Thursday, May 14, 2015
Lokiarchaeota - The shapeshifter bug in the mud
This is the story about a bug - a very special bug and how it was found. It is named Lokiarchaeota after the trixter god from ancient Nordic mythology (you might know him from the Marvel comics and movies where he is Thor's evil brother) and it is special because no one knew anything like that existed before. As all good stories it starts with mud.
Do you like to play in the mud? There is a team of scientists from Uppsala University (that's in Sweden) who sure does. And they found some really cool mud to play with. It comes from the bottom of the ocean, not that far from Iceland. When scientists play with mud they do it just like you do - they poke it with a stick, or they sift it and look for interesting things. But since they only had a few grams of the mud (they had to use a submarine to get it) and the interesting things they looked for was so small, they had to use a really, really good stick. The stick they used is called metagenomics.
Imagine that you were looking for insects in the mud, but all you found were bits and pieces. An antenna or a facet eye, a wing and lots and lots of legs. Then you would have to sit down and piece it all together, like a jigsaw puzzle. Connect the eyes to the head to the thorax to the legs and you get an ant. Other pieces become a ladybug or a fly. And you would have to be really good at puzzles to find where all the legs go. That's what the scientists from Uppsala did, only instead of legs and wings they used DNA, which is molecule inside the cells of all life - big and small (that's what metagenomics means - looking at DNA from all bugs at the same time, not one by one). And the scientists were really good at puzzles, so using only the DNA they could piece together almost the entire little bug - and it was the strangest bug they had ever seen.
But before I tell you about Lokiarchaea I want to tell you about bugs in general. Not "bug" as in insect but "bug" as in microbe, the tiny little things that you have to use a microscope to see. Do you know how small the bugs they were looking for are? Think of the smallest thing you can see without a magnifying glass. A little speck of dust, or the tip of the antenna of an ant or the dot in the end of this sentence. On that little speck, thousands or millions of microbes can fit quite cosily. They are about one micrometer long - that's a millionth of a meter. Each bug is a single cell - instead of being made from millions and millions of cells like you are, each cell is on their own. These kind of bugs are everywhere. Some like to swim in the ocean, some like to live in the soil. Some lives in your stomach and help you eat, and a few likes to get in your stomach and make you sick. Some are round and some are oblong, some stick to each other, some have little hairs that they use for swimming and some just float around.
There are three kinds of microbes. There are bacteria, who are almost everywhere. There are eukaryotes, who are bigger and like to eat the other two (Actually, not all eukaryotes are microbes - plants and mushrooms and dinosaurs and dogs and you are all eukaryotes too). And there are archaea, who not many people know about. They look a bit like bacteria but once you poke with them they are different - it's a bit like how birds and bats both have wings and can fly, but look really different when you look close. Archaea and bacteria have been around for almost as long as Earth - more than three billion years - but eukaryotes showed up "just" two billion years ago.
One thing that is interesting with eukaryotes is that they look a bit like archaea and a bit like bacteria (and a lot like none of them). And here is what's really interesting with Lokiarchaea. They have DNA that is shared with many other archaea, but they also have DNA normally found only in eukaryotes. In fact, they are more closely related to eukaryotes than any other archaea that we have ever seen before.
The Lokiarchaea have pieces of DNA - genes - that codes for actin. That is a protein that was previously only known from eukaryotes and is used for all sort of things that relates to the cell shape. It can be used to bend and form the cell. It can be used to send signal from one part to the other - and it can be used to pick up things from outside the cell. That last thing is exciting because one idea of how eukaryotes came to be is that an archaeal cell picked up a bacterial cell and that they stuck together after that. Maybe it was something much like the Lokiarchaeota that used the actin genes to pick up a bacteria. There are also other genes that are important for eukaryotes, including something that is called the ESCRT-system which is used to move things around in the cell and lots of genes for proteins called GTPases that are used as switches that control when things happens in the cell. We are not used to other things than eukaryotes having these genes, so that's why we think that the Lokiarchaea are actually more closely related to us than other archaea - a bit like how dinosaurs with feathers are more closely related to birds than other dinosaurs.
So that's the reason why this new bug is so exiting. It is a new kind of archaea we didn't know existed. It may very well be our closest relative among the archaea and bacteria, and it has taught us a lot about something really strange that happened two billion years ago. It has many genes that we didn't know existed outside eukaryotes that give us a rough idea of what genes the first eukaryotes had, and that's something we have wanted to know for a long time.
The thing is, bacteria and archaea are pretty easy compared to eukaryotes. They have small cells and not that much DNA, but the eukaryotic cells are huge and there are multiple compartments and lots and lots of DNA we don't know what it does, and we don't really now how a simple cell like an archaeon can evolve into a complex cell like an eukaryote. Well, thanks to Lokiarchaeota we now have a clue. Despite being rather simple, the Lokiarchaeota contains lots of the same genes as eukaryotes, and many of them are involved in changing how the cell is organized. That's why it is named after a shape shifting god. That, and because there is a place in the ocean floor not far away from where it was found that is called 'Loki's castle' (which is an incredible cool place - check it out).
The thing that I find most interesting with Lociarchaea is actually not what we know but what we don't know about them - because that is lots. Everything we know comes from the DNA, kinda like how most things we know about dinosaurs comes from their skeletons. We have never seen the cells of Lokiarchaea in a microscope or grown them in an aquarium, so we don't know if they are round or oblong, small or large. We don't know how they grow or what they like to eat, although we can make a few guesses. The mud they live in is cold and dark and doesn't contain much food of any kind, so they probably grow very slowly. We don't know how different they are from each other, we don't know how many there are (although there are probably lots, because there is so much mud in the sea floor). We don't know how they interact with bacteria, if they actually eat them or if they just ignore them, and we don't know what they use all these unusual genes for.
Still, it is pretty good for a little piece of mud and a really good stick. A lot of scientists have become existed about this - you can read more about what they are saying here and here, and read the original article here. If there is one thing this discovery tells us it is that there are lots of cool things out there to discover. So next time you play with mud - keep an eye out for any unusual bugs - who knows, maybe you will be the one to find the next one.