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Author Topic:   Mutations & structural modifications - Redux
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 1 of 22 (41838)
05-31-2003 6:51 AM


There was a previous thread on this topic which was derailed due to ontological argument. I have a particular interest in this topic so I would like to see it revived.
The original post was on the topic of polydactyly but I would like to widen the remit to all gross structural changes.
So what sources have been found for structural change? Single nucleotide mutations? Indels? Gene duplications? Chromosomal rearrangements? Whole genome duplications? How significant are each of these types of mutation in evolutionary terms? Any and all examples would be welcome. What non lethal mutations in humans lead to the loss or gain of an organ? What mutations lead to changes in organ/limb character?
One thing I would like to avoid is dwelling on HOX genes, brilliant as they are, a few examples would be great but I don't want to get swamped by homeotic mutant flies and syndactylys.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 2 of 22 (41842)
05-31-2003 10:54 AM


Point muttaiio in gene for FGF-3 receptor causes achondroplasia.

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 3 of 22 (41852)
05-31-2003 1:30 PM
Reply to: Message 1 by Wounded King
05-31-2003 6:51 AM


Having said I wanted to avoid HOX examples I now want to post one.
This is an example of a hindbrain patterning defect in Hoxa1 null mice. Rhombomeres 3 and 4 lose character but develop into a novel neural structure which can regulate breathing, although poorly. The mutants are post-natally lethal.
del Toro ED, Borday V, Davenne M, Neun R, Rijli FM, Champagnat J. Generation of a novel functional neuronal circuit in Hoxa1 mutant mice.
J Neurosci. 2001 Aug 1;21(15):5637-42.

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Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 4 of 22 (41922)
06-01-2003 6:16 PM
Reply to: Message 3 by Wounded King
05-31-2003 1:30 PM


Structure
Maybe we can expand the concept of structure a bit. One area of mutation that recieved quite a bit of attention a while back was structural aspects of protein domains. Tranquility Base and I had a running discussion concerning the evolution of protein families and protein domains. Would anyone object to adding protein structure and evolution/mutational changes to the general topic of structure?
One of the problems with mutation and larger structural changes is that the area is a VERY young field due to the complexity of the phenotypic blending of the particulate genotypes (are you reading this Syamsu?). Maybe we would get a larger and more fruitfull discussion if we broadened the scope. It's your call, Wounded you started the thread.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 5 of 22 (41932)
06-02-2003 5:27 AM
Reply to: Message 4 by Dr_Tazimus_maximus
06-01-2003 6:16 PM


Re: Structure
Protein family evolution is fascinating stuff, but I think that there is so much of it that it should really have a thread of its own. As you say the gross morphology linked mutations are not as established and lack the wealth of data available to discussions on protein evolution. Consequently I suspect that the structural mutations might be swamped by the protein evolution.
It goes without saying that pretty much all of the mutations affecting gross morphology are down to changes in either protein structure or expression, at least those we know of at the moment. So certain aspects of that are certainly going to be germane, however I think a general discussion of protein structure would deserve its own thread.

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Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 6 of 22 (41967)
06-02-2003 1:53 PM
Reply to: Message 5 by Wounded King
06-02-2003 5:27 AM


Re: Structure
How about this one for eye development then. I actually read about this a while ago where they were doing some of the intial work on PAX 6. The alterations may be due to differential downstream effects and binding vs. a defect in the gene itself. I am sure that there is more up to date material, I will see what I can dig up later.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 7 of 22 (41982)
06-02-2003 7:19 PM
Reply to: Message 6 by Dr_Tazimus_maximus
06-02-2003 1:53 PM


This paper ascribes the degeneration of the eye primordium to differences in Pax-6 expression. Suggesting that the major difference is either upstream in the signalling pathway or in the regulatory elements of the Pax-6 gene.
Strickler AG, Yamamoto Y, Jeffery WR.
Early and late changes in Pax6 expression accompany eye degeneration during cavefish development.
Dev Genes Evol. 2001 Mar;211(3):138-44.

