# Isolation and Characterization of a Novel Cyanophage Encoding Multiple Auxiliary Metabolic Genes
## 3 Results and Discussion
### AMGs Encoded by S-SZBM1 Re-Program Phase-Host Interactions  
Previous studies highlighted the prevalence of auxiliary metabolic genes (AMGs) derived from phage genomes and metagenomes, which play important roles in keeping host cell functioning and facilitate replication of phages during infection [18; 19; 48; 49; 50]. In other words, phages can re-program the metabolism of their host by introducing AMGs that are involved in energy and carbon metabolism, DNA and RNA processing, and other functions [48]. Among cyanophage S-SZBM1 and its most closely related 32 cyanophages, at least 13 AMGs are presented in a genome, and the frequencies of AMGs range from 3.03% (_hol_, _pyrE_, _purN_) to 100% (_psbA_, _talC_, _mazG_, _phoH_, and _hsp_) (Figure 4). A total of 25 ORFs in cyanophage S-SZBM1 are likely to participate in auxiliary metabolism reactions after infection, such as photosynthesis (_psbA_, _cepT_, _petF_, _speD_, _hli_), carbon metabolism (_talC_, _cp12_), nucleotide synthesis and metabolism (carbamoyltransferase), cell protection (_lsp_, _prnA_, _prdx_, _nrdC_), and other cell metabolism (_phoH_, _mazG_, 2 OG-Fe(II) oxygenase, _cobS_, cytidyltransferase). All of these AMGs are conserved in cyanophage S-SZBM1 genome,  
Figure 3: **(A)** Phylogenetic analysis showing the evolutionary relationship and taxonomy of cyanophage S-SZBM1. The GBDP phylogenetic tree was constructed using VICTOR based on complete amino acid profiles of compared phages. The numbers near branches of the phylogenetic tree are GBDP pseudobootstrap support values from 100 replications. The hosts, G+C content, genus cluster information, and genome size of these phages were obtained from the NCBI and the ICTV. **(B)** Heatmap generated by VIRIDIC incorporating intergenomic sequence similarities (right half) and alignment indicators (left half) for cyanophage S-SZBM1 and its most closely related 32 cyanophages. with the exception of the gene _hli_, while several of them (_psbA_, _mazG_, _phoH_, _hsp_, _hli_, and _cobS_) are described as T4-like core genes. Phage-encoded photosynthesis-related genes are the most representative AMGs to investigate phage-host interactions. Generally, utilization of cyanophage-encoded photosynthesis genes can boost the host photosynthetic performance during infection and, therefore, meet the energy demands for viral replication [48; 51; 52]. The _psbA_ and _psbD_ genes for the core photosystem II reaction center D1 and D2 encoded by genomes of phages were most well studied; these two proteins might potentially replenish the rapidly damaged host homologous proteins during infection [53; 54]. More recent studies showed that cyanophage _psbA_ under high light conditions would be up-regulated, which may increase the rate of delivery of D1 protein to PSII, resulting in an increase in the rate of photophosphorylation and more energy for cyanophage development [7; 55]. Among cyanophage S-SZBM1 and its most related 32 cyanophages, the _psbA_ gene is present in all cyanophages (100%), while the distribution of _psbD_ gene is more sporadic (72.73%), and this finding is consistent with previous studies [18; 19; 43; 51; 56; 57]. In addition, the _speD_ gene found in cyanophage S-SZBM1, which is a key enzyme in the biosynthesis of the polyamines spermine and spermidine, might involve in regulating the host PSII reaction center during infection [58]. The _speD_ gene was also reported to benefit phages in that polyamines are charge balance contributors in T4-like phage genome packaging processes [52; 59]. Moreover, cyanophage S-SZBM1 has a _hli_ gene, which has been reported to safeguard the host's photosynthetic apparatus by dissipating excess light energy [13; 60]. Cyanophage S-SZBM1 also contains a photosynthetic electron transport gene _petF_, and gene _cpeT_ which might be important for light-harvesting phycobilproteins assembly during infection [61].