Bacteria that tear themselves apart

Bacterial cell division is one of those fairly well studied areas, where time and much study has come forth with a nice standard model. One of the main proteins involved is FtsZ, which seperates one bacteria into two by forming a ring of protein around the middle of the bacteria and tightening it shut as shown below (figure from Nature paper):

Until quite recently it was thought that this was pretty much the only way to get bacteria to divide, until 1999, when the sequences of two Chlamydia species turned out not to contain genes for FtsZ. As Chlamydia are intracellular parasites (which I covered in more detail here) it was at first thought that they might be using some host proteins to complete the cell division, but after the discovery of an FtsZ-less free living archaea, and several more bacteria, it became apparent that the FtsZ-centric model of cell division (shown diagrammatically above) wasn't covering the behaviour of all bacteria.

In the archaeal species (in fact the entire archaeal kingdom Crenarchaea) the cell division was found to be based on a completely different cytoskeletal system. By screening for genes that were turned on at the onset of cell division, a three-gene operon was found to be involved. These genes coded for homologues of eukaryote vesicle trafficking proteins and their regulators, and it was suggested that they formed curved filaments which could pinch off sections of the membrane, forming new archaea. Although the method is similar, the 3D structure of the archaeal proteins is very different to that of FtsZ; the two proteins are not related, but have been coerced into doing the same job.

As well as finding bacteria without FtsZ, it was also discovered that taking a strain of Mycoplasma genitalium and removing the FtsZ didn't stop cell division and in fact showed the same growth kinetics as the wild type. The division mechanism in this case relied on the fact that Mycoplasma move by adhering to a surface and pulling their way along it (in a lab this will be on a glass or plastic surface). To pull their way forward they use a 'terminal organelle', a little protrusion that attaches to the surface and pulls the cell along (figure from the reference).

The diagram above shows Mycoplasma without FtsZ undergoing cell division. You can clearly see not one, but two little terminal organelles at either end of the long stretched cell. What's happening is that in the absence of proper organised proteins to sort out cell division the bacteria has taken matters into its own hands, and sent two terminal organelles determinedly heading off in opposite directions. The bacteria is literally tearing itself apart, splitting into two by ripping in half and letting the membrane close up behind.

It has been suggested that this might be an older method of cell division, used before FtsZ entered the Mycoplasma. It's certainly a lot more brutal than FtsZ-mediated division, and the bacteria has to spend a lot more time in stationary phase recovering from it. As this method only works in bacteria that can attach and hang onto surfaces, it is unlikely to be use by the Chlamydia species (the mechanism for their cell division is still unknown, although some work has been done with L-form bacteria). In the archaeal species it may even be the other way around, that the new filamentous system evolved to be even more efficient that FtsZ in certain species, and so the FtsZ has been dropped entirely.

All of this builds up a picture of just how diverse even simple systems like cell division can be within the bacterial kingdom. And, in my mind at least, is a compelling argument for not just working with model organisms...

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Erickson, H., & Osawa, M. (2010). MicroCommentary: Cell division without FtsZ - a variety of redundant mechanisms Molecular Microbiology DOI: 10.1111/j.1365-2958.2010.07321.x

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Life at 90°C

Prokaryotes are by far the most successful superkingdom in terms of types of both biochemical diversity and the variety of environments conquered. Bacteria can be found living in all kinds of adverse conditions; from high alkaline lakes, to below freezing temperature, to hot volcanic vents which in some cases can reach temperatures close to the boiling point of water.

Thermotoga is a small genus of bacteria that contains some of the most hyperthermophilic species known, some able to survive at 90°C although most prefer the cooler temperatures of 70-80°C. It’s called “thermotoga” because it lives at high temperatures (thermo) and contains a characteristic outer cell membrane known as the ‘toga’.

This was basically my mental image when I read that

One of the most interesting things about thermophilic bacteria (i.e bacteria that like living at very high temperatures) is their enzymes. Most normal enzymes, (most normal proteins in fact!) will break down and denature at very high temperatures, so bacteria like thermotoga will usually have their own set of enzymes. These enzymes are usually of great interest to people carrying out industrial processes, which all take place at higher temperatures. The most important enzyme in the PCR protocol (Taq polymerase, which synthesises DNA at temperatures of up to 80°C) was isolated from a marine thermophilic archaea.

