Comparative sequence analysis of CP12, a small protein involved in the formation of a Calvin cycle complex in photosynthetic organisms

Abstract

CP12, a small intrinsically unstructured protein, plays an important role in the regulation of the Calvin cycle by forming a complex with phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). An extensive search in databases revealed 129 protein sequences from, higher plants, mosses and liverworts, different groups of eukaryotic algae and cyanobacteria. CP12 was identified throughout the Plantae, apart from in the Prasinophyceae. Within the Chromalveolata, two putative CP12 proteins have been found in the genomes of the diatom Thalassiosira pseudonana and the haptophyte Emiliania huxleyi, but specific searches in further chromalveolate genomes or EST datasets did not reveal any CP12 sequences in other Prymnesiophyceae, Dinophyceae or Pelagophyceae. A species from the Euglenophyceae within the Excavata also appeared to lack CP12. Phylogenetic analysis showed a clear separation into a number of higher taxonomic clades and among different forms of CP12 in higher plants. Cyanobacteria, Chlorophyceae, Rhodophyta and Glaucophyceae, Bryophyta, and the CP12-3 forms in higher plants all form separate clades. The degree of disorder of CP12 was higher in higher plants than in the eukaryotic algae and cyanobacteria apart from the green algal class Mesostigmatophyceae, which is ancestral to the streptophytes. This suggests that CP12 has evolved to become more flexible and possibly take on more general roles. Different features of the CP12 sequences in the different taxonomic groups and their potential functions and interactions in the Calvin cycle are discussed.

Comparative Analysis of 126 Cyanobacterial Genomes Reveals Evidence of Functional Diversity Among Homologs of the Redox-Regulated CP12 Protein

“…This core sequence is implicated in GAPDH binding by trypsinprotection experiments (Lebreton et al, 2006); however, this region of CP12 is not visible in the electron density of either of the CP12-GAPDH structures (Matsumura et al, 2011;Fermani et al, 2012). Additionally, the N-terminal Gly-24, Ser-27, and His-46 and C-terminal Pro-65 residues are strongly conserved among all CP12 homologs (including those from eukaryotes), while the Gln-41 and Phe-57 residues following the AWD_VEEL sequence that have previously been noted as specific to cyanobacteria (Groben et al, 2010) are not strongly conserved among all cyanobacterial variants ( Fig. 2A).…”

“…PRK is very similar to another enzyme, uridine kinase, and annotations, COG (for Cluster of Orthologous Groups), and pfam assignments frequently contradict one another, suggesting that such computationally based functional assignments for this gene product are unreliable. However, it is clear that among the CP12 variants, the N terminus, which has been shown to interact with PRK (Groben et al, 2010), is overall less conserved than the GAPDH-interacting C terminus ( Fig. 2A).…”

“…CP12 is a small (approximately 80-amino acid) protein present in most photosynthetic organisms, including cyanobacteria, diatoms, red and green algae, and higher plants (Pohlmeyer et al, 1996;Wedel and Soll, 1998;Oesterhelt et al, 2007;Erales et al, 2008b;Groben et al, 2010). In eukaryotic organisms, CP12 is located in the chloroplast, where the only function thus far identified is in the regulation of the Calvin cycle in response to changes in light availability by reversibly binding glyceraldehyde-3-P dehydrogenase (GAPDH) and, subsequently, phosphoribulokinase (PRK; Wedel et al, 1997;Graciet et al, 2003aGraciet et al, , 2003bMarri et al, 2005aMarri et al, , 2008Erales et al, 2008a;Howard et al, 2008;Carmo-Silva et al, 2011).…”

Antisense Suppression of the Small Chloroplast Protein CP12 in Tobacco Alters Carbon Partitioning and Severely Restricts Growth

“…Given the complexity of the metabolic and developmental phenotype in the antisense plants, however, it is possible that CP12 may have additional functions. Bioinformatic and experimental evidence has shown that CP12 is an intrinsically unstructured protein (Graciet et al, 2003;Gardebien et al, 2006;Marri et al, 2009;Groben et al, 2010). Such proteins can have multiple partners and are frequently considered to be regulatory hubs (Tompa, 2002;Dunker et al, 2005).…”

Algal evolution in relation to atmospheric CO 2 : carboxylases, carbon-concentrating mechanisms and carbon oxidation cycles

“…There are also differences among algae in the regulation of enzymes of the PCRC [63]. Further work is needed to establish the relevance, if any, of atmospheric changes to these differences in the regulation of enzymes of the PCRC [63,64], and also the absence of Rubisco activase from algae with the form ID Rubisco in the few cases examined [61].…”