Evolvability due to Tandem Repeat Slippage

This forum is for the discussion of the evidence for evolution. Anyone is welcome to post, however, scripture is not allowed. As the title says, Science Only please!

Moderator: Moderators

Evolvability due to Tandem Repeat Slippage

Postby Timothy Chase » Sun Oct 22, 2006 6:44 pm

On another thread:

http://www.bcseweb.org.uk/forum/viewtopic.php?p=889#889

... Mikey and I touched on evolvability and how it itself is a product of the process of evolution - although the extent to which it itself is selectable is an open question. However, there is one area which may be of particular interest along these lines.

Variable Length Tandem Repeats

In recent literature, there is a fair amount of discussion involving tandem repeat slippage in variable length repeats. Much of the slippage being discussed is in coding sequences - which is a great deal easier to analyse than that we occurs in the promoter regions where transcription factors (typically regulatory proteins, although structural proteins may also act as transcription factors) bind to genetic sequences acting as inputs which determine the extent to which the protein which a gene codes for gets transcribed. Additionally, tandem repeats are being found in introns which control alternate splicing - and thus give rise to different proteins being coded for by the same gene.

PZ Meyers dealt with one of the technical papers a while back in his post:

Tandem repeats and morphological variation
Monday, January 03, 2005
http://pharyngula.org/index/weblog/comm ... variation/


This was in reference to the article at:

Molecular origins of rapid and continuous morphological evolution (YES!)
John W. Fondon, III *, and Harold R. Garner
PNAS | December 28, 2004 | vol. 101 | no. 52 | 18058-18063
http://www.pnas.org/cgi/content/full/101/52/18058


In essence, Fondon and Garner were able to trace much of the morphological variation in dogs back to variable numbers of amino acids in transcription factors - where this variability is itself the result of the variable length tandem repeats which code for these transcription factors.

Likewise, the antifreeze proteins of polar fishes appear to be the result of variable length tandem repeats. Here are a few articles in the area:

Cheng, C.-H.C. and DeVries, A.L. (2002) Origins and evolution of fish antifreeze proteins. In Molecular Aspects of Fish and Marine Biology Vol.1 - Monograph on Fish Antifreeze Proteins (Eds. C. Hew and V. Ewart), pp. 83-108, World Sci. Press, New Jersey.

Cheng, C.-H.C. and L. Chen (1999) Evolution of an antifreeze glycoprotein. Nature 40: 443-444.

Cheng, C.-H.C. (1998) Origin and mechanism of evolution of antifreeze glycoproteins in polar fish. In Evolution of the Antarctic Ichthyofauna (Eds. G. di Prisco and E. Pisano), pp. 311-328, Springer-Verlag, Italy.

Conservation of antifreeze protein-encoding genes in tandem repeats
Davies PL., Gene. 1992 Mar 15;112(2):163-70.
(Abstract) http://www.ncbi.nlm.nih.gov/entrez/quer ... t=Abstract


The following is are two articles on the role of variable length tandem repeats in the regulation of alternative splicing:

Non-technical:
New Study Explains Process Leading To Many Proteins From One Gene
Date: April 14, 2005
http://www.sciencedaily.com/releases/20 ... 142734.htm

Technical:
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats
Yun Lian and Harold R. Garner
Bioinformatics 2005 21(8 ):1358-1364
http://bioinformatics.oxfordjournals.or ... /21/8/1358


Likewise, here is an article on tandem repeats in a promoter region:
Technical:
Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila
Saurabh Sinha and Eric D. Siggia
Molecular Biology and Evolution 2005 22(4):874-885
http://mbe.oxfordjournals.org/cgi/content/full/22/4/874


But why are variable length tandem repeats and tandem repeat slippage important?

Because this form of mutation (where due to a kind of stuttering during the process DNA duplication occurs with repeat sequences - such as CGG, triplets will be added or subtracted from the genetic sequence) is up to a 100,000 times faster in modifying a genetic sequence. Incidentally, there is at least one other mechanism by which variable length tandem repeats may grow or shink - a process of unequal crossover during sexual recombination.

