Catching up

So I felt like I couldn’t put off the sixteen hundred articles twiddling their thumbs and tapping their feet in my RSS reader any longer. This is the first part of the crop that has accumulated since late December (yikes!). Legless axolotls, homing starfish, secretly related proteins, and more!

1. Axolotls are good at regenerating – until you make them grow up.

(Portrait of a pale lab/aquarium variety axolotl by Orizatriz, Wiki Commons.)

It’s probably not exactly obvious from my posting record, but a large part of my PhD work is about regeneration. It’s something we humans are pretty shit at, but many other vertebrates aren’t. Axolotls, these adorably dumb-faced salamanders, can easily regrow their legs. However, lab axolotls are kind of permanent babies. Although they can grow up in the sense that they are able to breed, they normally keep larval characteristics like gills throughout their lives. It’s reasonable to suspect that this influences their regenerative ability – after all, tadpoles lose their ability to regrow limbs the moment they turn into frogs.

It’s possible to make axolotls metamorphose, too, if you treat them with thyroxine (the same hormone that induces metamorphosis in “normal” amphibians). And when they turn into proper adult salamanders, they suddenly become much poorer regenerators. They can still replace a limb – kind of. But they take twice as long as non-metamorphosed axolotls of the same age and size, and they invariably wind up with small, malformed limbs, often missing bones. After amputation, new skin is slower to grow over their wounds, and the cells that gather under the new skin are sluggish to divide. Something about metamorphosis – that isn’t simply age – dramatically changes how they respond to amputation.

Reference: Monaghan JR et al. (2014) Experimentally induced metamorphosis in axolotls reduces regeneration rate and fidelity. Regeneration advance online publication, doi: 10.1002/reg2.8

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2. Similar cells repair muscles in crustaceans and vertebrates

“Regeneration” can cover a lot of different processes. For example, depending on the creature and the organ you’ve damaged, regenerated body parts can come from totally different kinds of cells. In planarian flatworms, a single kind of stem cell can replace anything else in the body. In the eyes of newts, mature cells of the iris transform into lens cells to replace a missing lens. In our muscles, there are special cells called satellite cells that are held in reserve specifically to make new muscle cells when needed.

This recent study of a little crustacean called Parhyale hawaiensis suggests that muscle regeneration in the fingernail-sized arthropod works in much the same way. Konstantinidis and Averof shot early embryos of Parhyale with DNA encoding a fluorescent marker, which randomly integrated into the genomes of some of the cells it hit. In a few “lucky” individuals, the marker ended up labelling just one cell lineage, and the pair used these animals to figure out which cells made which tissues in a regenerated limb.

It turned out that cells in Parhyale are limited in their potential. Descendants of the ectodermal lineage could make skin and nerves but not muscle, and the mesodermal lineage built muscle but not skin or nerves. Moreover, labelled cells only contributed to regeneration near their original location – animals with their left sides labelled never regrew glowing limbs on the right side. This is starting to sound a lot like vertebrates, but it’s still a very general observation. However, the similarities don’t end there.

Like vertebrate muscles, the muscles of the little crustaceans contain satellite-like cells derived from the mesodermal lineage that sit beside mature muscle cells and express the Pax3/7 gene. When the researchers transplanted some of these cells from animals with the glowy label into leg stumps of non-glowy animals, there were glowing muscle cells in some of the regenerated limbs. So like satellite cells, these cells can turn into muscle during regeneration. There’s little question that muscle cells have a common origin in vertebrates and arthropods like Parhyale, but it’s really cool to see that their mechanisms of regeneration also might.

Reference: Konstantinidis N & Averof M (2014) A common cellular basis for muscle regeneration in arthropods and vertebrates. Science, published online 02/01/2014, doi: 10.1126/science.1243529

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3. Convergent evolution is a poor explanation of rhodopsins

Proteins can be difficult. I mean, sometimes they do their darnedest to hide their family ties. A protein is a chain of amino acids (on average about 300 of them) often folded into a complex shape. Closely related proteins have obviously similar amino acid sequences. However, more distant relatives can be harder to identify. There are about 20 different kinds of amino acids in proteins, so the number of possible sequences is unimaginably vast. The same function can be carried out by very different sequences, and therefore enough evolution can completely erase sequence similarity.

Protein structures are generally thought to be more conserved than sequences. Like function, structure allows for a huge amount of sequence variation without significantly changing. However, theoretically, it’s possible that two unrelated proteins have similar structures because of their similar functions, not because of common ancestry. Apparently, this has been argued for the two types of rhodopsins – proteins that harvest light in systems as different as a the “solar generator” of a salt-loving microbe and the photoreceptors of our own eyes.

If Type I and Type II rhodopsins are similar despite being unrelated, one would assume that this is because they need to be that way to capture light. There are, after all, astronomical numbers of possible protein structures, and the chances of two protein families accidentally stumbling onto the same one without selection steering are slim to say the least. But, in fact, you can rearrange the structure of a rhodopsin in all kinds of cunning ways without destroying its function. This rather weakens the case for convergent evolution, and suggests that similarity of structure does indicate common ancestry here.

Reference: Mackin KA et al. (2014) An empirical test of convergent evolution in rhodopsins. Molecular Biology and Evolution 31:85-95

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4. Starfish can see their way back home

(Blue starfish, the beast featured in the paper, in its natural habitat. Richard Ling, Wiki Commons.)

Starfish aren’t widely known as visual creatures, but they do have eyes at the tips of their arms. The eyes are a bit… basic – no lenses, just a hundred or two little units filled with photoreceptors. Garm and Nilsson set out to find out how the starfish used their eyes. They measured or calculated the eyes’ visual fields (five arm-eyes together can see pretty much everywhere around the animal), resolution (very coarse), reaction speed (slow), and their sensitivity to various wavelengths (they are colour-blind, most sensitive to ocean blue).

