Tuesday, November 25, 2008

Trichoplax adhaerens and the development of eyes

On the development of eyes

Several types of eyes exist and these include the camera-type eye, the compound eye, and the mirror eye (Figure 1). Ernst Mayr proposed that eyes evolved in all animal phyla 40 to 60 times independently.
A monophyletic program governing the development of the different eye types is proposed and the Pax6 gene is posited to be the master control gene. The Pax6 gene also plays a part in controlling the development of the nose, ears and parts of the brain.

What is needed for the developmental program of eyes?

A few core genes include:
Pax6 (eyeless [eye]) in Drosophila)
Six-type genes (E.g. Six3)
Sox-type genes (E.g. Sox2)
atonal ( E.g. Atoh7)
Retinoid receptors
Fox transcription factors (E.g. FoxN4)

Fascinating experiments have been conducted by shuffling around the genetic program architecture of genes associated with eye development in various animals.
For example in Drosophila:
Ectopic eye structures are able to be induced on the antennae, legs, and wings of fruit flies. This is done by targeted expression of the eyeless gene (Pax6 Drosophila homologue) (Figure 2). The Pax6 gene from the mouse is able to do the same job as the Drosophila version (Figure 3). And in Xenopus embryos, ectopic eye structures in can also be induced by the Drosophila eyeless (Pax6) version (Figure 4).

What about the Trichoplax adhaerens genome? Any genes for eye development?
It seems quite a chunk of the circuitry needed for eye development is present. (From table 1)
PaxB (eyeless?)
Six genes
Sox gene
Atonal gene
Retinoid X Receptor
Fox transcription factors

All that is missing seems to be crystalins (plays a part in lens formation). However, Darwin posited that "The simplest organ which can be called an eye consists of an optic nerve, surrounded by pigment-cells and covered by translucent skin, but without any lens or other refractive body." Thus large chunks of the circuitry for eye development in Trichoplax is present but no eyes!

Now compare the developmental program to evolution.

Here is an interesting article that shows the parallels between evolution and development.

For development:
Primordial germ cells (PGC) are prevented from entering the somatic program and are demethylated (genome-wide erasure of existing epigenetic modifications). Then the gametes are imprinted (targeted DNA methylation) during gametogenesis, only to be demethylated again after fertilization. Then during development, DNA is methylated again, causing totipotential cells to become pluripotent. X-inactivation and reactivation (of the paternal gamete I think) also occurs. The whole process is governed by the genetic (and epigenetic?) program. During the unfolding of this somatic program, random variation and selection occur, ultimately leading to just a few endpoints, every time it is successful. The process is constrained (few end points) as a result of pre-existing information that is set up during the inititiation of the process. All this is controlled by information in the genome.

For evolution:
There also seems to be only a few endpoints (small subset, limited variation) out of all the possible endpoints.
In the article:
An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution
It is argued to be as a result of genetic instructions dating earlier in evolutionary time. Preadaptations...

As already seen in the evolution of eyes, as soon as these sets of genes were formed (E.g. Pax genes), through whatever mechanism), evolution seemed to have been biased to a few end points, and these few endpoints arose 40-60 times, independently, as a result of pre-existing (preadaptations) information in the case of eyes.

What other "biased" end points can there be? Nervous systems, smell, hearing? And why would evolution be biased, as in development, to only reach a few end points over and over?

Development, intrinsic control, biased evolution and facilitated evolution

ScienceDaily (Oct. 25, 2008) — Researchers have put forward a simple model of development and gene regulation that is capable of explaining patterns observed in the distribution of morphologies and body plans (or, more generally, phenotypes).
The study, by Elhanan Borenstein of the Santa Fe Institute and Stanford University and David Krakauer of the Santa Fe Institute was published in this month's issue of PLoS Computational Biology.

Nature truly displays a bewildering variety of shapes and forms. [b]Yet, with all its magnificence, this diversity still represents only a tiny fraction of the endless 'space' of possibilities, and observed phenotypes actually occupy only small, dense patches in the abstract phenotypic space.[/B] Borenstein and Krakauer demonstrate that the sparseness of variety in nature can be attributed to the interactions between multiple genes and genetic controls involved in the development of organisms – a much simpler explanation than previously suggested.

Borenstein and Krakauer further integrated their model with phylogenetic dynamics, allowing developmental plans to evolve over time. They showed that this hybrid developmental-phylogenetic model reproduces patterns that are observed in the fossil record, including increasing variation between taxonomic groups, accompanied by decreasing variation within groups. This pattern is consistent with the Cambrian radiation associated with a rapid proliferation of highly disparate, multicellular animals, and suggests that much of the variation seen today is as a result of simpler genetic controls dating from much earlier in evolutionary time.
These simpler genetic controls include hox genes that are responsible for body plans, nervous systems, eyes etc. As seen, many of these switches were present in animals at the base of the evolutionary tree without any of these body plans, nervous system or eyes etc.

The article continues...
The findings presented in this study also bear directly on issues of convergence (when very different organisms independently evolve similar features). By including a model of development, rather different genotypes can produce very similar phenotypes. Consequently, convergent evolution, which the vast space of genotypes would suggest to be rare, is allowed to become much more common.

One of the paradoxical implications of this study has been to show how innovations in development that lead to an overall increase in the number of accessible phenotypes, can lead to a reduction in selective variance. In other words, while the potential for novel phenotypes increases, the fraction of space these phenotypes occupies tends to contract.

