My apologies for not getting a new post up sooner – life got a bit busy over the past two weeks. However, I have put together a three part mini-series on some really interesting organisms called extremophiles. We’re going to cover some general information on them and their extreme living conditions first then I’ll focus on one particular organism, called Thermus aquaticus, and how one protein from that little bacterium makes lab life much easier for post docs like me.
So. What is an extremophile?
Literally, they are organisms that live/thrive/survive in extreme environments. Of course, “extreme” is in the eye of the beholder. In this case, the beholder is human so anything beyond our norms is considered extreme.
According to the article I read in Nature, Romans used the word “exter” to describe anything being on the outside. They eventually wanted (or “needed” depending on your view of the Romans) a word that meant anything really really beyond normal, so they coined the word “extremus,” which is now the English word “extreme.” I have already covered the root of “phile” (see Soap! post) but just to really hammer it home: “philos” is Greek for “lovers.”
When I was in college, I learned only about two types of extremophiles: thermophiles and halophiles. It appears that a whole world of extremophiles was known and that my deep chemistry education didn’t allow for more learning time on the subject. Sad!
I’m going to walk through a few of them, describe their environments, and discuss how they deal with their “extreme-ness.” Remember that all life uses the same basic molecules on Earth (amino acids, DNA, etc) and extreme conditions are harmful to them. These organisms must use these same tools but take advantage of their known characteristics to allow survival at these extreme conditions.
Thermophiles:
About: Some like it hot. Humans live in the range of 0°F/-17°C to 100°F/38°C (generally speaking) and are called mesophiles. Thermophiles like it a smidge hotter (140°F/60°C – 176°F/80°C) and hyperthermophiles achieve maximum growth at over 176°F/80°C! Yikes. The archaea bacterium Pyrolobus fumarii enjoys a balmy 234°F/113°C.
Where: Where on Earth can you find these ridiculous temperatures? Hotsprings, geyers, and deep in the ocean at the hydrothermal vents. Interestingly, many different life forms exist around those vents (examples: worms, shrimp, bacteria). It’s rather popular despite its location and hot climate.
Problems: membrane fluidity, protein/DNA denaturation
Solutions: Adjusting composition of membranes to decrease fluidity; changing protein structures to allow for more heat stability; using mono- and divalent ions to stabilize their DNA at these high temperatures.
Psychrophiles
About: Some like it cold. Psychrophiles enjoy temperatures below 59°F/15°C, which I’m sure doesn’t sound so daunting until I tell you that Himalayan midge is quite content at 0°F/-18°C.
Where: Very cold places like sea ice, artic soils, or deep ocean (not near hydrothermal vents, obviously).
Problems: membrane fluidity, ice crystals, protein function
Solutions: adjusting composition of membranes to increase membrane fluidity; rigidifying protein structure; proteins involved in keeping water from freezing
Halophiles
About: Some like it salty! Halophiles live in very very salty conditions.
Where: Salt flats, natural lakes and deep sea hypersaline basins
Problem: Retaining water.
A cell is separated from its environment by a semi-permeable membrane (meaning things can pass across the membrane if they meet the right requirements). If you make the area outside the membrane very salty, you will force water inside the cell to flow outside. Why? Science demands that the concentration of salt be the same on both sides of the semi-permeable membrane. The salt concentration outside is very high and the salt concentration inside the cell is lower. The easiest way to increase the salt concentration inside a cell is to remove water. Cells need water to survive so having it all flow out leads to death. (This is why you die if you drink salt water, by the way.)
Solution: The organisms utilize different strategies to sequester water inside their membranes so it is unavailable to flow out.
Alkaliphile
About: Humans maintain a pH inside their cells of ~ 7 and most biological processes occur around this range. However, alkaliphiles enjoy the pH much higher (> 9).
pH is simply a measure of how many protons are around. A lot of protons? Low pH. Only a few protons around? High pH.
Where: soda lakes or drying ponds
Problems: Protons are required for a cell to make energy. At high pH, protons are scarce.
Solutions: The organism tries to maintain pH of 7 inside their cells by bringing in as many protons as possible. The organisms also have unusual permeability properties to their membranes.
Acidophiles
About: Opposite of alkaphiles, acidophiles enjoy very low pH (< 3 or so). Their environments have a lot of protons floating around. Cyanidium caldarium (red alga) enjoys a pH of 0.5 while Dunaliella acidphila (greena alga) would prefer 0. Helicopbacter pylori can live in our stomachs (pH ~2) and can cause ulcers.
Where: sulphuric pools, geyers, hydrothermal vents, acid mine drainage, our own stomachs
Problems: protein denaturation
Solutions: Organisms have a lot of proton pumps to remove protons from their cells and bring the pH up inside their cells.
These are just some of the few. Other organisms exist that can live at incredibly high pressures, almost no water (or gravity!), high radiation or chemical extremes. Some can live in environments that are combination of these characteristics; these are called polyextremophiles.
Of course, this leads to two very interesting concepts: 1. Life in space, and 2. Usefulness of these organisms to the masses.
Learning that these extreme environments do not preclude life leads to some interesting questions about life on other planets. Places that we previously concluded were inhospitable to life may have it after all. Keep your eyes open!
As always, scientists (and business owners) are looking for new, cheaper or novel ways to make their products. What if we could find proteins directly involved in keeping psychrophiles running? What if we could purify them and apply them to frozen human organs? Currently, we can't reliably freeze human issue (or bodies. Want to revisit the Absolute Zero post?) due to ice crystal formation. However, we might be able to exploit psychrophile adaption methods for our own gains.
One area that we have been able to use extremophile adaptations is the laboratory. Most scientists have used a little enzyme called Taq Polymerase. It is an enzyme responsible for linking nucleotides together into DNA. It was purified from Thermus aquaticus and is currently sold to post docs like me.
Before we get into why this is so interesting, we first need to understand DNA.
Extremophile: an organism that lives in extreme environments
Polyextremophiles: an organism that lives in an environment that is extreme is more than one way.
REFERENCES
Rothschild and Mancinelli. "Life in Extreme Environments." Nature (2001) 409, pgs 1091 - 1101.
More info about hydrothermal vents:
http://www.onr.navy.mil/focus/ocean/habitats/vents1.htm
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