Then they took some poor starfish and dumped them a little way off the coral reefs they like staying on. The creatures could walk home from short distances (about 2 m or less), but if you take them too far away, they just wander around in random directions. Likewise if you take off their eyes (don’t worry, they regenerate) or do the experiment in the dark. In conclusion: starfish eyes aren’t exactly top-end cameras, but they are definitely useful to the animals. And what would a slow, brainless mopper-up of coral reef rubbish do with eagle eyes anyway?

(The paper states the walking speed of these starfish as about 4-5 cm per minute. I have a feeling this wasn’t the most exciting fieldwork these guys have done…)

Reference: Garm A & Nilsson D-E (2014) Visual navigation in starfish: first evidence for the use of vision and eyes in starfish. Proceedings of the Royal Society B 281:20133011

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5. What makes wormies settle

OK, Shikuma et al. (2014) one isn’t so much for its own news value, but I hadn’t known that my favourite worms need bacteria to settle until I saw this paper, so I think it deserves a mention. (Besides, it has beautiful pictures of baby Hydroides in it, which I couldn’t resist posting below. They are So. Cute. Yes, I’m weird.)

Shikuma_etal2014-hydroidesBabies

Tubeworms of the serpulid family have swimming larvae which are in many ways like the acorn worm larvae mentioned in my previous post (except cuter). They are tiny, look nothing like an adult worm, have bands of cilia for swimming and feeding, and live in the plankton until they’re ready to metamorphose. When they find a place they like, they settle and turn into adult worms. And apparently, this particular species (Hydroides elegans) not only needs a specific bacterium to like a place, it needs specific proteins produced by that bacterium.

The proteins in question are the components of a nasty device bacteria probably stole from viruses and then used to poke holes in one another. But to Hydroides larvae, they appear to be necessary for metamorphosis. Put healthy bacteria together with worm babies in a dish, and you’ll get happily settled little worms. Do the same with bacteria with damage to the relevant genes, and nothing happens. Use an extract containing the proteins but not the bacteria, and you still get metamorphosing worms. Use too much, though, and they start dying. Everything in moderation…

(Maybe my dismal failure at raising happy young worms years ago could have been remedied with the right bacteria?)

Reference: Shikuma NJ et al. (2014) Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 343:529-533

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6. Relative of animals does strange multicellularity with familiar genetics

Although this idea probably hasn’t reached popular perception, animals are surrounded by other multicellular lineages in the tree of life. Sure, most of them are only part-time multicellular, but that’s beside the point. What’s clear is that multicellularity, at least in its simpler forms, is rampant in our extended family. Slime moulds do it, fungi do it, our closest relatives choanoflagellates do it, and our next closest relatives, filastereans and ichthyosporeans also do it.

These latter two groups are really poorly known (the fact that only a taxonomist could like the latter’s name probably doesn’t help), but the situation is getting better with the attention they are receiving as relatives of animals. There are now genome sequences out, and some people are looking at the life cycles of the little creatures to search for clues to our own origins.

Iñaki Ruiz-Trillo recently published a paper describing an ichthyosporean that can form a weird kind of colony with many nuclei in the same membrane starting from a single cell (Suga and Ruiz-Trillo, 2013). Now his team describe a different kind of multicellularity in a filasterean, Capsaspora owczarzaki. Rather than developing from a single cell, this guy does something more akin to the slime mould way: take a load of individual cells and bring them together. (Below: a clump of Capsaspora cells from Sebé-Pedros et al. [2013]. On the right is a regular photograph of the colony. The two-coloured fluorescence on the left indicates that the colony formed by different cells coming together rather than a single cell dividing.)

Sebé-Pedros_etal2013-F4.capsasporaClump

But, interestingly, some of the genetics involved is similar to what animals use, despite the different ways in which the two groups achieve multicellularity. For example, we’ve known since all those genomes came out that the proteins animals use to glue cells together and make them talk to each other are often older than animals. Well, Ruiz-Trillo’s filasterean appears to ramp up the production of some of these when it goes multicellular. It also uses a gene regulation strategy that animals are really big on: it edits the RNA transcribed from many genes in different ways depending on cell type/life stage before it’s translated into protein.

A lot of the details are going to need further investigation, since this was a global RNA-sequencing study with a bird’s-eye view of what genes are doing. It’s still a nice reminder that, like most other innovations in evolutionary history, the multicellularity of animals didn’t spring fully formed out of nowhere.

References:

Suga H & Ruiz-Trillo I (2013) Development of ichthyosporeans sheds light on the origin of metazoan multicellularity. Development 377:284-292

Sebé-Pedros A et al. (2013) Regulated aggregative multicellularity in a close unicellular relative of metazoa. eLife 2:e01287

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Fifty thousand generations, still improving

I take all my hats off to Richard Lenski and his team. If you’ve never heard of them, they are the group that has been running an evolution experiment with E. coli bacteria non-stop for the last 25 years. That’s over 50 000 generations of the little creatures; in human generations, that translates to ~1.5 million years. This experiment has to be one of the most amazing things that ever happened in evolutionary biology.

(Below: photograph of flasks containing the twelve experimental populations on 25 June 2008. The flask labelled A-3 is cloudier than the others: this is a very special population. Photo by Brian Baer and Neerja Hajela, via Wikimedia Commons.)

