Going Green

Let’s take a closer look at some of the data patterns that emerged from the recently sequenced sponge genome. We are slowly getting to the point where we can begin to time the origin of complex genetic circuits essential for metazoan life.  For example, consider the figure below.  It represents the core elements of signal transduction pathways involved in cell-cell communication and coordinated growth:

From M Srivastava et al. Nature 466, 720-726 (2010)

Note the components are color-coded according to their distribution on the tree of life.  To help you visualize this, I used the same color-coded circles to identify the nodes below.

Of interest for purposes is that any component coded as green, purple, or red is found in unicellular life forms. And as you can see, the majority of the components are found in single-celled life form (I counted 43 gene products as part of this circuit and of these, 32 are found in unicellular life).  To make the transition from unicellular to animal life, the circuit only had to be tweaked with five components, three of those modulating receptor tyrosine kinase activity.

In other words, this system has long been preadpated to facilitate the emergence of animal life.

Imagine that the vast majority of components were pink.  In that case, if would be very difficult to argue that vertebrate-like life was front-loaded, as the lion’s share of innovations would not trace back to the original state, but would have co-evolved into existence long after along with the appearance of such life-forms.

We can also use the hypothesis of front-loading to make predictions – that more and more of the components colored as blue, yellow, and pink will, with more information, move into the realm of green, purple, and red.  In fact, the inertia from the hypothesis of front-loading would have us expect the circuitry to trend green.

Keep in mind these circuits represent a conservative estimate that is built upon sequence comparisons of a small sample.  But there are two problems with this method. First, our data base of single-celled eukaryotes is quite limited.  As we sequence more of these organisms, we can expect to find more “metazoan-specific” genes.  For example, consider the following research paper:

Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10142-7.

Ancient origin of the integrin-mediated adhesion and signaling machinery.

Sebé-Pedrós A, Roger AJ, Lang FB, King N, Ruiz-Trillo I.

The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi.

So here is another metazoan-specific complex that was recently identified only because someone characterized the genome of the apusozoan protist Amastigomonas sp.  Expect to see more of these findings from various other protozoans.

What’s more, if you look at the author’s figure, they code receptor tyrosine kinases as red, as if they appeared in the last common ancestor of choanoflagellates and animals.  But as we have seen, the tyrosine kinase circuit itself would be coded green.

Second, sequence data are not sensitive enough to rule out homology.  For example, there is the well-known example of the homology between FtsZ and tubulin.  This homology could not be detected by sequence data, but was only detected with biochemical and cell biology data.  As we gather more extensive biochemical and cell bio data about various protozoa, look for the circuits to trend green.

The bottom line is that the older and more extensive the preadaptations, the stronger the nudge signal and thus the potential to frame and guide subsequent evolution.  Of course, no one can say for sure just how strong this signal must be to be effective and just how much direction can be imposed, but it would stand to reason that if more and more components that move toward the green, the stronger the case for front-loading.

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One response to “Going Green

  1. Who said it’s not easy being green?

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