Viral eyes upon us?

“Viruses can’t see, right?”

“No, no, no  – viruses aren’t cells and its inside cells that you detect light.”

“So why do they have genes that make proteins that can sense light? “(1)


To explain this, we first need to talk about rhodopsin, a protein that absorbs the energy from sunlight to “do” things.  

Rhodopsin – a protein that is found embedded in plasma membranes and senses light. That white molecule is retinal – the reason you eat carrots. Well, its why I eat carrots.

In your eyes, rhodopsin absorbs the energy of light, causing it to change shape in a way that tickles your brain, allowing you to see under low light conditions (which is different from the cone opsins that allow you to see color).  Lots of other organisms have rhodopsins, including bacteria; a subset of the bacteriorhodopsins are the  proteorhodopsins.  There are lots of different kinds of proteorhodopsins – some pump ions across the plasma membrane when they absorb light (part of how many bacteria perform photosynthesis), others absorb light and cause the cell to move towards or away from the light, so called “sensory rhodopsins”.

Sensory rhodopsins are not “primitve eyes” but they serve an analogous function to the photoreceptors in your eyes – they tell the organism where the light is.  If you are a cell that relies on photosynthesis instead of jelly donuts, a sensory rhodopsin would be very useful in “seeing the light” (come on, admit it, it was funny).  Bacteria with these rhodopsins do not “see” anything mind you – vision requires a fairly complex tangle of cells called neurons to process and make sense out of what the light sensors are saying.  These bacteria are simply sensing the light.  In a crude way, they could tell a photosynthetic cell that it is moving AWAY from a light source, triggering that cell to stop swimming in that direction.  It might be kind of like if my eyes only told me if I was moving towards or away from the coffee pot – there are many mornings when that kind of system would prevent me from crawling onto the sofa, sleeping through my classes and losing my job.  Well, actually my KIDS wouldn’t let me do that, but you get the point.

Rhodopsins are very well studied, and certain amino acid residues in these proteins have been shown to influence  which wavelength of light is absorbed.  This means there are “flavors” of the rhodopsin gene that sense blue or red or green light.  In aquatic ecosystems, shorter wavelengths of light penetrate further into the water, so which rhodopsin-flavor a photosynthetic cell has is going to dictate in part where in the water column it can live.

Now the coolest part.

Cryo-electron microscopy of 2 Chlorellaviruses infecting a cell of the unicellular green algae, Chlorella. (Journal of Virology December 2013, Volume 87, Issue 24)

Phycodnaviridae is a large family of viruses that infect eukaryotic algae found in marine and fresh water. In the oceans they (along with other viruses of other phytoplankton) control massive blooms of algae by killing them and thus sending massive amounts of carbon to the bottom of the ocean annually; in freshwater they are not as well studied, but part of why I am interested in all this is to get a project up and running having my students quantify these viruses in local freshwater ecosystems.  They are also some of the largest viruses known.  They have been detected in lakes as remote as Antartica.  And, they have sensory rhodopsin genes.

If this doesn’t blow your mind, well, I probably can’t change that, but here is an attempt. Imagine the 2 different pirate stories below:

A pirate gets into a taxi that happens to be transporting hundreds of different human organs for transplant.  The pirate overpowers the driver and forces him to make clones of the pirate using the body parts in his cab.  The pirate clones fill up the cab and eventually break out, destroying the vehicle in order to get into other cabs to repeat the process.

In another city a second pirate also gets in a cab that also happens to be transporting hundreds of different human organs for transplant.  In addition to repeating the actions of the first pirate, this one hands the driver a map that allows him to find a restaurant with a drive through window.  Because he can eat, presumably the driver is able to last longer and make more or better pirate clones.  He and his cab are still destroyed in the end.

I am absolutely sure that we (the scientific royal we) don’t know what these viral rhodopsin genes actually do in infected cells. In my ill conceived pirate analogy I was imagining that they were in some way helping the cell find more sunlight, but that is pure speculation.  As long as they don’t interfere with virus reproduction, they don’t *need* to do anything.   Our genomes are filled to the brim with DNA sequences that don’t do squat*, but its tempting to speculate that the virus is bringing a gene which helps the cell “see things the viruses way” (said with a viral New Jersey accent)

Protein sequence line up of some viral and bacterial rhodopsins

Protein sequence line up of some viral and bacterial rhodopsins (modified from here)

Spectral tuning simply means “given all of the wavelengths of energy in sunlight, which specific ones does the protein absorb”. In the figure above, the amino acid position correlating with spectral tuning indicates this wavelength specificity. This is outside my area, so I will have to trust the author, Eugene Koonin,  that the methionine (“m”) found in all of the viral rhodopsins indicate that they absorb green light.  The lack of lysine or glutamate downstream of the spectral tuning residue apparently indicates that this is a sensory rhodopsin, not a rhodopsin involved in energy generation.  Eugene Koonin has an Erdos Numer of 2 (and I spent lots of time reading material he wrote in graduate school), so this seems legit.

Its important to admit here that this is NOT the first time a gene for a light sensing protein has been found in a virus.  For almost 10 years “we” have known that some marine bacterial viruses have been known to carry the genes for photosynthesis (for instance this 2004 report), but photosynthesis is a way to convert sunlight energy into chemical energy.  A virus that does that is just an Eagle Scout type virus.  But a virus that brings with it a little molecular “eye”?   Perhaps, the virus is helping the cell to “see things my way”.  That’s creepy.


(1) Natalya Yutin and Eugene V Koonin. “Proteorhodopsin genes in giant viruses”. Biology Direct. 34.7 (2012). Web 

* – if you hear anyone claim otherwise its likely they either don’t understand molecular biology or are being dishonest.


About SubOptimist

I am an Associate Professor in the Science Department at Georgia Perimeter College, Clarkston. I teach introductory biology courses at both the majors and non-majors level in addition to microbiology. Previous to that I spent 7 years as a postdoctoral researcher on different viruses. While I don't miss being on the "grant treadmill", I think better when I write and miss writing up data for papers and grants; this blog helps me with that a little. And sometimes my kids' insanely funny and cute antics need to be shared with the world. Any view expressed in this blog is that of me personally and not Georgia Perimeter College or the GPC Clarkston Science Department.
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2 Responses to Viral eyes upon us?

  1. jaksichja says:

    I enjoyed reading this post—some of it is beyond my formal training– but it is never too late to learn more and more. Thanks for posting it.

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