It doesn’t necessarily take many generations to see some mind-blowing things in evolution. An irreducibly complex new protein interaction (Meyer et al., 2012), the beginnings of new species and a simple form of multicellularity (Boraas et al., 1998) are only a few examples. However, a few generations only show tiny snapshots of the evolutionary process. Letting a population evolve for thousands of generations allows you to directly witness processes that you’d normally have to glean from the fossil record or from studies of their end products.

Fifty thousand generations, for example, can tell you that they aren’t nearly enough time to reach the limit of adaptation. The newest fruit of the Long-Term Evolution Experiment is a short paper examining the improvement in fitness the bacteria experienced over its 25 years (Wiser et al., 2013). “Fitness” is measured here as growth rate relative to the ancestral strain; the faster the bacteria are able to grow in the environment of the LTEE (which has a limited amount of glucose, E. coli‘s favourite food), the fitter they are. The LTEE follows twelve populations, all from the same ancestor, evolving in parallel, so it can also determine whether something that happens to one population is a chance occurrence or a general feature of evolution.

You can draw up a plot of fitness over time for one or more populations, and then fit mathematical models to this plot. Earlier in the experiment, the group found that a simple model in which adaptation slows down over time and eventually grinds to a halt fits the data well. However, that isn’t the only promising model. Another one predicts that adaptation only slows, never stops. Now, the experiment has been running long enough to distinguish between the two, and the second one wins hands down. Thus far, even though they’ve had plenty of time to adapt to their unchanging environment, the Lenski group’s E. coli just keep getting better at living there.

Although the simple mathematical function that describes the behaviour of these populations doesn’t really explain what’s happening behind the scenes, the team was also able to reproduce the same behaviour by building a model from known evolutionary phenomena. For example, they incorporated the idea that two bacteria with two different beneficial mutations in the same bottle are going to compete and slow down overall adaptation. (This is a problem of asexual organisms. If the creatures were, say, animals, they might have sex and spread both mutations at the same time.) So the original model doesn’t just describe the data well, it also follows from sensible theory. So did the observation that the populations which evolved higher mutation rates adapted faster.

Now, one of the first things you learn about interpreting models is that extrapolating beyond your data is dangerous. Trends can’t go on forever. In this case, you’d eventually end up with bacteria that reproduced infinitely fast, which is clearly ridiculous. However, Wiser et al. suggest that the point were their trend gets ridiculous is very, very far in the future. “The 50,000 generations studied here occurred in one scientist’s laboratory in ~21 years,” they remind us, then continue: “Now imagine that the experiment continues for 50,000 generations of scientists, each overseeing 50,000 bacterial generations, for 2.5 billion generations total.”

If the current trend continues unchanged, they estimate that the bugs at that faraway time point will be able to divide roughly every 23 minutes, compared to 55 minutes for the ancestral strain. That is still a totally realistic growth rate for a happy bacterium!

I know none of us will live to see it, but I really want to know what would happen to these little guys in 2.5 billion generations…

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References:

Boraas ME et al. (1998) Phagotrophy by a flagellate selects for colonial prey: a possible origin of multicellularity. Evolutionary Ecology 12:153-164

Meyer JR et al. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335:428-432

Wiser MJ et al. (2013) Long-term dynamics of adaptation in asexual populations. Science, published online 14/11/2013, doi: 10.1126/science.1243357

Viruses strike back

If you are a bacterium, life can be pretty dangerous. Wherever you live, you are surrounded by millions of viruses that can inject you with their DNA and turn you into a helpless factory of these (bacteriophage T4 by Adenosine, Wikipedia):

(They may kill you, but at least they look badass…)

In response to the constant threat of deadly viruses, bacteria and archaea have evolved an ingenious defence mechanism called the CRISPR system. The CRISPR region in the genome consists of repetitions of a short sequence (the actual CRISPRs), alternating with spacers containing foreign (often viral) DNA the bacterium snatched from invaders. Spacers can be pulled out later and used to recognise and destroy the same invader.

If you are a CRISPR-enabled cell and survive a virus attack long enough to add the attacker to your “library”, you and your offspring are protected against the same virus forever. (OK, in reality, if a virus doesn’t show up for many generations, the microbes can afford to lose their “memory” of it to mutations. But provided that the virus is around and exerting a selection pressure, the immunity remains.)

The CRISPR system is fascinating for more than one reason. First, it’s essentially an adaptive immune system in some of the simplest organisms alive today. Adaptive immune systems are uncommon even in multicellular creatures. They are known from two groups of vertebrates (jawless and jawed vertebrates probably evolved them independently) and possibly brown algae (Zambounis et al., 2012).*

Second, it’s eerily “Lamarckian”. Microbes with CRISPR can, in a way, “direct” their own evolution. They are acquiring new adaptations over their lifetimes, and passing these on to their descendants. And they aren’t doing it in the way most inheritance of acquired traits works – instead of tagging their DNA with signals that remain highly flexible in the long term, they are actually permanently incorporating the new information into their genomes.

Parasites are notorious for evolving a way around anything a host can throw at them, though, and bacteriophages are no exception. A new study not-quite-published in Nature (Bondy-Denomy et al., 2012) reports viral genes that enable the viruses to break through CRISPR-based defences. They experimented on cultures of a strain of the bacterium Pseudomonas aeruginosa. Their bacteria went into the experiment infected with a variety of viruses, but the viruses were kept in their dormant form that doesn’t hurt the host cell. When these bacteria were exposed to active viruses, most of them could defend themselves just fine, while genetically engineered bacteria who lack a CRISPR system die like flies from the exact same pathogens.

