Bacteriophage Lambda

Infection

Infection begins when a phage adsorbs to the lamB gene product, a receptor in the outer membrane of E. coli. The phage stores its DNA under pressure and so it can be injected into the cell, with the help of a cellular protein – ptsM. The DNA in the phage’s head is linear and double stranded but it has 12 base complementary single strang overhangs on each 5’ prime end, rich in G and C. These “sticky ends” mean that the DNA rapidly circularises. In most circumstances cII levels in the cell will not be high and so the phage will enter the lytic cycle typical of bacteriophages.

Lytic cycle

Immediate early (IE) stage

The phage’s lytic cycle uses three promoters PL, PR and PR’. These need to be strong promoters so that they can recruit the host polymerase. The host polymerase binds preferentially to these promoters to such an extent that if many copies of the promoters are artificially inserted the cell is unable to transcribe its own DNA and dies. PL promotes a transcript which initially terminates after transcription for N, an anti-termination protein. Transcription from PR produces cro, which is important in continuing the lytic cycle rather than lysogeny (see cI section). The PR’ transcript at this stage only produces a small inactive protein.

Figure 1: Immediate early stage
(click on any diagram to enlarge)

Delayed early (DE) stage

The immediate early stage produces the anti-termination factor N. There are areas around the PL and PR promoters called N utlilisation sites or nut sites. They cause N to bind to the transcriptional apparatus at the promoter. This prevents some of the the early termination that occurs in the immediate early stage. Most importantly for lysis, it allows the transcription of O, P and Q. O and P are needed for DNA synthesis to occur – they recruit the host’s machinery for DNA replication to a point near their locus. P prevents the host from synthesising bacterial DNA, working with cII. The machinery produces a number of copies of the phage’s circular DNA, each of which is used in rolling circle replication to produce around 10 phage genomes. Q is an anti-termination factor needed for progression to the late stage. Although int is part of the PL transcript, integrase is not synthesised because the transcript also contains the sib region which folds in a hair-pin loop and results in this section of the transcript being cleaved by RNaseIII.

Figure 2: Delayed early stage

Luzzati first showed that N was an anti-termination factor. He used a mutant lysogen which had a defect in N and a temperature sensitive transcriptional repressor which allowed transcription from PL and PR at 30ºC but not 40ºC. He superinfected the lysogen with a phage providing N at 30ºC but no transcription of the DE region of the original prophage took place. It was not until the temperature was raised to 40ºC that transcription began from PL and PR and was allowed to continue without termination by N, producing both IE and DE products. This proved that N did not create new promoters around the DE region but acted as an anti-termination factor.

Late stage

Once replication of the phage DNA has been initiated the other components of the new phages, heads and tails, are needed, as well as proteins for lysis. Q extends the PR’ transcript by binding to the transcriptional apparatus at a Q utilisation (qut) site close to the promoter. Once Q is bound termination does not occur as easily and so S, R and a number of genes coding for the heads and tails of the phage particles are transcribed. The head and tail proteins self assemble. R is an endolysin which is needed to cleave the cell wall for lysis.

Figure 3: Late stage

S produces mRNA with dual start sites for translation: one of these start sites produces S105, a holin; the other produces S107 which has an additional basic residue and acts as an antiholin because it cannot interact with the intact membrane correctly. Holin is produced twice as frequently as antiholin but binds preferentially to the anti-holin. This means that half of the holin molecules are disabled by antiholin. It is believed that this mechanism allows the sudden and rapid creation of many holes after a delay. Initially many S products are produced but there are few functional holin-holin dimers, not enough to create a single hole. When enough holin-holin dimers aggregate to form a hole in the membrane, its properties change and allow S107 to function as a holin. This immediately triples the number of S products available for hole creation, allowing rapid lysis.

Lysogeny

λ has an alternative lifestyle to the violence of lysis. It can integrate into the host’s genome and form a stable lysogen which continues to grow and divide. This is a stable state, even superinfection by the same phage willnot lead to lysis. There are some related phages which are heteroimmmune (e.g. 21 and 434); these can infect lambda lysogens and trigger lysis. Various experiments have been done to hone in on the ‘immunity substance’that provides protection from self superinfection.