They concluded that "The theory presented in our paper complements the view of development as a key component in the production of endless forms and highlights the crucial role of development in constraining (as well as generating) biotic diversity."
And there we have it... biasing (constraining) of evolutionary trends as a result of genetic information present in simpler genetic controls dating from the base of the evolutionary tree (preadaptations).

The free, online peer-reviewed article:

These findings complement the view of development as a key component in the production of endless forms and highlight the crucial role of development in constraining biotic diversity and evolutionary trajectories.
The role of development in generating, or constraining, biotic diversity has been one of the most active debates in evolutionary biology [32]–[34]. The roots of this debate go back to the study of homologies and questions over physico-chemical verses genetically-selected rules of growth. One merit of simple developmental models is to illustrate how these two positions reflect necessary, complementary properties of generic developmental programs. Regulatory epistasis introduces non-linearities into development, allowing similar genotypes to generate significant divergence among phenotypes, whereas degeneracy tends to contract the occupancy of morphospace and bias phenotypic samples. Of great interest is how these structural properties of development have themselves been modified over the course of evolutionary time, potentially changing the tempo and mode of the evolutionary process. One of the paradoxical implications of this study has been to show how innovations in development (arising through increasing regulatory dimensions) that lead to an increase in the volume of accessible phenotypes, can lead to a reduction in selective variance (through increasing regulatory epistasis), so whereas the potential for novel phenotypes increases, the fraction of space these phenotypes occupies tends to contract. Hence the evolutionary process moves from a macro-configuration, sampling distant regions of space sparsely, to a micro configuration, sampling local regions of space at high resolution. This is analogous to an annealing process, whereby as an optimization process proceeds, the solutions become more frequent and more densely localized around the putative solution points.
This is analogous to evolution being a memetic algorithm (nice paper discussing it) with a set fitness function in a pre-existing fitness landscape. Convergence is to be expected.

Take the following into consideration:
  • Evolution is constrained (biased) as a result of genetic information present in simpler genetic controls dating from the base of the evolutionary tree (preadaptations)..
  • We observe many preadaptations for multicellularity in primitive unicellular organisms.
  • Also several toolkits (also preadaptations) for the development of body plans (Hox genes), the nervous system and sensory organs in animals at the base of the eumetazoan tree.
  • Also, spectacular examples of convergence are observed in nature.

How do stem cells become specialized?
Many Paths, Few Destinations: How Stem Cells Decide What They'll Become
How does a stem cell decide what specialized identity to adopt -- or simply to remain a stem cell? A new study suggests that the conventional view, which assumes that cells are "instructed" to progress along prescribed signaling pathways, is too simplistic. Instead, it supports the idea that cells differentiate through the collective behavior of multiple genes in a network that ultimately leads to just a few endpoints -- just as a marble on a hilltop can travel a nearly infinite number of downward paths, only to arrive in the same valley.

Evolution seems to be biased towards a few endpoints. This is partly due to the massive amounts of preadaptations in organisms at the base of the evolutionary tree. Now evolution seems to learn....

Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments
One of the striking features of evolution is the appearance of novel structures in organisms. Recently, Kirschner and Gerhart have integrated discoveries in evolution, genetics, and developmental biology to form a theory of facilitated variation (FV). The key observation is that organisms are designed such that random genetic changes are channeled in phenotypic directions that are potentially useful. An open question is how FV spontaneously emerges during evolution. Here, we address this by means of computer simulations of two well-studied model systems, logic circuits and RNA secondary structure. We find that evolution of FV is enhanced in environments that change from time to time in a systematic way: the varying environments are made of the same set of subgoals but in different combinations. We find that organisms that evolve under such varying goals not only remember their history but also generalize to future environments, exhibiting high adaptability to novel goals. Rapid adaptation is seen to goals composed of the same subgoals in novel combinations, and to goals where one of the subgoals was never seen in the history of the organism. The mechanisms for such enhanced generation of novelty (generalization) are analyzed, as is the way that organisms store information in their genomes about their past environments. Elements of facilitated variation theory, such as weak regulatory linkage, modularity, and reduced pleiotropy of mutations, evolve spontaneously under these conditions. Thus, environments that change in a systematic, modular fashion seem to promote facilitated variation and allow evolution to generalize to novel conditions.
Biased evolution towards a few endpoints under intrinsic control.

And now proteins that control evolution...

Evolution's new wrinkle: Proteins with cruise control provide new perspective

Related articles: Number 1
Mutagenic Evidence for the Optimal Control of Evolutionary Dynamics

Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how [biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

Evolution is guided by the optimization of fitness measures that balance functionally beneficial properties.

Fitness functions actually guiding evolution?

Number 2:
Optimal control of evolutionary dynamics

From the conclusion:

The observation that coevolving biopolymer sequences may optimally control each other’s evolution raises the prospect of artificial optimal control of evolutionary dynamics. Possible applications include the control of replication fidelity in nucleic acid amplification reactions and the design of therapeutics that dynamically regulate the evolution of viral populations.

And again from this article:

The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues. Applying the concepts of control theory, a body of knowledge that deals with the behavior of dynamical systems..., .

the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism, analogous to a car's cruise control or a home's thermostat, allowing them to fine-tune and control their subsequent evolution.

Self-regulating systems biasing future evolutionary trajectories towards a few outcomes.

