I Don’t Think It Means What You Think It Means

Brad puts the dreaded “P-word” (Prokaryote) to rest and introduces the Archaea, the 3rd domain of life only recognized as distinct in 1977.

Brad Goodner here.  It is great to be back with you after some more student-hosted episodes of Genomics Revolution.  Did the title of today’s episode bring a chuckle or a smile to your face?  It is one of many memorable lines from one of my favorite movies – The Princess Bride.  Vizzini, the big-brained Sicilian kidnapper says “Inconceivable” every time the so-called “Man in Black” makes it past a huge obstacle.  Vizzini’s hired swordsman, the Spaniard Inigo Montoya finally turns to Vizzini and says “you keep using that word.  I don’t think it means what you think it means.”

Inigo Montoya’s phrase could also apply to a word all biologists know – prokaryote.  It is in my opinion, as I tell my students early and often, “the dreaded P-word” that has outlived its usefulness and should never be used again.

Prokaryote literally means “before kernel” or “without kernel” where kernel refers to a membrane-bound nucleus within a cell.  Prokaryote is literally the antonym of eukaryote which means “true kernel” or having a membrane-bound nucleus within a cell.  The prokaryote-eukaryote distinction played a major role in how biologists, and especially microbiologists like myself, looked at organisms in the mid- to late-20th century as biology became more cellular-focused.  The terms are attributed back to Edouard Chatton, a French biologist who studied protozoa.  As described in a great 2005 review by Jan Sapp (1), Chatton first used the terms prokaryote and eukaryote in a 1925 paper where he was trying to phylogenetically place a particular protozoan species.  Building on work that goes back to Haeckel and others in the late 19th century, Chatton made a case that his protozoan species of interest shared essential features seen in other eukaryotes: a membrane-bound nucleus, a flagella or cilia with associated basal bodies, and exhibited mitosis.  On the other hand, bacteria, spirochaetes, and blue-green algae, what we now call Cyanobacteria, lacked these structures and were lumped under the term prokaryote.  Chatton didn’t care about relationships within prokaryotes, but he did care deeply that his beloved protozoans were eukaryotes just like fungi, animals and plants.

So why should we care about this term prokaryote so much?  It turns out that Chatton’s terms gave two famous microbiologists, Roger Stanier and C.B. van Niel, a way out of a problem that had vexed them for over two decades.  Stanier and van Niel wanted a robust way to infer evolutionary relationships amongst bacteria like E. coli, Pseudomonas aeruginosa, Treponema pallidum, and Mycobacterium tuberculosis that we have heard about in past Genomics Revolution episodes.  They had tried using cell shape and biochemical tests with no success.  In their 1962 paper entitled “The Concept of a Bacterium” (2) Stanier and van Niel had reached a point of utter frustration, but Chatton’s terms at least gave them a way of saying what these bacteria WERE NOT.  They WERE NOT EUKARYOTES.  They were prokaryotes.

Whether or not Stanier and van Niel believed that all prokaryotes share a more recent common ancestor with each other than any of them shared with eukaryotes is not totally clear, it was this very  hypothesis that most microbiologists accepted just on the grounds of cell complexity.  Robert Whittaker in his 1969 Science article (3) appeared to agree with this hypothesis with his five kingdom model for classifying cellular life on Earth with all prokaryotes in the kingdom Monera.  Yet around this same time, data started emerging that held the real answer.  Emile Zuckerkandl and Linus Pauling in 1965 talked of DNA, RNA and protein sequences as information macromolecules of history because mutations were markers laid down over evolutionary time (4).  It kept getting easier and cheaper to sequence these linear polymers and in 1977, Carl Woese and George Fox had enough data for the right macromolecule, the 16S/18S rRNA found in all ribosomes in all cellular lifeforms, to answer the question (5).  Do all eukaryotes share a more recent common ancestor with each other than with prokaryotes?  YES.  Do all prokaryotes share a more recent common ancestor with each other than with eukaryotes.  NO.  The prokaryotes split into two groups that appeared to be equidistant from each other as they were from eukaryotes.  Woese and Fox called these two groups Eubacteria and Archaebacteria and suggested that these groups were two of three “primary kingdoms” for cellular life on Earth.  With more data in later papers, the names were shortened to Bacteria and Archaea to sit alongside of Eucarya not as “primary kingdoms” but rather as the three domains of life, the highest most encompassing evolutionary groupings.  Even the New York Times took notice and put it on the front page – “Third Domain of Life Found.”

As a freshman at Texas A&M University in the early 1980’s, I got the chance to hear George Fox give a series of visiting lectures on evolution.  I don’t think I really grasped at that time how much Woese and Fox had turned the microbial world upside down.  As more and more data accumulated, it became increasingly clear that the Archaea were a truly distinct group.  At first, we thought they were limited to a few weird extreme habitats, but now we know they are everywhere including inside our own GI tracts.

We heard about one Archaea genome several episodes ago, that of Thermoplasma acidophilum.  In the next few episodes we will hear about a few more genomes from this 3rd domain of life.  Stay tuned to expand your horizons, but please let the dreaded P-word Rest In Peace.  It doesn’t mean what you think it means. 

References:
(1)Sap, J., 2005.  Microbiology & Molecular Biology Reviews 69:292-305.  The prokaryote-eukaryote dichotomy: meanings and mythology.

(2)Stainer, R. & C.B. van Niel, 1962. Archives Microbiology 42:17-35.  The concept of a bacterium.

(3)Whittaker, R.H., 1969.  Science 163:150-163.  New concepts of kingdoms of organisms.

(4)Zuckerkandl, E. & L. Pauling, 1965.  Journal Theoretical Biology 8:357-366.  Molecules as documents of evolutionary history.

(5)Woese, C.R. & G.R. Fox, 1977.  Proceedings of National Academy of Sciences USA 74:5088-5090.  Phylogenetic structure of the prokaryotic domain: the primary kingdoms.