Another exciting thing about Thermotoga is it has the ability to produce hydrogen. In the lab, it uses carbohydrates from yeast extract or peptone to form sugars, which are oxidised to carbon dioxide (or acetic acid) using either sulphur or protons as the electron acceptor. Where protons are used, they get reduced to hydrogen as the carbon dioxide is formed. The yield of hydrogen from glucose is very high, and in many cases can approach the theoretical maximum yield of for 4 mole hydrogen from one mole off glucose. This represents almost twice the amount that can be obtained from other bacterial hydrogen producers. Because this process is taking place at high temperatures, the enzymes involved in the process could potentially be used inside high temperature reactors.

Thermotoga neopolitana has the potential to produce one of the highest hydrogen yields of all as it is able to respire microaerobically. This means that it would be theoretically possible for the cells to aerobically oxidise a small amount of the glucose, generating enough energy to ensure that all the remaining glucose is fully oxidised by hydrogen-generating pathways. As yet, the metabolic pathways for oxygen use within these organisms have not been identified, but it does look as if hydrogen generation depends almost exclusively on anaerobic processes.

Electron micrograph of Thermotoga, showing the large outer cell wall covering (the toga!).

As the majority of the research into hydrogen production of Thermotoga has focussed on yield, issues of productivity, stability and required substrates will all need to be address in order for this process to be fully understood and possibly implemented in an industrial setting. There are also issues with biomass concentration – which is restricted, possibly by free-flowing biofilms (and possibly due to the toga-like nature of the surrounding cell-wall capsules. However even if large scale hydrogen production proves to be unfeasible with these microorganisms, studies of the enzymatic processes used to produce hydrogen at high temperatures may have applications above and beyond using the entire bacteria for hydrogen production.

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Van Ooteghem, S., Beer, S., & Yue, P. (2002). Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana Applied Biochemistry and Biotechnology, 98-100 (1-9), 177-190 DOI: 10.1385/ABAB:98-100:1-9:177

Archaea, Eukaryotes and the evolution of DNA replication complexes

The relationship between bacteria, archaea and eukaryotes is an interesting one, and made slightly harder to approach as people tend to lump archaea and bacteria into the one grouping of 'prokaryotes' which is not much more than a scientific word for "blobs I don't care about". Delving deeper into the biochemistry of all three superkingdoms shows that while the metabolic pathways used by archaea are more similar to those in bacteria, their core DNA processes (such as replication and protein synthesis) are more similar to the processes in eukaryotes. (I talk more about the distinction between the three superkingdoms here)

There was an interesting paper in PLoS ONE lately that was looking at the evolution of DNA replication complexes in archaea, and seeing as this blog has been rather heavily bacteria-biased (i.e I haven't talked about archaea for a while) I decided to take a look at it. They were focussing on three main complexes that help in DNA replication and are found in both archaea and eukaryotes: proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacteria do use corresponding proteins, but they are far more distantly related.

Schematic of the structure and subunits of the three complexes.

The MCM complex is thought to act as a helicase; unwinding the two DNA strands to allow them to split in two to be replicated. The PCNA and RCF are known as the clamp and clamp loader and help to attach the RNA primer for replication to the Polymerase, which uses the primer to start replicating the DNA.

All of these three complexes consist of separate subunits, which are almost identical. PCNA, for example, is a trimer (in the diagram above each subunit is a separate colour). In eukaryotes these the subunits are identical, but in archaea variations are found between them. This general pattern, that subunit composition was far more variable within the archaea, was found in all three of the complexes. This method of gene duplication followed by gene modification to create two different proteins is an important one for evolution, and in the case of DNA replication it seems to have been exploited far more in archaea than in eukaryotes.

Changing some subunits also allows these complexes to carry out different tasks. It's been suggested that for some archaea there may be a functional difference between PCNA with all subunits the same (homotrimers) and PCAN with differing subunits (a heterotrimer). This allows multiple functions to be generated through simple DNA duplications - although all the functions are likely to relate to DNA replication in some way.

