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Author Topic:   Nature's Engines and Engineering
Wounded King
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Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


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Message 6 of 15 (668351)
07-20-2012 6:38 AM
Reply to: Message 1 by Genomicus
07-19-2012 6:52 PM


Lets do Science!
In particular, the design hypothesis predicts that molecular clocks will show that proteins with rapid substitution rates will have a later origin, while proteins with slow substitution rates will have an early origin.
Interesting, so on reading this I said to myself "Self, there must be some sort of data on substitution rates in flagellar proteins out there." I went looking but only found a couple of papers from a few basic search terms. One paper, Toft and Fares (2008), was focused on looking at the degeneration and neofunctionalisation of flagellar proteins in bacteria that were endosymbionts. This wasn't particularly relevant in itself but one of the sets of data they collected included synonymous and non-synonymous substitution rates in both endosymbiotic and free living bacteria, see supplementary data.
Since it is protein evolution we are interested in I took the non-synonymous values for the free-living bacteria and ranked them. Sadly they only looked at the genes which were still present in the endosymbiotic bacteria so there was no data for MotA/B or for FliJ.
This very first glance approach doesn't look great for your theory; out of 510 genes they had data for FliG was 303rd in terms of non-synonymous substitution rate with a rate of 0.0208 substitutions per site compared to 0.0525 for FliI (ranked 123rd) and 0.1029 for FliH (ranked 19th).
*ABE* I found amino acid and DNA sequences for FliJ, MotA and MotB from E. coli and S. typhimurium and used the PAML software to find a dN value. The values were as follows, MotA: 0.0389; MotB:0.0538; FliJ:0.0633.
So going by the substitution rates from highest to lowest the order comes out as FliH, FliJ, MotB, FliI, MotA and finally FliG. This seems to be almost exactly the opposite of what your theory predicts. Obviously we are missing the second variable of how much modification was needed for each particular protein to adapt it from the original.*/ABE*
Of course these were values from only a couple of bacterial species, E. coli and Salmonella typhimurium, so a wider survey might well turn up different average rates. It shouldn't be impossible to extract the protein sequence for the 6 proteins from your example from the NCBI, in fact the difficult part would be deciding which species to restrict ourselves to since, for example, there are ~26,000 entries for MotA. Maybe we could choose a dozen or so commonly studied bacteria or follow a strategy like Liu and Ochman (2007) and take 1 species from each of the 11 large bacterial groupings they identify since they are all species with flagellar systems.
Do you think this would be a worthwhile project?
TTFN,
WK
Edited by Wounded King, : Added values for MotA, MotB and FliJ.

This message is a reply to:
 Message 1 by Genomicus, posted 07-19-2012 6:52 PM Genomicus has replied

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 Message 11 by Genomicus, posted 07-20-2012 1:40 PM Wounded King has not replied
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