Here are a couple of articles on this:
Technical REVIEW
Mini- and microsatellite expansions: the recombination connection
Guy-Franck Richard & Frederic Paques
EMBO reports 1, 2, 122-126 (2000)
http://www.nature.com/embor/journal/v1/ ... bor606.pdf

Expansions and Contractions in a Tandem Repeat Induced by Double-Strand Break Repair
FREDERIC PAQUES, WAI-YING LEUNG, AND JAMES E. HABER
MOLECULAR AND CELLULAR BIOLOGY, Apr. 1998, p. 2045-2054 Vol. 18, No. 4


But where do such tandem repeats come from?

Although it is possible for them to originate, for example, as the result of point mutations, at least with the shorter sequences, larger tandem repeats are the result of retroelements.

Please see:
Technical REVIEW
Origin, evolution and genome distribution of microsatellites
Eder Jorge Oliveira, Juliano Gomes Pádua, Maria Imaculada Zucchi, Roland Vencovsky and Maria Lúcia Carneiro Vieira
Genetics and Molecular Biology, 29, 2, 294-307 (2006)
http://www.scielo.br/pdf/gmb/v29n2/a18v29n2.pdf


Furthermore, retroelements appear to be the relics of past retroviral invasions of the genome. As such, a great deal of the evolution of multicellular life is evidentally driven by the engine of retroviruses - which insert their sequences into the genomes of organisms, and, over time, these sequences become duplicated and then are subject to tandem repeat slippage.
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Evolvability due to Tandem Repeat Slippage

Postby Anonymous » Sun Oct 22, 2006 6:49 pm

Hi Timothy,

Here is the reference I was referring to:

Evolvability is a selectable trait
David J. Earl and Michael W. Deem
PNAS 2004;101 11531-11536
http://www.pnas.org/cgi/content/abstrac ... 11531?etoc

It will be freely available in pdf at the url.

Mike
Anonymous
 

Re: Evolvability due to Tandem Repeat Slippage

Postby Timothy Chase » Sun Oct 22, 2006 9:03 pm

mikeybrass wrote:Hi Timothy,

Here is the reference I was referring to:

Evolvability is a selectable trait
David J. Earl and Michael W. Deem
PNAS 2004;101 11531-11536
http://www.pnas.org/cgi/content/abstrac ... 11531?etoc

It will be freely available in pdf at the url.

Mike


Sounds great! I will be checking it out - although I might wait until I feel a little better. (Sinus headache, etc. - with me, stuff will bounce around a bit.)
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Postby molecanthro » Mon Oct 23, 2006 12:54 pm

During my undergraduate work in genetics, I read what I think is a really good book in this area: http://www.amazon.com/Darwin-Genome-Molecular-Strategies-Biological/dp/0071378227
'Darwin in the Genome' by Lynn Helena Caporale.
It's a good, accessible book about the non-randomness of mutations.
I think it would be worth a read.
Also, suprisingly, she had a webchat on Dembski's International Society for Complexity, Information, and Design http://www.iscid.org/lynn-caporale-chat.php
I like how she shut them down early with the statement:
But first, bottom line, my observations do not require an external intelligenct agency.

I think research into the evolution of evolvability and the non-randomness of mutations is going to be able to answer many questions. It would definately be something that I would be interested in looking into further. Thanks for those links. I'm currently researching Short tandem repeats, SNPs, and mtdna, but looking for an interesting side project and ideas for a PhD project I hope to begin next year. Are there any other evolutionary geneticists on this forum?
User avatar
molecanthro
 
Posts: 65
Joined: Mon Oct 16, 2006 8:29 pm
Location: London/Cambridge

Postby Timothy Chase » Mon Oct 23, 2006 2:05 pm

molecanthro wrote:'Darwin in the Genome' by Lynn Helena Caporale.
It's a good, accessible book about the non-randomness of mutations.
I think it would be worth a read.


I haven't had a chance to look at the book as of yet, but if I remember correctly, what she means by "non-randomness" is somewhat different from what is normally spoken of as non-randomness by geneticists. When an organism is under stress (e.g., e coli), mutations are more likely to occur, and with a marked preference for some locations over others, but whether these mutations are beneficial or detrimental to the organism is random. Stress, for example, results in the production of mutators.