This brings forth the interesting point of view that the truly 'ancestral' forms of these genes and proteins may be more like the proteins seen in the eukaryotes rather than the archaea! Archaea (and bacteria) can tolerate a lot more genetic change than eukaryotes can, and have a far shorter generation time, allowing them to change and evolve more quickly than the larger, less genetically mutable eukaryotes. On the other hand the lack of change and high level of conservation in eukaryotes means that the complexes remain very similar to those of the ancestral eukaryote from which they evolved. They may even be closer to the forms found in the last common ancestor between eukaryotes and archaea, before the eukaryotes gained a nucleus and became unable to share genes with the surrounding organisms.

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Chia N, Cann I, & Olsen GJ (2010). Evolution of DNA replication protein complexes in eukaryotes and Archaea. PloS one, 5 (6) PMID: 20532250

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How The Animal Lost Its Sensor

Two-Component Systems are one of the major sensory systems used by bacteria to detect and respond to changes in both their outside environment, and their internal state. I cover them in more detail here, but just in summary they consist of two proteins,a sensor and a responder. The sensor senses the change, and activates the responder, which binds to the bacterial DNA and leads the production of a protein that will enact a suitable response.

Although Two-Component Systems (TCS) are found in all three superkingdoms of life (Archaea, Bacteria and Eukaryotes) they are suspiciously absent from the animal kingdom. Plants have them, as do fungi and several protazoa, but they just aren't present in animals. For this reason they've been looked into as potential antibiotic targets as knocking out the Two-Component Systems of most bacteria is fatal.

Why don't animals use TCSs? To answer this you have to start looking at the evolution of the system itself, because despite being nominally present in eukaryotes such as plants and fungi, TCSs are used very differently in bacteria and archaea. Bacteria use TCSs for sensing a wide variety of signals; stress, metabolism, nutrient regulation, chemotaxis, pathogen-host interactions etc. in eukaryotes on the other hand, they are used sparingly, for ethylene responses and photosensitivity in plants and osmoregulation in fungi and slime moulds.

Bacteria (especially soil bacteria which have a lot of environment to sense) can contain up to 50 TCSs although many internal parasite bacteria (with a lot less to sense) contain far less. The maximum for Archaea is around 20 TCSs. Eukaryote number drop right down, with only one in the yeast Saccharomyces cerevisiae (one sensor kinase and three response regulators). None have yet been found in any animal genomes, or in the few partial protist genomes sequences (although I doubt if anyone's had a complete scan through the protist genomes for them).

Comparing the TCSs of Bacteria, Archaea and Eukaryotes leads to the interesting conclusion that the bacterial and eukaryotic systems are far more closely related than the archaeal, and in fact are thought to be monophyletic (all evolved from a single common ancestor). In contrast, the archaeal TCSs appear to be polyphyletic and some archaea lack TCSs entirely. It's therefore thought that TCSs originated in bacteria and spread by horizontal gene transfer to both archaea and eukaryotes (until the eukaryotes developed a nuclear membrane). In eukaryotes very little further diversification took place, whereas the bacterial TCSs diversified widely, and occasionally passed new systems back to the archaea. I've tried to show this in the diagram below:

Diagram made by Lab Rat. Red arrows show the movement (straight arrows) and duplication (curved arrows) of TCS genes. No horizontal gene transfer can take place in eukaryotes after the nuclear membrane (well....it *can* do but very, very rare) although gene duplication may still have occurred.

The eukaryotic kingdom appears not to have contained very many of these TCS genes to start with, and the animal kingdom may just have lost the very few it possessed. This makes sense from the point of view of cellular control because while TCSs are very useful in the small genomed and non-nuclear membrane containing bacteria, it's less clear how useful they are in eukaryotes as a whole. Introducing a membrane around the nucleus makes it harder for proteins to get in and bind to the DNA, and introducing systems of membranes inside a far bigger cell makes it harder for a simple two-component system to sense what's going on. Added to which, cells inside a multicellular organism don't really need to sense what's going on, they get told what's going on by the surrounding cells and circulating hormones.

