Editing Lambda phage (section)

==Protein function overview==
{| class="wikitable"
! scope="col" width="150px" | Protein
! scope="col" width="150px" | Function in life cycle
! scope="col" width="90px" | Promoter region
! scope="col" width="600px" | Description
|-
| cIII || Regulatory protein CIII.  Lysogeny, cII Stability || P<sub>L</sub> || (Clear 3) ''HflB'' (FtsH) binding protein, protects ''cII'' from degradation by proteases.
|-
| cII || Lysogeny, Transcription activator || P<sub>R</sub> || (Clear 2) Activates transcription from the P<sub>AQ</sub>, P<sub>RE</sub> and P<sub>I</sub> promoters, transcribing ''cI'' and ''int''. Low stability due to susceptibility to cellular ''HflB'' (FtsH) proteases (especially in healthy cells and cells undergoing the SOS response). High levels of ''cII'' will push the phage toward integration and lysogeny while low levels of ''cII'' will result in lysis.
|-
| cI || Repressor, Maintenance of Lysogeny || P<sub>RM</sub>, P<sub>RE</sub> || (Clear 1) Transcription inhibitor, binds O<sub>R</sub>1, O<sub>R</sub>2 and O<sub>R</sub>3 (affinity O<sub>R</sub>1 > O<sub>R</sub>2 = O<sub>R</sub>3, i.e. preferentially binds O<sub>R</sub>1). At low concentrations blocks the P<sub>R</sub> promoter (preventing cro production). At high concentrations downregulates its own production through O<sub>R</sub>3 binding. Repressor also inhibits transcription from the P<sub>L</sub> promoter. Susceptible to cleavage by ''[[RecA]]*'' in cells undergoing the SOS response.
|-
| cro || Lysis, Control of Repressor's Operator || P<sub>R</sub> || Transcription inhibitor, binds O<sub>R</sub>3, O<sub>R</sub>2 and O<sub>R</sub>1 (affinity O<sub>R</sub>3 > O<sub>R</sub>2 = O<sub>R</sub>1, i.e. preferentially binds O<sub>R</sub>3). At low concentrations blocks the pRM promoter (preventing ''cI'' production). At high concentrations downregulates its own production through O<sub>R</sub>2 and O<sub>R</sub>1 binding. No cooperative binding (cf. below for cI binding)
|-
| O || Lysis, DNA replication || P<sub>R</sub> || Replication protein O.  Initiates Phage Lambda DNA replication by binding at ''ori'' site.
|-
| P || Lysis, DNA Replication || P<sub>R</sub> || Initiates Phage Lambda DNA replication by binding to ''O'' and ''DnaB'' subunit. These bindings provide control over the host DNA polymerase.
|-
| {{anchor|gam}}gam || Lysis, DNA replication || P<sub>L</sub> || Inhibits host ''[[RecBCD]]'' nuclease from degrading 3' ends—allow [[rolling circle replication]] to proceed.
|-
| S || Lysis || P<sub>R'</sub> || [[Holin]], a membrane protein that perforates the membrane during lysis.
|-
| R || Lysis || P<sub>R'</sub> || [[Endolysin]], Lysozyme, an enzyme that exits the cell through the holes produced by Holin and cleaves apart the cell wall.
|-
| Rz and Rz1 || Lysis || P<sub>R'</sub> || Forms a membrane protein complex that destroys the outer cell membrane following the cell wall degradation by endolysin. Spanin, Rz1(outer membrane subunit) and Rz(inner membrane subunit).
|-

| F || Lysis || P<sub>R'</sub> || Phage capsid head proteins.
|-

| D || Lysis || P<sub>R'</sub> || Head decoration protein.
|-

| E || Lysis || P<sub>R'</sub> || Major head protein.
|-

| C || Lysis || P<sub>R'</sub> || Minor capsid protein.
|-

| B || Lysis || P<sub>R'</sub> || Portal protein B.
|-

| A || Lysis || P<sub>R'</sub> || Large terminase protein.
|-

| J || Lysis || P<sub>R'</sub> || Host specificity protein J.
|-

| M V U G L T Z || Lysis || P<sub>R'</sub> || Minor tail protein M.
|-

| K || Lysis || P<sub>R'</sub> || Probable endopeptidase.
|-

| H || Lysis || P<sub>R'</sub> || Tail tape measure protein H.
|-

| I || Lysis || P<sub>R'</sub> || Tail assembly protein I.
|-

| FI || Lysis || P<sub>R'</sub> || DNA-packing protein FI.
|-

| FII || Lysis || P<sub>R'</sub> || Tail attachment protein.
|-

| tfa || Lysis || P<sub>R'</sub> || Tail fiber assembly protein.
|-

| int || Genome Integration, Excision || P<sub>I</sub>, P<sub>L</sub> || [[Integrase]], manages insertion of phage genome into the host's genome. In Conditions of low ''int'' concentration there is no effect. If ''xis'' is low in concentration and ''int'' high then this leads to the insertion of the phage genome. If ''xis'' and ''int'' have high (and approximately equal) concentrations this leads to the excision of phage genomes from the host's genome.
|-
| xis || Genome Excision || P<sub>I</sub>, P<sub>L</sub> || [[Excisionase]] and ''int'' protein regulator, manages excision and insertion of phage genome into the host's genome.
|-
| N || Antitermination for Transcription of Late Early Genes || P<sub>L</sub> || [[Antiterminator]], RNA-binding protein and RNA polymerase cofactor, binds RNA (at Nut sites) and transfers onto the nascent RNApol that just transcribed the nut site. This RNApol modification prevents its recognition of termination sites, so normal RNA polymerase termination signals are ignored and RNA synthesis continues into distal phage genes (''cII, cIII, xis, int, O, P, Q'')
|-
| Q || Antitermination for Transcription of Late Lytic Genes || P<sub>R</sub> || [[Antiterminator]], DNA binding protein and RNApol cofactor, binds DNA (at Qut sites) and transfers onto the initiating RNApol. This RNApol modification alters its recognition of termination sequences, so normal ones are ignored; special Q termination sequences some 20,000 bp away are effective. Q-extended transcripts include phage structural proteins (A-F, Z-J) and lysis genes (''S, R, Rz and Rz1''). Downregulated by P''<sub>antiq</sub>'' antisense mRNA during lysogeny.
|-
| [[RecA]] || [[SOS Response]] || Host protein || DNA repair protein, functions as a co-protease during SOS response, auto-cleaving ''LexA'' and ''cI'' and facilitating lysis.
|}