Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii

RNA function and phosphorus use by photosynthetic organisms

Phosphorus (P) in RNA accounts for half or more of the total non-storage P in oxygenic photolithotrophs grown in either P-replete or P-limiting growth conditions. Since many natural environments are P-limited for photosynthetic primary productivity, and peak phosphorus fertilizer production is inevitable, the paper analyses what economies in P allocation to RNA could, in principle, increase P-use efficiency of growth (rate of dry matter production per unit organism P). The possibilities of decreasing P allocation to RNA without decreasing growth rate include (1) more widespread down-regulation of RNA production in P-limited organisms, (2) optimal allocation of P to RNA, both spatially among cell compartments and organs, and temporally depending on the stage of growth, and (3) a constant rate of protein synthesis through the diel cycle. Acting on these suggestions would, however, be technically demanding.

The evolution of autotrophy in relation to phosphorus requirement

The evolution of autotrophy is considered in relation to the availability of phosphorus (P), the ultimate elemental resource limiting biological productivity through Earth's history. Work on microbes and plants is emphasized, dealing in turn with the main uses for P in cells, namely nucleic acids, phospholipids, and water-soluble low molecular mass phosphate esters plus metabolically active inorganic orthophosphate. There is a greater minimum gene number and minimum DNA content in autotrophic than in osmochemoorganotrophic archaea and bacteria, as well as a lower rate of biomass increase per unit P (P-use efficiency) in autotrophs than in osmochemoorganotrophs, in eukaryotes as well as bacteria. This may be due to the diversion of rRNA from producing proteins common to all organisms to producing highly expressed proteins specific to autotrophs. The P requirement for phospholipids is decreased in oxygenic photolithotrophs, and some anoxygenic photolithotrophs, by substituting galactolipids and sulpholipids for phospholipids in the photosynthetic, and some other, membranes. The six different autotrophic inorganic carbon assimilation pathways have varying requirements for low molecular mass water-soluble phosphate esters. In oxygenic photolithotrophs, there is no clear evidence of a different P requirement for growth in the absence (diffusive CO2 entry) relative to the presence of CO2-concentrating mechanisms (CCMs). P limitation increases the expression of crassulacean acid metabolism (CAM) in facultative CAM plants, decreases the extent of inorganic carbon accumulation in algae with CCMs, and (usually) their inorganic carbon affinity and the water-use efficiency of growth of terrestrial plants, and the light-use efficiency of photolithotrophs.

De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq

BACKGROUND

Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular H2 under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of H2 photoproduction in this organism.

RESULTS

In this work, RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of H2 photoproduction. 156 million reads generated from 7 samples were then used for de novo assembly after data trimming. BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 34,136 contigs, which were then used as the reference contigs for RNA-Seq analysis. Our results indicated that more contigs were differentially expressed during the period of early and higher H2 photoproduction, and fewer contigs were differentially expressed when H2-photoproduction rates decreased. In addition, C. moewusii and C. reinhardtii share core functional pathways, and transcripts for H2 photoproduction and anaerobic metabolite production were identified in both organisms. C. moewusii also possesses similar metabolic flexibility as C. reinhardtii, and the difference between C. moewusii and C. reinhardtii on hydrogenase expression and anaerobic fermentative pathways involved in redox balancing may explain their different profiles of hydrogenase activity and secreted anaerobic metabolites.

CONCLUSIONS

Herein, we have described a workflow using commercial software to analyze RNA-Seq data without reference genome sequence information, which can be applied to other unsequenced microorganisms. This study provided biological insights into the anaerobic fermentation and H2 photoproduction of C. moewusii, and the first transcriptomic RNA-Seq dataset of C. moewusii generated in this study also offer baseline data for further investigation (e.g. regulatory proteins related to fermentative pathway discussed in this study) of this organism as a H2-photoproduction strain.

Plant SILAC: stable-isotope labelling with amino acids of arabidopsis seedlings for quantitative proteomics

Stable Isotope Labelling by Amino acids in Cell culture (SILAC) is a powerful technique for comparative quantitative proteomics, which has recently been applied to a number of different eukaryotic organisms. Inefficient incorporation of labelled amino acids in cell cultures of Arabidopsis thaliana has led to very limited use of SILAC in plant systems. We present a method allowing, for the first time, efficient labelling with stable isotope-containing arginine and lysine of whole Arabidopsis seedlings. To illustrate the utility of this method, we have combined the high labelling efficiency (>95%) with quantitative proteomics analyses of seedlings exposed to increased salt concentration. In plants treated for 7 days with 80 mM NaCl, a relatively mild salt stress, 215 proteins were identified whose expression levels changed significantly compared to untreated seedling controls. The 92 up-regulated proteins included proteins involved in abiotic stress responses and photosynthesis, while the 123 down-regulated proteins were enriched in proteins involved in reduction of oxidative stress and other stress responses, respectively. Efficient labelling of whole Arabidopsis seedlings by this modified SILAC method opens new opportunities to exploit the genetic resources of Arabidopsis and analyse the impact of mutations on quantitative protein dynamics in vivo.

Coping with abiotic stress: proteome changes for crop improvement

Plant breeders need new and more precise tools to accelerate breeding programs that address the increasing needs for food, feed, energy and raw materials, while facing a changing environment in which high salinity and drought have major impacts on crop losses worldwide. This review covers the achievements and bottlenecks in the identification and validation of proteins with relevance in abiotic stress tolerance, also mentioning the unexpected consequences of the stress in allergen expression. While addressing the key pathways regulating abiotic stress plant adaptation, comprehensive data is presented on the proteins confirmed as relevant to confer tolerance. Promising candidates still to be confirmed are also highlighted, as well as the specific protein families and protein modifications for which detection and characterization is still a challenge. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Sensitivity of Antarctic freshwater algae to salt stress assessed by fast chlorophyll fluorescence transient

In this study, we investigated the effects of salt stress (2 mM NaCl) on excitation energy transfer from light harvesting complexes to photosystem II (PS II) in two Antarctic algal species: Klebsormidium sp. and Zygnema sp. Short-term salt stress led to a significant changes in the shape of chlorophyll fluorescence transient (OJIP). Analyses of the polyphasic fluorescence transients (OJIP) showed that the fluorescence yield at the phases J, I and P declined considerably with the time of exposition to salt stress. In both experimental species, OJIP transients reached lowest values of chlorophyll fluorescence signal after 30/60 min. of NaCl exposition. Then, OJIP shape and chlorophyll fluo-rescence showed species-specific recovery and rised towards original values (about 2/3 of untreated control). Analyses of chlorophyll fluorescence parameters derived from OJIPs showed that salt stress led to a decrease in the maximal efficiency of PS II photo-chemistry (FV/FM) in Zygnema sp. but not Klebsormidium sp. The results indicated that the probability of excitation energy transfer before and beyond QA, and the yield of electron transport beyond QA is limited by salt-induced stress in Zygnema sp. In addition, salt stress resulted in a decrease in the photosynthetic electron transport per PS II reaction center, but both increase and decrease in the trapping per PS II reaction center was found. Performace index (PIabs) was affected negatively in Zygnema sp. but possitively Klebsormidium sp. indicating that the latter species was more resistant to salt stress than Zygnema sp.

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.

Gel-based and gel-free quantitative proteomics approaches at a glance

Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.