Whatever the reason though (and any other ideas would be welcomed, the above paragraph is mostly speculation) it is clear that despite this system being vital for bacteria it isn't used widely, or most likely at all, in animals. Research into this would be particularly useful against opportunistic pathogens which tend to have a large selection of two-component systems to allow them to adapt to different lifestyles depending on the conditions of their immediate environment.

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Kristin K. Koretke , Andrei N. Lupas , Patrick V. Warren , Martin Rosenberg , and James R. Brown (2000). Evolution of Two-Component Signal Transduction Mol Biol Evol, 17, 1956-1970

Wolanin PM, Thomason PA, & Stock JB (2002). Histidine protein kinases: key signal transducers outside the animal kingdom. Genome biology, 3 (10) PMID: 12372152

Paleoatmosphere

The first signs of life on earth appeared about 4.5 Ga (1 Ga is an American billion, ie. 10⁹ years) ago. It's not yet completely certain exactly how this life arose; hot volcanic mineral springs have been suggested, as have the more traditional lightning-struck primordial soups and (rather wonderfully) radioactive beaches. At any rate something happened (and there was certainly plenty of time for it to happen in) which lead to a little membrane-bound ball with internal nucleic acids which, crucially, could replicate...

Awesome little gif from here

And then it was all over really, bar the evolution.

What kind of world did these first little blobs of life appear in? The surrounding temperature is pretty much unknown, hypothesises for both warm and cold have been put forward and all that can really be agreed on is somewhere between 4-100 degrees. It was most definitely wet; water was in liquid form when life first started, a fact that was probably vitally important for the formation of life as we know it.

The atmosphere would have been very different, little oxygen and an abundance of carbon dioxide with plenty of methane being released into the atmosphere once the first life forms (appropriately called methanogens) started eking out an entropy-defying existence. In order to get energy to power cellular processes you need to set up redox pathways, which involve cycles of electron donors and acceptors. The main electron donors around at the time were H2, H2S and CH4 and the main acceptor probably nitrogenous. Water, the electron donor used for photosynthesis, was around in abundance, but none of the little proto-life-blobs quite had the energy required to split it (or the physical proteins required back then either) so it mostly stayed unused.

Carbon dioxide levels went down, methane levels went up, the planet warmed up a little due to global warming. Things stayed like that for a billion years or so (1 Ga) and then something quite special happened, something that would have mindblowingly devastating affects on the life surrounding it.

Photosynthesis. The uptake of carbon dioxide into the cell, and the reactions that stick it onto a carbon chain, effectively 'fixing' it as sugar; turning air into food. And as everyone hopefully was taught back in primary school, this process releases oxygen, which is good for us but was almost fatal for the life-forms around 3Ga (probably was fatal for some of them). When oxygen isn't being used for respiration, it can be highly toxic to cells. It screws up the internal redox potential, it creates dangerous free-radicals and it precipitates ions out into soluble forms.

Of course the oxygen produced by the photosynthesising proto-bacteria didn't go straight up into the atmosphere right away. There were too many ions floating around in solution to bind to it, and this caused a huge precipitation event; in common terms, everything rusted. Iron was pulled out to form large rust beds, which set down iron ore deposits to be dug up by humanity 2.5 billion years later and used in the Industrial revolution.

The arrival of this new resource (oxygen) lead to a change in the way organisms respired as well. Up until what is sometimes called the Great Oxidation Event (when oxygen started being released into the atmosphere by all the photosynthesising blobs) most respiration was anoxic, probably similar to anaerobic respiration (or fermentation) in anaerobic bacteria around today. This process, while enough t0 keep life going, is around sixteen times less efficient than aerobic respiration. The proto-life-blobs that managed to use the oxygen would therefore have gained a major energy boost.