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Mammuthus
Member (Idle past 6476 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 8 of 22 (41994)
06-03-2003 8:56 AM
Reply to: Message 1 by Wounded King
05-31-2003 6:51 AM


Sorry but here is more Hox stuff
Gene 2002 Apr 3;287(1-2):121-8 Related Articles, Links
Gene duplications in the prototypical cephalochordate amphioxus.
Minguillon C, Ferrier DE, Cebrian C, Garcia-Fernandez J.
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona., Avenida Diagonal 645, 08028 Barcelona, Spain.
The new discipline of Evolutionary Developmental Biology (Evo-Devo) is facing the fascinating paradox of explaining morphological evolution using conserved pieces or genes to build divergent animals. The cephalochordate amphioxus is the closest living relative to the vertebrates, with a simple, chordate body plan, and a genome directly descended from the ancestor prior to the genome-wide duplications that occurred close to the origin of vertebrates. Amphioxus morphology may have remained relatively invariant since the divergence from the vertebrate lineage, but the amphioxus genome has not escaped evolution. We report the isolation of a second Emx gene (AmphiEmxB) arising from an independent duplication in the amphioxus genome. We also argue that a tandem duplication probably occurred in the Posterior part of the Hox cluster in amphioxus, giving rise to AmphiHox14, and discuss the structure of the chordate and vertebrate ancestral clusters. Also, a tandem duplication of Evx in the amphioxus lineage produced a prototypical Evx gene (AmphiEvxA) and a divergent gene (AmphiEvxB), no longer involved in typical Evx functions. These examples of specific gene duplications in amphioxus, and other previously reported duplications summarized here, emphasize the fact that amphioxus is not the ancestor of the vertebrates but 'only' the closest living relative to the ancestor, with a mix of prototypical and amphioxus-specific features in its genome.
And a non-hox example though I don't have access to the full article
Plant Cell Physiol 2002 Apr;43(4):372-8 Related Articles, Links
The leaf index: heteroblasty, natural variation, and the genetic control of polar processes of leaf expansion.
Tsukaya H.
National Institute for Basic Biology (NIBB) and Center for Integrated Bioscience, Okazaki Research Institutes, Myodaiji-cho, Okazaki, 444-8585 Japan.
The morphology of the leaves of angiosperms exhibits remarkable diversity. One of the factors showing the greatest variability is the leaf index, namely, the ratio of leaf length to leaf width. In some cases, different varieties of a single species or closely related species can be distinguished by differences in leaf index. To some extent, the leaf index reflects the morphological adaptation of leaves to a particular environment. Moreover, physiological conditions or environmental factors can change the leaf index of an individual plant. No good tools have been available for studies of the mechanisms that underlie such biodiversity. However, we have recently obtained some, albeit fragmentary, information about molecular mechanisms of leaf morphogenesis as a result of studies of leaves of the model plant, Arabidopsis thaliana (L.) Heynh. For example, the ANGUSTIFOLIA gene, a homolog of animal CtBP genes, controls leaf width. ANGUSTIFOLIA appears to regulate the polar elongation of leaf cells via control of the arrangement of cortical microtubules. By contrast, the ROTUNDIFOLIA3 gene controls leaf length via the biosynthesis of steroid(s). We provide here an overview of the biodiversity exhibited by the leaf index of angiosperms. In particular, we consider information obtained from studies of mutants and transgenic strains of A. thaliana, from the so-called Evo/devo perspective.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 9 of 22 (42000)
06-03-2003 9:42 AM
Reply to: Message 8 by Mammuthus
06-03-2003 8:56 AM


Is there a specific morphological change that the Evx genes are being proposed to regulate Mammuthus? Are the duplications, seen in both cephalochordate and vertebrate lineages, linked to specific mnorphological changes themselves or do they simply provide a spare copy of the gene upon which natural selection can work to produce a distinct gene. Is there anything known about the effects of overexpression of even skipped or its homologues?

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Mammuthus
Member (Idle past 6476 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 10 of 22 (42002)
06-03-2003 10:07 AM
Reply to: Message 9 by Wounded King
06-03-2003 9:42 AM


