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The Bacterial Flagellum and Homology

December 25, 2011

The Bacterial Flagellum and Homology

In this brief analysis, I’m going to discuss the bacterial flagellum and the homology a number of its components share with non-flagellar proteins. The below table is a list of flagellar proteins found in the genus Salmonella, their length in terms of amino acid residues, and their homologs (if any). Protein lengths were taken from UniProt, and the data on homologs were taken from Pallen and Matzke’s 2006 paper in Nature Reviews Microbiology, “From the Origin of Species to the origin of bacterial flagella.”

Flagellar Protein Length (amino acid) Homology with non-flagellar proteins?
FlgA 219 Yes (CpaB)
FlgBCFG 138; 134; 251; 260 No; but homology with FlgBCEFGK
FlgD 232 No
FlgE 403 No; but homology with FlgBCFGK
FlgH 221 No
FlgI 367 No
FlgJ 316 No
FlgK 553 No; but homology with FlgBCEFG
FlgL 317 No; but homology with FliC
FlgM 97 No
FlgN 140 No
FlhA 692 Yes (YscV)
FlhB 383 Yes (YscU)
FlhDC 113; 192 Yes (other activators)
FlhE 130 No
FliA 239 Yes (RpoD, RpoH, RpoS)
FliB 401 No
FliC 200 Yes; homology with FlgL and EspA
FliD 467 No
FliE 104 No
FliF 579 Yes (YscJ)
FliG 331 Yes (MgtE)
FliH 235 Yes (YscL; AtpFH)
FliI 456 Yes (YscN; AtpD; Rho)
FliJ 147 Yes (YscO)
FliK 405 Yes (YscP)
FliL 155 No
FliM 334 Yes (FliN; YscQ)
FliN 137 Yes (FliM; YscQ)
FliO 125 No
FliP 245 Yes (YscR)
FliQ 89 Yes (YscS)
FliR 264 Yes (YscT)
FliS 135 No
FliT 122 No
FliZ 183 No
MotA 295 Yes (ExbB; TolQ)
MotB 309 Yes (ExbD; TolR; OmpA)

When these figures are added up, we get a total of 12,322 amino acid residues. Thus, it appears that Salmonella flagella are composed of roughly 12,322 amino acid residues. What percent of the Salmonella flagellum, in terms of amino acid residues, has absolutely no known homologs? A total of 3,195 amino acid residues belong to proteins in the flagellum that have no known homologs. This means that approximately 25.9% of the Salmonella flagellum lacks sequence homology.  Now, you will notice that a number of flagellar proteins only have homologs in the type III secretion system. However, the type III secretion system (TTSS) is not a pre-cursor system to the bacterial flagellum. It probably evolved directly from the flagellar export system (do note that Gophna et al. 2003 are a dissenting view, but in my humble opinion, the evidence is certainly in favor of the hypothesis that the type III secretion system evolved from flagella). So we can ask the question: what percent of the flagellum lacks homologs or only has homologs in the TTSS, which is not a pre-cursor system to the flagellum? A total of 2,804 amino acid residues only share sequence homology with TTSS components. This is added to 3,195, to get 5,999. Thus, approximately 48.7% of the Salmonella flagellum has no known homologs in systems that would pre-date the flagellum.  Finally, we ask the question: what percent of the flagellum have no known homologs in non-flagellar systems? Note that a number of flagellar proteins only share homology with other flagellar proteins and TTSS components. For example, FliM is homologous to FliN and YscQ. FliN is only homologous to FliM and YscQ. Since YscQ could not be a pre-cursor protein, one of these proteins do not share homology with a pre-cursor protein. If FliM is supposed to be a pre-cursor to FliN, then the homology FliN shares with FliM cannot be evidence that FliM descended through non-teleological evolution.  To arrive at a percent of the flagellum that has no homologs that provide evidence of a non-telic origin of the flagellum, in cases like FliM/FliN we will use the shorter protein. This will allow us to be as fair as possible to the non-telic position. We arrive at a total of 471 amino acid residues. Add this to 5,999 and about 52.5% of the Salmonella flagellum has no homologs that provide evidence of a non-teleological origin.

Conclusion

Several flagellar proteins only share structural similarity with other proteins. However, structural similarity can often be the result of convergent evolution – there are only a few thousand different protein folds, contrasted with trillions of different possible amino acid sequences.  Further, in some instances, sequence similarity can also be the result of convergent evolution.

From this brief analysis in this article, I found that more than half of the Salmonella flagellum, in terms of amino acid residues, lack any homologs that provide evidence that it evolved through non-teleological mechanisms.  Some of the remaining homologs can hardly be called significant. The flagellar protein, FliG, shares only about 20% sequence similarity with its only homolog, MgtE.  Also, from the angle of intelligent intervention, where the flagellum was designed at the dawn of life, the remaining proteins it does share fairly significant sequence similarity with could possibly be explained by convergent evolution. I suggest that convergent evolution at the molecular level may be more pervasive than many think.

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3 Comments leave one →
  1. themayan permalink
    March 6, 2012 1:48 am

    I’m not a scholar but I think this is at least some evidence for Behe’s argument. Am I wrong? Did I misunderstand?

    • March 6, 2012 3:39 am

      You are basically correct. The origin of the flagellum is still quite an obstacle to Darwinian evolution, and the evidence for the thesis that it evolved through non-teleological mechanisms is just a bit weak. As I show here, over half of the canonical (“classic”) flagellum has no known sequence homology with components that would be evolutionarily meaningful. If we find that the type III secretion system and the flagellum share a common ancestor, then my position would be weakened. But if the evidence indicates that the type III secretion system arose directly from the flagellar system, my teleological position would be strengthened. So, from the perspective of intelligent intervention, I predict that the type III secretion system arose from the flagellum.

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  1. Evolution of the the Bacterial Flagellum |Secret Done

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