Anyway, I am sure I have one of here articles here, but I am having a little difficulty looking it up at the moment. However, I did find the following link in among the stuff I've referenced:

Evolution of Evolution
Genomic Strategies for Evolutionary Adaptation:
The rate, location and extent of genetic variation is not monotonous
Lynn Helena Caporale
http://www.ceptualinstitute.com/genre/c ... le_IJ2.htm

There she deals with how the genetic code has been to some extent optimised for handing point mutations - due to its redundancy - something which I had mentioned in the earlier thread with Mikey.

molecanthro wrote:Also, suprisingly, she had a webchat on Dembski's International Society for Complexity, Information, and Design http://www.iscid.org/lynn-caporale-chat.php
I like how she shut them down early with the statement:
But first, bottom line, my observations do not require an external intelligenct agency.


A while back, Wells presented a paper there on the intelligent design "metatheory," that is, not actually something to be regarded as a theory in itself, but as a kind of framework for generating other theories. Real scientists came in, apparently as some kind of favour, then properly tore it to sheds. Her going there does not put her in a bad light, but I would personally advise no one to even inadvertently help them in maintaining their sham.

molecanthro wrote:I think research into the evolution of evolvability and the non-randomness of mutations is going to be able to answer many questions. It would definately be something that I would be interested in looking into further. Thanks for those links. I'm currently researching Short tandem repeats, SNPs, and mtdna, but looking for an interesting side project and ideas for a PhD project I hope to begin next year. Are there any other evolutionary geneticists on this forum?


The hypermutations which result from tandem repeat slippage is one of those areas, but there are others. For example, a transposon in the genetic code for nerve cells in the mammalian brain is responsible for their overproduction - so that those which make the "right" connections are preserved, and those which make the wrong connections undergo "programmed" cell death - apoptosis. This results in the unprecedently plasticity of the mammalian brain - when compared, for example, to the reptilian.

Likewise, the adaptive immune system has harnessed two transposons which are responsible for its ability to adapt to new pathogens - another instance of hypermutations. Then, if I remember correctly, there is a DNA virus which apparently underwent some form of fusion with an RNA virus, then uses the RNA during its replication to change its surface proteins to avoid recognition.
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Slippage Promoting Variation in Behavior...

Postby Timothy Chase » Mon Oct 23, 2006 3:43 pm

Here is another example of tandem repeat slippage in action - or at least what John Hawks refers to as microsatellite length polymorphisms - where microsatellites are shorter tandem repeats, and the length polymorphisms might possibly be due to unequal crossover during recombination rather than slippage. This time it is in the promoter regions of genes for neurotransmitters and hormones within voles affecting vole behaviour.

Microsatellite mutation and brain variation
http://www.johnhawks.net/weblog/reviews ... ior_2005.w
John Hawks wrote:Elizabeth Hammock and Larry Young (2005) report in Science that variation in behavioral traits among different species of voles is partly controlled by variation in microsatellite loci linked to neuroactive genes....

The theme here is that length polymorphisms in the regulatory regions of genes may have important impacts on gene expression. There are likely many genes related to behavioral variation. These include those coding for neurotransmitters and hormones, as well as genes related to the development of neural and brain structure. But most neurotransmitters and hormones are highly conserved molecules in vertebrates -- their gene sequences and consequent gene products have relatively little functional variation. The way that these molecules affect behavior is primarily modulated by the regulation of the genes. This makes mechanisms like microsatellite length polymorphisms potentially very important.
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Postby Timothy Chase » Mon Oct 23, 2006 3:52 pm

The article which John Hawks mentions on his blog requires a subscription to Science. However, I found another, earlier article by the same two authors on the same subject, and they likewise deal with the variation in vole behavior due to hypermutative microsatellite instability:

Functional Microsatellite Polymorphism Associated with Divergent Social Structure in Vole Species
Elizabeth A. D. Hammock and Larry J. Young
Mol. Biol. Evol. 21(6):1057-1063. 2004
http://mbe.oxfordjournals.org/cgi/conte ... /21/6/1057
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Postby Timothy Chase » Mon Oct 23, 2006 4:13 pm

Here is another open access article, this one from 2004, which investigates the distribution of microsatellites within the genome, that is, the extent to which they belong to intronic regions involved in alternate splicing, coding regions, promoter regions, or perhaps just to non-functional regions.

