Editing Lambda phage (section)

===Lytic life cycle===
{{Main|Lytic cycle}}
[[File:LambdaPlaques.jpg|thumb|Lysis plaques of lambda phage on ''[[Escherichia coli|E. coli]]'' bacteria]]
This is the lifecycle that the phage follows following most infections, where the cII protein does not reach a high enough concentration due to degradation, so does not activate its promoters.{{citation needed|date=October 2022}}
# The 'late early' transcripts continue being written, including ''xis'', ''int'', ''Q'' and genes for replication of the lambda genome (''OP''). Cro dominates the repressor site (see [[#Repressor|"Repressor" section]]), repressing synthesis from the ''P<sub>RM</sub>'' promoter  (which is a promoter of the lysogenic cycle).
# The O and P proteins initiate replication of the phage chromosome (see "Lytic Replication").
# Q, another [[antiterminator]], binds to ''Qut'' sites.
# Transcription from the ''P<sub>R'</sub>'' promoter can now extend to produce mRNA for the lysis and the head and tail proteins.
# Structural proteins and phage genomes self-assemble into new phage particles.
# Products of the genes ''S'',''R'', ''Rz'' and ''Rz1'' cause cell lysis. S is a [[holin]], a small membrane protein that, at a time determined by the sequence of the protein, suddenly makes holes in the membrane. R is an [[endolysin]], an enzyme that escapes through the S holes and cleaves the cell wall. Rz and Rz1 are membrane proteins that form a complex that somehow destroys the outer membrane, after the endolysin has degraded the cell wall. For wild-type lambda, lysis occurs at about 50 minutes after the start of infection and releases around 100 virions.

====Rightward transcription====
Rightward transcription expresses the ''O'', ''P'' and ''Q'' genes. O and P are responsible for initiating replication, and Q is another antiterminator that allows the expression of head, tail, and lysis genes from ''P<sub>R’</sub>''.<ref name="src3"/>

Pr is the promoter for rightward transcription, and the cro gene is a regulator gene. The cro gene will encode for the Cro protein that will then repress Prm promoter.  Once Pr transcription is underway the Q gene will then be transcribed at the far end of the operon for rightward transcription. The Q gene is a regulator gene found on this operon, which will control the expression of later genes for rightward transcription. Once the gene's regulatory proteins allow for expression, the Q protein will then act as an anti-terminator. This will then allow for the rest of the operon to be read through until it reaches the transcription terminator. Thus allowing expression of later genes in the operon, and leading to the expression of the lytic cycle.<ref>{{cite journal | vauthors = Thomason LC, Schiltz CJ, Court C, Hosford CJ, Adams MC, Chappie JS, Court DL | title = Bacteriophage λ RexA and RexB functions assist the transition from lysogeny to lytic growth | journal = Molecular Microbiology | volume = 116 | issue = 4 | pages = 1044–1063 | date = October 2021 | pmid = 34379857 | pmc = 8541928 | doi = 10.1111/mmi.14792 }}</ref>

Pr promoter has been found to activate the origin in the use of rightward transcription, but the whole picture of this is still somewhat misunderstood. Given there are some caveats to this, for instance this process is different for other phages such as N15 phage, which may encode for DNA polymerase. Another example is the P22 phage may replace the p gene, which encodes for an essential replication protein for something that is capable of encoding for a DnaB helices.<ref name="src3"/>

====Lytic replication====
# For the first few replication cycles, the lambda genome undergoes [[Theta structure|θ replication]] (circle-to-circle).
# This is initiated at the ''ori'' site located in the ''O'' gene. O protein binds the ''ori'' site, and P protein binds the DnaB subunit of the host replication machinery as well as binding O. This effectively commandeers the host DNA polymerase.
# Soon, the phage switches to a [[rolling circle replication]] similar to that used by phage M13. The DNA is nicked and the 3’ end serves as a primer. Note that this does not release single copies of the phage genome but rather one long molecule with many copies of the genome: a [[concatemer]].
# These concatemers are cleaved at their ''cos'' sites as they are packaged. Packaging cannot occur from circular phage DNA, only from concatomeric DNA.

