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| Fig. 5 from https://doi.org/10.1101/109447. Panel (a) shows the exponential decrease in the rate of evolution of reaction center proteins as a function of divergence times. The max rate is about 40 times larger than the average rate seen in the Proterozoic. See the paper for more details. Panel (a) was calculated assuming an origin of photosynthesis around 3.5 billion years ago |
I have recently performed a molecular clock of ChlL and BchX, subunits of protochlorophyllide reductase chlorophyllide reductase, enzyme needed for the synthesis of chlorophyll and bacteriochlorophyll respectively. These enzymes, as you may have seen from my previous post, is related to NifH of nitrogenase and CfbC of methanogenesis. Surprisingly, the results are very similar to those of Type II reaction centers, see above. The change in the rate of evolution of ChlL/BchX of all phototrophic bacteria follows an exponential decay as well! See below:
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| Change in the rate of evolution of ChlL as a function of time. Orange are ChlL at different time points. Blue are NifH and CfbC. Both cases are fitted with an exponential decay, but the decay of the rate of evolution of nitrogenases and CfbC is not as pronounce. This were calculated assuming that the origin of life occurred around 3.8 billion years ago, quite a conservative estimate, which then locates the origin of photosynthesis at about 3.5 billion years ago. For this molecular clock analysis I used a completely different set of calibrations in comparison to the graph above. So... is it a coincidence? |
The exponential decay of Type II reaction centers needs to be explained some how. This is what we wrote in our paper, quoting:
The phenomenon described here of an initial fast rate of evolution
followed by an exponential decrease demands an explanation. Two possible
mechanisms may account for this observation. The first one is the temperature
dependent deamination of cytosine, as suggested by Lewis and coworkers (2016). They calculated that as the Earth cooled
during its first 4 Ga, the rate of spontaneous mutation would have fallen
exponentially by a factor of more than 4000. That is to say that the rate of
spontaneous mutation during the earliest stages in the history of life would
have been about three orders of magnitude greater than those observed since the
Proterozoic. Lewis and coworkers (2016) calculated that 50% of all spontaneous
mutations occurred in the first 0.2 Ga, which matches well with the exponential
decay trend seen in Fig. 5A, especially if an origin of photosynthesis is
considered to be about 3.8 Ga. The second possibility is higher UV radiation on
the planet’s surface during the early Earth in the absence of an ozone layer,
which could have resulted in rates of DNA damage up to three orders of
magnitude greater than in present day Earth, as calculated by Cockell (2000); this higher rate of damage may have led as well
to faster rates of change. Alternatively, both mechanisms could have
contributed simultaneously.
The striking differences between ChlL/BchX and nitrogenase/CfbC is kind of interesting. I wonder if the sharp decrease in the rates of Type II reaction centers and ChlL means that it may have actually been due to higher exposure to UV light, given the fact that these are phototrophic organisms, so they had to be in the photic zone... and there was not an ozone layer at that time, so UV radiation was many times greater.
To my surprise there are no detailed analysis of the change in the rates of evolution across geological time. These may actually be the first ones... I wish I could compare many more proteins of ancient origins, but it is not trivial, it takes a lot of time, and I don't have funding for a project like this at the moment.
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