Amoeba: Much Wierder than You Think

Amoeba proteus extending pseudopodia to feed on a hapless ciliate. Note how the pseudopodia completely surround the ciliate, cutting off any escape, before they close in on it. A fantastic photo by Wim van Egmond - you owe it to yourself to visit that link.

I have been challenged (or at least, I think I have been challenged) to write some posts on amoebozoans, the clade of eukaryotes that includes such organisms as Amoeba and most slime moulds. As amoebozoans are unequivocally neat organisms, I'm happy to take up the challenge, but I thought Id start by focusing on the most famous amoebozoan genus of all, Amoeba itself. There are about five or so species of Amoeba (at least that I'm aware of), but most of what I'm going to say in this post applies equally to all of them. I think I'm safe in claiming that Amoeba is not just the most famous amoebozoan, it's also the most famous of all unicellular eukaryotes. Almost all general biology textbooks will include two examples of 'protists', and one of them will always be Amoeba (the other will be either Euglena or Paramecium). The funny thing about this ubiquity of the Amoeba exemplar, however, is that as unicellular protists go, Amoeba is actually (a) apparently not that common, and (b) seriously wierd*.

*Euglena and Paramecium aren't that typical either.

What makes Amoeba so odd? For a start, Amoeba is amoeboid* (kind of by definition, really). This might not seem so unusual at a glance (many micro-organisms are amoeboid), but the thing is that Amoeba is always amoeboid. It never possesses cilia. Many (if not most) other amoeboid eukaryotes transform into amoeboflagellates or flagellates for at least part of their life-cycle, or possess flagellated gametes, while the majority of unicellular eukaryotes are permanently flagellated**. Even among amoebozoans, cilia are not that unusual; they're still present in Breviata, Multicilia, Phalansterium, Mastigamoebidae, Pelomyxa and many Mycetozoa, though cilia have been entirely lost among amoebozoans at least nine times (Cavalier-Smith et al., 2004).

*Simply for the sake of avoiding confusion, I prefer to avoid the common use of the name "amoeba" to refer to any organism with an Amoeba-like morphology.

**A brief explanation about the terms "cilium" and "flagellum". Originally, the term "cilium" was used for small hair-like locomotory structures, usually present in large numbers, while "flagellum" referred to larger whip-like structures of which a cell would usually only have one or a few. As our knowledge of unicellular diversity broadened, the boundary between the two became increasingly blurred, and fundamentally they're all the same structure. On the other hand, "flagella" in bacteria, though superficially resembling flagella in eukaryotes, are structurally very different (eukaryote flagella are organelles formed of membrane-bound microtubules, while bacterial flagella are formed of a single protein strand). As a result, recent authors have tended to restrict the term "flagellum" to bacteria, and expand the term "cilium" to cover all eukaryote locomotory structures (a replacement term "undulipodium" never caught on [thankfully]). However, terms such as "flagellate" are still pretty well entrenched in their old sense.


Amoeba 'radiosa', photo by David Patterson & Aimlee Laderman. Despite the use of the name, there is not really such a species as 'Amoeba radiosa'. Rather, the name is used to indicate amoebae that have become detached from the substrate and are free-floating in the water column, where they abandon their usual flattened form and adopt a form with slender pseudopodia radiating from a spherical centre. Once they come back into contact with a solid surface, they will return to their normal morphology.

The second unusual thing about Amoeba (which is perhaps not unconnected to the first thing) is its reproductive habits. Most people are aware that Amoeba reproduce by division. That happens to be the only way that Amoeba reproduce (Chapman-Andresen, 1971); they are (so far as anyone knows) entirely asexual. While asexual reproduction is normal for many organisms, exclusively asexual lineages are something of a rarity. Most asexually reproducing organisms have more aphid-like life cycles - they reproduce asexually as long as conditions are favourable for doing so, but convert to sexual reproduction when times get tough. Even bacteria, which mostly don't engage in sexual reproduction per se, are able to engage in processes such as conjugation that still allow for gene flow.

And the third wierd thing about Amoeba has to be its genetics. Amoeba genomes are simply huge - the largest genomes known to exist, in fact. We humans have a genome that clocks in at a little under three billion base pairs of DNA. Amoeba proteus, the best-known species of Amoeba, has a genome containing closer to three hundred billion base pairs. And even that effort pales in comparison to Amoeba dubia, which carries around a whopping six hundred and seventy billion base pairs. That's right - the difference in genome size alone between the two species is larger than the total genome size of any other organism! The actual genetic structure of Amoeba, however, appears to be little-known. The genome of A. proteus is divided between more than five hundred chromosomes, which is hardly surprising considering its size. By means unknown, however, this enormous genome can be reduced to nearly a third of its normal size over the course of cell division (Parfrey et al., 2008). Presumably the normally polyploid amoeba jettisons excess chromosomes prior to division then recreates them from the remainder afterwards.


Amoeba proteus on the move (towards the top left of the photo). Note the knobbly bit at the bottom right corner. This is the uroid, and represents the trailing end of the cell. The form of the uroid has turned out to be surprisingly useful in identifying amoeboids. Another photo by David Patterson.

One other feature of the Amoeba nucleus is worth mentioning. The nucleus contains a number of stellate aggregations of condensed helical structures just inside the nuclear envelope that, when first observed, were not unreasonably thought to represent condensed chromosomes. However, further study showed that the nuclear helices were composed of a mixture of proteins and RNA (not DNA) and seemed to be able to be transported out of the nucleus into the surrounding cytoplasm (Minassian & Bell, 1976). The helices disappear over the course of cell division, but are regenerated afterwards. The exact function of these helices is still unknown. Minassian & Bell (1976) seem to have suggested (in a rather cagy way that would have allowed for ready back-tracking if they turned out to be wrong, and which I may have easily misinterpreted) that they could be related to ribosome formation. Gągola et al. (2003), in contrast, note the attachment of actin filaments to the helices, and imply that they may play a role in cell motility (Amoeba with removed nuclei are unable to move*, while amoeboid animals cells can continue to move even without their nuclei).

*Removing the nucleus from an Amoeba is as simple as slicing it in half.

REFERENCES

Cavalier-Smith, T., E. E.-Y. Chao & B. Oates. 2004. Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. European Journal of Protistology 40 (1): 21-48.

Chapman-Andresen, C. 1971. Biology of the large amoebae. Annual Review of Microbiology 25: 27-48.

Gągola, M., W. Kłopocka, A. Grębecki & R. Makuch. 2003. Immunodetection and intracellular localization of caldesmon-like proteins in Amoeba proteus. Protoplasma 222: 75-83.

Minassian, I., & L. G. E. Bell. 1976. Studies on changes in the nuclear helices of Amoeba proteus during the cell cycle. J. Cell Sci. 20: 273-287.

Parfrey, L. W., D. J. G. Lahr & L. A. Katz. 2008. The dynamic nature of eukaryotic genomes. Molecular Biology and Evolution 25 (4): 787-794.