Over the next 1.5 billion years the atmosphere changed from a highly reducing state (where the early proto-life-blobs developed) to a more oxidising environment. Endosymbiosis and the formation of mitochondria and chloroplasts allowed the first eukaryotes to specialise their metabolism even more. Rather than have the whole cell as a bundle of metabolic redox reactions, releasing potentially dangerous radicals into the cytoplasm, the energy production could be specialised inside it's own compartment, churning out enough energy for the cell to get bigger. Complex intracellular tubules allowed nutrients to be diffused all over this larger cell which would then commit what was from a bacterial point of view the biggest evolutionary mistake ever, and package the cell nucleus away in an inaccessible membrane. (Eukaryote cells then had to develop squishy things like sex in order to regain enough genetic plasticity to actually evolve.)

The effect of oxygen was not just limited to respiration; nowadays many metabolic pathways involve oxygen at some point, including those necessary for the production of sterols (used in signalling molecules and cholesterol, which is an important membrane component), indoles (found in the amino acid tryptophan) and several antibiotics. Oxygen can be an important resource if used correctly.

It's occasionally speculated just why life took so long to move out of the blob phase and into multicellularity. Spending over three billion years as blobs seems a little odd considering that the last billion years involved the branching out of multicellular organisms in a a whole myriad of forms and features, from velociraptors to cockroaches to annelid worms to highly specialised bacteria capable of forming complex networks of bacterial hunting packs. My personal opinion is that all that time was needed simply to get the metabolic background necessary for more complex cellular arrangements. Without the biochemical pathways necessary to generate reasonable amounts of energy, cells have severe limitations placed on their abilities. And biochemically, most organisms are remarkably similar. Differences between the eukaryotes, bacteria and archaea maybe, and plants and fungi have a few different bits of metabolic pathways, but otherwise the internal cellular reactions are remarkably conserved. Not just metabolic ones either; the finely tuned DNA replication machinary, protein synthesis, and even several signalling pathways remain conserved throughout the Kingdoms.

All those internal pathways had three billion years of self organisation and optimisation before they even had to begin to think about making multicellular creatures. No wonder they all fit together so well!

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Falkowski PG (2006). Evolution. Tracing oxygen's imprint on earth's metabolic evolution. Science (New York, N.Y.), 311 (5768), 1724-5 PMID: 16556831

Bacterial evolution: negative to positive?

The most commonly used distinction in bacterial populations is that of Gram negative and Gram positive bacteria. They are named after the method used to distinguish them: the Gram stain (developed by Hans Christian Gram). Gram positive bacteria have larger peptidoglycan cell walls, and therefore retain the crystal violet stain, whereas Gram negative bacteria have two membranes with a thin peptidoglycan wall between them, do not retain the crystal violet stain, and pick up the safranin counter-stain. The practical upshot of this is that you end up squinting at small blotched shapes under the microscope, trying to work out whether they look more pink or purple:

Gram +ve on the left, Gram -ve on the right.

As well as hinting that Mr Gram was one of those people who knows what shade 'fuchsia' is, the Gram stain is also one of the most important ways of telling what kind of bacteria you're dealing with. Despite being seemingly arbitrary, the composition of the cell wall plays a major role in determining behaviour. Gram negative bacteria (small cell wall, two cell membranes, see the picture below) tend to be motile, opportunistic, and able to colonise a wider range of environments. Gram positives on the other hand (big cell wall) are not so motile, but tend to have a huge range of excretory proteins to make up for this; almost all known antibiotics come from Gram positive bacteria.

Again, Gram +ve on the left, -ve on the right. Image from soil microbiology webpage

One thing that I've never really considered before is which one of them evolved from which. I haven't done much taxonomy, and the only time I really covered bacteria (unrelated to lab work) was in my Pathology course, which didn't seem too concerned about where different types of bacteria had come from, only what they were currently up to. The few times I did vaguely think about this though, I would have gone for the positive to negative direction. After all, surely you start with one cell membrane, and move on to two.

I recently came across a paper that came to the complete opposite conclusion, and therefore was too interesting not to read. The thing about bacterial taxonomy is that a lot of the major changes to morphology took place in Deep Time, and bacteria leave precious few fossils. Bacteria (and archaea...) had somewhere in the region of over one billion years to evolve before eukaryotic-things even started to be considered. That's a lot of time to try and sort out. To put that into context, one billion years ago from now things were just about starting to think about going multicellular. No dinosaurs, no plants even; the most complex form of life was something resembling a sofa cushion.

