Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii

Characterizing the anaerobic response of Chlamydomonas reinhardtii by quantitative proteomics

The versatile metabolism of the green alga Chlamydomonas reinhardtii is reflected in its complex response to anaerobic conditions. The anaerobic response is also remarkable in the context of renewable energy because C. reinhardtii is able to produce hydrogen under anaerobic conditions. To identify proteins involved during anaerobic acclimation as well as to localize proteins and pathways to the powerhouses of the cell, chloroplasts and mitochondria from C. reinhardtii in aerobic and anaerobic (induced by 8 h of argon bubbling) conditions were isolated and analyzed using comparative proteomics. A total of 2315 proteins were identified. Further analysis based on spectral counting clearly localized 606 of these proteins to the chloroplast, including many proteins of the fermentative metabolism. Comparative quantitative analyses were performed with the chloroplast-localized proteins using stable isotopic labeling of amino acids ([(13)C(6)]arginine/[(12)C(6)]arginine in an arginine auxotrophic strain). The quantitative data confirmed proteins previously characterized as induced at the transcript level as well as identified several new proteins of unknown function induced under anaerobic conditions. These proteins of unknown function provide new candidates for further investigation, which could bring insights for the engineering of hydrogen-producing alga strains.

An ancient light-harvesting protein is critical for the regulation of algal photosynthesis

Light is necessary for photosynthesis, but its absorption by pigment molecules such as chlorophyll can cause severe oxidative damage and result in cell death. The excess absorption of light energy by photosynthetic pigments has led to the evolution of protective mechanisms that operate on the timescale of seconds to minutes and involve feedback-regulated de-excitation of chlorophyll molecules in photosystem II (qE). Despite the significant contribution of eukaryotic algae to global primary production, little is known about their qE mechanism, in contrast to that in flowering plants. Here we show that a qE-deficient mutant of the unicellular green alga Chlamydomonas reinhardtii, npq4, lacks two of the three genes encoding LHCSR (formerly called LI818). This protein is an ancient member of the light-harvesting complex superfamily, and orthologues are found throughout photosynthetic eukaryote taxa, except in red algae and vascular plants. The qE capacity of Chlamydomonas is dependent on environmental conditions and is inducible by growth under high light conditions. We show that the fitness of the npq4 mutant in a shifting light environment is reduced compared to wild-type cells, demonstrating that LHCSR is required for survival in a dynamic light environment. Thus, these data indicate that plants and algae use different proteins to dissipate harmful excess light energy and protect the photosynthetic apparatus from damage.

Quantitation in mass-spectrometry-based proteomics

Mass-spectrometry-based proteomics, the large-scale analysis of proteins by mass spectrometry, has emerged as a new technology over the last decade and become routine in many plant biology laboratories. While early work consisted merely of listing proteins identified in a given organ or under different conditions of interest, there is a growing need to apply comparative and quantitative proteomics strategies toward gaining novel insights into functional aspects of plant proteins and their dynamics. However, during the transition from qualitative to quantitative protein analysis, the potential and challenges will be tightly coupled. Several strategies for differential proteomics that involve stable isotopes or label-free comparisons and their statistical assessment are possible, each having specific strengths and limitations. Furthermore, incomplete proteome coverage and restricted dynamic range still impose the strongest limitations to data throughput and precise quantitative analysis. This review gives an overview of the current state of the art in differential proteomics and possible strategies in data processing.

PGRL1 participates in iron-induced remodeling of the photosynthetic apparatus and in energy metabolism in Chlamydomonas reinhardtii

PGRL1 RNA and protein levels are increased in iron-deficient Chlamydomonas reinhardtii cells. In an RNAi strain, which accumulates lower PGRL1 levels in both iron-replete and -starved conditions, the photosynthetic electron transfer rate is decreased, respiratory capacity in iron-sufficient conditions is increased, and the efficiency of cyclic electron transfer under iron-deprivation is diminished. Pgrl1-kd cells exhibit iron deficiency symptoms at higher iron concentrations than wild-type cells, although the cells are not more depleted in cellular iron relative to wild-type cells as measured by mass spectrometry. Thiol-trapping experiments indicate iron-dependent and redox-induced conformational changes in PGRL1 that may provide a link between iron metabolism and the partitioning of photosynthetic electron transfer between linear and cyclic flow. We propose, therefore, that PGRL1 in C. reinhardtii may possess a dual function in the chloroplast; that is, iron sensing and modulation of electron transfer.

