Blogging will be slow the next few weeks, as I’m currently in the process of writing up my Master’s thesis, preparing the final presentation and generally finishing up the (last) internship of my MSc programme. After everything is over, I can hopefully call myself a Master of Science. It’s a strange feeling that 5 years of following courses, taking exams, giving presentations and doing experiments will finally culminate into this single degree.
A bioluminescent pyrosome
I also can’t help but think of the way the gentleman scientists of the Romantic and Victorian era obtained their knowledge of the natural world by travelling the seas and carefully observing this planet and the plants and creatures that live on it. Wallace did it. Von Humboldt did it. Darwin did it. And Huxley did it. The following entry in Huxley’s (aged 24) diary is enough to make anyone jealous:
I have just watched the moon set in all her glory, and looked at those lesser moons, the beautiful Pyrosoma, shining like white-hot cylinders in the water
~Thomas Huxley, Diary of the Voyage of H.M.S. Rattlesnake (1849)
With a few clicks, I can find out more about Pyrosoma than Huxley could dream of. I just found out that Pyrosoma lack any kind of nerve system, but instead communicate via the bioluminescence that Huxley admired so much. I can tell you that the Pyrosoma are like glowing colonial flagships, housing thousands of individual zooids. I now know that while they look like jellyfish, they are actually pretty closely related to us vertebrates, being urochordates.
But still, part of me would rather have stood on that deck in 1849, instead of sitting and procrastinating in front of my laptop in 2010.
finishing up my (last) internship of my MSc programme,
News sites left and right are picking up a story that “Scientists solved the chicken or egg problem”. Google News aggregated 164 news articles at the time of writing, with more being added every minute. The typical introduction runs like this:
It is the age-old question that has stumped the finest minds for thousands of years. But scientists claim to have finally discovered the answer to the conundrum of what came first – the chicken or the egg? ~Daily Express
Humanity would be in trouble indeed if its ‘finest minds’ are troubled by trivial questions like this! The articles go on to vaguely describe a particular protein that is involved in egg shell formation. While this is certainly interesting, it’s got little to do with chicken evolution or the famous chicken-or-egg ‘problem’. I tracked down the original publication and first online coverage to find out what went wrong here.
The 'who came first' question is trivial at best.
The original paper appeared over a month ago in a chemical journal of the German Chemical Society. It’s a nice study that describes how the carbon carbonate crystals that make up egg shells are formed. The British researched applied molecular modeling to calcium carbonate crystallization in the presence chicken protein ovocleidin-17 (OC-17).
Normally, small amorphous nanoparticles of calcium carbonate molecules don’t crystallize well because the energy barrier for the transition to the more stable crystalline phase is large. However, when OC-17 binds and coordinates the calcium carbonate particles with its arginine residues (described as a ‘clamp’), the energy barrier largely disappears and the calcium carbonate happily crystallizes. When the crystallizing particle starts growing, OC-17 detaches again. The whole mechanism Freeman and colleagues propose really is quite nice.
Ovocleidin-17 coordinates the carbon carbonate particles with its argenine residues, inducing crystallization.
The first online appearance of the story is in this press release of the University of Warwick. I have to admit, the press release really does cover the research pretty well. Of course it ends with some vague promises for crystallization and material science, but otherwise it is a fairly balanced piece. To spice up the article, the press writer decides to include an innocent reference to the famous ‘chicken or egg’ riddle:
The work may also give a partial answer to the age old question “what came first the chicken or the egg?” The answer to the question in this context is “chicken” or – at least a particular chicken protein.
~Warwick University press release
The anonymous writer is careful enough (“partial answer”, “in this context”), but merely being careful is never enough on the internet… The yolk really hits the fan when mainstream news stories pick up on this press release, with metro being one of the main champions of misinterpretation. The following quote from first author Colin Freeman doesn’t help much:
‘It had long been suspected that the egg came first but now we have the scientific proof that shows that in fact the chicken came first,’ said Dr Colin Freeman, from Sheffield University, who worked with counterparts at Warwick University.