Microsatellites Within Genes: Structure, Function, and Evolution
You-Chun Li, Abraham B. Korol, Tzion Fahima and Eviatar Nevo
Mol. Biol. Evol. 21(6):991-1007. 2004
http://mbe.oxfordjournals.org/cgi/conte ... t/21/6/991
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Re: Evolvability due to Tandem Repeat Slippage

Postby Timothy Chase » Mon Oct 23, 2006 7:52 pm

mikeybrass wrote:Hi Timothy,

Here is the reference I was referring to:

Evolvability is a selectable trait
David J. Earl and Michael W. Deem
PNAS 2004;101 11531-11536
http://www.pnas.org/cgi/content/abstrac ... 11531?etoc

It will be freely available in pdf at the url.

Mike


Actually, I had been thinking about that article when I included the question of whether evolvability is selectable. (Personally, I strongly believe it is - but I like to try and be conservative in my assertions - at least until I believe the mainstream of a given field has caught up.) Moreover, the view that it may be goes back at least as far as Gould and Eldridge's punctuated equilibria theory - where species which are better equipped to evolve (jacks of all trades rather than heavily invested specialists) would be more likely to have descendant species which adapt to a changing environment.

Anyway, here are some other articles which may be of interest along the same lines:

Stability and the Evolvability of Function in a Model Protein
Jesse D. Bloom * , Claus O. Wilke , Frances H. Arnold and Christoph Adami
Biophysical Journal 86:2758-2764 (2004)
http://www.biophysj.org/cgi/content/full/86/5/2758

Evolution of Genetic Potential
Lauren Ancel Meyers1,2*, Fredric D. Ancel3, Michael Lachmann4
Volume 1 | Issue 3 | AUGUST 2005
http://compbiol.plosjournals.org/perlse ... bi.0010032
(three distinct steady state conditions: (1) organismal flexibility, (2) genetic potential, and (3) genetic robustness.)

The Origin of Evolutionary Novelty
New Perspectives from Developmental Biology
http://www.mun.ca/biology/scarr/2900_Ev ... ovelty.htm
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Postby Timothy Chase » Sun Oct 29, 2006 6:19 pm

molecanthro wrote:During my undergraduate work in genetics, I read what I think is a really good book in this area: http://www.amazon.com/Darwin-Genome-Molecular-Strategies-Biological/dp/0071378227
'Darwin in the Genome' by Lynn Helena Caporale.
It's a good, accessible book about the non-randomness of mutations.


I just picked up the book - and it is going through much of the cutting-edge stuff, the targetted mutations involved in the adaptive immune system, the tandem repeat instabilities in the coding and promoter regions, the differences between various tandem repeats, hairpins, cruciforms, and structures I didn't even know about before - as well as a kind of overview of the mechanics involved - which is typically absent from the technical papers as it is commonly understood by those who read them. While highly accessible, it is also a fairly dense overview of much of what I consider the revolutionary developments of the past couple or so decades and what is often cutting-edge today.

I am going to find it helpful. I am also thinking of recommending it to my wife - a lit major who normally wouldn't get into this sort of thing. (She is much more at home in 19th and 20th century literature.) I think she would enjoy it - and would like the prose.

My only real complaint (other than the letter games) is that there aren't really any technical terms - they help me look things up. But you have the names of scientists and the names of organisms - so that should be enough.

In any case, thank you for recommending it. I had thought about getting it before, but it was your recent recommendation which made the difference.
User avatar
Timothy Chase
 
Posts: 532
Joined: Sat Oct 07, 2006 4:59 pm

Postby molecanthro » Sun Oct 29, 2006 6:33 pm

Yeah, I found the letter games annoying as well but I seem to remember her warning her readers about them. Glad you're liking it so far. I will probably give it another read as well now that I more fully understand the concepts. Though I'm going to be busy for the next few weeks interviewing for PhD positions...wish me luck.
User avatar
molecanthro
 
Posts: 65
Joined: Mon Oct 16, 2006 8:29 pm
Location: London/Cambridge

Postby Roger Stanyard » Sun Oct 29, 2006 7:03 pm

molecanthro wrote:Yeah, I found the letter games annoying as well but I seem to remember her warning her readers about them. Glad you're liking it so far. I will probably give it another read as well now that I more fully understand the concepts. Though I'm going to be busy for the next few weeks interviewing for PhD positions...wish me luck.


Best of luck there Mark!

Roger
User avatar
Roger Stanyard
Forum Admin
 
Posts: 6162
Joined: Sat Oct 07, 2006 4:59 pm


Return to Science Only

Who is online

Users browsing this forum: No registered users and 3 guests