Case study B · Investigate the molecules

The bacterial flagellum

A rotary motor in the cell envelope of many bacteria, driven by ion flow, that turns a long helical propeller. It is the best-known example in the irreducible-complexity debate, and also one of the best-studied machines in biology.

Drag to rotate · scroll to zoom · click a part. Schematic; not to scale (the filament is shortened about 100-fold).

Select a part, in the model or the list, to see its proteins, its job, the parts it works with, related systems elsewhere in biology, and what happens when the gene for it is knocked out.

The argument, and the replies

Irreducible complexity

The argument

Michael Behe (1996) defined an irreducibly complex system as one made of several well-matched, interacting parts that all contribute to the basic function, where removing any one part stops the system working. Such a system, he argued, cannot be produced directly by successive slight modifications of a precursor, because any precursor missing a part would not work. He offered the flagellum as an example.

The knock-outs in the model above are real: without stator units the flagellum is built but cannot turn; without the export gate nothing is built beyond the base.

The replies

Critics, including Miller (2004) and Pallen & Matzke (2006), accept that the argument rules out a direct route but say it does not rule out indirect ones, in which parts first served other functions and were co-opted. Many flagellar parts do have relatives elsewhere: the export gate in the injectisome, the ATPase in ATP synthase, the stator's architecture in other ion-driven motors.

Proponents answer that homologous parts are not a demonstrated pathway. Each step would still need to be functional and selectable, and no such series has been shown experimentally. The phylogenetic finding that the injectisome descends from the flagellum (Abby & Rocha 2012) bears on which parts could have been precursors.

Evidence and debate

Weighing the evidence

Addresses: The emergence of molecular machinesBiological evolution

01 What is observed?

  • EstablishedIn E. coli and Salmonella the flagellum is built from about two dozen structural proteins, and its gene clusters can include more than 50 genes when assembly and regulation are counted. (Liu & Ochman 2007; Macnab 2003)
  • EstablishedTorque comes from stator units (MotA/MotB, or PomA/PomB in sodium-driven motors) that pass ions across the inner membrane. E. coli motors hold at least 11 stator units, and strains lacking stator proteins build flagella that cannot turn. (Reid et al. 2006; Berg 2003)
  • EstablishedEach stator unit is a ring of five MotA around two MotB (A₅B₂). The same architecture appears in other ion-driven bacterial motors. (Santiveri et al. 2020; Deme et al. 2020)
  • EstablishedAssembly runs from the inside out. The export apparatus at the base sends rod, hook and filament subunits up the hollow centre to the growing tip, and assembly checkpoints control the order in which genes switch on. (Macnab 2003; Chevance & Hughes 2008)
  • EstablishedExport is driven mainly by the proton-motive force. Cells lacking the FliI ATPase can still export, weakly. (Minamino & Namba 2008; Paul et al. 2008)
  • EstablishedThe flagellar export apparatus is homologous to the injectisome (non-flagellar type III secretion system) that many pathogens use to inject proteins into host cells. Its ATPase, FliI, closely resembles the α/β subunits of F₁-ATP synthase, and FliJ resembles that enzyme's γ subunit. (Abby & Rocha 2012; Wagner et al. 2018; Imada et al. 2007; Ibuki et al. 2011)
  • EstablishedMotors differ between species: some have wider stator rings and extra scaffolding that produce more torque. (Beeby et al. 2016; Minamino & Imada 2015; Johnson et al. 2021)
  • EstablishedThe archaeal 'flagellum' is an unrelated machine whose structure resembles bacterial type IV pili. It has been renamed the archaellum. (Jarrell & Albers 2012)

02 What does evolutionary theory propose?

  • Active researchThe core axial proteins (rod, hook, filament) are related to one another, which suggests they arose by repeated duplication and modification of a few precursor genes, or even a single one. (Liu & Ochman 2007)
  • SpeculativeThe flagellum was assembled from parts that first served other functions (co-option, or exaptation): a protein-export system, an ion channel, adhesive filaments. On this view no 'leap' is needed. (Pallen & Matzke 2006; Pallen & Gophna 2007; Miller 2004)
  • Active researchPhylogenomic analysis of more than 1,000 genomes indicates that the injectisome evolved from the flagellum, not the other way round. Machines can be repurposed into new, equally complex machines. (Abby & Rocha 2012; Gophna et al. 2003)

