Adherens junctions poised to appear

In the previous posting (which was originally posted over a year ago), I was able to track down some papers which uncovered evidence for the existence of various adherens junctions proteins in unicellular organisms.  Well, a few days ago, I had the time to probe databases with sequence from human genes in search of homologs for adherens junction proteins in unicellular organisms.

Recall the basic components of an adherens junction as seen in the below figure:

As you can see, the cadherin is the membrane protein used to link cells together. The cadherin, in turn, is linked to the cytoskeletal microfilaments through a complex composed of beta-catenin, alpha-catenin, alpha-actinin, and vinculin.

Below is a table that lists what I found.

Front-loading and epithelial tissue

Your body is composed of four basic tissues: epithelial, connective, muscle, and nervous. Epithelial tissue is essentially a sheet of cells that is used to cover structures and line cavities and vessels. For example, your digestive and respiratory tracts are lined with epithelial tissue and the very surface of your skin is epithelial tissue. Furthermore, epithelial tissue is used to form all the glands in your body. Could unicellular creatures encode all, or most, of the machinery that would be needed to form such tissues?

More moonlighting

For years, I have used the hypothesis of front-loading to argue that multifunctional, moonlighting proteins would be expected to exist.  I explained the logic and provided many examples using the ribosome as a candidate of such front-loading.  In fact, as far as I know, I’m the only one to note that the gene for the ribosomal protein s5 also seems to code for a protein that is expressed in the mammalian brain (see here and here).

A fresh new study has just been published that fits seamlessly with the above essays:

Told ya so

The hypothesis of front-loading (or nudging) evolution is both reasonable and plausible and no one has shown otherwise.  In fact, it has become more reasonable and plausible as we have learned more about evolution over the years.  Doubt da bunny?  Consider the abstract for a paper that was published just this year:

Evolution. 2010 May;64(5):1189-201.
The importance of preadapted genomes in the origin of the animal bodyplans and the Cambrian explosion.
Marshall CR, Valentine JW.

The genomes of taxa whose stem lineages branched early in metazoan history, and of allied protistan groups, provide a tantalizing outline of the morphological and genomic changes that accompanied the origin and early diversifications of animals. Genome comparisons show that the early clades increasingly contain genes that mediate development of complex features only seen in later metazoan branches. Peak additions of protein-coding regulatory genes occurred deep in the metazoan tree, evidently within stem groups of metazoans and eumetazoans. However, the bodyplans of these early-branching clades are relatively simple. The existence of major elements of the bilaterian developmental toolkit in these simpler organisms implies that these components evolved for functions other than the production of complex morphology, preadapting the genome for the morphological differentiation that occurred higher in metazoan phylogeny. Stem lineages of the bilaterian phyla apparently required few additional genes beyond their diploblastic ancestors. As disparate bodyplans appeared and diversified during the Cambrian explosion, increasing complexity was accommodated largely through changes in cis-regulatory networks, accompanied by some additional gene novelties. Subsequently, protein-coding genic richness appears to have essentially plateaued. Some genomic evidence suggests that similar stages of genomic evolution may have accompanied the rise of land plants.

It’s Maguk

Ever hear of membrane-associated guanylate kinases?  I’ll let one team of researchers describe them:

Membrane-associated guanylate kinases (MAGUKs) form a family of scaffolding proteins, engaged in the organisation of multiprotein complexes, which are often associated with cellular junctions or signalling complexes, such as the vertebrate tight junction (TJ) or the Drosophila septate junction (SJ) in epithelial cells or the neuromuscular junction (NMJ). Their capacity to serve as a platform for recruiting larger protein assemblies results from the presence of several protein-protein interaction domains: one to three PDZ (PSD-95/Discs large/zonula occludens (ZO)-1)-domains, an SH3-(Src homology-3)-domain and a guanylate kinase (GUK)-domain. Some members additionally contain one or two L27 (Lin-2/Lin-7)-domains in their N-terminus.. This modular structure is ideally suited to recruit a variety of components into a protein complex, the composition of which often depends on the cell type and/or developmental stage. In addition, MAGUK-encoding genes often give rise to more than one isoform by alternative splicing, thus increasing the possibility of multiple interactions, localisations and/or functions. [1]

So we have a modular scaffold protein that associates with protein complexes involved in connecting cells together.  It is “ideally suited to recruit a variety of components into a protein complex” and its structure is poised to be exploited by alternative splicing. The MAGUKs play important regulatory roles in this multicellular context, “where they coordinate multiple binding partners, including cell adhesion molecules and ion channels.” [2]   The MAGUKs thus link these interactions to downstream signaling events.  Not surprisingly, they play an important role in brain function:

