Viruses at all levels

We’re all familiar with viruses that infect humans, from the common-cold rhinovirus to SARS-CoV-2. When I first heard about viruses that infect bacteria, I was really surprised! I’d never thought beyond viruses that infected animals or plants, much less considered that organisms as simple as bacteria might have their own immune systems.

Bacteria do fight back against potential invaders! There is a region of DNA in the bacterial genome that contains fragments of viral DNA, like a hit list for recognizing its enemies. A specialized DNA-cutting enzyme takes pieces of RNA transcribed from this genomic region and chops up DNA that matches the viral sequence. If a virus attempts to inject DNA into the bacterium, its DNA will be chopped to pieces before it can cause any problems.

It turns out that for pretty much every type of cell, there is a virus that infects it. But what if there were viruses that could… infect other viruses?

Viruses on viruses??

That’s the topic of this Kurzgesagt video, which outlines the 2003 discovery of GIANT VIRUSES (aka “giruses”). You should check out the video or its sources to learn more, but basically giruses are viruses many times larger and more complex than we knew viruses could be. They have many genes more typical of living cells than of viruses, and even more genes that we don’t understand. They might even have their own very basic metabolism. While giruses infect cells and turn them into girus-producing factories, much like typical viruses do, giruses can themselves be infected by smaller viruses called virophages. The virophages hijack the girus’s hijacking of the cell, causing it to produce more virophages instead of more giruses!

It’s even been suggested that giruses have their own immune systems, similar to CRISPR, that protect them from virophage attacks. Cells can also fight back against giruses by releasing their own virophages to hunt the giruses. The possibilities are dizzying.

Biology is full of surprises

There are so many cases in biology where what we thought we knew is turned upside down. There is often something truly remarkable lurking just under our misconceptions. Another awesome example is the discovery of introns and alternative splicing– the idea that one gene can spawn a huge variety of proteins, depending on which parts of its sequence are read in translation. To me, this illustrates the importance of keeping an open mind. There is always room for the completely unexpected in biology.

I love learning about the weird, wonderful, and surprising discoveries in biology. My close friends and family members know that I often start a sentence with “Did you know?” followed by a fun (and sometimes gross) fact. I’m starting to write down the cool things I learn to engage my sense of wonder and remind myself why I love science. It lets me use my intellectual energy in a way that’s just for fun, so I don’t get too bogged down in work. As I reach the end of my undergraduate degree, this is the kind of thing that gives me hope that a career in science will be as rewarding as it is challenging.

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Footnote 1: A note about CRISPR

A question that came to my mind as I was reviewing how CRISPR works for this blog post: If Cas9 is so good at cutting sequences that match fragments from viral DNA, why doesn’t it cut the same sequences of viral DNA stored in the bacteria’s own genome?

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The name refers to the original discovery of short repeat sequences in the bacterial genome that were evenly spaced apart. Further investigation of this strange pattern revealed that the sequences in between these repeats are actually fragments of virus genomes.

It turns out that if the sequence Cas9 is looking for is flanked by these short repeat sequences, Cas9 will not cut it. This means Cas9 only cuts actual viral DNA, not the part of its own immune system where viral DNA is stored for future reference.

Footnote 2: Course!

I studied the CRISPR-Cas9 system, as well as several variations on it, in a half-semester course called Genome Editing Biotechnology. I talked about it in my CMU science course reviews.