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Template:Taxobox begin Template:Taxobox begin placement virus Template:Taxobox group i entry Template:Taxobox ordo entry Template:Taxobox familia entry Template:Taxobox genus entry Template:Taxobox species entry Template:Taxobox end placement Template:Taxobox end Enterobacteria phage λ (lambda phage) is a temperate phage that lives in E. coli. Once the phage is inside its host, it may integrate itself into the host's DNA. In this state, λ is called a prophage and stays resident within the host's genome, without causing it much harm. This way, the prophage gets duplicated with every cell division of the host. The DNA of the prophage that is expressed in that state codes for proteins that look out for signs of stress in the host cell. Stress can be a large result of starvation, poisons (like antibiotics), and other factors that can damage or destroy the host. At that point, the prophage becomes active again, excises itself from the DNA of the host cell and enters its lytic cycle. The reactivated phage takes apart the host's DNA and "reprograms" its "protein factory" to produce new phages in multiple copies. When all resources of the host are depleted from building new phages, the cell is lysed (the cell membrane is broken down), and the new phages are released.

The integration of phage λ takes place at a special attachment site in the bacterial genome, called att. The sequence of the att site is called att and consists of the parts B-O-B', whereas the complementary sequence in the circular phage genome is called att and consists of the parts P-O-P'. The integration itself is a sequential exchange (see genetic recombination) via a Holliday structure and requires both the phage protein int and the bacterial protein IHF (integration host factor). Both int and IHF bind to att and built an intrasome, a DNA-protein-complex designed for site-specific recombination of the phage and host DNA. The original BOB' secuanes is changed by the integration to B-O-P'-phage DNA-P-O-B'. The phage DNA is now part of the host's genome.

Repressor

The represor found in the phage lambda is a notable example of the level of control possible over gene expression by a very simple system. It forms a 'binary switch' with two genes under mutually exclusive expression.

In the following, the convention that genes are italicized, while protein products are not, is followed, i.e. cI refers to the gene, whilst cI is the resulting protein encoded by that gene. The lambda repressor gene system consists of (from left to right on the chromosome):

• cI gene
• OR3
• OR2
• OR1
• cro gene

The lambda repressor is a dimer also known as the cI protein. It regulates the transcription of the cI protein and the Cro protein.

The life cycle of lambda phages is controlled by cI and Cro proteins. The lambda phage will remain in the lysogenic state if cI proteins predominate, but will be transformed into the lytic cycle if cro proteins predominate.

The cI dimer may bind to any of three operators, OR1, OR2, and OR3, in the order OR1 > OR2 > OR3. Binding of a cI dimer to OR1 enhances binding of a second cI dimer to OR2, an effect called cooperativity. Thus, OR1 and OR2 are almost always simultaneously occupied by cI. However, this does not increase the affinity between cI and OR3, which will be occupied only when the cI concentration is high.

• In the absence of cI proteins, the cro gene may be transcribed.
• In the presence of cI proteins, only the cI gene may be transcribed.
• At high concentration of cI, transcriptions of both genes are repressed.

Lifecycle

1. Bacteriophage Lambda binds to the target E.Coli cell, the tail fibres binding to maltose receptors.
2. The linear phage genome is injected into the cell, and immediately circularises.
3. Transcription starts, from the L, R and R' promoters producing the 'immediate early' transcripts.
4. Initially these produce N, Cro and a short inactive protein.
5. Cro binds to OR3 preventing access to the RM promoter preventing transcription and production of cI. N binds to the two Nut sites, on in the N gene, and one in the Cro gene.
6. The N bound in the L and R open reading frames extends the reading frames. The early translation products of these transcripts (the 'late early' transcripts) are more N and Cro along with cII and cIII.
7. cIII binds to cII partially preventing protease vulnerability. The stability of cII determines the lifestyle of the phage. In unstressed cells with abundant nutrients protease activity is high, and cII unstable. This leads to the lytic lifestyle. In stressed cells with limited nutrients protease activity is low, and cII stable. This leads to the lysogenic lifestyle.

Lytic Lifestyle

1. The 'late early' transcripts continue being written, including xis, int, Q and genes for replication of the lambda genome.
2. The lambda genome is replicated in preparation for daughter phage production.
3. Q binds to Qut sites.
4. Replication from the R' promoter can now extend to produce mRNA for the lysis and the structural proteins.
5. Structural proteins and phage genomes self assemble into new phage particles.
6. Lytic proteins build sufficiently far in concentration to cause cell lysis, and the mature phage particles escape.

1. 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.
2. The mRNA from the L promoter forms a stable secondary structure with a hairpin loop in the sib section of the mRNA. This targets the 3' end of the mRNA for RNAaseIII degradation, so a lower effective concentration of xis mRNA than int mRNA is found, so higher concentrations of xis than int.
3. Higher concentrations of xis than int result in no insertion or excision of phage genomes, the evolutionarily favoured action - leaving any pre-insterted phage genomes inserted (so reducing competition) and preventing the insertion of the phage genome into the genome of a doomed host.

