Wednesday, November 11, 2015

Fish Guts and Cancer – Giant Bacteria, part 2

The gut of a fish is a strange place to go looking for bacteria. It’s an even stranger place to find the second largest bacterium on Earth.

Epulopiscium fishelsoni (E. fishelsoni) hangs out in the intestinal tract of the brown surgeonfish, commonly called the lavender tang. While it seems logical that E. fishelsoni would be named for the site where it was found – inside a fish – it was actually named for its discoverer, Lev Fishelson of Tel Aviv University.  

Epulopiscium fishelsoni is shown in the left image. The white line is approximately 100 µm. On the right is the Lavender Tang.  E. fishelsoni lives in this fish’s gut, and only in this fish’s gut.

Before T. namibiensis (last week’s post) was discovered, E. fishelsoni was the biggest kid on the block, having been first seen in 1985. It can be seen with the naked eye, reaching a maximum length of 0.7 mm, but it also has large size variations. In fact, this is one of the keys to its success.

E. fishelsoni’s changing size is a daily routine. In the early morning, E. fishelsoni is only about 10 µm long, only 2-5 times bigger than typical bacteria. As the surgeonfish starts to feed, more food is available to the bacteria in its gut. With this signal, E. fishelsoni starts to grow. By late afternoon into evening, the maximum size has been reached and they can be seen with the unaided eye (if you happened to be in the fish’s gut to see it – I wouldn’t recommend it as a holiday destination).

However, after the night passes, you would find just the small cells again in the morning. You would also see that the number of bacteria has increased.  The large cells have divided into daughter cells, splitting their cellular contents between their two or three new partners. Then, as a new day passes and food becomes available in the gut, these cells grow large and divide overnight. 


Could you imagine having your baby grow 75x bigger in one day?
Think of it this way: you bring home your 22-inch long newborn baby in the morning and place it in its crib.  That night, you find that you have a baby that is 140 ft. tall. You start to build the world’s largest crib, but by morning, the giant is gone and you find two 22-inch babies in the crib. It would continue like this everyday. Parenting is difficult.

E. fishelsoni’s shape is also different than that of T. namibiensis. E. fishelsoni is shaped like a long grain of rice, as opposed to the spherical T. namibinesis. This can help meet diffusion needs (see this post), since the distance to travel is much shorter for molecules brought in on its long sides. The elongated shape is enough to make the new daughter cells viable. But as the cells grow during the day, merely being longer than they are wide isn’t enough to overcome diffusion rate, mixing rate, and traffic time limits. E. fishelsoni must know another trick in order to survive at is maximum size.

In the majority of molecular interactions, it is a cellular protein that partners with a molecule that has diffused into the cell. What might E. fishelsoni do to increase the chance that an enzyme will find its substrate (the molecule an enzyme acts on and changes in some way) quickly?

Remember in the “It’s all in the Numbers” post, we saw that one way to reduce traffic time was to increase the number of one or the other interacting molecule. It is impossible for the bacterium to raise the concentration of nutrients, but it can raise the number of proteins made by the bacterium.


The central dogma of molecular
biology.
We need a bit of background to help explain E. fishelsoni’s trick to producing more copies of its proteins. There is a central dogma (core belief) to cell molecular biology: DNA goes to RNA goes to protein. This means that DNA is transcribed to a message (mRNA), which is then translated into a protein. However, if you want to make more protein, you can’t just transcribe more RNA from the DNA in the cell. This process is highly regulated and can only be manipulated to a certain degree. The other problem with this solution is that the proteins would be produced near the site of the DNA, so these extra proteins would have to travel a long distance to mix through the entire cell – this wouldn’t solve the mixing time (diffusion) problem.

What if the cell made more copies of its DNA and spread them out through the cell? Then the cell could produce much more RNA and hence much more protein. Having the DNA spread throughout the entire bacterium would solve the mixing time problem.


Fold number of chromosomes is a cell’s ploidy. 
N= haploid number of chromosomes, N in humans = 23, 
but we are diploid, so the total number of 
chromosomes is 2 x 23 = 46.
How would a bacterium make more copies of its entire DNA (its genome)? Isn’t the number of copies of DNA determined and unchangeable? In general, bacteria are haploid, meaning that they have one copy of each (usually just one) chromosome. Human cells (except for sex cells) are diploid, meaning they have two copies of each chromosome (one from Ma and one from Pa). Some plants exhibit triploidy, especially the seedless varieties of fruit, like bananas and watermelons. Finally, while polyploid cells (poly = many and ploid = fold) can occur naturally in lower animals and some plants, in humans it is often associated with cancer cells. The more copies of the genome there are in a cancer cell, the worse the prognosis (predictable outcome) for the patient.

E. fishelsoni has found a way to make being polyploid work for it. The early morning version of the bacterium (the small cell) is haploid, but as the cell volume increases hour by hour, the amount of bacterial DNA also increases through the circadian cycle (the daily sequence of physiological events).


Green color in inset shows the huge amount of DNA dispersed throughout  
E. fishelsoni. Courtesy of: Ward, R.J., Clements, K.D., Choat, J,.H. 
and Angert, E.R..  2009.  Cytology of terminally differentiated  
Epulopiscium mother cells.  DNA and Cell Biology 28:  57-64.
By evening, the mega-E. fishelsoni has 85,000 copies of its genome! Scientists don’t have a -ploidy name for a number that big; just plain polyploid. This is a huge amount of DNA for a prokaryotic cell, and is 25% more DNA than contained in a human cell.  The new DNA copies are spread throughout the cytoplasm to provide thousands of local protein factories. Wherever there is a diffused nutrient, the proper protein it needs to interact with won’t be too far away. Therefore, E. fishelsoni can disregard the usual size limitations placed on it by diffusion.

This bacterium still has much to teach us; for instance, I wondered about all that extra DNA. If there are 85,000 copies in the parent cell, but the two or three daughters that result from it are haploid (1 copy/daughter cell), what happened to the other 84,997 or 84,998 copies of the genome? I asked Dr. Fishelson about this, and he said, “there are several questions concerning this enigmatic bacterium, one of which is what you are asking about - what is the fate of the ‘surplus DNA’ as the daughter cells are produced?” If we figure out how E. fishelsoni gets rid of its extra DNA, we could take advantage of the process. Wouldn’t it be something if we learned how to beat cancer by studying a bacterium in the gut of a fish?




Bresler V, Montgomery WL, Fishelson L, Pollak PE. (1998). Gigantism in a bacterium, Epulopiscium fishelsoni, correlates with complex patterns in arrangement, quantity, and segregation of DNA J Bacteriol., 180 (21), 5061-5611 : 9791108


  For more information and activities on ploidy, central dogma, see below:

Ploidy –

Central dogma –