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There
are recognized characteristics that all living
organisms
share. However, they are not black
and white; take a look at
these characteristics and
think about fire. Fire grows,
consumes energy, gives
off energy, metabolizes, reproduces.
So if fire can
be fit into some of these, maybe an argument
can be made for viruses? |
Many scientists do not consider viruses a form of life, but that doesn’t mean the idea is universal. Even virologists can’t agree. Viruses do blur the lines between life and non-life, and it gives us something to debate when parties get quiet. It makes for a great debate in Biology classes too, if you don't have a party to go to.
For many, it comes down to this - viruses don’t react to
changes in their environment, grow, or metabolize, so they can’t be alive. They
lack all these characteristics because these processes take energy, and viruses
themselves don’t make or consume energy. This is a big sticking point for
anyone trying to make an argument for including viruses as life.
But they seem to do O.K. at making their way in the world,
and are becoming quite the model for immune stimulation. A 2011 study at the Emory
Vaccine Center used virus-sized nanoparticles to try to induce life-long
immunity as natural viruses do. It is hypothesized that virus particles bind
to several different types of innate
immune receptors (called Toll-like receptors, TLRs) and this diverse
stimulation by one antigen is responsible for longer immunity.
The nanoparticles were composed of a synthetic polymer particle
complexed with two stimulators. One is similar to a part of the bacterial cell
wall, and the other mimics viral mRNA. The particles also stimulated several
different TLRs in mice, and it is hoped they will do similar in humans. Nice to see we can take advantage of
viruses, since they take advantage of us so often. Important to our topic today,
viruses can even take advantage of bacteria.
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What
a great image of a T2 bacteriophage. What
look
like layers are …. layers. Each is a protein and
what
is more, they self assemble! The head carries
the
nucleic acid, the legs attach to the bacterium, and
the
shaft creates the hole and injects the nucleic acid.
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Since bacteria are prokaryotes, it would be right to assume that the viruses that infect them look and act differently than the viruses that infect eukaryotic cells. They even have a different name – bacteriophages (backtron = small rod, and phage = to feed on). Infection of a bacterium by a virus may seem a trivial event - we have our own problems to deal with. But there are several ways in which this infection affects animals.
Bacteriophages insert their nucleic acid into the bacteria
from the outside; the virus doesn’t enter the cell. Similar to the bacteriocin delivery system recently discovered in bacteria, bacteriophage also use a spike system to punch a
hole in the target cell. Scientists in Switzerland, Russia, and Indiana
collaborated in 2011 to show that the bacteriophage spike has a single iron atom at the tip,
and it punches, not drills, a hole in the target bacterium.
Once inside, the nucleic acid can have different fates. In
many cases, the phage DNA is inserted into the bacterial chromosome and stays
there for a while, not harming anyone, but also not making new virus particles.
This is called lysogeny. Lysogens
(cells infected with lysogenic phage) will then pass on the prophage (the phage nucleic acid that
is integrated) on to their daughter cells.
Other bacteriophages don’t have the patience to just hang
out in the bacterial genome; they take over the cell, make many copies of
themselves and then destroy the bacterium by lysing it (breaking it open).
These are the lytic bacteriophages.
You might recognize that lysogenic phage DNA, just sitting
there in the chromosome, would die out with the cell (or daughter), so they
must have another side to themselves. These phages can be lysogenic if the environment
suits them, or lytic if they have the right signals, and they can switch from
lysogenic to lytic if the environment changes, so they are called temperate bacteriophage. Do I have to
point out that they can’t go the other direction (lytic to lysogenic); how could you insert yourself
into the bacterial genome if you have already caused bacterial destruction?!
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There
are 19 recognized bacteriophage types (probably
more
now). They have different kinds of head proteins, and
some
are filamentous. Cystovirus (cytovirus) is the only
virus
with RNA for a nucleic acid instead of DNA. Tectivirus
is the only phage that infects both archaea and bacteria.
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There are currently 19 different classes of bacteriophage that infect bacteria and archaea. That’s a bunch of different ways that a bacterium would have to defend itself, but it can. Bacteria have several different ways to prevent bacteriophage infection. In some cases, the bacteria will produce cell wall molecules to prevent phage binding or nucleic acid injection.
In other cases, the bacteria will identify its own nucleic acid,
usually by adding methyl groups to DNA. In some cases, the bacteria will methylate
its own DNA, and then cut up (called restriction,
this is where the restriction enzymes used in molecular biology come from) any
DNA that isn't methylated. In other cases, the bacteria will methylate the
incoming viral DNA and target all methylated DNA for restriction.