Trichoplax adhaerens: The Otp gene

The various versions:
Trichoplax: Function unknown at present. Interested in its function in a basal eumetazoan.
Human otp. Its function:
The role of Otx and Otp genes in brain development.
Over the last ten years, many genes involved in the induction, specification and regionalization of the brain have been identified and characterized at the functional level through a series of animal models. Among these genes, both Otx1 and Otx2, two murine homologues of the Drosophila orthodenticle (otd) gene which encode transcription factors, play a pivotal role in the morphogenesis of the rostral brain. Classical knock-out studies have revealed that Otx2 is fundamental for the early specification and subsequent maintenance of the anterior neural plate, whereas Otx1 is mainly necessary for both normal corticogenesis and sense organ development. A minimal threshold of both gene products is required for correct patterning of the fore-midbrain and positioning of the isthmic organizer. A third gene, Orthopedia (Otp) is a key element of the genetic pathway controlling development of the neuroendocrine hypothalamus. This review deals with a comprehensive analysis of the Otx1, Otx2 and Otp functions, and with the possible evolutionary implications suggested by the models in which the Otx genes are reciprocally replaced or substituted by the Drosophila homologue, otd.
The same for mice:
The murine Otp homeobox gene plays an essential role in the specification of neuronal cell lineages in the developing hypothalamus.
Hypothalamic nuclei, including the anterior periventricular (aPV), paraventricular (PVN), and supraoptic (SON) nuclei strongly express the homeobox gene Orthopedia (Otp) during embryogenesis. Targeted inactivation of Otp in the mouse results in the loss of these nuclei in the homozygous null neonates. The Otp null hypothalamus fails to secrete neuropeptides somatostatin, arginine vasopressin, oxytocin, corticotropin-releasing hormone, and thyrotropin-releasing hormone in an appropriate spatial and temporal fashion, and leads to the death of Otp null pups shortly after birth. Failure to produce these neuropeptide hormones is evident prior to E15.5, indicating a failure in terminal differentiation of the aPV/PVN/SON neurons. Absence of elevated apoptotic activity, but reduced cell proliferation together with the ectopic activation of Six3 expression in the presumptive PVN, indicates a critical role for Otp in terminal differentiation and maturation of these neuroendocrine cell lineages. Otp employs distinct regulatory mechanisms to modulate the expression of specific molecular markers in the developing hypothalamus. At early embryonic stages, expression of Sim2 is immediately downregulated as a result of the absence of Otp, indicating a potential role for Otp as an upstream regulator of Sim2. In contrast, the regulation of Brn4 which is also expressed in the SON and PVN is independent of Otp function. Hence no strong evidence links Otp and Brn4 in the same regulatory pathway. The involvement of Otp and Sim1 in specifying specific hypothalamic neurosecretory cell lineages is shown to operate via distinct signaling pathways that partially overlap with Brn2.
The Zebrafish version. Its function: More of the same.
Differential regulation of the zebrafish orthopedia1 gene during fate determination of diencephalic neurons
The homeodomain transcription factor Orthopedia (Otp) is essential in restricting the fate of multiple classes of secreting neurons in the neuroendocrine hypothalamus of vertebrates. However, there is little information on the intercellular factors that regulate Otp expression during development
In the sea urchin.
Evolution of OTP-independent larval skeleton patterning in the direct-developing sea urchin, Heliocidaris erythrogramma.
The Orthopedia gene (Otp) encodes a homeodomain transcription factor crucial in patterning the larval skeleton of indirect-developing sea urchins.
A clear example of a cooption, whereby the same gene plays a role in neurological development in vertebrates and skeletal development in the sea urchin. Recycling of pre-existing genes for various, distinct, developmental processes.

Trichoplax adhaerens: The Pitx gene

Pitx: Another neurologically associated Hox gene present in the Trichplax genome.

The various versions:
Trichoplax. Function unknown at present. Would be interesting to find out what it is.
Human Pitx1 Its function:
This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family are involved in organ development and left-right asymmetry. This protein acts as a transcriptional regulator involved in basal and hormone-regulated activity of prolactin.
Human Pitx2 Its function:
This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. The encoded protein acts as a transcription factor and regulates procollagen lysyl hydroxylase gene expression. This protein plays a role in the terminal differentiation of somatotroph and lactotroph cell phenotypes, is involved in the development of the eye, tooth and abdominal organs, and acts as a transcriptional regulator involved in basal and hormone-regulated activity of prolactin. Mutations in this gene are associated with Axenfeld-Rieger syndrome, iridogoniodysgenesis syndrome, and sporadic cases of Peters anomaly. A similar protein in other vertebrates is involved in the determination of left-right asymmetry during development. Alternatively spliced transcript variants encoding distinct isoforms have been described
Human Pitx3 Its function:
This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family act as transcription factors. This protein is involved in lens formation during eye development. Mutations of this gene have been associated with anterior segment mesenchymal dysgenesis and congenital cataracts.
Zebrafish Pitx1
Zebrafish Pitx2
Zebrafish Pitx3
Drosophila Ptx1 (fruitfly)