However, a few of the bacteria were unable to resist the assault despite a fully intact immune system. Since the only difference between the different bacterial samples was the kind of dormant virus they hosted, the reason had to be something related to the viruses. A look at the viral genomes turned up several genes that almost literally held smoking guns. When added to CRISPR-sensitive viruses, they enabled them to kill bacteria they couldn’t otherwise harm. When deleted from their source viruses, they prevented the viruses from killing CRISPR-enabled but not CRISPR-disabled bacteria. A series of such experiments demonstrated that these “anti-CRISPR” genes helped viruses evade the immune systems of their hosts. Interestingly, they didn’t work against the closely related CRISPR system of E. coli – the cheat codes, so to speak, were highly specific to the game.

A really interesting thing about the CRISPR resistance genes is their possible origin. It seems Pseudomonas may have wrought its own doom in this case! When the researchers searched for sequences similar to the resistance genes, some of the sequences they caught were actually from other strains of Pseudomonas itself. A possible explanation is this: since CRISPR-based immunity can work on any foreign DNA, the original benefit of some anti-CRISPR genes may have been to prevent the destruction of bacterial genes after being passed to other bacteria. Then the viruses somehow got their hands on the sequences, hacking poor microbes with their own code.

Evolutionary arms races are such weird and crazy and fascinating things!

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*I can’t really figure out whether some RNA interference based viral defence in plants counts. I’d have to go fact-hunting to find out if any of the interfering RNAs originate in a similar way to CRISPR spacers. The whole adaptive immunity angle is a digression, though, so I’m lazy enough to leave that up in the air.

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References:

Bondy-Denomy J et al. (2012) Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature advance online publication, available 16/12/2012, doi: 10.1038/nature11723

Zambounis A et al. (2012) Highly dynamic exon shuffling in candidate pathogen receptors… what if brown algae were capable of adaptive immunity? Molecular Biology and Evolution 29:1263-1276

So… much… STUFF!

Gods, this is what I’m faced with all the time. Someone needs to tell me how proper science bloggers pick articles to discuss, because I just get my RSS alerts, start squeeing, and end up not writing about anything because damn, I WANT TO WRITE ABOUT EVERYTHING!

I give up. I’ll just dump all the cool stuff that’s accumulated on my desktop and bookmark bar here and return to lengthy meandering whenever I don’t feel like I’ve been caught in a bloody tornado 😉

So, here is some Cool Stuff…

(1) A group measured the rate of DNA decay in 158 moa bones of known age from three sites. Really cool stuff, to go out and directly measure how ancient DNA disappears from dead things under more or less identical conditions. The unsurprising result is that DNA decays exponentially, a bit like radioactive material. This suggests that the main cause of the decay is random breaking of the strands. The surprising bit is that this happens much more slowly than previously estimated, suggesting that in ideal (read: frozen) conditions, it might be worth looking for preserved DNA in samples as old as a million years.

(On a side note, if you ever get a chance to see a talk by Eske Willerslev, one of the authors and a leading expert on ancient DNA, don’t miss it. The man is absolutely hilarious.)

– Allentoft ME et al. (2012) The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1745

(2) The beaks of the finches, or mixing and matching developmental recipes. This study examines the genetic basis of beak shape in three little birds closely related to Darwin’s famous finches. The three finches, just like Darwin’s, share the same basic beak shape, only bigger or smaller. However, there seem to be two distinct developmental programs at work, using different genes and parts of the skeleton to orchestrate beak development. One of the three newly investigated species (the one most closely related to Darwin’s finches) apparently uses the same developmental program as its more famous relatives, even though its beak is shaped more like the other two birds studied here. I told you – genetics, development and homology are complicated 😉

– Mallarino R et al. (2012) Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. PNAS 109:16222–16227

(3) Armoured fossil links worm-like molluscs to chitons. There’s a little-known group (or groups) of molluscs called aplacophorans that have only a coat of tiny spicules instead of shells and look more like worms than “proper” molluscs. Exactly where they fit into our picture of mollusc evolution has been controversial to say the least – they could represent an old lineage separate from other molluscs, they could be related to cephalopods, they could be related to chitons, they could be one group or they could be two lineages in completely different places on the tree… Well, a new fossil named Kulindroplax seems to argue for the chiton connection: the animal has the characteristic armour plates of a chiton on an aplacophoran-like body. Similar creatures have been discovered before, but this guy with its detailed 3D preservation provides the clearest evidence of the link so far.

– Sutton MD et al. (2012) A Silurian armoured aplacophoran and implications for molluscan phylogeny. Nature 490:94-97

(4) More cool fossils – this time straight from my beloved Cambrian. Nereocaris, a newly described Burgess Shale arthropod, suggests to its discoverers that the earliest arthropods weren’t predators prowling the seafloor, but swimmers who might have been filter feeders and certainly weren’t predators. The animal has a bivalved shell around its front end, similar to many other Cambrian swimming arthropods, and a long abdomen with paddles at the end. It bears the arthropod hallmark of a hardened and jointed exoskeleton, but it lacks specialised limbs such as antennae or mouthparts. In a cladistic analysis of arthropods and their nearest relatives, the new species comes out on the first branch within true arthropods, and the next few branches as we move towards living arthropods all contain similar shelled, swimming creatures. Since the non-arthropods closest to the real thing (i.e. anomalocaridids) were also fin-tailed swimmers, this arrangement makes the transition between them and true arthropods smoother than previously thought. It also suggests that the hard exoskeleton so characteristic of arthropods originally functioned in swimming – perhaps as an anchor for swimming muscles.

– Legg DA et al. (2012) Cambrian bivalved arthropod reveals origin of arthrodization. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1958

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And … there was also

… but it’s almost bedtime, and if I wanted to summarise every one of those, I’d be here all weekend 😦

See, this is why being a science nerd today is both amazing and frustrating. There’s just so. Much. Stuff.

