Various examples from the different domains of life all carry a similar lesson.
Mycoplasmas
Mycoplasmas are a group of bacteria that are so small they were once considered viruses. They are also considered good representatives of a “minimal life form” given that they possess the smallest genomes of all bacteria. For example, the species Mycoplasma genitalium has a genome that is only 580,000 nucleotides in length with only 484 genes. In comparison, Escherichia coli’s chromosome is over 4.6 million nucleotides in length and contains over 5000 genes.
Because of their small size, the mycoplasmas were once considered primitive organisms [1]. Genome sequencing establishes that mycoplasmas cluster with Bacillaceae. These are gram-positive bacteria that include the genera Clostridium, Lactobacillus, Bacillus, and Streptococcus. Rather than being primitive bacteria, mycoplasmas are derived, having undergone extensive reductive evolution from a much larger and more complex ancestral state. For example, the genomes of Clostridium.acetobutylicum, Lactobacillus plantarum , Bacillus subtilis, and Streptococcus pneumoniae have genomes with 4080, 3254, 5193, and 2219 genes, respectively. Thus, if we assume a last common ancestor connecting mycoplasmas and these other species of bacteria had a genome with about 3700 genes (the rough average of these four species), mycoplasma have lost over 80% of their genes.
The mycoplasmas underwent such massive gene loss as a result of their intimate parasitic relationship with eukaryotic hosts. They have shed their cell walls in order to facilitate a close connection with the host cell. And since the host cell supplies most of the nutrients for the bacteria, they have also lost most of their genes for a variety of synthetic reactions (for example, mycoplasmas can’t make their own amino acids or fatty acids). Because of this parasitic dependence, it is not truly accurate to think of mycoplasmas as “minimal life forms” given that they depend on the products of other life forms to exist.
Microsporidia
Microsporidia are unicellular eukaryotes. They are also the simplest and smallest eukaryote, existing as intracellular parasites. After the endosymbiont hypothesis really took root[2], scientists began to look for the descendents of those eukaryotes that existed prior to acquiring the mitochondria (a reasonable expectation). Microsporidia and several others seemed to fit perfectly. For example, microsporidia not only lack mitochondria (suggesting they branched off prior to other eukarya acquiring mitochondria), but they also lack golgi bodies, peroxisomes, and cilia. Their genomes are smaller than some bacteria (2.3 million nucleotides compared to E. coli’s 4.6 million). And it got even better. They have 70S ribosomes, the same size as bacteria. In fact, “the 5.8S and 28S rRNAs are fused, as they are in bacteria” and “there is no spacer sequence between the two in the rDNA, and the two are transcribed as a single molecule, as in bacteria.[3]Then it got better yet. Sequence analysis of rRNA showed microsporidia to be the deepest branching of all eukarya, practically confirming it split off very early on. So impressive was this evidence that biologist Cavalier-Smith invented a whole new kingdom for microsporidia and other unicellular organisms lacking mitochondria. The kingdom was called Archezoa.
Yet, the kingdom was short-lived. The first cracks in the wall developed when mitochondria genes were found in the genome of microsporidia, suggesting that this organism once had mitochondria and lost them. Then, further sequence analysis of several protein-coding genes (tubulin, TATA-binding protein, and others) indicate that microsporidia are close relatives to fungi [4].
Nanoarchaeum equitans
Archaea do not possess the same degree of diversity that is found among bacteria. While bacteria can be categorized into over 20 major groupings or phyla, all known cultivable archea fall into two phyla – Euryarchaeota and Crenarchaeota.
However, in 2002, Karl Setter and colleagues identified a novel archaebacterium that seems to constitute a third group [5]. They isolated a cell smaller than mycoplasma called Nanoarchaeum equitans. It exists as a hyperthemophile that lives on the surface of another archaebacterium known as Ignicoccus. Since N. equitans cannot live apart from Ignicoccus, it apparently represents the only known example of an archaeal parasite.
Having learned the lessons from mycoplasma and microsporidia, scientists did not immediately assume this small, parasitic archaebacterium was primitive. Instead, the genome was immediately sequenced to address this very issue [6]. While it was originally concluded that N. equitans represented a basal lineage, a second look uncovered evidence that shows a clear affinity with another another cluster among the Euryarchaeota known as Thermococcales [7]. This strongly suggests Nanoarchaea, like mycoplasma and microsporidia, are derived parasites that have undergone reductive evolution.
Nanoarchaeum has the smallest known genome, containing only 480,000 nucleotides. Yet the genome, with 552 genes, contains more genes that Mycoplasma genitalium. Unlike the mycoplasmas, Nanoarchaeum has little noncoding DNA. But like the mycoplasmas, the genome has been stripped of genes for the synthesis of lipids, amino acids, nucleotides, and various cofactors. There are, however, two interesting features of its genome. First, unlike the mycoplasmas,it contains the full set of DNA repair and recombination genes. Secondly, Nanoarchaeum has many split genes. These split genes code for different functional domains of the encoded protein and are found in different places along the chromosome. To get full function, the two domains must be synthesized independently and brought together. If Nanoarchaeum is a derived species, this helps us to see that evolution can take a complex gene and split it up into smaller functional modules.
Mitochondria
The champion of reductive evolution would have to be the mitochondria [2]. Mitochondria are derived from some Rickettsia type alpha-Proteobacteria. The last common ancestor of the mitochondria and Rickettsia is thought to have dated around 1.5 – 2 billion years ago. It is estimated that such an ancestor would have had around 1600 genes. In contrast, the range of gene content among mitochondria is 67 (Reclinomonas Americana)to 3 (Plasmodium falciparum. This is clearly the most extensive example of reductive evolution that was likely facilitated by input from the host(in yeast, the majority of mitochondrial proteins are coded for by eukaryotic-specific genes). What’s even more striking is that this reductive evolution may have been further catalyzed by viruses, as the bacterial RNA polymerase that would have been inherited from the alpha-Proteobacteria ancestor was quickly replaced by the simpler RNA polymerase from a T3/T7-like bacteriophage.
Summary
What we have is a Trifecta Plus One. The simplest organism among bacteria is derived. The simplest organism among eukarya is derived. The simplest organism among archaea is derived. The Three Domains of Life offer up the same lesson. And as a bonus, the simplest cellular genome (mitochondria) is derived. What is the common thread that ties this extreme evolution together? In every case, we have an intimate, symbiotic relationship. This would then allow us to predict that cell-level symbiotic relationships have the inherent potential to fall into flux of reductive evolution. So why might this be so significant?
The simplest class of biotic entities are viruses. In fact, they are so simple that many biologists do not consider them living organisms. Yet what is it that defines a virus? Its complete dependence on a host cell to carry out most of the work. In other words, the simplest biotic entity is also the most extreme form of parasite. Seen in the light of mycoplasmas, microsporidia, nanoarchaea, and mitochondria (and chloroplasts), we have good reason to predict that viruses, rather than reflecting some primitive state, represent the extreme end of this far-reaching, evolutionary trend.
Citations
1. Ross Hardison. 1997. More Information about Mycoplasma. See: http://globin.cse.psu.edu/html/pip/more_myco.html
2. Thoughts on the endosymbiotic theory”
5. Huber, H., Hohn, M.J., Rachel, R., Fuchs, T., Wimmer, V.C., and Stetter, K.O. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature417:63-67.
6. Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M. 2003. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A.100:12984-8.
7. Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterre P. 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol.6(5):R42. 8. Kurland CG, Andersson SG. 2000. Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev. 64:786-820.