More interesting facts about Pitx:
The Pitx homeobox gene in Bombyx mori: Regulation of DH-PBAN europeptide hormone gene expression
The diapause hormone-pheromone biosynthesis activating neuropeptide gene, DH-PBAN, is expressed exclusively in seven pairs of DH-PBAN-producing neurosecretory cells (DHPCs) on the terminally differentiated processes of the subesophageal ganglion (SG). To help reveal the regulatory mechanisms of cell-specific DH-PBAN expression, we identified a cis-regulatory element that regulates expression in DHPCs using the recombinant AcNPV-mediated gene transfer system and a gel-mobility shift assay. Bombyx mori Pitx (BmPitx), a bicoid-like homeobox transcription factor, binds this element and activates DH-PBAN expression. The BmPitx was expressed in various tissues, including DHPCs in the SG. Suppression of DH-PBAN expression by silencing of the BmPitx successfully induced non-diapaused eggs from a diapause egg producer. To the best of our knowledge, this report is the first to identify a neuropeptide-encoding gene as a target of the Pitx transcriptional regulator in invertebrates. Thus, it is tempting to speculate that functional conservation of Pitx family members on neuropeptide gene expression occurs through a "combinational code mechanism" in both vertebrate and invertebrate in neuroendocrine systems.

PITX genes are required for cell survival and Lhx3 activation

Zebrafish pitx3 is necessary for normal lens and retinal development.

And the trend of neurologically associated genes present in this basal eumetazoan continues

Trichoplax adhaerens: Hex and Dbx genes

More preadaptations from Trichoplax:
Its function?
Critical element in the development of the liver:
The role of Hex in hemangioblast and hematopoietic development.
The homeoprotein Hex is required for hemangioblast differentiation.
The homeobox gene HEX regulates proliferation and differentiation of hemangioblasts and endothelial cells during ES cell differentiation.

Detoxification of free radicals and damaging molecules play a crucial part in cellular homeostasis as well as systems homeostasis. The liver is mainly responsible for system homeostasis as it contains the highest concentration cells (hepatocytes do the heavy lifting) capable of detoxification, modification and excretion of hazardous molecules. It would be interesting to see what a gene that is associated with the development of the liver is doing in this simple organism at the base of the eumetazoan tree.

The trend of neurologically associated homeobox genes continues.
Regulation and function of Dbx genes in the zebrafish spinal cord.
Dbx homeodomain proteins are important for spinal cord dorsal/ventral patterning and the production of multiple spinal cord cell types. We have examined the regulation and function of Dbx genes in the zebrafish. We report that Hedgehog signaling is not required for the induction or maintenance of these genes; in the absence of Hedgehog signaling, dbx1a/1b/2 are expanded ventrally with concomitant increases in postmitotic neurons that differentiate from this domain. Also, we find that retinoic acid signaling is not required for the induction of Dbx expression. Furthermore, we are the first to report that knockdown of Dbx1 function causes a dorsal expansion of nkx6.2, which is thought to be the cross-repressive partner of Dbx1 in mouse. Our data confirm that the dbx1a/1b/2 domain in zebrafish spinal cord development behaves similarly to amniotes, while extending knowledge of Dbx1 function in spinal cord patterning. 2007 Wiley-Liss, Inc

Trichoplax adhaerens: The Hmx gene

Another Hox gene in the Trichoplax genome involved in central nervous system development.

Its function:
Hmx homeobox gene function in inner ear and nervous system cell-type specification and development.
The Hmx homeobox gene family is comprised of three members in mammals, Hmx1, Hmx2, and Hmx3, which are conserved across the animal kingdom and are part of the larger NKL clustered family of homeobox genes. Expression domains of Hmx genes in distantly related species such as Drosophila and mouse suggest an ancestral function in rostral central nervous system development. During vertebrate evolution, the Hmx genes appear to have been recruited into additional roles in inner ear morphogenesis and specification of vestibular inner ear sensory and supporting cell types. Being derived from a common ancestor, the vertebrate Hmx gene family is thus a strong candidate to investigate functional overlap versus the unique roles played by multiple genes belonging to the same family. The functions of Hmx2 and Hmx3 were investigated via directed gene mutagenesis and the primary regions where Hmx2 and Hmx3 exert their individual functions are consistent with their expression domains, such as the vestibule and uterus. Meanwhile, it is notable that some tissues where both Hmx2 and Hmx3 are extensively expressed were not severely affected in either of the Hmx2 or Hmx3 single mutant mice, suggesting a possible functional overlap existing between these two genes. Compound Hmx2 and Hmx3 double mutant mice showed more severe defects in the inner ear than those displayed by either single knockout. Furthermore, novel abnormalities in the hypothalamic-neuroendocrine system, which were never observed in either of the single mutant mice, confirmed a hypothesis that Hmx2 and Hmx3 also function redundantly to control embryonic development of the central nervous system.
The Trichoplax Hmx sequence. BLAST it.

Where is this critter's brain? Did its mind get lost somewhere along the line, or is it just ready for a bit of cooption here and there?

Trichoplax adhaerens: The Mnx (aka HB9) gene

The Trichoplax Mnx sequence: ABC86118
Comparison of this sequence with a few others: Cladogram

The human Mnx1 gene.

The fly Mnx gene (exex)
The Zebrafish Mnx gene

What does it do?
It is involved in the development of the pancreas and motor neurons.
1) Zebrafish mnx genes in endocrine and exocrine pancreas formation.
2) The Mnx homeobox gene class defined by HB9, MNR2 and amphioxus AmphiMnx.
The HB9 homeobox gene has been cloned from several vertebrates and is implicated in motor neuron differentiation. In the chick, a related gene, MNR2, acts upstream of HB9 in this process. Here we report an amphioxus homologue of these genes and show that it diverged before the gene duplication yielding HB9 and MNR2. AmphiMnx RNA is detected in two irregular punctate stripes along the developing neural tube, comparable to the distribution of 'dorsal compartment' motor neurons, and also in dorsal endoderm and posterior mesoderm. We propose a new homeobox class, Mnx, to include AmphiMnx, HB9, MNR2 and their Drosophila and echinoderm orthologues; we suggest that vertebrate HB9 is renamed Mnx1 and MNR2 be renamed Mnx2.