The importance of minding your own business

One of the defining characteristics of life is responding to stuff that the environment throws at it. At the level of cells, such responses are often accomplished by what we call signalling pathways. These are chains of interacting proteins that detect a stimulus (chemicals, voltage differences, pressure, light, etc.) on one end, and affect gene regulation or modify the activity of cellular components on the other end. One of the most common way of passing a message from one protein to another is phosphorylation – an enzyme called a kinase attaches phosphate groups to another protein, changing its behaviour. Kinases that phosphorylate proteins are unsurprisingly called protein kinases. (Their families are named after their favourite amino acid to phosphorylate, so we have tyrosine kinases, histidine kinases, etc.)

There are shitloads of protein kinasess. Legend has it that the acronym JAK, which officially refers to the “two-faced” Janus kinases, originally stood for “Just Another Kinase”. (I guess “Just Another Damned Kinase” didn’t abbreviate so well.) Every cell encounters many different stimuli, each of which may require a different response, and a diversity of signalling pathways can provide a more sophisticated ability to handle all conceivable circumstances. And sometimes, it’s best if such pathways keep to themselves.

Capra et al. (2012) investigate a curious property of a simple signalling pathway in bacteria. This pathway reacts to a shortage of phosphate, and consists only of the histidine kinase PhoR, and the regulatory protein it phosphorylates (PhoB). (Presumably there is still enough phosphate for the enzyme to work when the reaction kicks in…) The PhoR-PhoB pathway is found in all sorts of bacteria. In each major group, the handful of amino acids that determine the specificity of the interaction are strongly conserved. However, these “specificity residues” sometimes differ markedly between groups. Their conservation within groups suggests that changing them has dire consequences. So how and, most importantly, why were they changed anyway?

The study focused on three groups of bacteria: the alpha, beta and gamma classes of proteobacteria, which include familiar bugs like E. coli. In fact, E. coli (a gamma-proteobacterium) was one of the two main experimental species, the other one being the alpha-proteobacterium Caulobacter crescentus. The alpha bugs have an odd set of PhoR specificity residues compared to other proteobacteria, and the researchers hypothesised that this isn’t accidental. Instead, they thought, it might prevent PhoR from meddling with another signalling pathway that gamma-proteobacteria like E. coli lack.

The differences certainly aren’t without consequence. PhoR from E. coli can barely phosphorylate PhoB from alpha-proteobacteria, while it works quite happily on the same protein from other gamma-proteobacteria. It also does reasonably well on PhoB from the beta class, in accordance with the greater similarity of their specificity residues. C. crescentus PhoR only really works on PhoB from its own class.

How about that hypothesised other pathway? Well, when E. coli and C. crescentus PhoR are tested on the regulatory proteins from all similar pathways in C. crescentus, one particular molecule stands out. NtrX is the member of a pathway that has been duplicated in alpha- but not gamma-proteobacteria – and E. coli PhoR phosphorylates it! Is this duplication the reason why PhoR took a strange direction in this class of bacteria?

Multiple lines of evidence indicate that the researchers’ hunch was right. Replacing just one of the three altered specificity residues in C. crescentus PhoR to match the sequence in the other classes causes it to start interacting with NtrX at the expense of its normal function. C. crescentus with such “gamma-like” PhoR grows just as lousily in a  phosphate-poor environment as C. crescentus with no PhoR at all, but only if NtrX is also present – delete the ntrx gene from the genome, and the disadvantage almost completely disappears. (NtrX isn’t disposable, though – under normal circumstances, it’s NtrX-deficient bacteria who perform badly.) A gamma-like PhoR can still interact normally with its correct target*, but it’ll simply ignore poor PhoB when NtrX is also around.

[*Which suggests to me that more than those few amino acids are involved in the PhoR-PhoB interaction, since a C. crescentus PhoR with specificity residues completely identical to those of E. coli still phosphorylates C. crescentus PhoB much better than PhoR from E. coli. However, those three do seem to be the main culprits in the NtrX mix-up.]

(In an interesting twist, it turns out that beta-proteobacteria also possess the NtrX pathway, but they tweaked NtrX instead of PhoR. The result is the same – each protein minds its own business, peace and prosperity and mad procreation ensue.)

The authors hypothesise that the Ntr pathways must have duplicated and diverged at a time when phosphate limitation didn’t come up often, given how much of a nuisance NtrX becomes to old-fashioned PhoR when phosphate is scarce. When phosphate did become a problem, the bugs were stuck with an already established NtrX pathway that they couldn’t just boot out of their genomes. Under those circumstances, any mutation getting NtrX out of PhoR’s way would have been the definition of beneficial.

Avoiding crosstalk seems to be a general feature of this kind of pathway: when you compare the specificity residues of all the signalling kinases and kinase targets from the same kind of bacterium, it’s as though they’re all doing their darnedest to be as different as possible. Capra et al. note that signalling pathways relying on a small set of amino acids to ensure specificity are very common in all life forms. They also often proliferate by gene duplication, which would make the crosstalk-avoidance issue a huge force in protein evolution. Good thing that so few mutations are needed, then – where would the complexity of the living world be if duplicated pathways all died, stuck between being redundant and screwing the organism?

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Reference:

Capra EJ et al. (2012) Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families. Cell 150:222-232

An ode to sponges, skeletons and bacteria

Sponges are not what you’d normally think of as “exciting” animals. They are simple creatures that spend the entirety of their adult lives sitting around, patiently sifting immense amounts of water for microscopic food. The closest most of them get to “doing” anything is popping out a few babies every now and then. (Exception: deadly shrimp-killin’ predators :o) However, these (mostly) placid filter feeders have a lot to offer once we move past the usual coolness filters that make our inner ten-year-old a Velociraptor fan*.