Hfr strains of E. coli lysogenic for λ can be mated with wild type bacteria. They do not form recombinants, the Hfr strain transfers it’s entire genome and the prophage becomes lytic (zygotic induction). If the wild type cells are first made lysogenic then recombinants are formed. This demonstrates that the immunity substance is a cytoplasmic factor. In another experiment, λ is added to a population of E. coli cells on a petri dish. A turbid plaque is formed for wildtype λ which is made up of lysogens and periodically some lysis. Mutations in some genes (cI, cII and cIII) give clear plaques, meaning that all cells have gone into lysis. Every one of these factors is needed to establish lysogeny. Using temperature sensitive mutations to each gene it has been shown that only cI is needed to maintain lysogeny once established. It is the repressor, or immunity substance. A very few mutants are unable to establish lysogeny even in the presence of cI and always go into lytic cycle, these are dubbed virulent.

cI was isolated using a double labelling experiment. Wild type phage protein was labelled with one radioactive amino acid marker and protein from a cI strain was labelled with another. Proteins were pooled and separated by chromatography. The protein fraction which only had the wildtype label was cI. This was confirmed by the fact that it did not bind to the DNA of virulent mutants.

cII

The ultimate factor which determines whether λ will go into a lytic or lysogenic cycle after infection is the level of cII in the cell. If cII levels are high enough a lysogen will be formed, otherwise a lytic cycle will ensue. But cII is broken down by ftsH, a protease. cIII inhibits ftsH by binding to it competitively and so allows cII levels to remain high. This is why both cII and cIII are essential for the establishment of lysogeny.

Figure 4: Initial establishment of lysogen – cII active but low cI

cII is a transcriptional activator which acts on three promoters, PRE, Pint and PQ’. PRE promotes a transcript which produces cI and also the antisense to the normal mRNA to cro (which is being transcribed as usual in the delayed early stage.) This is important as it binds to the sense mRNA and prevents translation. PQ’ performs the same task for Q. This is necessary to stop the extension of the PR’ transcript which would send the cell into lysis. Pint has a short transcript which is translated to an integrase. Since it is not affected by N it terminates before the sib region and so no hairpin loop forms, so the RNA is not a target for RNase III.

cI

The areas around PL and PR are the operators OL and OR. These allow control of the promoters: each has three sites to which transcription factors can bind. cI forms a dimer and binds best to site 1, then site 2 and worst to site 3. When it binds to OL1 it is well positioned to interact with other cI dimers to allow them to bind cooperatively to OL2. Once these two sites are bound, transcription from PL is repressed. This is important to prevent xis being produced which would excise the integrated prophage, and generally to avoid a waste of resources on unnessessary products. There is a similar story for OR, with initial binding to OR1 and then cooperative binding to OR2. But here the binding to OR2 activates another promoter PRM in addition to repressing PR. Repression of PR stops the production of Cro and Q, removing the dependence of the phage on PRE and PQ’ (and hence cII) and prevents O and P from initiating replication on the integrated genome.

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Figure 5: Lysogenic state – cII levels now low, cI levels at optimum

PRM is the promoter for the maintenance for lysogeny. Its transcript produces cI, which we have established is the only factor needed to maintain the lysogenic state. In lytic state thispromoter is repressed by the action of cro which cannot bind cooperatively and binds best to OR3.This is why cro levels must be kept down for lysogeny. At very high concentrations in lytic cells, cro will bind to OR2 and OR1 to regulate its own production by negative feedback. cI has a similar regulatory mechanism, at high concentrations it will bind to OR3 and so repress PRM.

Integration and induction

The integrase produced by the Pint transcript results in the insertion of the prophage at attB, which lies between the galactose catabolic operon and the biotin biosynthetic operon. The inserted prophage is a circular permutation of the phage DNA in the particle, with int on one side and the sib region on the other.Once inserted the prophage will be replicated with the rest of the bacterial genome and so lie dormant, being passed into all the bacterial progeny.

In general the lysogenic state is observed to be very stable, 1 in 105 cells would normally go into lysis in a culture. This process is called induction. Lysis can be reliably induced by exposure to UV light. This damages DNA, which is one of the triggers for the cell’s SOS response – a postreplication mechanism for DNA repair.The genes for the SOS response are repressed in normal cells by a dimer called lexA. In the SOS response, recA is made active by binding to single stranded DNA and cleaves lexA, removing the repression.But cI has the same motif that makes lexA a target for cleavage and so in lysogens it is cleaved too.

cI levels fall and so cI no longer binds to the operators; PR and PL are no longer repressed. PRM is no longer activated so no further cI can be made. The situation now looks very like Figure 1 except that the DNA is now part of the bacterial genome and not a small loop of phage DNA. The same process happens – N istranscribed which allows the elongation of the PR and PL transcripts. The PL transcript no longer has the sib region because of the circular permutation, and so no hairpin loop is formed and RNase III attack does not occur. This means that xis (and int) are expressed. Both these factors and a bacterial gene product called fis are needed to allow excision. The excised circular DNA proceeds as in the lytic cycle.

Figure 6: Induction of a lysogen – cI has been cleaved

Lysis or lysogeny?