Interesting research:

Directed Evolution of Motor Neurons from Genetically Engineered Neural Precursors.
Stem cell-based therapies hold therapeutic promise for degenerative motor neuron diseases such as amyotrophic lateral sclerosis and for spinal cord injury. Fetal neural progenitors present less risk of tumor formation than embryonic stem (ES) cells but inefficiently differentiate into motor neurons, in line with their low expression of motor neuron-specific transcription factors and poor response to soluble external factors. To overcome this limitation, we genetically engineered fetal rat spinal cord neurospheres to express the transcription factors HB9, Nkx6.1 and Ngn2. Enforced expression of the three factors rendered neural precursors responsive to sonic hedgehog and retinoic acid and directed their differentiation into cholinergic motor neurons that projected axons and formed contacts with co-cultured myotubes. When transplanted in the injured adult rat spinal cord, a model of acute motor neuron degeneration, the engineered precursors transiently proliferated, colonized the ventral horn, expressed motor neuron-specific differentiation markers and projected cholinergic axons in the ventral root. We conclude that genetic engineering can drive the differentiation of fetal neural precursors into motor neurons which efficiently engraft in the spinal cord. The strategy thus holds promise for cell replacement in motor neuron and related diseases.
What did these guys do? They enforced the expression of 3 genes associated with neuronal development in order to direct the development of motor neurons. Sonic hedgehog also played a role.
So four genes played a role:
  1. HB9
  2. Nkx6.1
  3. Ngn2
  4. Sonic hedgehog

Are similar genes present in the Trichoplax genome?
1. HB9 (mnx)
Yes (see above).

2. Nkx6.1
Here is the human Nk6 gene
And here is the Trichoplax version

3. Ngn2
Here is the human neurogenin 2 (ngn2) gene
And here is the Trichoplax version.
A quick BLAST (blastp) the human genome shows this sequence to be closely related to ngn2 (E-value = 3^-8).

4. Sonic hedgehog (shh)
Here is the human shh gene
This gene seems to absent in from the Trichoplax genome, however, the presence of shh in Monosiga brevicollis (unicellular eukaryote that diverged before Trichoplax) suggest the possibility of gene loss in this lineage.

Wonder what will happen if shh is co-expressed and together with mnx, Nk6 and ngn2 in Trichoplax, or whether these genes will function like their counterparts in higher animals.

A complex array of neurologically associated developmental pathways present in this eumetazoan that has no nerves, sensory cells and muscle cells, and there is more

Trichoplax adhaerens: The Dlx gene

More Trichoplax preadaptations:
The Dlx gene

What does it do (wiki)?
  • Dlx genes are required for the tangential migration of interneurons from the subpallium to the pallium during vertebrate brain development [3].
  • It has been suggested that Dlx promotes the migration of interneurons by repressing a set of proteins that are normally expressed in terminally differentiated neurons and act to promote the outgrowth of dendrites and axons [4]. Mice lacking Dlx1 exhibit electrophysiological and histological evidence consistent with delayed-onset epilepsy [5].
  • Dlx2 has been associated with a number of areas including development of the zona limitans intrathalamica and the prethalamus.
  • Dlx5/6 expression is necessary for normal lower jaw patterning in vertebrates [6].
  • Dlx7 is expressed in bone marrow
A quick BLAST of the sequence reveals it is closely related to human Dlx1, as well as Dlx1 in other vertebrates (including Zebrafish, the mouse, rat opossum, dog etc.)

More specifically, what does Dlx1 do?
This gene encodes a member of a homeobox transcription factor gene family similiar to the Drosophila distal-less gene. The encoded protein is localized to the nucleus where it may function as a transcriptional regulator of signals from multiple TGF-{beta} superfamily members. The encoded protein may play a role in the control of craniofacial patterning and the differentiation and survival of inhibitory neurons in the forebrain. This gene is located in a tail-to-tail configuration with another member of the family on the long arm of chromosome 2. Alternatively spliced transcript variants encoding different isoforms have been described.
It is possible to create a homology of this protein to look at its possible structure. The closest match is the human Dlx 5 protein structure. Sequence alignment places the Dlx sequence of Trichoplax closer to human Dlx5 than to human Dlx1.

What does Dlx 5 do?
This gene encodes a member of a homeobox transcription factor gene family similar to the Drosophila distal-less gene. The encoded protein may play a role in bone development and fracture healing. Mutation in this gene, which is located in a tail-to-tail configuration with another member of the family on the long arm of chromosome 7, may be associated with split-hand/split-foot malformation.
The homology model of the protein:
A good quality protein was generated

So, a Hox gene responsible for a sundry of neurologically associated developmental processes present in an organism with no nerve, sensory or bone cells at the base of the evolutionary tree.

Trichoplax adhaerens.

