Field of Science

My creative contributions to the Festive Tree of Life

Last week I got a thick padded envelope from the Wellcome Trust. My colleagues were a bit surprised... I told them it was a grant, and well it kind of was, only not wads of cash, but lumps of modelling clay!

As part of their Festive Tree of Life project, the Wellcome trust sent out free packs of colourful modelling clay in the run up to the festive season. The idea is that you make science-inspired decorations and either hang them on their physical Christmas tree if you're somewhere in the vicinity, or post them on the Festive Tree of Life Flicker page.

I had a fun afternoon the other day making my decorations. Here they are:



Ribosome, with three tRNAs and EF-Tu. The pink thing is supposed to be mRNA, while the string is the nascent polypeptide chain coming out the exit tunnel... scale is overrated anyway.

The clay started to dry up by the time I got to the ribosome, and got less sticky and more tricky to deal with. After a few hours, the tRNAs fell off, and the subunits have now almost dissociated. All of this in the absence of termination and ribosome recycling factors too!

Happy holidays!

Bacterial genes in eukaryotes - function and phylogeny

There have been a couple of interesting papers recently on those eukaryotic genes that are more closely related to bacterial, than archaeal homologues. Such proteins are often organellar (athough they may be encoded in the nucleus), having entered eukaryotes with the bacterial endosymbiosis event that gave rise to the mitochondrion (or the event that gave rise to the chloroplast in the case of plants).

Giant, glowing mitochondria in the Deutsches Museum, Munich

The first paper, published in GBE, considers humans alone:

The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences.
David Alvarez-Ponce and James O. McInerney

This paper tests whether human genes of different ancestries (bacterial versus archaeal) have different effects on phenotype, essentiality of the gene (as judged by lethality in mice), function, selective constraint, expression and position in protein-protein interaction network (PIN). Proteins were classified as bacteria- or archaea-like based on best hit scores in Blast searches.

They found that human genes of archaeal ancestry, although fewer in number, tend to be have higher and broader expression levels, are more likely to be essential, are involved in core information processes, are under greater selection, and tend to be central in the PIN, as compared with bacteria-like genes.

I don't think they mention whether the archaea-like genes they identified have (more distant) homologues in bacteria too... if they do, then we're likely looking at the characteristics of universal, usually essential, core information processing genes. Whether archaeal-like genes that have been lost in bacteria are just as central in eukaryotes as universal genes, it isn't clear.

It's also not clear just how many of the bacteria-like genes are endosymbiotic in origin. 7,884 human genes were found to be bacteria-like, but the human mitochondrion is predicted to contain only 1000-1500 proteins. Of the remainder, while some are likely to be endosymbiotic in origin, but have acquired non-mitochondrial functions,  an unknown proportion may actually be of archaeal ancestry, but have been lost in archaea, and so are actually nothing to do with mitchondria. As these proteins are not universally essential, it follows that they would have a less central role in the cell... maybe the two gene populations that are considered in this paper are more like essential for life versus non-essential for life.

Anyway, it's a very interesting paper, particularly the finding that archaeal-like genes are less likely to be involved in inherited diseases. It's also surprising just how many genes did not have an identifiable homologue in either bacteria or archaea (58%).

The second paper, published in MBE addresses the evolutionary history of mitochondrial genes from a broad distribution of eukaryotes:

Rooting the eukaryotic tree with mitochondrial and bacterial proteins
Romain Derelle and B. Franz Lang

The idea here is that the endosymbiosis event happened more recently than the divergence of eukaryotes from archaea, and this can be exploited for rooting the eukaryotic tree of life with a less divergent outgroup. Usually eukaryotic phylogenies are made using archaea-like information processing genes, rooted with archaea. However, there is a problem of long branch attraction to the very distant outgroup. This is the phenomenon in molecular phylogenetics where fast evolving, and therefore long branched sequences that should be nested within the tree are pulled down to the base of the tree because of spurious similarities to the outgroup. Using mitochondrial genes to make trees rooted with bacteria theoretically reduces the distance to the outgroup and, therefore, the problem of LBA.

The idea is very neat and I like it in principle. There are a couple of issues though that I think might not help the LBA problem, and in fact might exacerbate the problem.

1. We don't know just how much more recently the mitochondrion was acquired after the divergence of eukaryotes from archaea. Some people might argue that this was the event was involved in the separation of the two lineages.
2. Mitochondrial genes have a faster rate of evolution than their cytoplasmic counterparts. 

Still, its interesting to see the results of rooting the eukaryotic tree in this way. The paper doesn't use best hits as in the above paper, but specifically targets known mitochondrial and mitochondrially targeted genes, such as cytochromes and two of the three universal mitochondrial translational GTPases, mIF2 and mEF-Tu. The third, mEF-G was likely excluded because it does not group with alpha-proteobacteria. Although... come to think of it, I don't see mEF-Tu or mIF2 grouping clearly with alphas in my trees... maybe EF-G was excluded because of its duplication early in eukaryotic evolution... though, mEF-Tu has also been duplicated in its history, and actually mEF-G1 is quite a conservative marker... anyway, this paper isn't about trGTPases specifically so I shouldn't drift off topic.

So, the root. They find the root between monophyletic unikonts (opisthokonts and amoebozoa) and bikonts (other eukaryotes), supporting one of the most popular hypotheses. There seems to good statistical support for this topology using the Bayesian inference method, however, maximum likelihood support is only achieved with much filtering of the dataset. It's an interesting new take on rooting the eukaryotic tree, but not one that will convince everyone.

As is so often the conclusion, we're just going to need more eukaryotic protist genomes!

Alvarez-Ponce D, & McInerney JO (2011). The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome biology and evolution, 3, 782-90 PMID: 21795752 Derelle R, & Lang BF (2011). Rooting the eukaryotic tree with mitochondrial and bacterial proteins. Molecular biology and evolution PMID: 22135192