Auxiliary metabolic genes
Auxiliary metabolic genes are found in many bacteriophages but originated in bacterial cells. AMGs modulate host cell metabolism during infection so that the phage can replicate more efficiently. For instance, bacteriophages that infect the abundant marine cyanobacteria Synechococcus and Prochlorococcus carry AMGs that have been acquired from their immediate host as well as more distantly-related bacteria. Cyanophage AMGs support a variety of functions including photosynthesis, carbon metabolism, nucleic acid synthesis and metabolism. AMGs also have broader ecological impacts beyond their host including their influence on biogeochemical cycling.
Classes
AMGs employ diverse functions including pathways not involved in metabolism despite what the name suggests. They are categorized in two classes based on their presence in the Kyoto Encyclopedia of Genes and Genomes. AMGs do not encompass metabolic genes involved in typical viral functions, such as nucleotide and protein metabolism since their functions achieve direct viral reproduction, rather than augmenting host function to indirectly enhance it.Class I
Class I AMGs encode for metabolism pathways in the cell and are found in KEGG. In particular, these genes are found in photosynthesis and carbon metabolism. psbA is almost a ubiquitous photosynthetic AMG for the photosystem Il reaction center D1 found in Synechococcus and Prochlorococcus cyanophages. Photosynthetic machinery for other reaction centers and electron transport are also found in many viruses infecting phototrophs. Phages encode for nearly all genes involved in carbon metabolism. In particular, viruses redirect host metabolism to increase dNTP biosynthesis for viral genome replication. glgA can induce starvation by converting glucose-6-phosphate to glycogen, forcing the host to compensate by deriving ribulose-5-phosphate from glyceraldehyde-3-phosphate and fructose-6-phosphate.Class II
Class II AMGs encode for peripheral functions absent from the KEGG metabolic pathways. This includes genes typically involved in transport and assembly. Major representatives of this class are involved in balancing TCA cycle intermediates. Additionally, the acquisition of biogenic elements outside of carbon like phosphate, governed by pstS, are prevalent for this class. Confidence of AMG identification for Class II AMGs is reduced without a database for reference.Abundance
Virus survival through inclusion of AMGs is governed by the laws of natural selection and has been made highly selective through co-evolution with their hosts. As such, the AMGs that confer a fitness advantage to the virus's ability to infect a host and reproduce will be more abundant. AMG abundance is largely dictated by the lifestyle of the virus, environmental conditions surrounding it, and host characteristics.Lifestyle
Lytic and lysogenic viruses have different lifestyles which impact what AMGs they acquire. Lytic viruses tend to use AMGs to repurpose host cell metabolism and steal nutrients when in high cell density. Therefore, AMGs related to metabolism and transport are found more abundantly in lytic viruses. Lytic viruses also encompass a more diverse set of AMGs than lysogenic viruses, in part due to their larger host range and higher infection frequency. Temperate viruses, on the other hand, may employ AMGs to improve host fitness and virulence due to their often longer lifespan in the cell as a prophage. Gene density in these viruses is higher when compared to their lytic counterparts. Higher rates of HGT in lysogenic viruses allows for more AMG transfer but also lowers overall gene diversity.Photosynthesis capacity has also been correlated to AMG diversity. Aphotic viral communities possess greater AMG diversity than those in the photic zone.
Environmental conditions
Pathways utilizing nutrients found in low concentrations in the local environment are generally found in higher abundance in the virus. In marine environments, AMGs can confer fitness advantages for both host and viruses under relatively nutrient-limited conditions compared to sediment and strong ultraviolet stress of water. In sunlit versus dark ocean waters, AMGs in distinct pathways are unequally distributed to reprogram host energy production and viral replication based on available nutrients. In sedimentary environments, carbon and sulfur metabolism AMGs are typically more prevalent to outcompete other organisms for the abundant resources.Host factors
A virus's host range determines which host it can acquire AMGs from. Additionally, the abundance of a host surrounding a virus will affect its likelihood to acquire genes from the host. Virus populations increasingly occupy lytic lifestyles as bacterial production increases. The strong evolutionary connection between viruses and their hosts makes AMG acquisition mirror the host's own adaptation to its environment over time.Synechococcus and Prochlorococcus are the most abundant picocyanobacteria, accounting for up to 50% of primary production in the marine environment. As such, many AMGs characterized have been discovered in phages of these host systems.