~Metro
After the Metro story launched, other mainstream news sites jumped on the bandwagon for a ride. It’s funny and sad to see the whole story turn into a game of Chinese Whispers. ‘Ovocleidin-17′ becomes ‘vocledidin-17′ on Fox News. On various news sites, the study of OC-17 gets reduced to a single sentence. The resulting article doesn’t make sense any more and has become confusing as hell.
Luckily, many readers are smarter than the science ‘journalists’ that have mindlessly copied and pasted this story:
What a silly article. This finding does not “prove” that the chicken came first. After all, if the first chicken did not come from an egg, it was not a chicken. All this really says is that a protein was identified which controls eggshell formation.
… What overblown sensationalist reporting…
~Gabriel on Metro
I didn’t exactly hold mainstream science journalism in high esteem, but I’m amazed that science journalists continue ‘covering’ science stories in this way, even when readers are calling them out. While the trouble may have started with a misleading introduction and a quirky quote, it is the journalist’s responsibility to check facts and put a story into a context. Coverage like this does more harm than good for the public image of science reporting and scientists themselves:
Another brilliant revelation from the British scientific community, but could the tens of millions of pounds of taxpayers’ money that they receive in research grants not be used to discover something of value like the discovery of a new source of cheap, clean energy!
~David, on Metro
Luckily we’ve still got Wikipedia to guide us when we’re misguided and confused:
Wikipedia entry for "Chicken or the Egg"
Oh, wait a minute…
Freeman, C., Harding, J., Quigley, D., & Rodger, P. (2010). Structural Control of Crystal Nuclei by an Eggshell Protein Angewandte Chemie International Edition, 49 (30), 5135-5137 DOI: 10.1002/anie.201000679
You might not think much of sponges. Maybe you feel that they’re only good for rubbing your back and cleaning your kitchen sink. While you’re absolutely right that sponges have to be admired for their absorbing qualities, they have much more to offer this world. Like on the front of early animal evolution: new research by a Croatian team of scientists shows that these simple creatures harbour a genomic complexity that matches our own!
Sponges really are pretty cool animals. As an example, Henry van Peters Wilson discovered the regenerative abilities of sponges in 1907: after putting a living sponge through a sieve, fragmenting its cells in this way, he saw that the remaining clumps of cells found each other again to form what he called ‘plasmodial masses’. After a while, complete sponges emerged again from these ‘masses’!
This remarkable regenerative flexibility might partly reflect the transition that their ancestors underwent from a colonial to a multicellular species (scientists believe sponges evolved from colonies of protozoans much like Monosiga brevicollis). Sponges can lay claim to being the first animals on this planet, and the common ancestor of all animals might very well have been a very sponge-like critter.
Spongia officinalis, or "kitchen sponge". It is dark grey because it is alive, unlike the dried out yellow one in your bathtub. Source.
Sponges are morphologically not very complex. They depend on the flow of water to obtain food and oxygen and remove their waste products. Their porous body structure and skeleton are built to optimize this flow of water, making it flow through all interconnected chambers. Sponges have a number of different cell types, with some that can generate the water flow with their beating flagella, some that can contract and transmit signals like muscle cells and others that maintain and repair the sponge ‘skeleton’.
Such a simple animal must have a pretty simple genome right? Not exactly. Matija Harcet and colleagues sequenced a large set of expressed genes from two different sponges and compared them to their homologs from sea anemone , sea squirt , nematode , fruit fly, sea urchin and human. As you can see in the phylogenetic tree below, the sponges (porifera) occupy a basal position on the tree of metazoans. Consider the surprise when most sponge gene transcripts mapped back to the human and sea anemone proteomes, whereas nematodes and fruit flies ranked the lowest on the list!
Phylogenetic relationships between sponges (porifera) and other animals. We humans are hiding within "Chordata", sea squirts within "Tunicata" and sea urchins in "Echinodermata".
Moreover, the sponge transcripts not only matched the most genes in sea anemones and humans, the protein sequences were also much more similar to human genes than those of other species. You can see this for yourself in the beautiful figure below. Every dot is a transcript that is placed closest to the species it is most similar to. The sponge transcripts most often fall in the human or sea anemone (N. vectensis) quadrants.