Hi WK,
From the paper
quote:
Both sequence comparisons and expression patterns clearly indicate that AmphiEvxA is a prototypical chordate Evx gene. The basal chordate role of Evx genes was the pan-bilaterian function in gastrulation and neurogenesis, plus a probable pan-chordate role in tail bud development. The expression of Evx around the MHB is probably a vertebrate innovation, perhaps linked to the evolution of the MHB organizer activity in vertebrates. Appendages, and the function of Evx in their development, evolved within the vertebrates. In summary, an ancestral Evx gene was duplicated in the amphioxus genome, giving rise to a prototypical Evx gene (AmphiEvxA) and a fast evolving gene (AmphiEvxB), that is no longer involved in typical Evx functions.
and
quote:
Amphioxus morphology may have remained astonishingly invariant since the origin of vertebrates, but the amphioxus genome has not escaped evolution. Gene duplication events are not so rare, as perhaps should be expected in any lineage with a long independent evolutionary history. Amphioxus has undergone duplication of developmentally important genes (Emx). Such duplications raise questions about the chordate and vertebrate ancestors; for example, Hox14 and how many Posterior Hox genes were there? Also duplication of genes can lead to very divergent members of their respective classes (AmphiEvxB), which may have unusual, atypical expression for the class, if indeed they are not recently formed pseudogenes. Gene duplications in amphioxus are not restricted to homeobox genes (see Table 2), and so when analysing an amphioxus gene to trace the history of a given gene family in chordates, special attention should be paid to the fact that amphioxus is not the ancestor of vertebrates, but `only' the closest living relative to the vertebrate ancestor, an invaluable position to help understand the origin of vertebrates.
So it is not entirely clear what the function of the second Evx gene is...but the duplicated gene has a different expression pattern. I think the interesting point is that amphioxus is not an ancestor (which is often assumed in discussing the Hox clusters) but is the closest living relative which is a major distinction...searching medline does not reveal any work on deletion or overexpression studies of Evx in amphioxus. The second Evx seems to be a spare copy that may have taken on a novel and exclusive function in amphioxous...or as they suggest, is an expressed pseudogene and does nothing.
I can look around later for even skipped overexpression..though I must admit that developmental bio is not my expertise....and "evo devo" literature is really pretty thin since it is a very new field.
However, it is interesting that a morphologically static organism like amphioxus has only had minor duplications of the major developmental genes whereas all the more complex organisms, particularly vertebrates, have had several duplications i.e. a (rough) correlation between morphological complexity and genome duplications of developmental critical genes.

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 Message 11 by Wounded King, posted 06-03-2003 11:54 AM Mammuthus has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 11 of 22 (42007)
06-03-2003 11:54 AM
Reply to: Message 10 by Mammuthus
06-03-2003 10:07 AM


Doesnt it almost go without saying that no currently extant species is ancestral to any other? That doesnt mean that the single Hox cluster of amphioxus cannot inform our views on the ancestral hox cluster, as does that of drosophila.
There are quite a few instances of duplicate genes in amphioxus which are related to duplicated genes in vertebrates but appear to be independent, the AmphiEmxs and Amphioxus myogenic regulatory genes for example.
I prefer this example from Ciona where one gene has two splice variants with properties similiar to two related proteins in vertebrates.
Meedel TH, Farmer SC, Lee JJ.
The single MyoD family gene of Ciona intestinalis encodes two differentially expressed proteins: implications for the evolution of chordate muscle gene regulation.
Development. 1997 May;124(9):1711-21.
http://www.ncbi.nlm.nih.gov:80...
{Shortened display form of URL, to restore page width to normal - AM}
[This message has been edited by Adminnemooseus, 06-03-2003]

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 Message 12 by Mammuthus, posted 06-03-2003 12:08 PM Wounded King has replied

  
Mammuthus
Member (Idle past 6476 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 12 of 22 (42010)
06-03-2003 12:08 PM
Reply to: Message 11 by Wounded King
06-03-2003 11:54 AM


quote:
Doesnt it almost go without saying that no currently extant species is ancestral to any other? That doesnt mean that the single Hox cluster of amphioxus cannot inform our views on the ancestral hox cluster, as does that of drosophila.
Right you are. However, it depends on how far one takes the comparative approach. If one assumes that amphioxus is similar to the ancestral state and it actually is not, rather than informing it will be misleading. At a cartoonish extreme it would be like the creationist arguement that "living fossils" refute evolution becasue they don't vary when that is clearly not the case. At the molecular level amphioxus has a lot of evolution under its belt. It does not appear to be the case for the Hox cluster but Evx, Mox genes and a few others may not be similar to the ancestral state in amphioxus.
Since you seem to be more up on this subject, do you have any references regarding Hox-like genes or developmental homologues in basal metazoans or even in yeast? I ask because a while back I got into a rather ridiculous argument with Tranquility Base where he was stating that because I could not say what or where the original Hox gene (s) came from, they could not have evolved (this is a very rough paraphrasing of the debate and does not do TB's usually good debating style credit). I was wondering if you know of any literature on the search for pre-hox like genes in non-segmented or unicellular organisms...I assume they would have a drastically different function..but then prions have been found in yeast so I would not be surprised to find a distant hox relative there as well.

