## 3 The Photosynthetic Machinery Used by Cyanobacteria
### AMGs with the Potential to Impact the Biogenesis of the PBS  
Photosynthetic pigments are biosynthesized and then formed into the PBS, an assemblage of chromophorylated proteins anchored to thylakoid membranes. In cyanobacteria, the biosynthesis of PEB **1**, as well as the associated pigments phycocyanabilin **2** and phytochromobilin **3**, starts with the heme oxygenase (HO)-mediated cleavage of heme to an open-chain product biliverdin IXa (BV) **4** through an aerobic reaction [47; 48]. Of the 153 sequenced cyanophage genomes, 8 could be seen to contain a gene encoding an additional copy of HO (XIII in Figures 2 and 3B. Table 2). Ferredoxin oxidoreductase, encoded by _pebA_, is employed to catalyze the two-electron reduction of biliverdin IXa (BV) **4** to 15,16 dihydrohliverdin (DHBV) **5**[49]. The conversion of DHBV **5** to phycoerythrobilin (PEB) **1** is subsequently mediated by PebB (Phycoery  
Figure 3: Photosynthesis affected by phage infection. (**A**) The three multicomponent photosynthetic complexes used by cyanobacteria [43]. (**B**) Biosynthesis of the chromophores Phycoerythrobilin (PEB) [44], Phycocyanobilin 2, and Phytochromobilin 3. Enzymes that we note to be encoded by AMGs, through our analyses of cyanophage genomes, are depicted in an orange sphere. For the full list of cyanophages that encode HO, PcyA, PebS, and PEB, see Figure 2 entries XIII, IV, VII, and VIII, respectively. PEB could also be found in four myocyanophage genomes. (**C**) The polypeptide composition of and electron transport in the photosystem II complex [45]. AP: Allophycocyanin, PE: phycoerythrin, PC: phycocyanin, P680: reaction center chlorophyll a dimer, Phe: pheophytin, Q\({}_{\text{A}}\): plastoquinone tightly bound to the D2 protein, Q\({}_{\text{B}}\): exchangeable plastoquinone bound to the D1 protein, PQ: plastoquinone and PQH\({}_{2}\): plastohydroquinone. (**D**) Modifications to photosynthetic pathways caused by phage infection [46]. The photosynthetic machinery and mechanisms of uninfected (**top**) and phage-infected cyanobacteria (**bottom**). Cyanphage genes involved in the photosystem are gene _psbA_ encoding photosystem II reaction center protein D1, _psbD_ encoding photosystem II D2 protein, _ptox_ encoding plastoquinol terminal oxidase (PTOX), _petF_ encodingferredoxin, and _petE_ encoding plastocyanin and the NADH dehydrogenase gene (shown in red bold font). NDH, NAD(P)H dehydrogenase. COX, cytochrome c oxidase. PTOX, plastoquinol terminal oxidase. PC, plastocyanin. throughin: ferredoxin oxidoreductasenetase). The direct conversion of BV **4** to PEB **1** mediated by PebS (phycoerythrobilin synthase), is also possible. Intriguingly, of the 153 sequenced cyanophage analyzed, 9 of them may be seen to contain a gene encoding PebS (VII in Figures 2 and 3B; Table 2). Phyocyanobilin:ferredoxin oxidoreductase(PcyA) belongs to the ferredoxin-dependent bilin reductase (FDBR) family [50; 51] and mediates the conversion of BV **4** to phycocyanobilin (PCB) **2**. Through the catalysis of PcyA, the substrate BV **4** can be converted to phycocyanobilin (PCB) directly [50; 52]. The gene encoding PcyA may be seen in 16 of the 153 sequenced genomes (IV in Figures 2 and 3B, Table 2). Once the chromophores are biosynthesized, they are integrated into the PBPs through the formation of thioester links with cysteine residues. They are then assembled into the PBS. A putative phycobiliprotein lyase (CpeT) [8], likely involved in supporting the attachment of PEB to the apo-phycobiliprotein, provides a scaffold for the pigment to ensure binding in the right conformation to facilitate correct stereospecific ligation to a conserved cysteine residue within the phycobiliprotein. CpeT belongs to the so-called T-type lyases, and phycocyanobilin-specific homologs of CpeT (i.e., CpeT) were shown to specifically serve the position equivalent to cysteine 153 in the -subunit of phycocyanin (PC) [53]. Therefore, the analogous CpeT lyases may serve the Cys-153 of PE.