I’ve been getting quite fond of sponges recently. It’s mostly a byproduct of the reading I do for my work, which partly concerns the mineralised hard parts of animals. All sponges have skeletons, and the majority of them make hard(ish) skeletons from one of two minerals: either amorphous silica (think glass) or calcium carbonate (think chalk, limestone, clam shell, etc.) (The rest, including bath sponges, use proteins.) Siliceous sponges in the class Hexactinellida (= glass sponges proper) can have beautiful, intricate skeletons like this one from a Venus’s flower basket (Euplectella sp. by NEON ja, Wikimedia Commons):

They are not only gorgeous, but, at least in some cases, also insanely strong and bendy – nature’s fibreglass fishing rods, if you like. See this photo from sponge guru Werner Müller’s group for a demonstration. That glass rod is the skeleton of Monorhaphis chuni, a deep-sea glass sponge that anchors itself with the largest known single structure made of silica in the living world. This “giant spicule” can be up to 3 m long, and flexible enough to bend around in a circle (Levi et al., 1989).

Some sponges have both glassy and calcareous (or “chalky”, if you like) skeletons. And such sponges are giving me all kinds of squee moments lately. Something I’ve only learned recently is that sponges often live in close association with a variety of bacteria. Now it turns out that these symbiotic bacteria contribute to their skeleton-building abilities!

Last year, Dan Jackson and his team published evidence that a sponge species stole a gene it uses to make its calcareous skeleton from a bacterium (Jackson et al., 2011). The gene in question occurs only in bacteria – and sponges. While the sponge species used in the study does harbour bacteria in the cells that produce the calcareous portion of its skeleton, multiple lines of evidence indicate that the gene in question sits in its own genome, and has done so for a long time. It is only active in the skeleton-forming cells, and its protein product is present in bits of skeleton isolated from the animal, suggesting that it does in fact function in building the skeleton. (As of that study, its exact role is still unknown.)

(Above: Astrosclera willeyana, coralline sponge and convicted gene thief. The living animal forms a crust over an ever-growing bulk of dead skeleton. From Jackson et al. [2011])

Most recently, another “spongy” research team found that members of a different sponge lineage have the actual bacteria in their cells make their skeletons for them. Uriz et al. (2012) examined three species of crater sponges, belonging to the “siliceous” sponge genus Hemimycale. In certain cells of the animals, they saw tiny round objects that molecular genetic tests revealed to be bacteria. The bacterial cells were surrounded by a coat of varying thickness that, when the researchers probed its elemental composition using X-rays, proved to be made of calcium carbonate. According to their observations, the bacteria live and divide inside membrane-enclosed vacuoles. They accumulate calcareous material as they mature, and finally the host cell spits them out to form a mineral crust around the animal. (Below: colonies of Hemimycale columella, one of the three species used in the study, from the Encyclopedia of Marine Life of Britain and Ireland via Encyclopedia of Life)

The bacteria look like they’ve had a long-standing partnership with their host sponges. They were abundant in all examined individuals of all three species. Unlike free-living bacteria, they appear to lack cell walls. They are also inherited by baby sponges. Mother Hemimycale sponges nurture their embryos in their bodies (apparently this is common among sponges). Sponges provide their embryos with so-called nurse cells, which, in the case of these species, contain some mineral-making bacteria. The young sponge eventually eats the nurse cells, thereby acquiring the bacteria. By the time it becomes independent and settles on a comfortable rock, its body is littered with tiny mineral spheres made by its inherited symbionts.

On closer examination, it seems that Hemimycale is far from the only sponge genus to harbour similar hired skeleton-builders. Uriz and colleagues tell us that they have found previously overlooked evidence of such “calcibacteria” in several other sponges – one of which is only distantly related to Hemimycale. Could calcibacteria be ancient partners of these animals, inherited by many different sponges from a distant common ancestor? Could bacteria even hold the key to the origin of calcareous animal skeletons?

(FWIW, I don’t really buy the second idea. As far as I know, all non-sponge animals that have been investigated make their skeletons with their own genes – nothing suspiciously bacterial-like the way Jackson et al.‘s spherulin is. [Caveat: there remain plenty of groups that haven’t been investigated in sufficient molecular detail.] However, the idea that sponges as a whole may have acquired their calcareous skeletons this way is fascinating. Incidentally, though the ID isn’t 100% certain yet, the calcibacteria may belong to the same bacterial class as mitochondria and these insidious bastards. Do alpha-proteobacteria have a special knack for endosymbiosis?)

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*Not to say Velociraptor isn’t cool, but being a vicious toothed, raptor-clawed killer bird is, well, not the only road to coolness 😛

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ETA: 42nd post, yay! (Also yay: random Hitchhiker’s Guide reference in completely unrelated post :D)

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References:

Jackson DJ et al. (2011) A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy. BMC Evolutionary Biology 11:238

Levi C et al. (1989) A remarkably strong natural glassy rod: the anchoring spicule of theMonorhaphis sponge. Journal of Materials Science Letters 8:337-339

Uriz MJ et al. (2012) Endosymbiotic calcifying bacteria: a new cue to the origin of calcification in Metazoa? Evolution early online view, doi: 10.1111/j.1558-5646.2012.01676.x

A virus with half a wing

Richard Lenski’s team is one of my favourite research groups in the whole world. If the long-term evolution experiment with E. coli was the only thing they ever did, they would already have earned my everlasting admiration. But they do other fascinating evolution stuff as well. In their brand new study in Science (Meyer et al., 2012), they explore the evolution of a novelty – in real time, at single nucleotide resolution.