The intriguing genome of the Trichoplax (Placozoa meaning flat animals):
Trichoplax Genome Sequenced: 'Rosetta Stone' For Understanding Evolution

Currently there is only one named species in the phylum: Trichoplax adhaerens.
It's a flattened blob, a few millimeters across and made up of a few thousand cells. It's main claim to fame is its remarkable simplicity: it is a multicellular animal that consists of only four apparent cell types, and the only obvious organization is into an upper and lower surface. The upper surface consists of a sheet of covering cells, while the lower surface contains two cell types: the gland cells that secrete digestive enzymes onto whatever the animal is sitting on, and the cylinder cells that absorb whatever nutrients are released. In between is a loose network of fiber cells that are responsible for the animal's movement.
Nerves, sensory cells and muscle cells are absent.
Interestingly (from the link):
One other strange thing: in culture, Trichoplax is consistently asexual and reproduces by fission, but older cultures at high density begin to produce small motile presumptive sperm cells, and as individual animals desintegrate, they spew out ova. The two have never been observed to come together, though, so there is no fertilization, and while the ova may divide a half dozen times, they all eventually die. It is possible that there is another stage in the life cycle that is not viable under laboratory conditions and has never been observed.
The genome of this critter is even more fascinating.
From the nature article:
The Trichoplax genome and the nature of placozoans

Table 1 | Developmental transcription factors in the Trichoplax genome
Homeobox (Hox genes)
  • A) ANTP-class: Trox-2 (Hox/ParaHox-like), Not, Dlx, Mnx, Hmx, Hex, Dbx and seven others.
  • B) PRD-class (paired box and homeobox): PaxB, Pitx, Otp, Gsc and five others
  • C) POU-class(POU domain and homeobox): POU class 4 (Brn-3), one other
  • D) LIM-class (LIM domain and homeobox): islet, apterous, Lhx1/5 and one other
  • E) SIX-class (sine oculis homeobox): Six3/6 and one other
  • F) TALE-class: Pbx/Exd, Irx, Meis
  • G) HNF-class: Hnf

Going down the list, what are the functions of these Hox genes?
1) Trox-2 (Hox/ParaHox-like)
Hox/paraHox-like genes are involved in axial patterning in bilaterarian organisms. Basically, they control the formation of the anterior–posterior (AP) axis. Function of Trox-2?
We speculate that Trox-2 functions within a hitherto unrecognized population of possibly multipotential peripheral stem cells that contribute to differentiated cells at the epithelial boundary of Trichoplax.
2) Not
In mice, Not controls the development of the caudal notochord. What is the notochord?
The notochord is a flexible, rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In lower vertebrates, it persists throughout life as the main axial support of the body, while in higher vertebrates it is replaced by the vertebral column. The notochord is found on the ventral surface of the neural tube.
What does it do in this flat, simple organism?
The homeobox gene Not is highly conserved in Xenopus, chicken and zebrafish with an apparent role in notochord formation, which inspired the name of this distinct subfamily. Interestingly, Not genes are also well conserved in animals without notochord such as sea urchins, Drosophila or even Hydra, but appear to be highly derived in mammals. A search for homeobox genes in the placozoan Trichoplax adhaerens, one of the simplest organisms available today, revealed only two homeobox genes: a Not homologue and the previously described gene Trox-2, which is most similar to the Gsx subfamily of the Hox/ParaHox cluster genes. Not has a unique expression profile in Trichoplax. It is highly expressed in folds of intact animals and in the wounds of regenerating animals. The dynamic expression pattern of Trichoplax Not is discussed in comparison with the invariable expression pattern of Trox-2 and the putative secreted protein Secp1. The high sequence conservation of Not from Trichoplax to lower vertebrates, but not to mammals, represents a rare example of an apparent gene decay in the lineage leading to humans.
Interesting preadaptations. It gets better.

Next, a look at the other Hox genes in this organism and their functions in higher animals.
Dlx, Mnx, Hmx,Hex, Dbx etc...

Hox genes video
Nice overview of Hox genes.

Sea urchin

The sea urchin is another interesting creature (Green circle, yellow circle = divergence time):

It provides valuable knowledge for cancer, Alzheimer's and infertility research:

Sea Urchins' Genetics Add To Knowledge Of Cancer, Alzheimer's And Infertility

What is even more interesting is what lurks in its genome. According to present models, they originated at least 450 million years ago. These organisms have no eyes, ears or a nose, yet they have the genes humans have for vision, hearing and smelling (see above link). They also have a surprisingly complex immune system, which surpasses the human one by far.

Now the genes in the genetic toolkit (nice video) in animals responsible for assigning specific properties of the various body parts are known as Hox genes. Here is a nice overview of Hox genes. A great deal of Hox genes are found in the sea urchin, the pattern of gene expression just differs, resulting in a different body plan.

Right at the base of the animal tree, a sundry of genes necessary for sight, smell, hearing as well as the various body plans were present in the genome of the common ancestor.


More interesting preadaptations:
This time sponges (wiki).
Sponges are among the simplest animals. They lack gastrulated embryos, extracellular digestive cavities, nerves, muscles, tissues, and obvious sensory structures, features possessed by all other animals.
Nice site about sponges.
Evolutionary history of sponges (Sponges = light blue, Divergence time = yellow)

Choanoflagellates had a lot of the toolkits necessary to develop a nervous system as well as multi-cellularity, even though they are simple uni-cellular organisms that do not form colonial assemblages.

Now the Origin of Nerves are Traced to Sponges
Sponges are very primitive animals. They don't have nerves cells (nor muscles nor eyes nor a lot of other things we commonly associate with animals). So scientists figured sponges split from the tree of life before nerves evolved.