So how to sort out what was going on in that billion years or so? There are four main ways of going about it:

• Paleontological evidence. Bacteria don't form a huge number of fossils, but they can occasionally leave some physical evidence of their presence. For example, bacteria that eat iron will leave behind little fossilised iron cases; those that eat rocks can leave microscopic drilling holes. These provide temporal evidence for changes in structure and metabolism.
• Transition analysis. This is used to polarise major changes by turning them into a simple before-or-after question, and uses comparative, developmental, and selective arguments for determining answers. For example: did legs or wings develop first? Or, in bacterial cases: Which came first, Gram negative or Gram positive?
• Congruence testing. This searches for similarities across whole evolutionary trees, enabling loss or gain of evolutionary abilities (wings, feathers, second membranes etc) to be identified and polarised. As this is a comparison of many species, it allows potential mistakes from the arguments made in transition analysis to be found.
• Sequence trees. Sequence trees are ... problematic, but at the same time indispensably useful. They are formed by taking DNA sequences from a range of organisms and then using algorithms to tell the 'relatedness' between sequences and using these 'relatedness' levels to make evolutionary trees. They tend to be biased towards your sample distribution, undirectional, unable to properly account for generation times, and go somewhat screwy when you try to introduce horizontal gene transfer. Nevertheless they were instrumental data in showing that archaea and bacteria are two very distinct super-kingdoms (and I will freely admit that most of my distrust for them occurs because I can't get the damn things to work whenever I try them)

So...using these techniques can we get a clearer idea what was happening with bacterial membranes during those 1 billion-odd years before the arrival of eukaryotes? On the face of it; positive-to-negative seems to make more sense: start with one membrane, gain a second, possibly by gene duplication.

However like many evolutionary stories, that one falls apart a little when closer examined. Because Gram positive bacteria are not simply 'one cell membrane' they also have a massive cell wall surrounding them. Developing a second cell membrane on top of that seems absurd. And then why would the cell wall shrink? And how would anything get through this suddenly developed cell membrane. Transport proteins for the outer membrane tend to form a protein structure called a beta-sheet, while those for the inner membrane form an alpha-helix. That's a whole new system of protein folding that has to evolve pretty quickly, because otherwise the bacteria will starve, nothing can get through its outer membrane (which is balancing precariously on top of the huge cell wall...)

In view of this, the schematic seen on the right starts to make a little more sense (figure taken from the reference below). 'Murein' means 'peptidoglycan cell wall' and the cytoplasm denotes the inside of the cell. In this scenario, the double-membraned proto-bacteria (which has spend the last half-a-billion years or so evolving a well adjusted double membrane system) suddenly looses the outer membrane. A very simple genetic change would lead to a massively overgrown cell wall, which would rip the outer membrane away. The cell looses all it's outer membrane porins, and signal systems, but in return gains a highly protective cell wall, which potentially allows it to survive in different niches. How these aspects are lost genetically is another matter, and the paper rather hand-waves away by saying that unused genes tend to get lost eventually. Which is true in bacteria, they have such a small genome they don't want it getting filled up with unnecessary genes, but I have a feeling genes tend to leave something behind. Even so, the question of where the now-unnecessary genes go is possibly one of the weaker parts of this arguments (to my untrained student eyes at least.).

One thing that would really support this hypothesis would be to show that Gram positive bacteria formed a 'mono-clade' i.e came from a single universal common ancestor. Unfortunately this data is proving hard to pin down, not helped by the bacterial trick of swapping DNA around with all and sundry. Another confounding factor is the sheer space of time. Trying to determine whether a range of different modern bacteria all came from the same blob several million years ago is a daunting task. You can sort of get RNA sequence trees that support the mono-cladal Gram positives, but only if you close one eye and squint, which is not generally accepted scientific practise.

I don't think I'll ever end up going into taxonomy, even of bacteria. but it does produce fascinating ways to look at the world; how it changed, how it evolved, and how it finally turned into the way it is now. Orwell wrote, fairly famously, "He who controls the past commands the future", and when you're trying to figure out how bacterial resistance works, and preferably how to stop them getting it, that phrase takes on a whole new meaning beyond the political.