For their experiments, they used a pair of old enemies: the common gut bacterium and standard lab microbe E. coli, and one of its viruses, the lambda phage. Phages (or bacteriophages, literally “bacterium eaters”) are viruses that infect bacteria. They are also some of mother nature’s funkiest-looking children. Below is an example, because if you haven’t seen one of them, you really should. I borrowed this electron micrograph of phage T4 from GiantMicrobes, where you can get a cute plushie version 😛

Phages work by latching onto specific proteins in the cell membrane of the bacterium, and literally injecting their DNA into the cell, where it can start wreaking havoc and making more viruses. Meyer et al.‘s phage strain was specialised to use an E. coli protein called LamB for attachment.

The team took E. coli which (mostly) couldn’t produce LamB because one of the lamB gene’s regulators had been knocked out. Their virus normally couldn’t infect these bacteria, but a few of the bacteria managed to switch lamB on anyway, so the viruses could vegetate along in their cultures at low numbers. Perfect setup for adaptation!

Meyer and colleagues performed a lot of experiments, and I don’t want to go into too much detail about them (hey, is that me trying not to be verbose???). Here are some of their intriguing results:

First, the phages adapted to their LamB-deficient hosts. They did so very “quickly” in terms of what we usually think of as evolutionary time scales (naturally, “evolutionary time scales” mean something different for organisms with life cycles measurable in minutes). Mutations in the gene coding for their J protein (the one they use to attach to LamB) enabled them to use another bacterial protein instead. Not all experimental populations evolved this ability, but those that did succeeded in less than 2 weeks on average.

The new protein target, OmpF, is quite similar to LamB, which might explain how the viruses evolved the ability to use it so quickly. But more interesting than the speed is the how of their innovation. Amazingly, all OmpF-compatible viruses shared two specific mutations. Another mutation always occurred in the same codon, that is, it affected the same amino acid in the J protein. A fourth mutation invariably occurred in a short region near the other three. Altogether, these four mutations allowed the virus to use OmpF. Plainly, we are dealing with more than mere convergent evolution here. Often, many different mutations can achieve the same thing (see e.g. Eizirik et al., 2003), but in this case, a very specific set of them appeared necessary. I’ll briefly revisit this point later, but first we have another fascinating result to discuss!

By comparing dozens of viruses that did and didn’t evolve OmpF compatibility, the researchers determined that all four mutations were necessary for the new ability. Three were not enough; there were many viral strains with three of the four mutations that couldn’t do anything with LamB-deficient bacteria. On the surface, this sounds almost like something Michael Behe would say (see Behe and Snokes, 2004), except the requirement for more than one mutation clearly didn’t prevent innovation here. Given the distribution of J mutations, it’s also likely that they were shaped by natural selection, even in virus populations that didn’t evolve OmpF-compatibility. So what did the first three mutations do? What use was, as it were, half a new J protein?

The answer would delight the late Stephen Jay Gould: the new function was a blatant example of exaptation. Exaptations are traits that originally had one function, but were later co-opted for another. While three mutations predisposed the J gene to OmpF-compatibility, they also improved its ability to bind its original target. Thus, there was a selective advantage right from the first mutation. And, in essence, this is what we see over and over again when we look at novelties. Fish walk underwater, non-flying dinosaurs cover their eggs with feathered arms, and none of them have the first clue that their properties would become success stories for completely different reasons.

In the paper, there is a bit of discussion on co-evolution and how certain mutations in the bacteria influenced the viruses’ ability to adapt to OmpF, but I’d like to go back to the convergence/necessity point instead. I have a few half-formed thoughts here, so don’t expect me to be coherent 😉

We’ve seen cases where the same outcome stems from different causes, like in the cat colour paper cited above. Then there is this new function in a virus that seems to always come from (almost) the same set of mutations. Why? I’m thinking it has to do with (1) the complexity of the system, (2) the type of outcome needed.

Proteins interact with other proteins through very specific interfaces. Sometimes, these interactions can depend on as little as a single amino acid in one of the partners. If you want to change something like that, there is simply little choice in what you can do without screwing everything up. On the other hand, something like coat colour in mammals is controlled by a whole battery of genes, each of which may be amenable to many useful modifications. And when it comes to even more complex traits like flying (qv. aside discussing convergence and vertebrate flight/gliding in the mutations post), the possibilities are almost limitless.

So there’s that, and there is also what you “want” with a trait. There may be more ways to break a gene (e.g. to lose pigmentation) than to increase its activity. When the selectively advantageous outcome is something as specific as a particular protein-protein interaction, the options may be more restricted again. (To top that, the virus has to stick to the bacterium with a very specific part in its structure, or the whole “inject DNA” bit goes the wrong way.) Now that I read what I wrote that sounds like there will be very few “universal laws” of evolutionary novelty (exaptation being one of them?). Hmm…

References

Behe MJ and Snoke DW (2004) Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Science 13:2651-2664

Eizirik E et al. (2003) Molecular genetics and evolution of melanism in the cat family. Current Biology 13:448-453

Meyer JR et al. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335:428-432

Bacteria invented multicellularity – then thought better of it

I get content alerts from a whole host of journals, some specialist publications focusing on my field, some more general. The majority of even the former is stuff I couldn’t care less about, and the ratio of interesting to irrelevant from generalist journals like PNAS or Nature is lower still. Nevertheless, sometimes you stumble on a title that isn’t directly related to your main interests, but still makes the whole rummaging through the Pile of Irrelevance worth it.

This was the case with a paper (Schirrmeister et al., 2011) just published in the online, open-access journal BMC Evolutionary Biology. It’s so fresh that they haven’t even formatted it – the full text is only available as a “provisional” pdf where all the figures are dumped at the back of the file, separated from their captions (why they can’t wait with publication until the damned thing is in readable format escapes me).

