Editing Lytic cycle (section)

==Gene regulation biochemistry==
There are three classes of genes in the phage genome that regulate whether the lytic or lysogenic cycles will emerge. The first class is the immediate early genes, the second is the delayed early genes and the third is the late genes. The following refers to the well-studied temperate phage lambda of ''E. coli.''{{cn|date=October 2022}}

# Immediate early genes: These genes are expressed from promoters recognized by the host RNA polymerase, and include ''Cro'', ''cII'', and ''N''. CII is a transcription factor that stimulates expression of the main lysogenic repressor gene, ''cI'', whereas Cro is a repressor for ''cI'' expression. The lysis-lysogeny decision is mainly influenced by the competition between Cro and CII, resulting in the determination of whether or not sufficient CI repressor is made. If so, CI represses the early promoters and the infection is shunted into the lysogenic pathway. N is an anti-termination factor that is needed for the transcription of the delayed early genes.
# Delayed early genes: These include the replication genes ''O''  and ''P'' and also ''Q'', which encodes the anti-terminator responsible for transcription of all the late genes.
# Late genes:{{More detail needed}}

Q-mediated turn-on of late transcription begins about 6–8 min after infection if the lytic pathway is chosen. More than 25 genes are expressed from the single late promoter, resulting in four parallel biosynthetic pathways. Three of the pathways are for production of the three components of the virion: the DNA-filled head, the tail, and the side tail fibers. The virions self-assemble from these components, with the first virion appearing at about 20 min after infection. The fourth pathway is for lysis. In lambda 5 proteins are involved in lysis: the holin and antiholin from gene ''S'', the endolysin from gene ''R'' and the spanin proteins from genes ''Rz'' and ''Rz1''. In wild-type lambda, lysis occurs at about 50 min, releasing approximately 100 completed virions. The timing of lysis is determined by the holin and antiholin proteins, with the latter inhibiting the former. In overview, the holin protein accumulates in the cytoplasmic membrane until suddenly forming micron-scale holes, which triggers lysis. The endolysin R is released to the periplasm, where it attacks the peptidoglycan. The spanin proteins Rz and Rz1 accumulate in the cytoplasmic and outer membranes, respectively, and form a complex spanning the periplasm through the meshwork of the peptidoglycan. When the endolysin degrades the peptidoglycan, the spanin complexes are liberated and cause disruption of the outer membrane. Destruction of the peptidoglycan by the endolysin and disruption of the outer membrane by the spanin complex are both required for lysis in lambda infections.{{cn|date=October 2022}}

Lysis inhibition: T4-like phages have two genes, ''rI'' and ''rIII'', that inhibit the T4 holin, if the infected cell undergoes super-infection by another T4 (or closely related) virion. Repeated super-infection can cause the T4 infection to continue without lysis for hours, leading to accumulation of virions to levels 10-fold higher than normal.<ref>{{cite web|url=http://nemetoadreviews.weebly.com/lytic-cycle-of-viruses.html|title=The Lytic Cycle of the T-Even Bacteriophage|website=nemetoadreviews.com|access-date=January 9, 2018}}</ref>{{Better source needed|date=June 2024}}