A possible explanation for this observation could be that genes have been evolving slowly in both sponges and humans, whereas the proteins of nematodes and drosophila have been evolving in overdrive. Since these species have much shorter generation times and larger population sizes, they can acquire mutations at a much higher rate, speeding up the sequence evolution of their genes.
Each dot is an EST plotted at the appropriate relative sequence distance from the other species.
The team also compared the sponge gene repertoire to that of our closest unicellular nephew: the Monosiga brevicollis that was mentioned before. They found more than a thousand genes which were unique to sponges, of which most are predicted to be involved in signalling pathways and cel adhesion processes. This would mean that most gene expansions and genomic innovations that are found in animals today, were already present in the Urmetazoan ancestor of all animals.
Whatever in happened in that great-great grandmother of animals, it was enough to spawn the whole breadth of animals of the Cambrian explosion and those that live today. Sometimes, simple appearances hold complex and fascinating stories. Not bad, for a ‘simple’ sponge!
1.Wilson, H. (1907). On some phenomena of coalescence and regeneration in sponges Journal of Experimental Zoology, 5 (2), 245-258 DOI: 10.1002/jez.1400050204 2.Matija Harcet, Masa Roller, Helena Cetkovic, Drago Perina, Matthias Wiens, Werner E.G. Müller, and Kristian Vlahovicek (2010). Demosponge EST sequencing reveals a complex genetic toolkit of the simplest metazoans Molecular Biology and Evolution : 10.1093/molbev/msq174
For those of you unfamiliar with the concept of a blog carnival: a carnival is like a monthly digest of the blogosphere concerning a particular subject. Any blogger can submit their blogposts on the subject of molecular or cellular biology to the carnival hosts. The first Monday of every month, one of the hosts will shortly describe and link to the posts that have been submitted that month.
If you’ve written a blogpost on the subject of molecular or cellular biology, you’re very welcome to submit your posts to the blog carnival online here. From the Carnival description:
This carnival focuses on cellular and molecular biology in different systems: the discussion of peer-review articles, techniques, book reviews and related topics, are all welcomed. Specific areas of interest include, but are not limited to: structure and function of proteins, nucleic acids and other macromolecules, gene expression and its regulation, signal transduction, apoptosis, developmental biology, cell cycle and cell growth, microbiology, biochemistry, structural biology, membrane dynamics and many others. Systems and synthetic biology-related posts are also welcomed.
A blog carnival is a great way of exposing a larger and interested audience to your writing, so spread the word via twitter, e-mails, friendfeed etcetera. The first carnival will be published on the second of August, so waste no time submitting your blogposts! We look forward to receiving your contributions!
In my high school text books, bacteria were primarily defined in terms of what they were not. “Bacteria don’t have a nucleus”, “bacteria don’t have mitochondria”, “bacteria are not capable of complex membrane trafficking” and so on. But such boundaries seem to blur as more and more “eukaryote specific” properties pop up in some corners of the prokaryotic world, with bacterial endocytosis being the latest discovery. The simple finding that some bacteria can ‘eat’ the same way as your and my cells do, could have huge implications for our understanding of the evolution of eukaryotes.
To understand what is so special about endocytosis in bacteria, we’ll first have to take a look at what bacteria normally do and don’t do. If a bacterium wants to take up particles from its surroundings, it does so in non-specific ways. Small molecules or peptides can be taken up passively via channels in the membrane, or actively via importing ‘pumps’. Normal proteins are far too big to be taken up in this way, so the only way bacteria can gobble up a protein is if it’s completely smashed to bits (by proteases for example).
Eukaryotes have more sophisticated importing mechanisms, allowing them to import molecules as large as entire proteins. When eukaryotic receptors sense a protein the cell wants to import, Part of its cell wall invaginates as membrane coat proteins line the newly formed pit. The invagination gets deeper and deeper until the membrane closes and an internal vessicle is formed. This vesicle now contains part of the extracellular fluid and any (macro)molecules that where floating around at the time. The vesicle can now be internalized for further processing in the endosomes. The entire process is known as endocytosis, which you can see beautifully animated using electron microscropy pictures in the video below.