The study by Schirrmeister and others deals with an unusual group of bacteria. Cyanobacteria are probably still better known as blue-green algae, even though they have nothing to do with anything else we call an alga (well, in truth they have everything to do with algae, but in a rather more interesting way, as we’ll see below). If I had to pick one group of organisms that had the greatest impact on the history of our planet, cyanobacteria would be it. For more than two billion years, they have contributed huge amounts of biomass to the global carbon cycle. They are solely responsible for the oxygen-rich atmosphere of the earth – and, by extension, for most eukaryotic life and all animals. They are among the distinguished group of bacteria that can fix nitrogen – a vital ingredient of DNA and proteins – straight from the air, making it available for other organisms. Without them, the world would be a vastly different place, and we wouldn’t be possible. As Andrew Knoll puts it in his wonderful book Life on a Young Planet (consider this a recommendation ;)): “animals may be evolution’s icing, but bacteria are the cake”.

Cyanobacteria live everywhere there is light, from hot springs to the ocean to puddles to stone walls (as components of lichens). They also live inside the cells of every single eukaryote capable of photosynthesis: plants, red and green algae, brown algae, diatoms, dinoflagellates, euglenids (and any others I forgot to mention). The chloroplast is a pared down cyanobacterium – a symbiont that has lost most of its genes, but the ones that remain, together with its structure, still tell of its ancestry. Plants owe all their green splendour to these tiny buggers.

Cyanobacteria are not just immensely important, they are also quite unusual among prokaryotes. As the post title implies, they invented multicellularity. Multicellular cyanobacteria display a range of complexity. Some of them are just chains of identical cells. Others, though, have up to three different cell types. Heterocysts, thick-walled cells that ensure the oxygen-free environment that these bacteria require for nitrogen fixation, sit at regular intervals among “normal” cells, and when necessary, the “normal” cells can also differentiate into hardy resting cells that can survive bad times. The most complex cyanobacteria not only have filaments with different cell types, but also introduce branching into these filaments. This is the most complex prokaryotes get.

Filaments of an unbranched, differentiated cyanobacterium. The oversized heterocysts are quite obvious in some of them. Image by Kristian Peters, from Wikimedia Commons.

The new study raises an interesting possibility: that at least the simple form of multicellularity (i.e. undifferentiated filaments) occurred very early in the history of cyanobacteria. According to Schirrmeister et al., the vast majority of modern cyanobacteria descend from multicellular ancestors, even though a great many of them are single-celled today. Even more intriguingly, they find a lineage that might have re-evolved multicellularity after losing it. I don’t pretend to fully understand the methods used to come to these conclusions, but I have to say that it’s built on an impressive dataset – the group selected 58 cyanobacterial species for more detailed study from an original phylogenetic tree built from over a thousand taxa. They then constructed trees of this smaller dataset using two separate methods, and finally, tried to reconstruct the ancestral states at various points in those trees using several different statistical methods again. The analyses all agree: multicellularity is a very ancient trait in cyanobacteria, and it was lost left and right during their three-billion-year history.

These findings go against our ingrained view of evolution as an inexorable march towards increasing complexity. We, mammals, are among the (if not the) most complex organisms the earth has ever produced. We are assemblages of some 200 distinct cell types organised into a finely regulated machinery of a multitude of specialised organs. When we look at the large-scale patterns in the fossil record, we also see that this complexity has accumulated from much simpler beginnings over the aeons. We can be forgiven for thinking, in a characteristically self-centred way, that complexity is where evolution is intrinsically headed. But every now and then, nature reminds us that “more complicated” does not necessarily equal “favoured”.

Parasites are probably best known for their tendency to become simplified – after all, if you are bathed in your host’s digestion products all the time, why waste your energy on growing your own gut? However, simplification is abundant in organisms that make their own living, too. For example, two entire phyla of distinctly unsegmented, baglike worms – spoon worms and peanut worms -, likely came from more sophisticated segmented worms (Struck et al., 2007). Now, cyanobacteria join the club, and new questions surge in their wake. Why did they go back to unicellularity? How difficult is it for them to become multicellular? Such questions, of course, can be asked about any complex trait that followed a similar evolutionary trajectory.

Most intriguingly, these tiny microbes seem to violate another “law” of evolution, known as Dollo’s law: that once lost in a lineage, a complex trait won’t reappear. If the inferences of Schirrmeister et al. are correct, then either simple multicellularity isn’t such a big deal at all for these bacteria, or Dollo’s law isn’t as much of a law as we thought.

(Actually, the latter is probably the case however the history of cyanobacteria turns out. Dollo’s law has been questioned by others, and it was recently dealt a spectacular blow by a frog that almost certainly re-evolved teeth in its lower jaw (Wiens, 2011) after at least 200 million years of not having them.)

Evolution is a fascinating story. As the example of cyanobacterial multicellularity suggests, it can also be as complex as any good novel. I for one think this makes for a much more interesting and fulfilling narrative than simplistic listings of “what’s new” through the ages.

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References:

Schirrmeister BE, Antonelli A and Bagheri HC (2011) The origin of multicellularity in cyanobacteria. BMC Evol Biol 11:45

Struck TH et al. (2007) Annelid phylogeny and the status of Sipuncula and Echiura. BMC Evol Biol 7:57

Wiens JJ (2011) Re-evolution of lost mandibular teeth in frogs after more than 200 million years, and re-evaluation of Dollo’s Law. Evolution advance online publication, DOI: 10.1111/j.1558-5646.2011.01221.x