What do you think when hearing “a virus”?...
The most common thoughts might be the cold virus or HIV. Indeed, these are forms of viral particles that infect humans and cause disease. However, “a virus” means much more than diseases. In this post, I will talk about a specific form of virus, this type is known for infecting bacteria. This type of viruses are the bacteriophages and were first discovered by Frederick Twort and Félix d'Herelle in 1915 when they observed that a filtered solution produced the absence of bacteria. This phenomenon was observed several times therefore the particles in the solution must have been eaten the bacteria. However, the shape, size, and other features of these particles were unknown.
Figure 1.- Three main families of bacteriophages based on their morphology. This image was produced by Nobrega et al., (Nat Rev. Microb., 2018)(1).
Nowadays, technology has allowed us to understand that there are multiple shapes of viral particles. This includes the shapes that bacteriophages can have. In figure 1 three different shapes for bacteriophages are shown. Because of their complex viral capsids (heads), or morphology, typical bacteria eaters are classified into three main families: Myoviridae, Podoviridae, and Siphoviridae. The abundance of bacteriophages is paramount. In all the World, there is no biological entity that can compete in number with the bacteriophages. An estimated of 10 thousand billion billion billion (10^31) bacteriophages shape the whole bacterial population thus the ecosystems and the entire biosphere.
The bacteriophages move and they do it fast
About 1 million billion billion (10^24) infections happen per second(2) therefore the bacteriophage-bacteria interactions are constant. In other words, every time that you observe the signs of bacteria there is a huge chance that there are five to ten times more bacteriophages in the same spot. This means that we live actually in a World dominated by this type of viruses and yet they are not alive. Bacteriophages, as all other viruses, are composed of genetic material (DNA or RNA) inside a capsid, therefore, they require a host to replicate. This is the main reason that these overwhelming abundant and dynamic biological entities are not living organisms.
Bacteriophages act like highly sophisticated machines when they infect a host. Typically, bacteriophages undergo a lytic cycle which will produce a burst of the infected bacteria. In this most common state, the bacteriophages will 1) attach to the surface of the bacteria, 2) inject the genetic material contained in the capsid, 3) synthesize phage proteins inside the host utilizing the bacteria machinery, 4) assemble themselves in mature bacteriophages inside the bacteria and 5) lyse the cell which will release the new bacteriophages ready to infect more bacteria. This process is shown in Figure 2A.
Figure 2.- Viral cycles. (A) Lytic cycle occur most of the time and this process shapes the type of bacteria in a given environment. (B) The lysogenic cycle promote the recombination of viral particles with host genome. In case of certain conditions the viral genetic material could start to stimulate the viral replication.
This precise mechanism of bacteriophage expansion is tightly controlled by both the bacterial metabolism and the bacteriophage genome. This suggests a fascinating set of genes in the bacteriophage genome that perform very interesting tasks. In fact, diverse bacteriophage-derived elements are utilized every day in molecular biology laboratories and the majority of advances in this field required of these particular viruses.
The genome of the bacteriophages has been historically rich in answers
Paradoxically, the bacteriophages mostly employ a random-like process called illegitimate recombination which produces several features in the genome of the bacteriophage. Some typical patterns in the DNA sequences of the bacteriophage genome are repeated, inverted, and segmented sequences. These disordered blocks of DNA sequences in the genome of bacteriophages produce mosaics that have been linked to their evolution(3). But…
Can bacteriophages evolve while eating bacteria?
The shuffling of bacteriophage DNA might include bacterial genomic DNA. This implies that the bacteriophage genetic information can recombine with the bacterial chromosome and produce a hybrid-like version of the bacteriophage. This is possible because the bacteriophages can undergo two cycles depicted in Figure 2. As mentioned, the lytic cycle will destroy the host cell and release the progeny of newly synthesized bacteriophages. On the other hand, the lysogenic cycle causes the bacteriophage genetic material to be integrated into the bacterial chromosome. This bacteriophage-material, in the bacterial chromosome, might or not be induced by the environment to switch back to the lytic cycle. The amount and the diversity of recombinases in the bacteriophage can further promote DNA shuffling. So, yes, bacteriophages do evolve while infecting bacteria. As mentioned by Dr. Graham Hatfull from the University of Pittsburg in iBiology video found on YouTube:
“If you want to discover genes with new functionality, the best way is to look at the genome of the bacteriophages”
The genome of the bacteriophages and the bacterial immune system inspired one of the most popular gene-editing tools, CRISPR-cas9. More interestingly, one of the limitations of this tool to be widely applicable to eukaryotic systems is its off-target effects. Several research groups are investigating this process and improving the efficiency of a particular microorganism. The off-target effects are caused by a class of random-like recombination called non-homologous end joining (NHEJ). Interestingly, this type of recombination is typical of bacteriophages in their process to produce mosaics in their genomes.
Would it be possible that bacteriophages have once again a solution for the limitation of CRISPR-cas9?
Besides gene editing, more direct applications for bacteriophages have been mentioned. Probably the oldest application is the idea of employing phage therapy. The Russian army treated bacterial infections in wounds utilizing bacteriophages during World War II(4). Although the lack of knowledge made difficult to treat antibiotic-resistant bacterial infections with bacteriophages in the last decades, recently several studies have suggested this a promising alternative.
When are the bacteriophages considered a problem?
Bacteriophages have allowed us to understand some molecular biology mechanisms, other viruses, perform gene editing, they might help us to eradicate at least some antibiotic-resistant bacteria, but they remain to be a serious threat to some other areas. Specifically, for industrial fermentations where bacteria are employed as biocatalyst. The abundance of bacteriophages might promote “spontaneous” phage contamination events. This is particularly an issue for dairy fermentations that utilize lactic acid bacteria (5).
More exhaustive studies of the structure of bacteriophages, their receptors, their abundance, their optimal conditions of amplification, and their mechanisms will further contribute to molecular biology and antibiotic resistance fields at the same time of preventing phage contamination issues in large-scale bacterial fermentations.
Next time you look at any element in nature (sea, sand, forest, snow, etc.) or hear about CRISPR, bacteria, viruses, antibiotic resistance or industrial fermentations, remember who the shapers of the biosphere are, how much we don’t know about them yet, and what other bacteriophage-derived tools will be developed in the near future.
References
1. F. L. Nobrega et al., Targeting mechanisms of tailed bacteriophages. Nat. Rev. Microbiol. (2018), , doi:10.1038/s41579-018-0070-8.
2. S. W. Wilhelm, C. A. Suttle, Viruses and Nutrient Cycles in the Sea: Viruses play critical roles in the structure and function of aquatic food webs. Bioscience (1999), doi:10.2307/1313569.
3. M. Belcaid, A. Bergeron, G. Poisson, Mosaic graphs and comparative genomics in phage communities. J. Comput. Biol. (2010), doi:10.1089/cmb.2010.0108.
4. S. T. Abedon, S. J. Kuhl, B. G. Blasdel, E. M. Kutter, Phage treatment of human infections. Bacteriophage (2011), doi:10.4161/bact.1.2.15845.
5. M. B. Marcó, S. Moineau, A. Quiberoni, Bacteriophages and dairy fermentations. Bacteriophage (2012), doi:10.4161/bact.21868.