Deg2 protease is similar to those in wild-type plants. Therefore, we propose that several redundant D1 protein degradation pathways might exist in vivo.     

Overexpression of AtPTPA in Arabidopsis increases protein phosphatase 2A activity by promoting holoenzyme formation and ABA negatively affects holoenzyme formation

AtPTPA is a critical regulator for the holoenzyme assembling of protein phosphatase 2A (PP2A) in Arabidopsis. Characterization of AtPTPA improves our understanding of the function and regulation of PP2A in eukaryotes. Further analysis of AtPTPA-overexpressing plants indicates that AtPTPA increases PP2A activity by promoting PP2A''s AC dimer formation, thereby holoenzyme assembling. Plant hormone abscisic acid (ABA) reduces PP2A enzyme activity by negatively affects PP2A''s AC dimer formation. Therefore, AtPTPA is a positive factor that promotes PP2A holoenzyme assembly, and ABA is a negative factor that prevents PP2A holoenzyme assembly.     

Growth phase and growth rate dependence of ribosomal peptidyltransferase activity status in Escherichia coli

Ribosomes from a clinical isolate of E coli were purified and characterized. The structural features of these ribosomes were identical to wild-type E coli ribosomes, with the exception that rRNA in general, but especially 23S rRNA, was degraded as a result of the transition from early to late logarithmic growth phase, on different growth media. Analysis of the ribosomal protein by gel electrophoresis indicated that the L12/L7 molar ratio increases during early logarithmic phase, reaching a maximum value of about 1.6 at midlogarithmic phase, and then falling to 0.7 in late logarithmic phase. Concomitantly with L12/L7 alterations, the activity status of ribosomal peptidyltransferase was found to undergo a striking shift. Reconstitution experiments demonstrated that the two effects are closely related. Moreover, L12/L7 molar ratio as well as peptidyltransferase activity increased with increasing growth rate. In the latter case, however, the acetylation level of L12 protein per se seemed to be inadequate to modulate the peptidyltransferase activity.     

Quantification of mRNA and protein and integration with protein turnover in a bacterium

Biological function and cellular responses to environmental perturbations are regulated by a complex interplay of DNA, RNA, proteins and metabolites inside cells. To understand these central processes in living systems at the molecular level, we integrated experimentally determined abundance data for mRNA, proteins, as well as individual protein half‐lives from the genome‐reduced bacterium Mycoplasma pneumoniae. We provide a fine‐grained, quantitative analysis of basic intracellular processes under various external conditions. Proteome composition changes in response to cellular perturbations reveal specific stress response strategies. The regulation of gene expression is largely decoupled from protein dynamics and translation efficiency has a higher regulatory impact on protein abundance than protein turnover. Stochastic simulations using in vivo data show how low translation efficiency and long protein half‐lives effectively reduce biological noise in gene expression. Protein abundances are regulated in functional units, such as complexes or pathways, and reflect cellular lifestyles. Our study provides a detailed integrative analysis of average cellular protein abundances and the dynamic interplay of mRNA and proteins, the central biomolecules of a cell.     

Latitudinal variation in plant size and relative growth rate in Arabidopsis thaliana

Latitude is an important determinant of local environmental conditions that affect plant growth. Forty ecotypes of Arabidopsis thaliana were selected from a wide range of latitudes (from 16°N to 63°N) to investigate genetic variation in plant size and relative growth rate (RGR) along a latitudinal gradient. Plants were grown in a greenhouse for 31 days, during which period three consecutive harvests were performed. Plants from high latitudes tended to have smaller plant size in terms of seed size, cotyledon width, rosette size, number of rosette leaves, size (leaf area) of the largest leaves, total leaf area, and total dry weight per plant than those from low latitudes. The mean (±SE) RGR across ecotypes was 0.229 (±0.0013) day⁻¹. There was, however, significant ecotypic variation, with RGR being negatively correlated with latitude. The two main components of RGR, leaf area ratio (LAR) and unit leaf rate (ULR), were also correlated with latitude: LAR increased with increasing latitude while ULR decreased with increasing latitude. It was also found that RGR tended to be negatively correlated with LAR, specific leaf area (SLA) and specific root length (SRL) but to be positively correlated with mean area per leaf (MAL) and ULR. The variation in RGR among ecotypes was relatively small compared with that in the other traits. RGR may be a conservative trait, whose variation is constrained by the trade-off between its physiological (i.e. ULR) and morphological (i.e. LAR) components. Received: 2 November 1997 / Accepted: 28 February 1998     