====Q antitermination====
{{multiple image
| width     = 400
|direction = vertical
|align = center
|footer =  The Q protein modifies the RNA polymerase at the promoter region and is  recruited to RNA polymerase. The Q protein turns into a RNA polymerase subunit after it is recruitment to RNAP and modifies the enzyme into a processive state.  Note that NusA can stimulate the activity of the Q protein.<ref name="Korlach 2008">{{cite journal | vauthors = Santangelo TJ, Artsimovitch I | title = Termination and antitermination: RNA polymerase runs a stop sign | journal = Nature Reviews. Microbiology | volume = 9 | issue = 5 | pages = 319–329 | date = May 2011 | pmid = 21478900 | pmc = 3125153 | doi = 10.1038/nrmicro2560 }}</ref>

| image1    =Qantitermination1.jpg|
| alt1      = Step 1

|image2 = QantiterminationSupplement.jpg

| image3    = Qantitermination2.jpg
| alt3      = Step 2
}}
Q is similar to N in its effect: Q binds to [[RNA polymerase]] in ''Qut'' sites and the resulting complex can ignore terminators, however the mechanism is very different; the Q protein first associates with a DNA sequence rather than an mRNA sequence.<ref name="Deighan, P. and Hochschild, A.">{{cite journal | vauthors = Deighan P, Hochschild A | title = The bacteriophage lambdaQ anti-terminator protein regulates late gene expression as a stable component of the transcription elongation complex | journal = Molecular Microbiology | volume = 63 | issue = 3 | pages = 911–920 | date = February 2007 | pmid = 17302807 | doi = 10.1111/j.1365-2958.2006.05563.x | doi-access = free }}</ref>
# The ''Qut'' site is very close to the ''P<sub>R’</sub>'' promoter, close enough that the σ factor has not been released from the RNA polymerase holoenzyme. Part of the ''Qut'' site resembles the -10 [[Pribnow box]], causing the holoenzyme to pause.
# Q protein then binds and displaces part of the σ factor and transcription re-initiates.
# The head and tail genes are transcribed and the corresponding proteins self-assemble.

====Leftward transcription====
[[File:Phage Lambda int xis Retroregulation.jpg|thumb|right|300px|Diagram showing the retro-regulation process that yields a higher concentration of xis compared to int. The mRNA transcript is digested by bacterial RNase starting from the cleaved hairpin loop at sib.]]
Leftward transcription expresses the ''gam,'' ''xis'', ''bar'' and ''int'' genes.<ref name="src3"/> Gam proteins are involved in recombination. Gam is also important in that it inhibits the host RecBCD nuclease from degrading the 3’ ends in rolling circle replication. Int and xis are integration and excision proteins vital to lysogeny.{{Citation needed|date=November 2023}}

===== Leftward transcription process =====

# Lambda phage inserts chromosome into the cytoplasm of the host bacterial cell.
# The phage chromosome is inserted to the host bacterial chromosome through DNA ligase.
# Transcription of the phage chromosome proceeds leftward when the host RNA polymerase attaches to promotor site ''p''L resulting in the translation of gene ''N.''
## Gene N acts a regulatory gene that results in RNA polymerase being unable to recognize translation-termination sites.<ref name="pmid6241940">{{cite journal | vauthors = Brammar WJ, Hadfield C | title = A programme for the construction of a lambda phage | journal = Journal of Embryology and Experimental Morphology | volume = 83 | issue = Suppl | pages = 75–88 | date = November 1984 | pmid = 6241940 | doi = | url = }}</ref>

===== Leftward Transcription mutations =====
Leftward transcription is believed to result in a deletion mutation of the ''rap'' gene resulting in a lack of growth of lambda phage. This is due to RNA polymerase attaching to pL promoter site instead of the pR promotor site. Leftward transcription results in ''bar''I and ''bar''II transcription on the left operon. Bar  positive phenotype is present when the ''rap'' gene is absent. The lack of growth of lambda phage is believed to occur due to a temperature sensitivity resulting in inhibition of growth.<ref>{{cite journal | vauthors = Guzmán P, Guarneros G | title = Phage genetic sites involved in lambda growth inhibition by the Escherichia coli rap mutant | journal = Genetics | volume = 121 | issue = 3 | pages = 401–409 | date = March 1989 | pmid = 2523838 | pmc = 1203628 | doi = 10.1093/genetics/121.3.401 }}</ref>

===== xis and int regulation of insertion and excision =====
# ''xis'' and ''int'' are found on the same piece of mRNA, so approximately equal concentrations of ''xis'' and ''int'' proteins are produced. This results (initially) in the excision of any inserted genomes from the host genome.
# The mRNA from the ''P<sub>L</sub>'' promoter forms a stable secondary structure with a [[stem-loop]] in the ''sib'' section of the mRNA. This targets the 3' (''sib'') end of the mRNA for RNAaseIII degradation, which results in a lower effective concentration of ''int'' mRNA than ''xis'' mRNA (as the ''int'' cistron is nearer to the ''sib'' sequence than the ''xis'' cistron is to the ''sib'' sequence), so a higher concentrations of ''xis'' than ''int'' is observed.
# Higher concentrations of ''xis'' than ''int'' result in no insertion or excision of phage genomes, the evolutionarily favoured action - leaving any pre-inserted phage genomes inserted (so reducing competition) and preventing the insertion of the phage genome into the genome of a doomed host.