The relative abundance of wheat Rubisco activase isoforms is post-transcriptionally regulated

Diurnal rhythms and light availability affect transcription-translation feedback loops that regulate the synthesis of photosynthetic proteins. The CO2-fixing enzyme Rubisco is the most abundant protein in the leaves of major crop species and its activity depends on interaction with the molecular chaperone Rubisco activase (Rca). In Triticum aestivum L. (wheat), three Rca isoforms are present that differ in their regulatory properties. Here, we tested the hypothesis that the relative abundance of the redox-sensitive and redox-insensitive Rca isoforms could be differentially regulated throughout light-dark diel cycle in wheat. While TaRca1-β expression was consistently negligible throughout the day, transcript levels of both TaRca2-β and TaRca2-α were higher and increased at the start of the day, with peak levels occurring at the middle of the photoperiod. Abundance of TaRca-β protein was maximal 1.5 h after the peak in TaRca2-β expression, but the abundance of TaRca-α remained constant during the entire photoperiod. The redox-sensitive TaRca-α isoform was less abundant, representing 85% of the redox-insensitive TaRca-β at the transcript level and 12.5% at the protein level. Expression of Rubisco large and small subunit genes did not show a consistent pattern throughout the diel cycle, but the abundance of Rubisco decreased by up to 20% during the dark period in fully expanded wheat leaves. These results, combined with a lack of correlation between transcript and protein abundance for both Rca isoforms and Rubisco throughout the entire diel cycle, suggest that the abundance of these photosynthetic enzymes is post-transcriptionally regulated.

Long photoperiod affects the maize transition from vegetative to reproductive stages: a proteomic comparison between photoperiod-sensitive inbred line and its recurrent parent

Maize (Zea mays L.) is a typical short-day plant that is produced as an important food product and industrial material. The photoperiod is one of the most important evolutionary mechanisms enabling the adaptation of plant developmental phases to changes in climate conditions. There are differences in the photoperiod sensitivity of maize inbred lines from tropical to temperate regions. In this study, to identify the maize proteins responsive to a long photoperiod (LP), the photoperiod-insensitive inbred line HZ4 and its near-isogenic line H496, which is sensitive to LP conditions, were analyzed under long-day conditions using isobaric tags for relative and absolute quantitation. We identified 5259 proteins in maize leaves exposed to the LP condition between the vegetative and reproductive stages. These proteins included 579 and 576 differentially accumulated proteins in H496 and HZ4 leaves, respectively. The differentially accumulated proteins (e.g., membrane, defense, and energy- and ribosome-related proteins) exhibited the opposite trends in HZ4 and H496 plants during the transition from the vegetative stage to the reproductive stage. These results suggest that the photoperiod-associated fragment in H496 plants considerably influences various proteins to respond to the photoperiod sensitivity. Overall, our data provide new insights into the effects of long-day treatments on the maize proteome, and may be useful for the development of new germplasm.

Targeted quantitative analysis of a diurnal RuBisCO subunit expression and translation profile in Chlamydomonas reinhardtii introducing a novel Mass Western approach

RuBisCO catalyzes the rate-limiting step of CO2 fixation in photosynthesis. Hypothetical mechanisms for the regulation of rbcL and rbcS gene expression assume that both large (LSU) and small (SSU) RuBisCO subunit proteins (RSUs) are present in equimolar amounts to fit the 1:1 subunit stoichiometry of the holoenzyme. However, the actual quantities of the RSUs have never been determined in any photosynthetic organism. In this study the absolute amount of rbc transcripts and RSUs was quantified in Chlamydomonas reinhardtii grown during a diurnal light/dark cycle. A novel approach utilizing more reliable protein stoichiometry quantification is introduced. The rbcL:rbcS transcript and protein ratios were both 5:1 on average during the diurnal time course, indicating that SSU is the limiting factor for the assembly of the holoenzyme. The oscillation of the RSUs was 9h out of phase relative to the transcripts. The amount of rbc transcripts was at its maximum in the dark while that of RSUs was at its maximum in the light phase suggesting that translation of the rbc transcripts is activated by light as previously hypothesized. A possible post-translational regulation that might be involved in the accumulation of a 37-kDa N-terminal LSU fragment during the light phase is discussed.

BIOLOGICAL SIGNIFICANCE

A novel MS based approach enabling the exact stoichiometric analysis and absolute quantification of protein complexes is presented in this article. The application of this method revealed new insights in RuBisCO subunit dynamics.

Why measure enzyme activities in the era of systems biology?

Information about the abundance and biological activities of proteins is essential to reveal how genes affect phenotypes. Over the past decade, mass spectrometry (MS)-based proteomics has revolutionized the identification and quantification of proteins, and the detection of post-translational modifications. Interpretation of proteomics data depends on information about the biological activities of proteins, which has created a bottleneck in research. This review focuses on enzymes in central metabolism. We examine the methods used for measuring enzyme activities, and discuss how these methods provide information about the kinetic and regulatory properties of enzymes, their turnover, and how this information can be integrated into metabolic models. We also discuss how robotized assays could enable the genetic networks that control enzyme abundance to be analyzed.

Rice proteomics: a model system for crop improvement and food security

Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040.

