Tuesday, July 13, 2010

Peroxisome Puzzles..

Gene. 2010 Jan 15;450(1-2):18-24.
Duhita N et al (Japan)

Gene. 2010 Jun 25. [Epub ahead of print]
Gabaldón T et al (Spain)

Phylogenetic analysis of Pex1/6 proteins was used as basis for determining the relatedness of these peroxins to actinobacterial or ER proteins and to determine the evolutionary ancestor of peroxisomes.
At least one of the paper has to be wrong. or there is third possibility that phylogenetic analysis of Pex1/6 itself is insufficient criteria to determine the origin of peroxisomes.!

3 comments:

  1. Hi Vishal,

    Your third possibility is actually what we conclude in the paper (Gabaldón et. al.). Pex1/6 is a highly divergent family, as illustrated by the long branches that appear in the trees and by the fact that many alternative scenarios are not statistically distinguishable from each other in terms of support from the sequence. In a previous paper (Gabaldón et. al 2006: http://www.biology-direct.com/content/1/1/8), we based the possibility of an evolutionary origin from the ER on several suggestive findings:

    - Several components (not only Pex1/6) of the import machinery show functional and sequence homology to the ER-based ERAD system.
    - The fraction of proteins with bacterial origin in the peroxisome is reduced as the family is more widespread (i.e more ancient)
    - We showed that many bacterial-derived proteins in the peroxisome are actually recently retargetted from other compartments.
    - In extant species novel peroxisomes can be formed at the ER, as shown by experiments from Henk Tabak's group.

    I agree that no current hypothesis is 100% conclusive, but I believe that current data are more compatible with an origin from within the eukaryotic cell rather than an endosymbiotic event.

    In any case, it is a fascinating discussion. Thank you for bringing this up here and congratulations on your blog.


    Toni Gabaldón

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  2. Thanks for the Comment Dr.Gabaldón.
    Current evidences do strongly suggest ER origin of peroxisomes than endosymbiotic origin.
    Thank you for the detailed insight in this conundrum.
    I get fascinated by some unique organisms that lack many of the common organelles. for e.g Giardia which lacks peroxisomes, mitochondria and golgi. How do they carry out the pathways normally localized in these organelles? I dont know if they have (Bioinformatically!)similar proteins with organelle targetting signals but no organelles at all! What is your opinion?

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  3. Hi Vishal,

    These examples are indeed fascinating. Actually in the case of mitochondria these organisms do possess highly reduced mitochondria, called mitosome or relic mitochondrion, that lacks DNA and most of the typical pathways, but they still transport some proteins there like those involveed in Fe-S clusters assemblies.
    For the case of peroxisomes, some organisms do clearly like them. For most of them it looks like secondary losses, with peroxisomal pathways being lost or present elsewhere in the cell. In any case, there is still much research to be done in that direction.

    I discuss some of these aspects in a recent review:
    http://rstb.royalsocietypublishing.org/content/365/1541/765.abstract

    you may be interested in reading it.

    Nice talking to you.

    Cheers, Toni

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