Proteomic analysis of chromate-induced modifications in Pseudokirchneriella subcapitata

In this work, we have analyzed the changes in the protein expression profile elicited by chromium (Cr) exposure in the freshwater green alga Pseudokirchneriella subcapitata, a well known bio-indicator of water pollution. We tested two experimental conditions, namely 0.2 and 1ppm of potassium dichromate; this concentration range includes the environmentally-relevant concentrations. Results show that neither concentration of potassium dichromate tested inhibited algal growth. However, the proteomic approach allowed the identification of relevant modifications in protein expression. In fact, among 800 protein spots detected by two-dimensional electrophoresis, 16 Cr-regulated proteins, including predicted and novel ones, were identified using tandem mass spectromic protein analysis. The results demonstrate a Cr-specific action in altering several photosynthetic proteins, such as ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), RuBisCO activase, Light Harvesting Chla/b protein complex, and stress related Chla/b binding protein1. Although Cr toxicity with respect to photosynthesis has been already documented, here we have identified, for the first time, the target proteins of this toxicity. Cr also induced a modulation of some proteins involved in the metabolism of the amino acids glutamine, arginine and methionine. These data are supported by changes in cellular polyamine (PA) accumulation. Present findings provide new insight into the molecular mechanisms underlying Cr toxicity in P. subcapitata.

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

Background

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism.

Results

In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification.

Conclusion

ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under .

Sub-proteome analysis in the green flagellate alga Chlamydomonas reinhardtii

In the past years, research on the flagellate unicellular alga Chlamydomonas reinhardtii has entered a new era based on the availability of its complete genome. Since this green alga can be grown relatively easy in a short time-range, sufficient biological material is available to efficiently establish biochemical purification procedures of sub-cellular fractions. Combined with the available genome sequences, this paved the way to perform analysis of specific sub-proteomes by mass spectrometry. In this review, several approaches that provided comprehensive lists of components of certain sub-cellular compartments and their biological relevance will be described. These include proteins of chloroplast ribosomes, of flagella, of the eyespot as well as posttranslational and environmentally modified sub-proteomes. The power of such proteome approaches lies in the identification of novel components and modifications of a given sub-proteome that have not been discovered before. Information is usually gained at a large scale and is very valuable to further understand biological processes of a given cellular sub-compartment. But clearly the arduous task has then to be performed to further analyze the function of specific proteins/genes by RNA interference technology, mutant analyses or methods for identifying the protein interaction network within a sub-proteome.

Peroxiredoxins: a less studied component of hydrogen peroxide detoxification in photosynthetic organisms

Peroxiredoxins (Prx) are ubiquitous thiol-dependent peroxidases capable of reducing a broad range of toxic peroxides and peroxinitrites. A cysteinyl residue of peroxiredoxins reacts with the peroxides as primary catalytic center and oxidizes to sulfenic acid. The regeneration of the reduced form of Prx is required as a next step to allow its entry into next catalytic cycle. Several proteins, such as thioredoxin, glutaredoxin, cyclophilin, among others, are known to facilitate the regeneration of the reduced (catalytically active) form of Prx in plants. Based on the cysteine residues conserved in the deduced amino acid sequence and their catalytic mechanisms, four groups of peroxiredoxins have been distinguished in plants, namely, 1-Cys Prx, 2-Cys Prx, Type II Prx and Prx Q. Peroxiredoxins are known to play an important role in combating the reactive oxygen species generated at the level of electron transport activities in the plant exposed to different types of biotic and abiotic stresses. In addition to their role in antioxidant defense mechanisms in plants, they also modulate redox signaling during development and adaptation. Besides these general properties, peroxiredoxins have been shown to protect DNA from damage in vitro and in vivo. They also regulate metabolism in thylakoids and mitochondria. The present review summarizes the most updated information on the structure and catalysis of Prx and their functional importance in plant metabolism.

The dynamics of photosynthesis

Despite recent elucidation of the three-dimensional structure of major photosynthetic complexes, our understanding of light energy conversion in plant chloroplasts and microalgae under physiological conditions requires exploring the dynamics of photosynthesis. The photosynthetic apparatus is a flexible molecular machine that can acclimate to metabolic and light fluctuations in a matter of seconds and minutes. On a longer time scale, changes in environmental cues trigger acclimation responses that elicit intracellular signaling between the nucleo-cytosol and chloroplast resulting in modification of the biogenesis of the photosynthetic machinery. Here we attempt to integrate well-established knowledge on the functional flexibility of light-harvesting and electron transfer processes, which has greatly benefited from genetic approaches, with data derived from the wealth of recent transcriptomic and proteomic studies of acclimation responses in photosynthetic eukaroytes.

Analysis of environmental stress response on the proteome level

Thousands of man-made chemicals are annually released into the environment by agriculture, transport, industries, and other human activities. In general, chemical analysis of environmental samples used to assess the pollution status of a specific ecosystem is complicated by the complexity of the mixture, and in some cases by the very low toxicity thresholds of chemicals present. In that sense, a proteomics approach, capable of detecting subtle changes in the level and structure of individual proteins within the whole proteome in response to the altered surroundings, has obvious applications in the field of ecotoxicology. In addition to identifying new protein biomarkers, it can also help to provide an insight into underlying mechanisms of toxicity. Despite being a comparatively new field with a number of caveats, proteomics applications have spread from microorganisms and plants to invertebrates and vertebrates, gradually becoming an established technology used in environmental research. This review article highlights recent advances in the field of environmental proteomics, mainly focusing on experimental approaches with a potential to understand toxic modes of action and to identify novel ecotoxicological biomarkers.