Recent evidence show that bacteria even have a version of
adaptive immunity. The CRISPR system
takes spacer DNA (short repeats outside genes) from the bacteriophage and
places them in specific CRISPR spots in its own chromosome. These serve as a memory in case that
bacteriophage is encountered again. If it is, the appropriate spacer can be
turned in to a piece of RNA that will target the phage DNA for destruction
(called RNAi, the “i” stands for interfering, the process for another
discussion).
Finally, bacteria can oppose phage by giving up. Like the apoptosis in our cells or the
plant hypersensitive reaction
we have discussed, bacteria can kill themselves in order to prevent themselves from
becoming virus factories. In the case of bacteriophage-infected bacteria, the
process is called high frequency of
lysogeny. This system prevents the bacterium from carrying the prophage and
passing it on to daughter cells by having the cell die before it replicates.
So bacteria infected by phage can defend themselves, but in
some cases, they don’t need to. In fact, it may help them out. Consider a
lysogenic phage of one type and lytic phage of another type. Which would a
bacterium consider living with – certainly not the lytic phage. But many
viruses, including phage have mechanisms to prevent superinfection (infection
with a second virus); phage of one type cannot survive in a bacterium infected
with a phage of another type. If the lysogenic phage got there first,
it could actually protect the bacterium from a death by a lytic phage.
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Cholera
toxin is carried by the CTX bacteriophage.
The
phage needs TCP, a type IV pillus to infect the
V. cholerae. Once the bacterium is
growing on the
intestinal
surface, the phage is activated, reproduces,
infects
other bacteria, and the cholera toxin is
produced.
So to cause disease, the bacteria must
undergo
horizontal gene transfer to gain the pillus,
and be infected by the CTX phage.
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We may chuckle at the idea of bacteria getting infected – in many cases it serves them right – but it can also affect us. Certain bacteriophages possess DNA that can make an infected bacterium even better at causing humans distress. The cholera toxin of Vibrio cholerae is carried by the CTX bacteriophage, and the diphtheria toxin gene of Cornybacterium diphtheriae is also transferred from bacterium to bacterium by a phage.
But phage may also be turned from the dark side and used to
help mankind. In the spirit of our recent discussions on when it is beneficial
to be infected, how about letting your doctor infect you with bacteriophage to
kill off your bacterial infection?
It is no secret that antibiotic resistance is becoming a
large problem in medicine. If we know that viruses can infect bacteria, why
don’t we use them as a type of antibiotic? This may very well be a good idea,
but it isn’t a new one.
Before the advent of penicillin and other traditional
antibiotics, bacteriophages were used to treat bacterial infections in the
Soviet Union and Eastern Europe. However, the 1920-30's trials were not without
their flaws, mostly because scientists didn’t have a good idea of how phages
worked. For many years the West remained behind, because Soviet research was not
widely distributed.
To kill bacteria, lytic phages would be the tools of choice.
But there is a downside, we use bacteria to stay alive. You wouldn’t want to
kill of your gut flora, you need them to digest food and absorb vitamins. So,
bacteriophage must be delivered to the site of the infection only, replicate
there but not travel, and kill only the target bacteria. This is a tall order, but
trials are in progress for bacteriophage as antibiotics against drug resistant
Staphylococcus and others. Bacteriophages are even being tested in bacterially-infected
plants.
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The
SOS system is one way a bacterium can repair
DNA
damage. The damage stimulates RecA protein
function.
This is an important protein. It works in
many
forms of DNA repair, as well as being responsible
for
homologous recombination. The SOS repair genes
are
controlled by RecA degrading the protein that
represses
their production. They go on to fix the DNA
problem.
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On another front, research at MIT and Boston University from 2010 suggests that it may be possible to inhibit bacterial antibiotic resistance mechanisms, and once again making the resistant bacteria susceptible to conventional antibiotics. In this case, bacteriophage were engineered to target the bacterial DNA repair system in the target cells. The SOS system (see picture to right) is induced when bacteria are treated with antibiotics, but the bacteriophage-treated cells were more susceptible to the antibiotic. This could prevent resistance from developing, but may also be useful in strains that have developed some other antibiotic resistance mechanism.
Another potential bacteriophage aid to humanity has nothing
to do with disease. May 2012 work from the University of California has made use of the mechanical
energy of the bacteriophage inside bacteria, turning it into electrical energy
(piezoelectricity, piezo = to press or squeeze). While this
is a very small amount of power per cell, it is hoped that this may soon be
harnessed to run your smart phone and iPad.
Next week we will start a series on heat in Biology.
Lu, T., & Collins, J. (2009). Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy Proceedings of the National Academy of Sciences, 106 (12), 4629-4634 DOI: 10.1073/pnas.0800442106
For
more information or classroom activities, see:
Bacteriophage
–
phage
therapy –
http://www.popsci.com/science/article/2011-04/bleaching-threatens-coral-phage-therapy-could-prevent-ghost-coral