Not all the factors that influence the levels of cII – and so the fate of an infected cell – are understood. The nutritional status of cells is certainly important and there are proteases other than ftsH which can breakdown cII and are regulated by the cell cycle. Although a model organism for the study of bacterial infection, λ still holds its mysteries.

A fish’s tale – explaining the origins of major groups of jawed fish

Our story begins long ago with an ancient jawless fish from whom came every tetrapod, from an axolotl to a zebra-finch, and almost every fish in the seas, lakes and rivers. This fish’s parents were ostracoderms (hard shelled dermis), extinct fishes covered in an armour made from scales of dermal bone. They had cartilaginous endoskeletons to provide some structural support. But this fish was on its way to gaining a feature which would separate it from the ostracoderms, developing a jaw. The first stage was to develop jointed branchial arches rather than the one-piece branchial basket we now see in lampreys, this in itself allowed better ventilation which provided the oxygen needed for a fish that was becoming an active pelagic predator. Over generations these joints would have become more pronounced, until eventually they were such that they allowed the next step in the journey towards jaws.

The two front gill arches developed into the mandibular and hyoid arches. The former the jaw itself, and the latter the support from which it hung. This allowed a buccal pumping mechanism to better ventilate the gills. The gill slit between them became the spiracle or in our case the ear cavity. This jaw was adapted for co-option into the predatory life style as a weapon.

Some of these gnathostome fish (jawed mouth fish) were living in freshwater, they made their bodies more dilute in an attempt to become more isotonic with the water. These fish, still heavy with their dermal bone used their fins as wings to generate lift and wafted a heterocercal tail to force water downwards generating lift. This required a great deal of energy and so posed a problem, it was solved differently in two different groups.

In one which would give rise to the chondrichthyans (cartilaginous fish) the dermal bone was lost and replaced with dermal denticles, a skin of tooth-like projections. This decreased the density of the fish and allowed them a role as important pelagic predators, still beating their tails to generate lift and using an oily liver to increase their buoyancy. Their only structural support came from cartilage, which they made stronger in their vertebrae by using calcium phosphate, creating a form known as prismatic cartilage. The chondrichthyans would go on to form the sharks, skates and rays and the chimaeras.

Another group of gnathostomes would give rise to the osteichthyans (bony fish). They would have lived in anoxic conditions, perhaps caused by vegetation decomposing in warm water. Such fish would have stayed near the surface of the water, where oxygen would be most concentrated and here they evolved the strategy of swallowing air from above the surface, so that it passed through their gut. It could be inefficiently absorbed as it passed through the gut. But there was selective pressure for an invagination of the gut wall to allow a greater surface area for oxygen absorption. Gradually this pocket would have become a specialised lung. This lung provided a store of air in the body, decreasing its density. This allowed the potential for the evolution of endochondral bone, created by the ossification of cartilage by osteoblasts laid down during development, the feature that gives the osteichthyans their name.

The buoyancy these fish now enjoyed freed their fins from generating lift as wings, they could now be adapted as flexible appendages for steering. This was achieved in two different ways by different groups.

The actinopterygians (ray finned) withdrew their endoskeleton and left their fins supported by rays connected by webs of skin. This gave them greater flexibility and manoeuvrability but did not provide very much strength. However when surrounded by water strength is not a very important characteristic and the actinopts have gone on to dominate the sea, comprising 95% of all fish species. Many moved out of anoxic environments and separated their lungs from the gut, so that it was used simply for buoyancy and known as a swim bladder. Only the basal Polypterus has lungs that look very similar to those of other osteichthyans. Many moved into marine environments but they betray their freshwater past with hypotonic bodies. A major group, the Teleosts, use their original lungs as swim bladders but have re-evolved secondary lungs. The electric eel is one which has a secondary lung in its mouth. The actinopts also no longer needed their heterocercal tail for upthrust given their newfound buoyancy and so withdrew the notochord which had run along the top of their ventral tail. This formed a symmetrical, homocercal tail with which to generate simply thrust.

The sarcopterygians are another group of osteichthyans which took a different path when their fins were freed up. Again they achieved greater fin flexibility, but they did so without withdrawing their endoskeleton. Instead they reduced the number of basal elements to allow flexibility while maintaining strength. In the water column this was probably not of great significance. But such strong limbs were ready to be co-opted firstly for strong underwater movement along the bottom of water, as in Acanthostega, and later after further skeletal modifications, to form the terrestrial tetrapods to which we belong. Sarcopts also adopted a different approach to modifying their freed tail to provide forward thrust instead of upthrust. They did not withdraw their notochord but placed it down the middle of a symmetrical, diphycercal tail.