## 3 The Photosynthetic Machinery Used by Cyanobacteria
### AMGs with the Potential to Repair Photosystem II following Oxidative Damage  
As a large common protein complex, photosystem II (PSII) extracts the electrons from water and releases molecular oxygen [55]. Polypeptide D1 and D2, encoded by _psbA_ and _psbD_, respectively, form the core heterodimer of the PSII reaction center. Together with the necessary cofactors, PSII enables the generation of a strong oxidant that can be used to extract electrons from water (Figure 3C). The generation of this strong oxidant results in abundant levels of molecular oxygen, which can cause photo-oxidative damage. The polypeptides D1 and D2, especially D1, are particularly vulnerable to photodamage [56]. This could irreversibly inhibit the function of PSII. Stress conditions, such as high light, high salt concentration, or high or low temperatures, may exacerbate the damage [57]. To counteract the damage, cyanobacteria have evolved a PSII repair mechanism, whereby damaged D1 can be degraded and complemented by the newly synthesized D1 polypeptides. If the synthesis of D1 polypeptides can complement the damage, then photosynthesis would not be affected. However, if the synthesis of D1 polypeptides cannot complement the damage, photoinhibition occurs, and the growth of cells would be affected. In a recent study, the phototrophs treated with protein synthesis inhibitors were shown to inhibit the synthesis of D1 polypeptides and result in photoinhibition [58; 59]. This demonstrates that D1 peptide synthesis is especially important for the PSII repair cycle against photoinhibition. Different species and growth conditions can affect the half-life of D1 polypeptides. For example, in higher plants, the half-life of D1 is about 2-6 h. The half-life of D1 in _Synechococcus_ WH7803 is about 3-4 h [57].  
Photodamage to the D1 polypeptide is unavoidable, regardless of the prevailing light conditions. Most of the investigated viruses contain AMGs encoding D1 (111/153). Basedon our analyses, 16/33 podocyanophages and 95/103 myocyanophages contain a copy of _psbA_. AMGs encoding D2 were also prevalent in the myocyanophages analyzed (78/103) but absent in podoviridae and siphoviridae.  
Previous studies have indicated that shortly after infection, archetypal myovirus T4 can block host DNA replication, transcription, and translation and degrade the host DNA [57]. In _Synechococcus_ WH7803 cells, S-PM2 infection exerts a similar effect on the host. One effect of infection would be to prevent the D1 protein re-synthesis. Indeed, the transcription of the gene _psbA_ is markedly and progressively reduced following S-PM2 infection [57]. Thus, compared with uninfected cells, the infected cells would be more sensitive to photoinhibition. This also explains why the acquisition of a copy of the _psbA_ gene would confer a fitness advantage to the phage. By encoding its own copy of D1, S-PM2 maintains the PSII repair cycle after the synthesis of D1 proteins in host cells have been shut down, thus permitting the continuation of photosynthesis and providing the necessary energy for phage replication.  
It could be postulated that after infection, more _psbA_ genes need to be transcribed to complement the loss of D1 polypeptides. The _psbD_ AMG-encoding D2 polypeptide was found in 78 of the 153 cyanophage that we analyzed.  
In _Prochlorococcus_ myoviruses P-SSM2 and P-SSM4 [60], there are putative promoter and transcriptional terminators flanking the genes _psbA_ and _psbD_, indicating they can be expressed autonomously [61]. Gene _psbA_ and the essential and highly expressed phage capsid genes in the podocyanophage P-SSP7 have the same promoters and terminators, enabling simultaneous transcription, implying that _psbA_ has become an integral part of phage genomes [61].