Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation

Abstract

Chlamydomonas reinhardtii, a unicellular green alga, has been exploited as a reference organism for identifying proteins and activities associated with the photosynthetic apparatus and the functioning of chloroplasts. Recently, the full genome sequence of Chlamydomonas was generated and a set of gene models, representing all genes on the genome, was developed. Using these gene models, and gene models developed for the genomes of other organisms, a phylogenomic, comparative analysis was performed to identify proteins encoded on the Chlamydomonas genome which were likely involved in chloroplast functions (or specifically associated with the green algal lineage); this set of proteins has been designated the GreenCut. Further analyses of those GreenCut proteins with uncharacterized functions and the generation of mutant strains aberrant for these proteins are beginning to unmask new layers of functionality/regulation that are integrated into the workings of the photosynthetic apparatus.

Proton Gradient Regulation 5-Mediated Cyclic Electron Flow under ATP- or Redox-Limited Conditions: A Study of ƊATPase pgr5 and ƊrbcL pgr5 Mutants in the Green Alga Chlamydomonas reinhardtii

“…These results support the hypothesis that the redox state of the cells controls CEF, which was previously suggested: when stromal redox carriers are reduced, which is the case under light anaerobic conditions, Fdmediated CEF is strongly activated (Kessler, 1973;Alric, 2010;Alric et al, 2010;Terashima et al, 2012;Takahashi et al, 2013). It also shows that, like PGRL1 (Petroutsos et al, 2009;Tolleter et al, 2011) Figure 1A shows that an absence of PGR5 results in reduced photosynthetic growth and ultimately, light sensitivity when the cells are grown on minimal medium in air.…”

“…The flow rate determined from the dark relaxation kinetic is given in charges (electrons or protons) transferred per second per PSI reaction center, with the amplitude of one electron per PSI determined by the absorbance change induced after a single turnover saturating flash (one charge separation); in this instance, the value is approximately 3 3 10 23 . In aerobic conditions, in the presence of DCMU, the rates of CEF were very similar in the wild-type line and pgr5 cells at 9.5 6 3.3 s 21 and 11.5 6 4.8 s 21 (Table I), which supports the suggestion that the NADPH-mediated CEF is the dominant pathway for recycling reducing equivalents under these conditions (for review, see Alric, 2010). Under anaerobic conditions, there was a much greater difference in the CEF between the wild-type line (60.6 6 9.2 s 21 ) and pgr5 mutant (16.3 6 6.3 s 21 ) cells.…”

“…4A), with a rereduction rate of 6.56 (61.45) e 21 s 21 (Supplemental Fig. S2C), which is typical for CEF in such conditions (Alric et al, 2010). However, as also shown in Figure 4A, the quantity of oxidizable P 700 was severely reduced in the pgr5 mutant compared with the wild-type line after growth in moderate/high light.…”

“…Indeed, according to Hertle et al (2013), in Arabidopsis, PGR5 is a lowabundance protein, approximately 7 times less abundant than its binding partner PGRL1, with PGRL1 being one-half as abundant as cyt f. A C. reinhardtii pgr5 mutant (the putative protein is orthologous to Arabidopsis PGR5) was isolated in a large screen for identifying mutants defective in their responses to high light (Dent et al, 2005). The PGR5 protein is also included in the GreenCut set of proteins derived from phylogenomic analysis, many of which are likely to be involved in chloroplast function and photosynthesis (Merchant et al, 2007;Grossman et al, 2010;Karpowicz et al, 2011;Heinnickel et al, 2013). Here, we report that the functional attributes of the C. reinhardtii pgr5 mutant are congruent with those attributes observed for the analogous mutant in vascular plants as well as those attributes of the Crpgrl1 mutant.…”

Eukaryotic algae: where lies the diversity of oxygenic photosynthesis

“…Reinforcing the dominant position of Chlamydomonas, the availability of its nuclear genome sequence (Merchant et al 2007) made also possible the identification of a minimal set of proteins (designated the GreenCut) that were likely involved specifically in chloroplast function within the green lineage. Recent advances in approaching the functions of these proteins are highlighted in this special issue (Grossman et al 2010). Many pioneering works and more recent findings on the regulation of photosynthetic electron transport arose from studies on eukaryotic microalgae, such as chlororespiration (Bennoun 1982) and cyclic electron flow (Iwai et al 2010) in Chlamydomonas, or state transitions in the green alga Chlorella pyrenoidosa (Bonaventura and Meyers 1969).…”