Evidence for autophagy-dependent pathways of rRNA turnover in Arabidopsis

Ribosomes account for a majority of the cell''s RNA and much of its protein and represent a significant investment of cellular resources. The turnover and degradation of ribosomes has been proposed to play a role in homeostasis and during stress conditions. Mechanisms for the turnover of rRNA and ribosomal proteins have not been fully elucidated. We show here that the RNS2 ribonuclease and autophagy participate in RNA turnover in Arabidopsis thaliana under normal growth conditions. An increase in autophagosome formation was seen in an rns2–2 mutant, and this increase was dependent on the core autophagy genes ATG9 and ATG5. Autophagosomes and autophagic bodies in rns2–2 mutants contain RNA and ribosomes, suggesting that autophagy is activated as an attempt to compensate for loss of rRNA degradation. Total RNA accumulates in rns2–2, atg9–4, atg5–1, rns2–2 atg9–4, and rns2–2 atg5–1 mutants, suggesting a parallel role for autophagy and RNS2 in RNA turnover. rRNA accumulates in the vacuole in rns2–2 mutants. Vacuolar accumulation of rRNA was blocked by disrupting autophagy via an rns2–2 atg5–1 double mutant but not by an rns2–2 atg9–4 double mutant, indicating that ATG5 and ATG9 function differently in this process. Our results suggest that autophagy and RNS2 are both involved in homeostatic degradation of rRNA in the vacuole.     

The TIR-NBS protein TN13 associates with the CC-NBS-LRR resistance protein RPS5 and contributes to RPS5-triggered immunity in Arabidopsis

Nucleotide-binding site (NBS)–leucine-rich repeat (LRR) domain receptor (NLR) proteins play important roles in plant innate immunity by recognizing pathogen effectors. The Toll/interleukin-1 receptor (TIR)-NBS (TN) proteins belong to a subtype of the atypical NLRs, but their function in plant immunity is poorly understood. The well-characterized Arabidopsis thaliana typical coiled-coil (CC)-NBS-LRR (CNL) protein Resistance to Pseudomonas syringae 5 (RPS5) is activated after recognizing the Pseudomonas syringae type III effector AvrPphB. To explore whether the truncated TN proteins function in CNL-mediated immune signaling, we examined the interactions between the Arabidopsis TN proteins and RPS5, and found that TN13 and TN21 interacted with RPS5. However, only TN13, but not TN21, was involved in the resistance to P. syringae pv. tomato (Pto) strain DC3000 carrying avrPphB, encoding the cognate effector recognized by RPS5. Moreover, the regulation of Pto DC3000 avrPphB resistance by TN13 appeared to be specific, as loss of function of TN13 did not compromise resistance to Pto DC3000 hrcC⁻ or Pto DC3000 avrRpt2. In addition, we demonstrated that the CC and NBS domains of RPS5 play essential roles in the interaction between TN13 and RPS5. Taken together, our results uncover a direct functional link between TN13 and RPS5, suggesting that TN13 acts as a partner in modulating RPS5-activated immune signaling, which constitutes a previously unknown mechanism for TN-mediated regulation of plant immunity.     