A while ago I wrote a guest post on Lab Rat’s blog on the discovery of typical eukaryotic membrane coat proteins in some bacteria. This finding of compartments and membrane coat proteins in the bacterial branch of Planctomycetes was suspicious of course: do these bacteria actually use all this machinery for endocytosis? A month ago, the exciting answer was published in PNAS with one of the most simple and elegant experiments I have seen in a long time. To show that the Planctomycete Gemmata obscuriglobus (literally ‘strange ball’) is taking up proteins via endocytosis, Lonhienne and colleagues incubated the bacteria with green fluorescent protein. Within 5 minutes of incubation the cells were glowing like christmas trees, proving that the bacteria had taken up the complete protein! A normal bacterium would cleave the GFP to bits and pieces, and import the remaining peptides into the cell. There’s no way the GFP would still be fluorescent if Gemmata had taken up the GFP in this way. In other words, Gemmata carefully took in the light bulbs it found on its doorstep, whereas other bacteria would first smash them before dragging in the pieces.
When incubated together with fluorescent proteins (GFP), Gemmata obsuriglobus happily gobbled it up and started glowing!
The next step was looking where the fluorescent proteins ended up. In eukaryotes, a specific organelle called the endosome is the first stop for endocytosed proteins. From there it is decided whether the protein will be degraded, returned to the membrane or passed on for further processing in the Golgi apparatus. The team labeled the GFP proteins in the cell with little gold particles, so that they would show up as distinct black spots on electron microscopy pictures. As you can see in the picture below, most of the proteins are localized in a special compartment: the paryphoplasm, which seems to be an expansion of the bacterial periplasm. The authors discovered that proteins got degraded in this paryphoplasm. Moreover, the team found invaginations and vesicle like structures within the cell that are normally associated with endocytocis. That certainly sounds like complex membrane trafficking to me!
Most GFP proteins (little black dots) localize to the paryphoplasm (marked with "P").
So where does that leave us? Endocytosis, comparmentalization and membrane sorting are no longer exclusive to eukaryotes. This could mean that the entire endocytosis machinery evolved before the latest eukaryotic ancestor did. If this is what happened, we would expect to find the system conserved and retained in a few bacterial phyla, such as the planctomycetes. Bacteria in this phylum have other ‘strange’ and eukaryote-like properties (for a bacterium at least): they reproduce via budding, surround their genetic material with membranes, synthesize sterols and don’t have peptiodglycan in their cell walls. The origin of eukaryotes may well lie with an ancestor that has many of the properties planctomycetes have today. If it’s true that planctomycetes are the prokaryotes most closely related to eukaryotes, Carl Woese’s famous tree of 1991 may need to be redrawn. That would be about time too, because that thing is getting close to ancient for a field that is moving so quickly as evolutionary biology! It’s interesting to note that this scenario of eukaryotic evolution is also in direct conflict with the hypothesis that eukaryotes arose after the endosymbiosis of an archaeon by a bacterium, so expect to see some fireworks as experts debate how to integrate these findings into our current understanding of evolution..
I’m not an expert on eukaryotic evolution, but I can tell you that the discovery of a bacterium with so many distinct ‘eukaryotic’ features will impact on our ideas and views of the history of life on this planet. Before the dust settles, the song “Take it in” by Hot Chip strikes me as wonderfully appropriate:
Lonhienne, T., Sagulenko, E., Webb, R., Lee, K., Franke, J., Devos, D., Nouwens, A., Carroll, B., & Fuerst, J. (2010). Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1001085107
If coral reefs are the rain forests of the tropical oceans, kelp forests are the woodlands of the Northern seas. Kelp is one of the algal species that can survive the harsh conditions of the North Sea that I know and love, together with other hardy seaweeds like bladder wrack. All these seaweeds are part of the larger family of the brown algae, which are generally good at dealing with unfavorable conditions, such as large fluctuations in light, temperature and salinity. The evolutionary past of Brown Algae is particularly interesting, as it is assumed that they arose via the fusion of two eukaryotes (their chloroplasts have four membranes)!
