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, 2012, 164690

Genomewide Analysis of Carotenoid Cleavage Dioxygenases in Unicellular and Filamentous Cyanobacteria

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Genomewide Analysis of Carotenoid Cleavage Dioxygenases in Unicellular and Filamentous Cyanobacteria

Hongli Cui et al. Comp Funct Genomics.

Abstract

Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the oxidative cleavage steps from carotenoids to various carotenoid cleavage products. Some ccd genes have been identified and encoded enzymes functionally characterized in many higher plants, but little in cyanobacteria. We performed a comparative analysis of ccd sequences and explored their distribution, classification, phylogeny, evolution, and structure among 37 cyanobacteria. Totally 61 putative ccd sequences were identified, which are abundant in Acaryochloris marina MBIC 11017, filamentous N(2)-fixing cyanobacteria, and unicellular cyanobacterial Cyanothece. According to phylogenetic trees of 16S rDNA and CCD, nced and ccd8 genes occur later than the divergence of ccd7, apco, and ccd1. All CCD enzymes share conserved basic structure domains constituted by a single loop formed with seven β-strands and one helix. In this paper, a general framework of sequence-function-evolution connection for the ccd has been revealed, which may provide new insight for functional investigation.

Figures

Figure 1
Figure 1
Phylogenetic tree of the sequenced cyanobacterial strains and the distribution of ccd sequences genes. Left: 37 fully sequenced cyanobacteria strains were performed based on 16 s rRNA as described in the methods section. An identical topology was obtained with two different methods (ML, NJ) and different models applied (for ML, generalized time reversible (GTR); for NJ, Kimura 2-parameter). Numbers at the node indicated bootstrap values (%) for 1,000 replicates. Right: the distribution of ccd genes across 37 cyanobacterial strains. Circular boxes represented the different ccd sequences that were labeled in the distinct color. The numbers of ccd sequences were presented by the numbers of circular boxes.
Figure 2
Figure 2
Maximum-likelihood tree of CCD enzymes of cyanobacteria, bacteria, eukaryotic algae, fungi, and higher plants. The model of LG+I+G was applied to construct ML tree using PHYML as described in the methods section. Numbers at the node indicated bootstrap values (%) for 1,000 replicates. Cyanobacterial CCD enzymes IDs and the strain names are as in Table 2 and Figure 1. Red line: CCD7, green: APCO, blue: CCD1, CCD4, and NCED, pink: CCD8. Species belonged to similar clade were represented by colored boxes. Orange: fungi, wheat: bacteria, purple: eukaryotic algae, barium: higher plants, cyan: cyanobacterial Prochlorococcus marinus, blue: Thermosynechococcus elongates, Synechococcus elongates, and Synechococcus, ruby: cyanobacterial Cyanothece, and smudge: filamentous cyanobacteria. Unlabeled species included Synechocystis sp. PCC 6803 (sll1541 and slr1648), Gloeobacter violaceus PCC 7421 (gll3689 and gll2774), Microcystis aeruginosa NIES-843 (MAE09040 and MAE60600).
Figure 3
Figure 3
The conserved motifs of the cyanobacterial CCD enzymes. Schematic representation of motifs identified in cyanobacterial CCD enzymes using MEME motif search tool and ClustalW. The results were edited by hand. Length of box did not correspond to length of motif. Boxes represented the same or similar motifs that were labeled in the same color. (a) CCD7 from Synechococcus and Prochlorococcus marinus, (b) CCD7 from other cyanobacterial strains, (c) APCO, and (d) CCD1 and NCED.
Figure 4
Figure 4
Model of structure of CCD enzymes from cyanobacteria strains. (a) The structure model of CCD7 from Prochlorococcus MIT9312 (PMT9312_0282), (b) the structure model of CCD7 from Nostoc punctiforme ATCC 29133 (Npun_F0298), (c) the structure model of APCO from Cyanothece sp. PCC 7424 (PCC7424_5321), (d) the structure model of CCD1 from Anabaena sp. PCC 7120 (all1106).
Figure 5
Figure 5
Sketch of the chain-fold of CCD enzyme showing the seven-bladed β-sheet as the basic motif. Distinct types of β-sheets were presented by colored arrowheads. Bottle green boxes stand for α-helix. (a) The second structure of CCD7 enzyme from Prochlorococcus MIT9312 (PMT9312_0282), (b) CCD7 from Nostoc punctiforme ATCC 29133 (Npun_F0298), (c) APCO from Cyanothece sp. PCC 7424 (PCC7424_5321), (d) CCD1 from Anabaena sp. PCC 7120 (all1106).

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