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 Message 13 by Wounded King, posted 06-03-2003 5:39 PM Mammuthus has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 13 of 22 (42025)
06-03-2003 5:39 PM
Reply to: Message 12 by Mammuthus
06-03-2003 12:08 PM


It depends what you mean by HOX. If you mean the Genes in the Hox cluster specifically then no there are no obvious homologues that I am aware of in yeast. There are certainly homeobox proteins found in Yeast, fungi and plants.
The origin of the HOX cluster itself is somewhat obscure as you say. They are plentiful in the basal metazoa however and the devlopment of the HOX cluster has been suggested as a major contributor to the cambrian explosion. The cnidaria are probably the most studied basal group.
Yanze N, Spring J, Schmidli C, Schmid V.
Conservation of Hox/ParaHox-related genes in the early development of a cnidarian.
Dev Biol. 2001 Aug 1;236(1):89-98.
Slightly further up though there is a lot of work on the nematodes especially C. elegans.
Aboobaker AA, Blaxter ML.
Hox Gene Loss during Dynamic Evolution of the Nematode Cluster.
Curr Biol. 2003 Jan 8;13(1):37-40.
Van Auken K, Weaver DC, Edgar LG, Wood WB.
Caenorhabditis elegans embryonic axial patterning requires two recently discovered posterior-group Hox genes.
Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4499-503.
Just a moment...
Here is a paper hot off the presses touching on the character of the protohox cluster before its split into the HOX and paraHOX clusters.
Minguillon C, Garcia-Fernandez J.
Genesis and evolution of the Evx and Mox genes and the extended Hox and ParaHox gene clusters.
Genome Biol. 2003;4(2):R12.
Application Unavailable | Springer Nature

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Mammuthus
Member (Idle past 6476 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 14 of 22 (42033)
06-04-2003 4:00 AM
Reply to: Message 13 by Wounded King
06-03-2003 5:39 PM


Hi WK,
Thanks for the references. I am actually working a bit on transposons in coelenterates but have not read up much on their dev bio.
But I am also interested if you know what the current state of research into homeobox proteins in yeast is...that they don't have a hox cluster is not surprising. But is anyone trying by phylogenetic approaches to re-create the ancestral hox gene like has been done (to a limited extent) with RNase H (I think RNase H cant remember anymore)? What do the homeobox genes do in yeast, fungi, and plants?
cheers,
M

This message is a reply to:
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Mammuthus
Member (Idle past 6476 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 15 of 22 (42038)
06-04-2003 4:19 AM
Reply to: Message 13 by Wounded King
06-03-2003 5:39 PM


Ah..just found this
Dev Genes Evol 2003 Feb;213(1):50-2 Related Articles, Links
The homeobox genes of Encephalitozoon cuniculi (Microsporidia) reveal a putative mating-type locus.
Burglin TR.
Department of Biosciences at Novum and Center for Genomics and Bioinformatics, Karolinska Institutet, Sodertorns Hogskola, Alfred Nobels Alle 7, 141 89, Huddinge, Sweden, thomas.burglin@biosci.ki.se
Homeobox genes have been found in animals, fungi, and plants. Recently, the complete genomic sequence of Encephalitozoon cuniculi has become available and it was shown that this Microsporida species is related to fungi. Given this close relatedness to fungi, I have searched the genome of E. cuniculifor homeobox genes. There are 12 homeobox genes as well as one STE12 orthologue. The large number of homeobox genes when compared to the annotations, which only list one, suggests that possibly other smaller genes may have been overlooked in the published analysis and E. cuniculi may have more than 1,997 genes. Sequence and phylogenetic analyses show that the E. cuniculi homeobox genes also fall into two distinct groups, with two TALE and ten typical homeobox genes being present. Like in the mating-type locus of yeast and other fungi, one TALE and one typical homeobox are found in close proximity of each other on the chromosome, suggesting that Microsporidia also contain a mating-type locus.
I did not realize the mating type loci were homeobox genes....cool.

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