Lysenogenic (or Lysogenic) Lifestyle

1. The 'late early' transcripts continue being written, including xis, int, Q and genes for replication of the lambda genome. Although the stable cII also acts to promote transcription from the RE, I and antiq promoters.
2. The antiq promoter produces antisense mRNA to the Q section of the R promoter transcript switching off Q production. The RE promoter produces antisense mRNA to the cro section of the R promoter transcript, turning off cro production, along with sense mRNA for cI, turning on cI production. The I promoter produces mRNA for int, resulting in high concentrations of integrase.
3. No Q results in no extension of the R' promoter's reading frame, so no lytic or structural genes are made. Elevated levels of integrase (to much higher than that of xis) result in the insertion of the lambda genome into the hosts genome (see diagram). Production of cI leads to the binding of cI to the OR1 site in the R promoter, turning off cro production. cI also binds to the L promoter, turning off transcription there too.
4. Lack of cro leaves the OR1 site is left unbound, so transcription from the RM promoter may occur, maintaining levels of cI.
5. Lack of transcription from the L and R promoters leads to no further production of cII and cIII.
6. As cII and cIII concentrations decrease, transcription from the antiq, RE and I stop being promoted.
7. Only the RM and R' promoters are left active, producing a short inactive transcript and cI. The genome is inserted in the host and is in a dormant state.

Induction

1. The host cell, containing a dormant phage genome, experiences DNA damage due to a high stress environment, and starts to undergo the SOS response.
2. RecA (a cellular protein) detects DNA damage and becomes activated, RecA*, a highly specific protease.
3. Normally RecA* cleaves LexA (a transcription repressor), inactivating it, and allowing production of DNA repair proteins. In infected cells this response is hijacked, and RecA* cleaves cI.
4. Cleaved cI can no longer dimerise, and looses its affinity for DNA binding.
5. The R and L promoters are no longer repressed and switch on, and the cell returns to the lytic sequence of expression events (note that cII is not stable in cells undergoing the SOS response). There is however one notable difference.

1. The phage genome is still inserted in the host genome and needs excision for DNA replication to occur. The sib section of the normal L promoter transcript is, however, no longer included in this reading frame (see diagram).
2. No sib domain on the L promoter mRNA results in no hairpin loop on the 3' end, so no longer targeted for RNAaseIII degradation.
3. The fully intact transcript has one intact copy of both xis and int, so approximately equal concentrations of xis and int proteins are produced.
4. Equal concentrations of xis and int result in the excision of the inserted genome from the host genome for replication and later phage production.

Protein Function Overview

cro; Transcription inhibitor, binds OR3, OR2 and OR1 (affinity OR3 > OR2 > OR1, ie. prefferentially binds OR3). At low concentrations blocks the RM promoter (preventing cI production). At high concentrations downregulates its own production through OR2 and OR1 binding.

cI; Transcription inhibitor, binds OR1, OR2 and OR3 (affinity OR1 > OR2 > OR3, ie. prefferentially binds OR1). At low concentrations blocks the R promoter (preventing cro production). At high concentrations downregulates its own production through OR2 and OR3 binding. Also inhibits transcription from the L promoter. Succeptable to cleavage by RecA* in cells undergoing the SOS response.

cII; Transcription activator, binds cIII. Activates transcription from the antiq, RE and I promoters. Low stability due to succeptability to cellular proteases (especially in healthy cells and cells undergoing the SOS response), slightly stabilised by binding to cIII.

cIII; cII binding protein, protects cII from degradation by cellular proteases.

N; DNA binding protein and RNApol cofactor, binds DNA (at Nut sites) and transfers onto any oncoming RNApol. Alters the recognition of stop codons, so normal stop codons are ignored and special N stop codons are effective instead.

Q; DNA binding protein and RNApol cofactor, binds DNA (at Qut sites) and transfers onto any oncoming RNApol. Alters the recognition of stop codons, so normal stop codons are ignored and special Q stop codons are effective instead.

xis; excisionase and integrase regulator, manages excision and insertion of phage genome into the host's genome.

int; 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 the n 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.

A, B, C, D, E, F, Z, U, V, G, T, H, M, L, K, I, J ; structural proteins, self assemble with the phage genome into daughter phage particles.

S, R ; lysis promoters, cause the host cell to undergo lysis at high enough concentrations.

OP ; DNA replication promoter, promotes the specific replication of only the phage genome.

sib ; Forms a stable hairpin loop structure in transcribed mRNA. Attracts degradation of mRNA by RNAaseIII.

attp ; point of action of int and xis in insertion and excision of the phage genome into the host's genome. Corresponding attb found in the host's genome at the point of insertion.

• Caudovirales
• Model organisms