## 3 The Photosynthetic Machinery Used by Cyanobacteria
### AMGs with the Potential to Impact Electron Transport  
Plastocyanin (PC), encoded by the gene _petE_, can transfer the electron flow from cytochrome b6\(f\) to photosystem I in cyanobacteria (XII in Figures 2 and 3D). However, studies indicate that PC encoded by cyanophages may have a different function [50]. The hydrophobic core region of PC directly follows the signal peptide of the cyanophage PC without a C-terminal domain [62]. The N-terminal signal peptide of the cyanophage PC is also modified. Compared with the host, cyanophage PC also contains many unique amino acid residues [38]. In cyanobacteria, the isoelectric point (pI) is essential for the interactions of PC and PSI. However, the cyanophage PC has a substantially different pI compared to the host (Kruskal-Wallis: H1 = 50.21, \(p<0.001\)). All of these findings may imply a potential functional difference in PC between the host and cyanophage. After the acceptance of electrons from the cytochrome b6\(f\) complex, cyanophage PC may not reduce the PSI, but could, instead, transfer electrons to cytochrome c oxidase (COX) directly [63]. Following the reduction of COX, the proton is transferred across the thylakoid [59]. Through this electron transfer pathway, electrons could accumulate for ATP synthesis by ATP synthase. Furthermore, the over-production of the PQ pool (plastoquinol, reduced; plastoquinone, oxidized) caused by the cyanophage infection may be alleviated in this way, which could prevent the photosystem from undergoing photoinhibition [38]. Of the 153 sequenced cyanophage genomes, 70 of them contain the PC-encoded gene _petE_ and are all from myocyanophages. According to a recent study, following phage infection, the COX expression level may be enhanced, which may support the above hypothesis for the role of this complex in accepting electrons from the plastocyanin (PC) pool during infection [46]. Cyanophages can also encode type I NAD(P)H dehydrogenase, also known as the NDH -1 complex, which can transfer electrons to quinol and participate in photosynthesis and CO\({}_{2}\) uptake [64]. Through metagenomic analysis, cyanophages have been shown to have the _ndhl_ gene-encoded NADH dehydrogenase subunit 1 [65], the _ndhlD_-gene encoded NADH dehydrogenase subunit 4 [66], as well as the _ndhlP_ gene-encoded single transmembrane small subunit of the NDH-1 complex [67]. In the genome of P-TIM40, we also identified the _ndhl_ gene (IX in Figure 2 and Table 2) that encoded a Fe-S protein. The cysteine residues that directly bind the two Fe-S centers (N6a and N6b) of the protein are completely conserved in the suspected cyanophage homolog, suggesting that NdhI may play a key role in electron transfer through the complex directly to reduce plastoquinol [65]. Electrons are then transferred from plastoquinol to PC through the cytochrome bof complex. To date, the mechanism of electron donation to NdhI has not been clearly understood, although there are several hypotheses [64; 68; 69]. It is also difficult to know whether there are any functional differences between cyanobacterial NdhI and the cyanophage NdhI. In cyanobacteria, ferredoxin (Fd), encoded by the _petF_ gene, can transfer electrons from photosystem I to ferredoxin NADP\({}^{+}\) reductase (FNR), which, in turn, reduces NADP to NADPH for carbon fixation (Figure 3D). However, according to some hypotheses, electron flow may be redirected from Fd to the NDH-1 complex after infection [38]. Furthermore, the ferredoxin-dependent bilin reductases (FDBRs) can catalyze BV reduction, where Fd provides electrons for this reaction [70]. As a class of radical enzymes, FDBRs are able to catalyze the biosynthesis of both PEB and PCB [50; 70; 71]. Among the 153 sequenced cyanophage genomes, the gene _petF_ encoding Fd was found in 44 of them. In a recent study, the transcriptome difference between a cyanophage (P-HM2) and its host (_Prochlorococcus_ MED4) throughout infection was analyzed.