FER1 and FER2 encoding two ferritin complexes in Chlamydomonas reinhardtii chloroplasts are regulated by iron

Two unlinked genes FER1 and FER2 encoding ferritin subunits were identified in the Chlamydomonas genome. An improved FER2 gene model, built on the basis of manual sequencing and incorporation of unplaced reads, indicated 49% identity between the ferritin subunits. Both FER1 and FER2 transcripts are increased in abundance as iron nutrition is decreased but the pattern for each gene is distinct. Using subunit-specific antibodies, we monitored expression at the protein level. In response to low iron, ferritin1 subunits and the ferritin1 complex are increased in parallel to the increase in FER1 mRNA. Nevertheless, the iron content of the ferritin1 complex is decreased. This suggests that increased expression results in increased capacity for iron binding in the chloroplast of iron-limited cells, which supports a role for ferritin1 as an iron buffer. On the other hand, ferritin2 abundance is decreased in iron-deprived cells, indicative of the operation of iron-nutrition-responsive regulation at the translational or post-translational level for FER2. Both ferritin subunits are plastid localized but ferritin1 is quantitatively recovered in soluble extracts of cells while ferritin2 is found in the particulate fraction. Partial purification of the ferritin1 complex indicates that the two ferritins are associated in distinct complexes and do not coassemble. The ratio of ferritin1 to ferritin2 is 70:1 in iron-replete cells, suggestive of a more dominant role of ferritin1 in iron homeostasis. The Volvox genome contains orthologs of each FER gene, indicating that the duplication of FER genes and potential diversification of function occurred prior to the divergence of species in the Volvocales.

Ferritin is required for rapid remodeling of the photosynthetic apparatus and minimizes photo-oxidative stress in response to iron availability in Chlamydomonas reinhardtii

Ferritin is a key player in the iron homeostasis due to its ability to store large quantities of iron. Chlamydomonas reinhardtii contains two nuclear genes for ferritin (ferr1 and ferr2) that are induced when Chlamydomonas cells are shifted to iron-deficient conditions. In response to the reduced iron availability, degradation of photosystem I (PSI) and remodeling of its light-harvesting complex occur. This active PSI degradation slows down under photo-autotrophic conditions where photosynthesis is indispensable. We observed a strong induction of ferritin correlated with the degree of PSI degradation during iron deficiency. The PSI level can be restored to normal within 24 h after iron repletion at the expense of the accumulated ferritin, indicating that the ferritin-stored iron allows fast adjustment of the photosynthetic apparatus with respect to iron availability. RNAi strains that are significantly reduced in the amount of ferritin show a striking delay in the degradation of PSI under iron deficiency. Furthermore, these strains are more susceptible to photo-oxidative stress under high-light conditions. We conclude that (i) ferritin is used to buffer the iron released by degradation of the photosynthetic complexes, (ii) the physiological status of the cell determines the strategy used to overcome the impact of iron deficiency, (iii) the availability of ferritin is important for rapid degradation of PSI under iron deficiency, and (iv) ferritin plays a protective role under photo-oxidative stress conditions.

A plastid protein crucial for Ca2+-regulated stomatal responses

* Guard cell movements are regulated by environmental cues including, for example, elevations in extracellular Ca(2+) concentration. Here, the subcellular localization and physiological function of the Ca(2+)-sensing receptor (CAS) protein was investigated. * CAS protein localization was ascertained by microscopic analyses of green fluorescent protein (GFP) fusion proteins and biochemical fractionation assays. Comparative guard cell movement investigations were performed in wild-type and cas loss-of-function mutant lines of Arabidopsis thaliana. Cytoplasmic Ca(2+) dynamics were addressed in plants expressing the yellow cameleon reporter protein YC3.6. * This study identified CAS as a chloroplast-localized protein that is crucial for proper stomatal regulation in response to elevations of external Ca(2+). CAS fulfils this role through modulation of the cytoplasmic Ca(2+) concentration. * This work reveals a novel role of the chloroplast in cellular Ca(2+) signal transduction.

Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii

We present an integrated analysis of the molecular repertoire of Chlamydomonas reinhardtii under reference conditions. Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins and metabolites, resulting in the detection of 1069 proteins and 159 metabolites. Of the measured proteins, 204 currently do not have EST sequence support; thus a significant portion of the proteomics-detected proteins provide evidence for the validity of in silico gene models. Furthermore, the generated peptide data lend support to the validity of a number of proteins currently in the proposed model stage. By integrating genomic annotation information with experimentally identified metabolites and proteins, we constructed a draft metabolic network for Chlamydomonas. Computational metabolic modeling allowed an identification of missing enzymatic links. Some experimentally detected metabolites are not producible by the currently known and annotated enzyme set, thus suggesting entry points for further targeted gene discovery or biochemical pathway research. All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. Information of identified peptides is also available directly via the JGI-Chlamydomonas genomic resource database (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html).