A new study has surprised researchers, however.

"We are pretty confident it was after the sponges split from trunk of the tree of life and sponges went one way and animals developed from the other, that nerves started to form," said Bernie Degnan of the University of Queensland. "What we found in sponges though were the building blocks for nerves, something we never expected to find."

In humans and other animals, nerves deliver messages to and from the brain and all the parts of a body.

Degnan and colleagues studied a sea sponge called Amphimedon queenslandica. "What we have done is try to find the molecular building blocks of nerves, or what may be called the nerve's ancestor the proto-neuron," Degnan said. They found sets of these genes in sponges.
Nice .
Free, online peer-reviewed article:
A Post-Synaptic Scaffold at the Origin of the Animal Kingdom
There are even more fascinating findings from the genome of the sponge.
"But what was really cool," he said, "is we took some of these genes and expressed them in frogs and flies and the sponge gene became functional — the sponge gene directed the formation of nerves in these more complex animals.

The research, announced this month, was published in the journal Current Biology.
Article with the details:
Article abstract:
Sponge Genes Provide New Insight into the Evolutionary Origin of the Neurogenic Circuit
The nerve cell is a eumetazoan (cnidarians and bilaterians) synapomorphy [1]; this cell type is absent in sponges, a more ancient phyletic lineage. Here, we demonstrate that despite lacking neurons, the sponge Amphimedon queenslandica expresses the Notch-Delta signaling system and a proneural basic helix loop helix (bHLH) gene in a manner that resembles the conserved molecular mechanisms of primary neurogenesis in bilaterians. During Amphimedon development, a field of subepithelial cells expresses the Notch receptor, its ligand Delta, and a sponge bHLH gene, AmqbHLH1. Cells that migrate out of this field express AmqDelta1 and give rise to putative sensory cells that populate the larval epithelium. Phylogenetic analysis suggests that AmqbHLH1 is descendent from a single ancestral bHLH gene that later duplicated to produce the atonal/neurogenin-related bHLH gene families, which include most bilaterian proneural genes [2]. By way of functional studies in Xenopus and Drosophila, we demonstrate that AmqbHLH1 has a strong proneural activity in both species with properties displayed by both neurogenin and atonal genes. From these results, we infer that the bilaterian neurogenic circuit, comprising proneural atonal-related bHLH genes coupled with Notch-Delta signaling, was functional in the very first metazoans and was used to generate an ancient sensory cell type.
Whole parts of the nervous system were present in animals that do not have a nervous system, yet these parts are interchangeable and function just like they should in animals that do have a nervous system.


Interesting article about amoebas from 2005 (University of California):
Biologists determine genetic blueprint of social amoeba
An international team that includes biologists at the University of California, San Diego has determined the complete genetic blueprint of Dictyostelium discoideum, a simple social amoeba long used by researchers as a model genetic system, much like fruit flies and laboratory mice, to gain a better understanding of human diseases.

The scientific details of this seven-year-long genetic sequencing effort, which involved 97 scientists from 22 institutions in five countries, are contained in a paper featured on the cover of the May 5 issue of the journal Nature.

The international team's achievement will have an immediate application for biomedical researchers, who can now mine the Dictyostelium genome for a host of genes that cause human disease, thus gaining a new and efficient way to study those human diseases with a simple organism in their laboratories.

For evolutionary biologists, the genetic blueprint of Dictyostelium, the first amoeba genome to be sequenced, has clarified the place that Dictyostelium occupies in the hierarchy of life.

"It is more closely related to fungi and animals than we had previously thought," says Adam Kuspa, a professor of biochemistry and molecular biology at Baylor College of Medicine in Houston and a senior author of the Nature paper.

The discovery will also improve geneticists' understanding of how the genes from Dictyostelium and other genetic model organisms have been conserved or adapted through evolution in humans and other organisms.

"The cells which gave rise to plants and animals had more types of genes available to them than are presently found in either plants or animals," explains William Loomis, a professor of biology at UCSD and one of the key members of the international sequencing effort. "Specialization appears to lead to loss of genes as well as the modification of copies of old genes. As each new genome is sequenced, we learn more about the history and physiology of the progenitors and gain insight into the function of human genes."

In 1989, Loomis and Kuspa, then a postdoctoral fellow in Loomis' laboratory, initiated a critical portion of the effort when they began the arduous task of constructing a physical map of the genes located on the six chromosomes of Dictyostelium.

The scientists mapped the location of several hundred genes on those chromosomes based on landmarks that had been discovered over the years, then created a set of 5,000 large DNA clones, each about 200,000 nucleotide bases long, that proved useful for other researchers in assembling the genetic sequences of Dictyostelium's genome. Another UCSD biologist involved in the genome effort, Christophe Anjard, an assistant project scientist in Loomis' laboratory, analyzed families of Dictyostelium genes and uncovered relationships with these genes in both animals and plants.

Dictyostelium is used as a model organism for studying cell polarity, how cells move and the differentiation of tissues. It also exhibits many of the properties of white blood cells.

Three years ago, another team of UCSD biologists discovered that two genes that are used by Dictyostelium to guide the organism to food sources are also used to guide human white blood cells to the sites of infections and play a role in the spread of cancer. (see: http://ucsdnews.ucsd.edu/newsrel/science/mcchemo.htm)

Dictyostelium usually exists as a single cell organism that inhabits forest soil, consuming bacteria and yeast. When starved, however, the single cells come together, differentiate into tissues and become a true multicellular organism with a fruiting body composed of a stalk with spores poised on top. This increases its utility in a variety of studies.

