Saturday, October 17, 2015

BtB#5- An intro to Bacteriophages


Viruses represents the ultimate of pathogens. They represent simplest of chemical replication machinery, totally host dependent. Interestingly, some viruses themselves have their own set of hackers called as Virophages. It is widely acknowledged, there isn't any life form on Earth that doesn't have its own set of viral infections. Among the different category, bacteriophages is the current leading interest. They can be useful as a therapeutic agent. See my earlier post on Phage therapy. However, far less people understand the basics of a bacteriophage or what we commonly call as the phage.

Fig 1: Generalized phage structure.
Bacteriophages, first described by Frederick Twort and Felix d'Herelle are viruses that attack the bacteria. They ubiquitously distributed in environment. The association of phage and bacteria is so profound that if you can find the phage in a system, it associated bacteria should be there, with reverse also being true. Several phages have been well studied in lab and several new has been described in recent years.

A classic textbook figure of structure is shown in Fig 1. The figure shows the structure of T4 phage. The structure consists of a head which holds the genetic material. The head is made up of capsid which is in turn made up of capsomeres and roughly prism shaped. This structure is more or less the same across all of the bacteriophages. The capsid is a tough covering and usually resistant to environmental stress thus being protective to the genetic material. The second component is the tail which is connected to head through a Neck (or sometimes referred to as collar). Tail is not a constant feature, as many members don't have a tail. Tail is often a hollow tunnel through which the genetic material can be transferred. This is surrounded by a covering called as sheath. Some of the complex phages at the end of tail has a specialized structure called as base plate. This holds tail fibres which are responsible for hooking of phages to particular receptors.

Fig 2: Size distribution of sequenced
Bacteriophage genomes. Source
There is great deal of genetic diversity when it comes to the bacteriophages. Phage metagenomics is a reality and a lot of what is called as genetic dark matter is in these phages. Nothing is known about these sequences. Fig 2 captures a summary of genetic size variation considering some of the known phages. Phages also comes in a variety of genetic makeups- DNA or RNA, single or double stranded. Each different type has a different replication strategy. Depending on the structure and organisation of the phage, there are at least 12 distinct group of bacteriophages known. Their properties are summarized in Table 1 (Adapted from source).

Table 1: Characters of various families of Bacteriophages
The basic steps in bacteriophage replication is quite common- Phage adsorption, Genetic entry, Genetic replication, synthesis of virus particle, assembly and finally phage release. The details differ based on the type of phage and host. The phage receptor complex (PRC) are usually located in an accessible region of the outer membrane of bacterial host (exceptions exist where entry mechanism is more complex). Most of the PRC that I have read about in literature are somehow related to porins regulated by operons. For example, in case of E coli lambda phage, J protein in the tail tip interacts with maltose outer membrane porin (part of maltose operon) and then DNA passes through mannose permease complex in the inner membrane.

There are 2 modes of life cycle when it comes to phages- Lytic and Lysogenic life cycle. Lytic life cycle represents a quick paced infection and replication and then burst out of the cell. Lysogeny is a more relaxed life cycle, where the viral genome integrates with the bacterial genome and keeps silent. The bacteria replicates the gene for virus. Someday, if the viral gene decides that its time to leave, the machinery becomes active and turns up into a lytic cycle. Though it appears superficially to be a random process, each type of life cycle is a carefully guarded decision.

Here is a simple explanation. Lytic life cycle is a process which allows the phage to infect new bacteria. Lysogeny is a mode where the phage takes advantage of bacterial replication machinery, without having to do anything by itself. Lytic life cycle would thus be useful only when the bacterial host is possibly in danger of loss such as stress. In other cases, lysogeny may help. It is arguable that this whole process has to do something with quorum sensing, but I'm not aware of any articles that has shown a direct relationship. Indeed, when the phage is in lysogenic state, phages can be awakened to their lytic state by inducing stress such as UV radiation. Interesting enough, quorum sensing mechanisms are demonstrated to induce resistance to phage invasion.

Fig 3: The lambda repressor switch.  Source
At molecular level, the things are a little bit more complex. As an example, let us take the example of E coli phage lambda. Though the exact mechanism differs from phage to phage the overall principle remains nearly the same. The simplest principle can be stated as follows. There exists a competition between two phage repressor molecule: CI and Cro. In the event that CI repressor gains upper hand, lambda DNA becomes a quiescent prophage that integrates into the host chromosome and expresses only one gene, cI. If Cro gets the lead, then the phage turns on the lytic mode. The decision of which repressor wins is based on the expression pattern of other genes, A simplified circuit is shown in Fig 3. Now what determines the underlying gene expression pattern? One well known idea is the multiplicity of infection. In the event that several phages infect the same bacteria CI is made in more numbers. This leads to lysogenic conversion. This is useful since more phages per cell would mean that there are less number of bacteria available to infect and hence lytic cycle wouldn't be useful.

Table 2: Phage encoded toxins in bacteria. Source
Phage forms a very important interest these days. Phages are the next generation antibiotics. You would not like the phages to undergo lysogenic conversion if they are to be used as an antibiotic. This can be achieved by genetically engineering viral strains to not have lot of CI production. Also, Phages are some of the best medium for genetic exchange in bacteria. Further, phages themselves can contribute genes to bacteria that may increase the virulence. Many bacterial toxins are actually phage encoded genes. There also several examples of phage derived genetic product that are involved in antigenic conversion, effector proteins, enzymes, resistance factors etc.

In this post I have talked about bacteriophages in a very short format, just in a introductory format. The genetics and molecular switches involved in decision making process is quite complex, and probably I could put a post on that on some other day. Bacteriophages form a different entity. Phages exist for others such as fungal and parasites. The working mode of fungal phages are still bizarre. For example, some fungal phages never leave the cell. They are transmitted via spores through mating. Perhaps all these are a topic for another future post.
Hendrix RW (2003). Bacteriophage genomics. Current opinion in microbiology, 6 (5), 506-11 PMID: 14572544

Høyland-Kroghsbo NM, Maerkedahl RB, & Svenningsen SL (2013). A quorum-sensing-induced bacteriophage defense mechanism. mBio, 4 (1) PMID: 23422409

Oppenheim AB, Kobiler O, Stavans J, Court DL, & Adhya S (2005). Switches in bacteriophage lambda development. Annual review of genetics, 39, 409-29 PMID: 16285866

Boyd EF, & Brüssow H (2002). Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends in microbiology, 10 (11), 521-9 PMID: 1241961

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