Most aquatic photoautotrophs depend on CO₂-concentrating mechanisms (CCMs) to maintain productivity at ambient concentrations of CO₂, and carbonic anhydrase (CA) plays a key role in these processes. Here we present different lines of evidence showing that the protein LCIP63, identified in the marine diatom Thalassiosira pseudonana, is a CA. However, sequence analysis showed that it has a low identity with any known CA and therefore belongs to a new subclass that we designate as iota-CA. Moreover, LCIP63 unusually prefers Mn²⁺ to Zn²⁺ as a cofactor, which is potentially of ecological relevance since Mn²⁺ is more abundant than Zn²⁺ in the ocean. LCIP63 is located in the chloroplast and only expressed at low concentrations of CO₂. When overexpressed using biolistic transformation, the rate of photosynthesis at limiting concentrations of dissolved inorganic carbon increased, confirming its role in the CCM. LCIP63 homologs are present in the five other sequenced diatoms and in other algae, bacteria, and archaea. Thus LCIP63 is phylogenetically widespread but overlooked. Analysis of the Tara Oceans database confirmed this and showed that LCIP63 is widely distributed in marine environments and is therefore likely to play an important role in global biogeochemical carbon cycling.

Mitochondria play a key role in the life and death of eukaryotic cells, yet the full spectrum of mitochondrial functions is far from being fully understood, especially in photosynthetic organisms. To advance our understanding of mitochondrial functions in a photosynthetic cell, an extensive proteomic survey of Percoll-purified mitochondria from the metabolically versatile, hydrogen-producing green alga Chlamydomonas reinhardtii was performed. Different fractions of purified mitochondria from Chlamydomonas cells grown under aerobic conditions were analyzed by nano-liquid chromatography–electrospray ionization–mass spectrometry after protein separation on sodium dodecyl sulfate polyacrylamide gel electrophoresis or on blue-native polyacrylamide gel electrophoresis. Of the 496 nonredundant proteins identified, 149 are known or predicted to reside in other cellular compartments and were thus excluded from the molecular and evolutionary analyses of the Chlamydomonas proteome. The mitochondrial proteome of the photosynthetic alga reveals important lineage-specific differences with other mitochondrial proteomes, reflecting the high metabolic diversity of the organelle. Some mitochondrial metabolic pathways in Chlamydomonas appear to combine typical mitochondrial enzymes and bacterial-type ones, whereas others are unknown among mitochondriate eukaryotes. The comparison of the Chlamydomonas proteins to their identifiable homologs predicted from 354 sequenced genomes indicated that Arabidopsis is the most closely related nonalgal eukaryote. Furthermore, this phylogenomic analysis shows that free-living α-proteobacteria from the metabolically versatile orders Rhizobiales and Rhodobacterales better reflect the gene content of the ancestor of the chlorophyte mitochondria than parasitic α-proteobacteria with reduced and specialized genomes.

The rapid growth in silver nanoparticles (AgNPs) commercialization has increased environmental exposure, including aquatic ecosystem. It has been reported that the AgNPs have damaging effects on photosynthesis and induce oxidative stress, but the toxic mechanism of AgNPs is still a matter of debate. In the present study, on the model aquatic higher plant Spirodela polyrhiza, we found that AgNPs affect photosynthesis and significantly inhibit Photosystem II (PSII) maximum quantum yield (F_v/F_m) and effective quantum yield (Φ_PSII). The changes of non-photochemical fluorescence quenching (NPQ), light-induced non-photochemical fluorescence quenching [Y(NPQ)] and non-light-induced non-photochemical fluorescence quenching [Y(NO)] showed that AgNPs inhibit the photo-protective capacity of PSII. AgNPs induce reactive oxygen species (ROS) that are mainly produced in the chloroplast. The activity of ribulose-1, 5-bisphosphate carboxylase–oxygenase (Rubisco) was also very sensitive to AgNPs. The internalized Ag, regardless of whether the exposure was Ag⁺or AgNPs had the same capacity to generate ROS. Our results support the hypothesis that intra-cellular AgNP dissociate into high toxic Ag⁺. Rubisco inhibition leads to slowing down of CO₂ assimilation. Consequently, the solar energy consumption decreases and then the excess excitation energy promotes ROS generation in chloroplast.

In aquatic environments, the concentration of inorganic carbon is spatially and temporally variable and CO₂ can be substantially oversaturated or depleted. Depletion of CO₂ plus low rates of diffusion cause inorganic carbon to be more limiting in aquatic than terrestrial environments, and the frequency of species with a CO₂-concentrating mechanism (CCM), and their contribution to productivity, is correspondingly greater. Aquatic photoautotrophs may have biochemical or biophysical CCMs and exploit CO₂ from the sediment or the atmosphere. Though partly constrained by phylogeny, CCM activity is related to environmental conditions. CCMs are absent or down-regulated when their increased energy costs, lower CO₂ affinity, or altered mineral requirements outweigh their benefits. Aquatic CCMs are most widespread in environments with low CO₂, high HCO₃⁻, high pH, and high light. Freshwater species are generally less effective at inorganic carbon removal than marine species, but have a greater range of ability to remove carbon, matching the environmental variability in carbon availability. The diversity of CCMs in seagrasses and marine phytoplankton, and detailed mechanistic studies on larger aquatic photoautotrophs are understudied. Strengthening the links between ecology and CCMs will increase our understanding of the mechanisms underlying ecological success and will place mechanistic studies in a clearer ecological context.

Protein–protein interactions are involved in many metabolic pathways. This review will focus on the role of such associations in CO₂ assimilation (Benson–Calvin cycle) and especially on the involvement of a GAPDH/CP12/PRK complex which has been identified in many photosynthetic organisms and may have an important role in the regulation of CO₂ assimilation. The emergence of new kinetic and regulatory properties as a consequence of protein–protein interactions will be addressed as well as some of the questions raised by the existence of these supramolecular complexes such as composition, function, and assembly pathways. The presence and role of small intrinsically unstructured proteins like the 8.5 kDa protein CP12, involved in the regulation and/or assembly of these complexes will be discussed.