In the postsynaptic density of excitatory glutamatergic synapses, membrane associated guanylate kinase (MAGUK) proteins, such as Post-Synaptic Density 95 (PSD-95), organize ionotropic glutamate receptors and their associated signalling proteins regulating the strength of synaptic activity. Modifications of MAGUK proteins function in the glutamatergic synapse such as alterations of MAGUK proteins interaction with N-Methyl-D-Aspartate (NMDA) receptors regulatory subunits are common events in several neurodegenerative disorders. Thus, a better knowledge and understanding of MAGUK structure and function as well as of the molecular events regulating MAGUK-mediated interactions in the glutamatergic synapse could lead to the identification of new targets for pharmaceutical intervention for neurodegenerative diseases. [3]

It would seem that the MAGUKs would be a very useful component of any genomic toolkit that was front-loaded to facilitate the emergence of metazoan life.  So when did these MAGUKs originate?

A reductive evolution from a complex community of ancestors as a general trend in the evolution of life.

Meet the Pompeii Worm (Alvinella pompejana).

This little creature is famous among biologists because it is the most heat tolerant animal known to exist – it lives buried in the sides of hydrothermal vents and is thus regularly exposed to water temperatures up to 176 degrees Fahrenheit.  To survive in such an extreme environment, the worm lives in a close symbiotic relationship with thermophilic bacteria:

Scientists believe the bacteria on the worms’ backs act like firefighters’ blankets, shielding the worms from intermittent blasts of hot, metal-rich water.

http://news.nationalgeographic.com/news/2005/01/0117_050117_tubeworms.html

While this shows us another example of the way the global bacterial superorganism can facilitate the evolution and survival of other eukaryotic organisms, right now, let’s focus on the gene content of this worm, as a library of 15,858 unique cDNAs has just been described. [1]

10 Signs of Intellectual DIShonesty

A new blog by A.robustus takes a very interesting twist on the Ten Signs of Intellectual Honesty.  A. robustus writes:

I did a search of the web to see what information was available to an inquisitive reader trying to learn more about the intellectual honesty concept.  There’s quite a lot – much of it, unsurprisingly, from colleges and universities from all over the world.  The stand-out candidate appears to be 10 Signs of Intellectual Honesty available from the website of one Mike Gene.

While Mike Gene is an intelligent design apologist (who is bound to become the focus of future posts!), I have to admit that his 10 Signs post is splendid.  Looking at the number of others who have linked to this particular page I am not alone in that assessment.  I recommend it to anybody who is searching for a checklist to ensure that their argument is developed and progresses from a foundation of intellectual honesty.

A. robustus then offers his/her clever twist by outlining the 10 Signs of Intellectual Dishonesty:

Ten Signs of Intellectual Honesty

I can never post this too much…

When it comes to just about any topic, it seems as if the public discourse on the internet is dominated by rhetoric and propaganda. People are either selling products or ideology. In fact, just because someone may come across as calm and knowledgeable does not mean you should let your guard down and trust what they say. What you need to look for is a track record of intellectual honesty. Let me therefore propose 10 signs of intellectual honesty.

Another Unicellular Genome

Another genome from a single-celled organism has been sequenced. This time it is the green algae, Chlorella. Chlorella are tiny algae that can reproduce quite rapidly. Yet despite the stream-lined nature of the organism, it retains most of the phytohormone biosynthesis pathways necessary to the development and growth of land plants.

Check it out:

Another interesting feature of the NC64A genome was the presence of homologs of receptors and biosynthetic enzymes of land plant hormones, such as abscisic acid, auxin, and cytokinin. The presence of these homologs does not necessarily imply the existence of plant hormones and their related functions in Chlorella but supports the hypothesis that genes involved in phytohormone biosynthesis and perception were established in ancestral organisms prior to the appearance of land plants.

Not only does this genome add more evidence to the growing plausibility of front-loading, but it also seems to offer a clue that the horizontal transfer of genetic information played a key role in the evolution of one of its key features – it’s unique chitin cell wall.

Food science

Some people don’t like McDonalds. To support their agenda, they often claim that science shows there is something unnatural about the burgers and fries. Consider this video:

Of course, there is nothing scientific about the video. All you have are a set of observations across time. And yes, while the food does not decay, there is no reason to think these observations mandate the belief that there is something wrong or unnatural about the food. What’s more, it is not going to help to come up with some mathematical analysis that argues it is extremely unlikely for the food to resist decay, therefore something unnatural is happening.

If you want to make a scientific case against McDonalds, then you need to go beyond the realm of observation and speculation. You need to come up with specific hypotheses and then test them with experiments. That is, you would need to consider a range of possible explanations for the food not decaying and then test each explanation. And the experiment is key, because you need to design the experiment to include both positive and negative controls. This is the only way to eliminate confirmation and disconfirmation bias.