REVIEW: An Ancient Divergence among Bacteria

When you learned about life in school, you most likely learned the FIVE KINGDOM system, shown below:

 In this system,

Animalia are the various self propelled animals of the world including humans, elephants, platypi, and octopi.

Plantae are are the green things out there.

Fungi are just things to put on pizza.

Protista are eukaryotic single celled organisms, such as yeast for making bread.

Finally, monera are prokaryotic organisms, like E. coli the workhorse of most scientific work!

 This classification system was fine and good, because it made sense with the current state of science. Things that looked alike belonged together. Well, with the discovery of DNA as our genetic material and the improvement in techniques to sequence DNA, people got to wondering if the genetic code also reflected the system that was previously devised. Today's paper that establishes that the five kingdom system is flawed and (through later work) that there are THREE DOMAINS OF LIFE!!!!

Spider-man was drawn by Skottie Young, Bat-mite by Ryan Sook, and I don't know for Mr. Mxyzptlk.

 Why does sequencing DNA matter so much? Can't we just look at the bacterium and compare create a more refined tree for the five kingdom system? The problem with that is that bacteria look pretty much the same. There are some that are really different, but most of them look like a squiggling speck. The DNA sequences though are passed down through time and when comparing to other sequences they can reveal a great many details! This was back when comparing DNA sequences didn't make you a molecular biologist, it made you a MOLECULAR PALEONTOLOGIST!!!

 There is a problem though. At this time (1977), DNA sequencing "technology" consisted of some GUNG-HO graduate student, an organism, and an arduously long procedure to get the DNA sequences by hand. Nowadays, there are machines that determine the DNA sequence and can do so in an afternoon. Since it takes forever and a day to get a DNA sequence, you cannot just sequence an entire genome. To really hammer the point home, it took 13 years to sequence the human genome and that was with significant help from the US government. The first bacterial genome was not completed until 1995, eight years before the human genome was completed. So, what gene or region of the DNA do you sequence? Obviously, the one that changes the least. This gene turned out to be the 16S ribosomal RNA sequence. 

 The ribosome is a large structure of RNAs (ribonucleic acids) and some proteins that are responsible for taking your messenger RNA and translating it into proteins. All Earth bound organisms have a ribosome and they are all very similar. Since there are several RNAs that make up the ribosome, they choose the the 16S ribosomal RNA to sequence. Why the 16S? Previous research pointed towards it being the best.

 The researchers took two bacteria-like organisms (Methanobacterium ruminantium and Methanobacterium thermoautotrophicum) and sequenced the 16S ribosomal RNA and then compared it to the other 16S ribosomal RNAs and they found a surprise. When compared to the sequences of the other bacteria, the two that they sequenced were extremely different and points to a divergence from bacteria that antedates the previously oldest division of bacteria!!!