The first brown algal genome sequences will be entered in sequence databases soon, since scientists published the Ectocarpus genome in Nature a few weeks ago. As the first representative of brown algae, Ectocarpus has the honour of joining the ranks of giant pandas and body lice in having its genome sequenced, promising exciting insights in how multicellularity can evolve.
Kelp blowing in the "wind" in Diamond Bay. Kelp forests are one of the most productive ecosystems of temperate and cooler seas. Source: saspotato on Flickr
The genome is of course rich in interesting nuggets of molecular insights into biological observations. For example, brown algae are known to have some strange polysacharides in their cell walls, such as alginates, which give seaweeds their gummy feeling. The genes involved in the biosynthesis of alginates were first described in bacteria, but the brown algal genes have were never identified. Now with the Ectocarpus genome in hand, the researchers still couldn’t find any homologs of the bacterial genes. This probably means that brown algae independently evolved enzymes to synthesize these funny polysacharides. Whatever biological problem arises, evolution will find a (different) way!
The Ectocarpus genome is also rich in genes dedicated to harvesting light in fluctuating conditions, containing 53 light harvesting complex genes. What’s more, the team found an enzyme (DPOR) that can synthesize chlorophyll in dim light or in the dark. The DPOR enzyme cannot be find in many terrestrial plants, and seems to be more commonly found in green algae.
On to the real interesting stuff. Brown algae are one of the few clades that can lay claim to inventing multicellularity. Because contrary to what simple overviews of evolution tell you, the emergence of multicellular life wasn’t a single ‘big leap’ in the evolution of life on earth. ‘Multicellular leaps’ occurred in at least five different branches of the tree of life: the metazoans (animals), fungi, green algae / plants, red algae and brown algae.
The place of brown algae and Ectocarpus within eukaryotes. All five multicellular lineages have been coloured, with brown algae unsurprisingly in brown and us metazoans in funky blue.
In an attempt to explain why certain species became multicellular, the authors analyzed the total gains and losses of gene families in separate lineages. I’m not a big fan of this approach, it reeks a bit of the ‘the deflated ego problem’ where we assume that ‘complexer organisms’ must have more genes than ‘less complex’ lineages. To support their statement that ‘multicellular organisms have lost fewer gene families and evolved more new gene families than unicellular lineages’, they predicted the gains and losses of different gene families in some eukaryotic lineages (below). I am not really convinced: Ectocarpus and Laccaria seem to fall within the range of half of the unicellular lineages analyzed. The authors themselves have to admit that they fail to detect significant trends.
The gains and losses of gene families in different lineages of eukaryotes.
The authors however do find several gene families that could have contributed to developing multicellularity. Of particular interest are the integrins, that are not found in other stramenopile genomes (Oomycetes and Diatoms in the phylogeny above). In animals integrins are vital for ‘sticking’ cells together, so it’s easy to see why they would be important for other multicellular organisms. The team also found many ion channels that are unique to animals, including the IP3 receptor. This receptor plays a central role in the very fast calcium signaling, which animal cells use to quickly react to stimuli (it is used in muscle contraction, for example).
This typical combination of metazoan and algal genes in the Ectocarpus genome reflects its interesting evolutionary past, where two eukaryotes fused to give rise to a successful lineage. Considering the many genes derived from algae , the chimera maybe arose from a photosynthetic algal-like eukaryote and a (heterotrophic?) eukaryote that is closer to the metazoan lineage. Consider the identity crisis the poor guy must have faced! Luckily, by keeping the right sets of genes and ditching the obsolete ones, the brown algae overcame this crisis and blossomed into a rich and diverse branch on the tree of life.
Cock, J., Sterck, L., Rouzé, P., Scornet, D., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J., Badger, J., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Cho, G., Coelho, S., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F., Lang, D., Le Bail, A., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D., Nyvall-Collén, P., Peters, A., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Van de Peer, Y., & Wincker, P. (2010). The Ectocarpus genome and the independent evolution of multicellularity in brown algae Nature, 465 (7298), 617-621 DOI: 10.1038/nature09016
This is a science blog, where I will be writing about interesting papers on evolution in an understandable fashion. I like science that's on the intersection of molecular, evolutionary and computational biology. Leave a comment behind if you're amazed, baffled or offended by what I wrote!
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