Irreducible complexity and the flagellum

From: Peter Ruest (pruest@pop.mysunrise.ch)
Date: Thu Oct 24 2002 - 00:53:24 EDT

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    Some time ago, on this list, Behe's and Dembski's use of the bacterial
    flagellum as a system of irreducible complexity was dismissed with the
    claim that it probably evolved out of the type III protein secretion
    system. I tried to check the evidence available to support this claim.

    A comprehensive review of the type III system is found in Hueck C.J.,
    "Type III protein secretion systems in bacterial pathogens of animals
    and plants", Microbiology and Molecular Biology Reviews 62 (1998),
    379-433.

    The type III system investigated most thoroughly is the one of the pest
    (or bubonic plague) pathogen Yersinia pestis and two other Yersinia
    species. There are 10 genes showing some sequence similarity between the
    Yersinia type III system and flagellar proteins (of Escherichia coli,
    Salmonella typhimurium, and Bacillus subtilis). All of these flagellar
    proteins belong to the basal body of the flagellum which is inserted
    into the cytoplasmic (inner) membrane. According to Hueck's drawing, the
    basal body of the flagellar system consists of the MS (outer) and C
    (inner) rings, encased in what I call the bearing, and the ATPase
    attached on the cytoplasmic side. The basal body constitutes (together
    with other components) the export system for flagellar constituents and
    the driving machinery for flagellar rotation. The corresponding Yersinia
    proteins also belong mostly to the part of the type III system
    presumably embedded in the cytoplasmic membrane. At least 30 other
    proteins of the flagellar system, comprising the flagellar hook, the
    connection (P ring) of the hook to the basal body, the bearing (L ring)
    of the hook within the outer membrane, and the flagellum proper, have no
    homologs in the type III system. The Yersinia type III system, as well,
    comprises at least 25 other proteins having no homologs in the flagellar
    system. The 10 presumed homologs (or partial homologs) are as follows:

    Flagellum: Length: Location: Function: Type III: Length: Function:
    FliF 560 MS ring YscJ 236
    FliG 331 C ring torque YscD 419
    FliN 137 C ring YscQ 307
    FliH 235 bearing 1 YscL 223
    FliP 245 bearing 2 YscR 217
    FliQ 89 bearing 3 YscS 88
    FliR 261 bearing 4 YscT 261
    FlhB 383 bearing 5 export YscU 354
    FlhA 692 bearing 6 LcrD 704 export
    FliI 456 cytoplasm ATPase YscN 439 ATPase

    The flagellum proteins are those of E.coli or S.typhimurium, the type
    III system proteins those of Y.pestis, Y.pseudotuberculosis, or
    Y.enterolytica. The lengths are in amino acid residues. The location of
    most type III system proteins is unknown, but inferred from that of the
    flagellar homologs. The functions are usually unknown.

    Synteny in the genome is restricted to FliP-Q-R with YscR-S-T.

    The similarities between the FliP-Q-R / YscR-S-T systems and
    (especially) the FliN-G / YscD-Q systems are weak.

    In some cases, e.g. FliF / YscJ, the similar proteins are probably
    unrelated. The FliF-like domain in YscJ may reflect their binding to
    other components of the export apparatus. Systems III are unlikely to
    have an MS ring analog, but may form a bridge across the periplasm to
    the outer membrane.

    FliI / YscN, which have ATPase activity, show similarities to the alpha
    and beta subunits of the F1 component of the F0F1 proton translocating
    ATPases; the most highly conserved regions are two GTP-binding domains
    and the Mg2+-binding motif around the ATPase-catalytic domain. FliI
    provides the energy for the export of flagellum units. The similarity
    between FliI and YscN appears to be due to similar requirements of their
    common ATPase functions.

    Thus, the flagellum and the type III export system are two very complex
    systems composed of a few dozen specific proteins, of which 25-30% show
    some sequence similarities between the two systems. The 10 similar
    proteins constitute the majority of the proteins found in all type III
    export systems, as well as the flagellar basal body, whereas the parts
    of the type III systems lying outside the cytoplasmic membrane show
    homologies to different export systems, such as the type II secretion
    systems and other transport pathways, but not to the flagellar system.
    Hueck therefore suggests that the type III system may have evolved from
    a combination of a flagellar basal body and a type II secretion system.
    Notice that he doesn't propose that the flagellar system arose from a
    type III export system!

    In any case, the similarities between flagellum and type III export are
    very restricted, making any derivation claim highly speculative. Whether
    the sequence similarities which do exist derive from divergence from
    common ancestral genes or from functional convergences remains equally
    uncertain.

    Does this situation "explain" the flagellum and demonstrate that it is
    not "irreducibly complex"? I doubt it. The claim remains to be
    substantiated.

    Peter

    -- 
    Dr. Peter Ruest, CH-3148 Lanzenhaeusern, Switzerland
    <pruest@dplanet.ch> - Biochemistry - Creation and evolution
    "..the work which God created to evolve it" (Genesis 2:3)
    


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