Carotenoids have important functions in photosynthesis, nutrition, and protection against photooxidative damage . They are produced by all photosynthetic organisms–plants, algae and bacteria as well as many species of nonphotosynthetic eubacteria. Cyanobacteria are a group of eubacteria that can be traced back 3.5 billion years, based on the fossil and molecular evidence [2,3]. Carotenoids in cyanobacteria have two main functions: they serve as light –harvesting pigments in photosynthesis and they protect against photooxidative damage .Thus, over hundreds of millions ago, cyanobacteria had photosynthetic activity.
Extensive studies have been done on the biosynthetic pathway for carotenoids (Fig.1) [5-7]. Farnesyl pyrophosphate (FPP) combining with C5-isoprenoid units is extended to C20 molecules, geranylgeranyl pyrophosphate (GGPP) by geranylgeranyl pyrophosphate synthase (crtE). The common C40 carbon results from the condensation of two C20 molecules by phytoene synthase (crtB). The sequential desaturation steps and cyclization of the ends of the molecule to generate carotenes are catalyzed by phytoene desaturase (crtP/crtI), ζ-carotene desaturase (crtQ) and lycopene cyclase. Finally, the carotenes are further modified by the enzymes such as β-carotene ketolase (crtW or crtO) and β-carotene hydroxylase (crtR) to generate a various C40 carotenoids. The general aspects of chemical structures, functions, molecular genetics of carotenoids and molecular evolution of enzymes involved in carotenoid biosynthesis have been reported [8-12]. More recently the cyanobacterial genomes results in the focus on the enzymes involved in carotenoid biosynthesis from cyanobacteria. CrtQs from Anabaena sp. PCC 7120 (crtI-like sequence) , Synechocystis sp. PCC 6803 (plant crtQ-like) , and crtI-type phytoene desaturase from Gloeobacter violaceus PCC 7421 have been functionally identified. Although only one monoketolase CrtO from Synechocystis has been functionally characterized , two distinct β-carotene ketolases-crtO and crtW from Anabaena sp. PCC 7120 , and two carotenoid ketolase genes (crtW) from Nostoc punctiforme PCC 73102  have been characterized. In generally, the biosynthetic pathways of the carotenoids are similar, but the carotenoids among these species are different in composition and diverse in category.
Now whole-genome information is being generated for a number of cyanobacteria.16 cyanobacterial genomes have been fully sequenced and 2 in the draft format and more than 20 are in the process of being sequenced (http://img.jgi.doe.gov/pub/main.cgi?Page=restrictedMicrobes&domain=Bacteria; http://www.ncbi.nlm.nih.gov/).The complete genome sequences of cyanobacteria allowed us to obtain a comprehensive data set of genes encoding enzymes in the carotenoid biosynthetic pathway. Moreover, even if experimental studies have become possible to reconstruct the pathway on the basis of a prediction of the genes and its function from the complete genome sequence data. Genome-wide screening of crt genes based on the genome-sequencing project provided us a new and comprehensive insight into the cyanobacterial carotenoid biosynthetic pathway. In this article, emphasis is centered on the comparative analysis of cyanobacteria and shedding light on the diversity of the carotenoid biosynthesis pathway based on the information of genomes.