"An organism's relationship to humans depends on how related the proteins are that are found in the two cell types," says Kuspa. "You can make direct analogies, or you could learn general principles about how cells regulate their behavior. Both things will apply in the studies we do."

He and the other members of the international sequencing team found that there are more protein coding genes in the organism than they had thought and nearly twice as many as there are in fungi
. Their unraveling of the genome also allowed Rolf Olsen, a postdoctoral fellow working in Loomis' laboratory, to generate a tree of life and show that amoebozoa, the group to which Dictyostelium belongs, evolved from the common ancestor of eukaryotes (the group of organisms that contain all animals, plants, algae, protozoa, slime mold and fungi) before fungi. Dictyostelium has about 12,000 genes that produce a greater variety of proteins than the approximately 6,000 found in fungi. And its genes are more closely related to human genes than are the genes from fungi.

"That really speaks to how much we will relate the gene function information we find to humans," Kuspa says. "It makes Dictyostelium a better model for looking for targets against which drugs can act."

Key collaborators in the project at Baylor included Richard Gibbs and George Weinstock, co-directors of Baylor's Human Genome Sequencing Center, and Richard Sucgang, an assistant professor of biochemistry. Baylor performed about one half of the sequencing work.
Phylogenetic analysis suggest Dictyostelium discoideum diverged after plants and before metazoa.

Any idea how many preadaptations for multi-cellularity existed? E.g.: Unicellular programmed cell death (autophagic, apoptotic metabolic catastrophe and necrotic processes), differentiation, adhesion, calcium toolkits, tyrosine kinase signaling cascades? More later.

Monosiga brevicollis and multicellularity preadaptations

Preadaptations (aka exaptations) are features that perform a function but was not produced by natural selection for its current use. It could be argued that an exaptation forms as a result of co-option from a preadaptation, however Daniel Dennett denies exaptation differs from preadaptation. A simple example of a preadaptation is a feather that evolved (through natural selection) for warmth and was coopted into a new function, flight.

The genomes of various ancient organisms have been sequenced and it is interesting to view the presence of several preadaptations in the genomes of these creatures. The purpose of this thread is to highlight several of these interesting findings. If anyone come across any interesting findings, post it here .

Various trees of life exist. For example:

For the purpose of this thread, tree #2 (Dhushara, trevol.jpg) will be used as it is a nice representation of the evolution of animals (especially vertebrates). Horizontal gene transfer and endosymbiotic events are however not clear and tree #7 (Doolittle) is probably a better way of looking at evolution. Therefore keep #2 and #7 in mind and try and piece them together.

Preadaptations in the genome of the choanoflagellate, Monosiga brevicollis:

Choanoflagellates (link) are single-celled organisms thought to be most closely related to animals. The divergence time of this organism was about >600 million years ago (Link) (Blue circle in image).

Tyrosine Kinases are crucial for multicellular life to exist and play pivotal roles in diverse cellular activities including growth, differentiation, metabolism, adhesion, motility, death (link). More than 90 Protein Tyrosine Kinases (PTKs) have been found in the human genome. Interestingly Monosiga brevicollis has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan.

Adherens junctions are also crucial components of multicellular life and function to communicate and adhere together in tissues. Even though Monosiga brevicollis are single-celled and do not form colonial assemblages, it is interesting to know they posses about 23 cadherins genes (Cadherins) usually associated with multicellular organisms.

Calcium signaling toolkits also play a crucial role in multicellular signaling. Calcium signaling plays a crucial part in contraction, metabolism, secretion, neuronal excitability, cell death, differentiation and proliferation. Thus, it is also interesting to note that Monosiga brevicollis has an extensive calcium signaling toolkit and emerged before the evolution of multicellular animals.

Tyrosine kinases, calcium signaling, and adherens junctions all play a part in neural signaling and other multecellular systems. Monosiga brevicollis does not have a nervous system. Thus it is also interesting to find the presence of the hedgehog gene in the genome of Monosiga brevicollis. Signaling by Sonic hedgehog (Shh) controls important
developmental processes, including neural stem cell proliferation. (Link).
Nice article:
Multigene Phylogeny of Choanozoa and the Origin of Animals
Compare the hedgehog gene of Monosiga brevicollis to that of humans.

Another interesting fact about the genome of the Monosiga brevicollis is noted in this article.
Interestingly, the choanoflagellate has nearly as many introns - non-coding regions once referred to as "junk" DNA - in its genes as humans do in their genes, and often in the same spots. Introns have to be snipped out before a gene can be used as a blueprint for a protein and have been associated mostly with higher organisms.

The choanoflagellate genome, like the genomes of many seemingly simple organisms sequenced in recent years, shows a surprising degree of complexity, King said. Many genes involved in the central nervous system of higher organisms, for example, have been found in simple organisms that lack a centralized nervous system.

Likewise, choanoflagellates have five immunoglobulin domains, though they have no immune system; collagen, integrin and cadherin domains, though they have no skeleton or matrix binding cells together; and proteins called tyrosine kinases that are a key part of signaling between cells, even though Monosiga is not known to communicate, or at least does not form colonies.
(Emphasis mine)

Fascinating multicellular preadaptations very early on in the evolution of single-celled organisms.


A blog dedicated to the massive amounts of preadaptations of organisms at the base of the eumetazoan (and other) tree.