by Merry Youle
Lysogeny — a nasty time bomb or a mutually beneficial symbiosis? A prophage gone lytic will murder its host, but a symbiotic picture can well be argued. Here are some thoughts about the ongoing give-and-take. More details are still emerging.
1. If you are a phage, why be temperate?
For a phage, temperance offers the obvious advantage of providing a safe haven when host cells are few and far between or when conditions are not good for their rapid growth. Indeed, one does find more lysogens in nutrient-poor environments or during winter months. While nestled within a host chromosome, the prophage is faithfully replicated pari passu with host DNA. If the host clone prospers, so does the prophage. Here the prophage is protected from the heat-labile factors (proteases secreted by bacteria?) that can chew up a virion. Even while inside an intact virion, the phage DNA can be damaged by UV light. In sunlit waters, the number of infective virions is typically less than the number of intact virions, the difference being accounted for by virions that contain UV-damaged DNA. Prophages are also subject to UV damage, but being a segment of the host chromosome the damage is often mended by the host's DNA repair machinery. Of course, there are trade-offs here. Lysogeny eliminates the risky business of extra-cellular survival and locating a host, but one hungry protist can end the game for all concerned.
2. If you are a bacterium, why tolerate a prophage?
Having a prophage on board burdens you with more DNA to be replicated and with a passenger that just might kill you should conditions change. But said prophage protects you from infection by related phages and often supplies genes of immediate usefulness. Good examples of the latter are prophage-encoded toxins and other virulence factors, such as those essential for the pathogenesis of V. cholerae, E. coli O157, and C. diphtheriae. Even the temperate lambdoid phages of E. coli provide genes that make their hosts resistant to killing by serum complement. Some adaptations of nonpathogenic bacteria to a specific ecological niche almost surely also rely on useful prophage genes. It is thought that most of these genes had been acquired from previous hosts. Their conveyance by phage is central to horizontal gene transfer among prokaryotes.
This role of prophage as a source of new genes is of colossal importance. Bacterial genomes are composed of a core genome shared by virtually all members of a species, plus a halo of strain-specific genes. Prophage (along with related genomic islands) appear to be a primary source of these defining genes.
3. How do prophage genomes evolve?
Looking at this evolutionarily, one would not expect an entire prophage to become fixed in the bacterial genome since it is only the rare prophage gene that increases host fitness. If any of the prophage genes necessary for induction are inactivated, all the better for the host. The time bomb has been defused without the loss of potentially useful genes. (Click here for a paper about an archaeal prophage that has lost the ability to excise but still protects its host from viral infection and, under conditions of starvation, makes a lytic enzyme that lyses the host.) Once the prophage can no longer go lytic, its genes are released from selection pressure and gradually decay. Thus, in hindsight, it is not surprising to find many bacteria carrying noninducible prophages that have suffered varying degrees of gene loss. The rare useful genes, typically ones picked up by the phage from a former host, may become part of the host genome—testaments to horizontal gene transfer.
4. Are prophage genes active?
Prophages account for a significant fraction of the host genome, especially in pathogens. E. coli O157:H7 strain Sakai contains 18 prophage elements that total 16% of its DNA; the 4-6 prophages found in Streptococcus pyogenes make up 12% of its genome. The percentages in non-pathogens are lower, but still prophages contribute many genes to the lysogen. Early studies on a few model systems (the temperate lambdoid phages of E. coli in particular) suggested that most prophage genes are repressed, that only the few regulators needed to maintain lysogeny are transcribed. When more lysogens were scrutinized, more prophage genes were found to be active during lysogeny. In some cases transcription is up- or down-regulated in response to changes in host state or environmental conditions. Expression of some prophage genes is under host control, such as the diphtheria toxin gene that is governed by the same mechanism that regulates the expression of some bacterial genes in the presence of iron. In free-living bacteria, transcription of some prophage genes of unknown role (morons) is constitutive.
5. How common is lysogeny?
Many numbers are bandied about. Of all terrestrial bacteria cultured as of 1987, 47% were reported to be lysogens. A 2008 paper estimated that 60–70% of all sequenced bacterial genomes contain prophages. Those with 6 or more are mostly pathogens. Prophages are less common in Archaea and in bacterial endosymbionts that have undergone pronounced genome reduction. All of these numbers are best viewed as approximations. Since formerly active prophages in varying stages of decay can linger in the host genome, when does a decaying prophage cease to qualify as a prophage? This is like asking when that burrito you had for breakfast ceases to be a burrito. Should one count only those prophages that can be induced to enter the lytic cycle by mitomycin C or UV irradiation? By that criterion, roughly half of the marine bacterial isolates contain prophages. This gives you some idea of how many bacteria likely harbor active prophages that might be induced under various environmental conditions.
Suppose that you want to know how many bacteria carry prophage genes, not just those with inducible prophages. For bacteria whose genome has been sequenced, the first step would be to scan their genome using ab initio gene prediction software to locate every potential gene—an imperfect business in itself. Next, use BLASTx to compare the ORFs, one by one, to all known phage genes. When you find an ORF that has significant similarity to a phage gene, closely examine its neighborhood for more phage-related genes. Find a cluster of phage-related genes and you might have located a prophage genome. One major flaw here: all of the currently "known" phage genes are estimated to represent less than 0.0002% of the total number in existence. So a lot of prophages and prophage relics can be missed.
You could instead zero in on one particular prophage gene. For example, all active prophages encode an integrase (the enzyme that catalyzes the insertion of the prophage into the host genome). Integrases can be efficiently detected by in silico analysis, but spotting an integrase does not necessarily mean you've found a prophage since integrases are used by other types of mobile elements, as well.
So to answer the original question, we don’t know exactly how many, but there are a lot of lysogens out there, and prophage relics abound.
Meanwhile, a sixth and clearly unanswerable question has come to mind. If lysogeny is so great, why aren't all bacteria lysogens? John Paul offered some thoughts on this. Phages typically have very narrow host ranges. Thus, when a prophage protects its host from infection by related phages, this may protect it from virtually all infection. It follows that as the percentage of lysogens increases, it becomes more and more unlikely that a phage virion will meet up with a susceptible host. At some point, the phage population would decline and lytic infection would come to a halt. That might sound like a boon for the bacteria, but not really. In aquatic environments lytic infection plays an important evolutionary role by fostering bacterial diversity through "kill-the-winner" dynamics. Paul posited that it may be that one could not have more than half lysogens and still keep lytic processes and kill-the-winner ongoing. And about half is what we have.
Canchaya, C., Fournous, G., & Brussow, H. (2004). The impact of prophages on bacterial chromosomes Molecular Microbiology, 53 (1), 9-18 DOI: 10.1111/j.1365-2958.2004.04113.x
Paul, J. (2008). Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? The ISME Journal, 2 (6), 579-589 DOI: 10.1038/ismej.2008.35