Impact of transamination reactions and protein turnover on labeling dynamics in (13)C-labeling experiments

A dynamic model describing carbon atom transitions in the central metabolism of Saccharomyces cerevisiae is used to investigate the influence of transamination reactions and protein turnover on the transient behavior of (13)C-labeling chemostat experiments. The simulations performed suggest that carbon exchange due to transamination and protein turnover can significantly increase the required time needed for metabolites in the TCA cycle to reach isotopic steady state, which is in agreement with published experimental observations. On the other hand, transamination and protein turnover will speed-up the net rate of incorporation of labeled carbon into some free and protein-bound amino acids. The simulation results indicate that the pattern of labeled carbon incorporation into amino acids obtained from biomass hydrolysate shows significant deviation from the commonly assumed first-order kinetics behavior until after three residence times. These observations suggest that greater caution should be used while also pointing to new opportunities in the design and interpretation of (13)C-labeling experiments.     

Divergent low water potential response in Arabidopsis thaliana accessions Landsberg erecta and Shahdara

The Arabidopsis thaliana accession Shahdara (Sha) differs from Landsberg erecta (Ler) and other accessions in its responses to drought and low water potential including lower levels of proline accumulation. However, Sha maintained greater seedling root elongation at low water potential and a higher NADP/NADPH ratio than Ler. Profiling of major amino acids and organic acids found that Sha had reduced levels of all glutamate family amino acids metabolically related to proline, but increased levels of aspartate‐derived amino acids (particularly isoleucine), leucine and valine at low water potential. Although Sha is known for its different abiotic stress response, RNA sequencing and co‐expression clustering found that Sha differed most from Ler in defence/immune response and reactive oxygen‐related gene expression. HVA22B and Osmotin34 were two of the relatively few abiotic stress‐associated genes differentially expressed between Ler and Sha. Insensitivity to exogenous glutamine and a different expression profile of glutamate receptors were further factors that may underlie the differing metabolism and low water potential phenotypes of Sha. These data define the unique environmental adaptation and differing metabolism of Sha including differences in defence gene expression, and will facilitate further analysis of Sha natural variation to understand metabolic regulation and abiotic/biotic stress interaction.     

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

Although elevated CO₂ (eCO₂) significantly affects the α‐diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO₂ impacts on the geographic distribution of micro‐organisms regionally or globally. Here, we examined the β‐diversity of 110 soil microbial communities across six free air CO₂ enrichment (FACE) experimental sites using a high‐throughput functional gene array. The β‐diversity of soil microbial communities was significantly (P < 0.05) correlated with geographic distance under both CO₂ conditions, but declined significantly (P < 0.05) faster at eCO₂ with a slope of ?0.0250 than at ambient CO₂ (aCO₂) with a slope of ?0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO₂ at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P < 0.05) contributed to the observed microbial β‐diversity. This study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO₂ continues to increase.     

WVD2 is a novel microtubule-associated protein in Arabidopsis thaliana

Arabidopsis WAVE-DAMPENED 2 (WVD2) was identified by forward genetics as an activation-tagged allele that causes plant and organ stockiness and inversion of helical root growth handedness on agar surfaces. Plants with high constitutive expression of WVD2 or other members of the WVD2-LIKE (WDL) gene family have stems and roots that are short and thick, have reduced anisotropic cell elongation, are suppressed in a root-waving phenotype, and have inverted handedness of twisting in hypocotyls and roots compared with wild-type. The wvd2-1 mutant shows aberrantly organized cortical microtubules in peripheral root cap cells as well as reduced branching of trichomes, unicellular leaf structures whose development is regulated by microtubule stability. Orthologs of the WVD2/WDL family are found widely throughout the plant kingdom, but are not similar to non-plant proteins with the exception of a C-terminal domain distantly related to the vertebrate microtubule-associated protein TPX2. in vivo, WVD2 and its closest paralog WDL1 are localized to interphase cortical microtubules in leaves, hypocotyls and roots. Recombinant glutathione-S-transferase:WVD2 or maltose binding protein:WVD2 protein bind to and bundle microtubules in vitro. We speculate that a C-terminal domain of TPX2 has been utilised by the WVD2 family for functions critical to the organization of plant microtubules.