(It's not a perfect quote for this post. "Understands the past" would work better. But I'm not quite pretentious enough to go trawling through the quote archives to find something better. Any suggestions would be appreciated :p )

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Cavalier-Smith T (2006). Rooting the tree of life by transition analyses. Biology direct, 1 PMID: 16834776

On the classification of blobs

The first forays into microscopy revealed a whole world of blobs, tiny microscopic organisms that were invisible to the naked eye. These went through a range of different names, from the 'animalcule' denomination given by Anton van Leeuwenheok (which he used to describe everything small he saw under the microscope, including his own sperm) through 'monera' (a more specific name for certain types of blobs, namely those that weren't eukaryotic) to 'prokaryotes', a name that still stands.

Prokeryote means, literally, 'no nucleus', and it's use allows the world of living organisms to be split up into two groups: Prokaryotes and Eukaryotes. Eukaryotes are things with a nucleus, a membrane covered partition to hold DNA, as well as many separate organelles existing within their cells, such as mitochondria, endoplasmic reticulum, the Golgi apparatus...

Prokaryotes are...uh...everything else.

Which means that the label 'prokaryote' was always waiting to fall apart. After all, they may just be blobs but there are a lot of them, and some are very different blobs. Around the 1970's people started noticing that there were a group of the prokaryotes that behaved differently, mainly through studies done by Carl Woese and George E. Fox who created classification tables based on the genetic sequences of ribosomal RNA (the part of the genome most likely to be conserved, this is often used for classification, especially of things in Deep Time). This showed that there was a distinct group of prokaryotes with a mostly separate evolutionary history (more on the mostly later) to the rest of the prokaryotes. They were originally named 'archaebacteria', and together with 'eubacteria' (true-bacteria) were put in the prokaryotes group. They were blobs without a nuclei, and that was where they belonged.

However, things started to get a bit more complicated the more people looked at archaebacteria. They weren't just a group of slightly odd bacteria, they were something else. Something different. Although their metabolic pathways are similar to bacteria, their methods of turning DNA into proteins more resembles eukaryotic processes. Their flagella (tentacle like structures used for movement) have a markedly different structure from bacterial flagella. Like bacteria, they reproduce asexually and (also like bacteria) they can share their DNA around, in fact they can also share there DNA with bacteria, which makes taxonomists tear their hair out. It's very difficult to classify something when it keeps giving its DNA away, and collecting bits from other sources.

It is proposed in the SGM journal (Society for General Microbiology-journal not available on line) that the term 'prokaryote' should be scrapped altogether. As well as being an incorrect label for a large group of organisms it also produces an incorrect evolutionary perspective. The use of the eukaryote/prokaryote terms suggests a very human based linear "One upon a time there were blobs with no nuclei and then they got nuclei and then they were better" sort of story. A more correct view is that of all three superkingdoms; bacteria, archaea and eukaryotes splitting away from each other. Eukaryotes safely packaging their DNA away, allowing a more complex system to build up, yet forfeiting the ability to share bits of DNA. The archaea and bacteria on the other hand, continued to share their genetic material, just became more selective about it as they diverged (hense the 'mostly' seperate history).

Or maybe not. It might be that the archaea/eubacteria formed a very selective group of blobs, which then split further when some developed a nucleus, while the others continued to share their DNA with the bacteria, picking up different metabolic secrets. It's hard to work out; especially given that similarities between the DNA of archaea and bacteria does not necessarily show their relatedness; it might be a gene that has remained conserved in both of them for millions of years, or it might just be one that was exchanged last week.

There a several arguments against removing the 'prokaryote' as a naming system but most of them boil down to the very multicellular-centric argument of: "but they're all just blobs!" The three superkingdoms of archaea, bacteria and eukaryote are a far more accurate, and scientifically and taxonomically correct way of looking at things than the prokaryote/eukaryote model.

My only complaint is that I spent ages in secondary school trying to learn how to spell 'prokaryote'... removing the name means I could have spent that time doing something far more useful...like building paper planes and reading 'Redwall'.