Sweet immunity in the plant circadian regulatory network

All organisms have an internal timing mechanism, termed the circadian clock, to anticipate the light/dark cycle. The clock, with an oscillating rhythm that approximates 24h, is a rather robust system persisting to a great extent in continuous light and dark. It is widely accepted that plant growth and development are regulated by the clock, hormones, and sugar signals. On the one hand, sugar signalling can affect circadian rhythms by altering the expression pattern of clock-regulated genes. More in particular, the clock seems to be particularly sensitive to sucrose-mediated signalling which is also associated with immunity and abiotic stress responses. Also, hormonal interaction with the clock can contribute to appropriate plant immune responses. Recent data show a prominent role for the clock in growth and stress responses. On the other hand, the clock seems to be essential in controlling the gene expression and activity of an array of carbohydrate-metabolizing enzymes, suggesting a complex reciprocal relationship between the clock and metabolic signalling processes. Therefore, the clock fulfils a crucial role at the heart of cellular networks. The players involved in the complex plant circadian network and their possible contribution to the novel 'sweet immunity' concept are discussed.

Disturbances, organisms and ecosystems: a global change perspective

The present text exposes a theory of the role of disturbances in the assemblage and evolution of species within ecosystems, based principally, but not exclusively, on terrestrial ecosystems. Two groups of organisms, doted of contrasted strategies when faced with environmental disturbances, are presented, based on the classical r-K dichotomy, but enriched with more modern concepts from community and evolutionary ecology. Both groups participate in the assembly of known animal, plant, and microbial communities, but with different requirements about environmental fluctuations. The so-called "civilized" organisms are doted with efficient anticipatory mechanisms, allowing them to optimize from an energetic point of view their performances in a predictable environment (stable or fluctuating cyclically at the scale of life expectancy), and they developed advanced specializations in the course of evolutionary time. On the opposite side, the so-called "barbarians" are weakly efficient in a stable environment because they waste energy for foraging, growth, and reproduction, but they are well adapted to unpredictably changing conditions, in particular during major ecological crises. Both groups of organisms succeed or alternate each other in the course of spontaneous or geared successional processes, as well as in the course of evolution. The balance of "barbarians" against "civilized" strategies within communities is predicted to shift in favor of the first type under present-day anthropic pressure, exemplified among others by climate warming, land use change, pollution, and biological invasions.

Progress in understanding and engineering primary plant metabolism

The maximum yield of crop plants depends on the efficiency of conversion of sunlight into biomass. This review summarises recent models that estimate energy conversion efficiency for successive steps in photosynthesis and metabolism. Photorespiration was identified as a major reason for energy loss during photosynthesis and strategies to modify or suppress photorespiration are presented. Energy loss during the conversion of photosynthate to biomass is also large but cannot be modelled as precisely due to incomplete knowledge about pathways and turnover and maintenance costs. Recent research on pathways involved in metabolite transport and interconversion in different organs, and recent insights into energy requirements linked to the production, maintenance and turnover of the apparatus for cellular growth and repair processes are discussed.

The interactions between the circadian clock and primary metabolism

Primary metabolism in plants is tightly regulated by environmental factors such as light and nutrient availability at multiple levels. The circadian clock is a self-sustained endogenous oscillator that enables organisms to predict daily and seasonal changes. The regulation of primary metabolism by the circadian clock has been proposed to explain the importance of circadian rhythms in plant growth and survival. Recent transcriptomic and metabolomic analyses indicate a wide spread circadian regulation of different metabolic processes. We review evidence of circadian regulation of pathways in primary metabolism, discuss the challenges faced for discerning the mechanisms regulating circadian metabolic oscillations and present recent evidence of regulation of the circadian clock by metabolites.

Proteomic analysis reveals an aflatoxin-triggered immune response in cotyledons of Arachis hypogaea infected with Aspergillus flavus

An immune response is triggered in host cells when host receptors recognize conserved molecular motifs, pathogen-associated molecular patterns (PAMPs), such as β-glucans, and chitin at the cell surface of a pathogen. Effector-triggered immunity occurs when pathogens deliver effectors into the host cell to suppress the first immune signaling. Using a differential proteomic approach, we identified an array of proteins responding to aflatoxins in cotyledons of peanut (Arachis hypogaea) infected with aflatoxin-producing (toxigenic) but not nonaflatoxin-producing (atoxigenic) strains of Aspergillus flavus. These proteins are involved in immune signaling and PAMP perception, DNA and RNA stabilization, induction of defense, innate immunity, hypersensitive response, biosynthesis of phytoalexins, cell wall responses, peptidoglycan assembly, penetration resistance, condensed tannin synthesis, detoxification, and metabolic regulation. Gene expression analysis confirmed the differential abundance of proteins in peanut cotyledons supplemented with aflatoxins, with or without infection with the atoxigenic strain. Similarly, peanut germination and A. flavus growth were altered in response to aflatoxin B1. These findings show an additional immunity initiated by aflatoxins. With the PAMP- and effector-triggered immune responses, this immunity constitutes the third immune response of the immune system in peanut cotyledon cells. The system is also a three-grade coevolution of plant-pathogen interaction.