03 What are the unresolved questions and criticisms?

  • Active researchBehe argued that a system of several interacting parts, each needed for the basic function, cannot be produced directly by numerous successive slight modifications. He called such systems irreducibly complex, with the flagellum as his example. Knockouts do abolish motility: without stators the filament does not turn, and without the export apparatus nothing beyond the base is built. (Behe 1996; Reid et al. 2006; Macnab 2003)
  • Active researchCritics reply that the argument rules out only direct routes. Indirect routes, in which parts are borrowed from other systems and change function along the way, are not excluded, and homologies show that many parts do have relatives elsewhere. (Miller 2004; Pallen & Matzke 2006)
  • Active researchHomology shows that parts share ancestry; it does not by itself show a pathway in which every intermediate worked and was selected. No such step-by-step pathway has been demonstrated experimentally. Pallen & Matzke described what an experimental programme might look like. (Pallen & Matzke 2006)
  • Active researchIf the injectisome is derived from the flagellum, it cannot be the flagellum's ancestor. What the export system did before the flagellum existed is not known. (Abby & Rocha 2012)

04 What evidence would help distinguish competing explanations?

  • Laboratory evolution of motility from a cell given only part of the system.
  • Natural intermediate systems with a demonstrated, selectable function. Abby & Rocha describe an intermediate form of the injectisome that still exists in Myxococcales.
  • Resurrected ancestral axial and export proteins, tested for the activities a proposed pathway requires.
  • For each proposed step, an estimate of how many coordinated changes it needs. Those numbers can then go into the Probability Simulator's population-genetics model.

Established Measured or observed repeatedly; not in serious dispute.Active research An open research question, or a claim that specialists still dispute.Speculative A proposed explanation that has not yet been tested directly.

Methodology and limitations

How this works, and what it leaves out

Method

  • The model follows the architecture of the Salmonella and E. coli flagellum described in reviews and cryo-EM structures (Macnab 2003; Berg 2003; Minamino & Imada 2015; Johnson et al. 2021). Shown are 12 components and 11 stator units (E. coli motors can hold at least 11; Reid et al. 2006).
  • Knock-out effects summarise published mutant phenotypes, with sources on each component.
  • Pressing "clockwise" reverses the rotor, as happens when CheY-P binds the C ring.

Limitations

  • Schematic: shapes and proportions are approximate, and the filament is shortened about 100-fold. Positions of the export gate and ATPase are simplified.
  • Flagella vary between species in stator number, scaffolds and sheaths (Beeby et al. 2016); this is one well-studied type.
  • Knock-outs here remove one part at a time. Real mutations can be partial, and a few phenotypes, such as the FliH–FliI double mutant, are leaky.
Your conclusions

Before you move on

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References

  1. Abby SS, Rocha EPC (2012). The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genetics 8:e1002983. doi:10.1371/journal.pgen.1002983
  2. Beeby M, Ribardo DA, Brennan CA, et al. (2016). Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold. PNAS 113:E1917–E1926. doi:10.1073/pnas.1518952113
  3. Behe MJ (1996). Darwin's Black Box: The Biochemical Challenge to Evolution. Free Press. Book, not a peer-reviewed journal article.
  4. Berg HC (2003). The rotary motor of bacterial flagella. Annual Review of Biochemistry 72:19–54. doi:10.1146/annurev.biochem.72.121801.161737
  5. Chevance FFV, Hughes KT (2008). Coordinating assembly of a bacterial macromolecular machine. Nature Reviews Microbiology 6:455–465. doi:10.1038/nrmicro1887
  6. Deme JC, Johnson S, Vickery O, et al. (2020). Structures of the stator complex that drives rotation of the bacterial flagellum. Nature Microbiology 5:1553–1564. doi:10.1038/s41564-020-0788-8
  7. Gophna U, Ron EZ, Graur D (2003). Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312:151–163. doi:10.1016/s0378-1119(03)00612-7
  8. Ibuki T, Imada K, Minamino T, et al. (2011). Common architecture of the flagellar type III protein export apparatus and F- and V-type ATPases. Nature Structural & Molecular Biology 18:277–282. doi:10.1038/nsmb.1977
  9. Imada K, Minamino T, Tahara A, Namba K (2007). Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits. PNAS 104:485–490. doi:10.1073/pnas.0608090104
  10. Jarrell KF, Albers SV (2012). The archaellum: an old motility structure with a new name. Trends in Microbiology 20:307–312. doi:10.1016/j.tim.2012.04.007
  11. Johnson S, Furlong EJ, Deme JC, et al. (2021). Molecular structure of the intact bacterial flagellar basal body. Nature Microbiology 6:712–721. doi:10.1038/s41564-021-00895-y
  12. Liu R, Ochman H (2007). Stepwise formation of the bacterial flagellar system. PNAS 104:7116–7121. doi:10.1073/pnas.0700266104
  13. Macnab RM (2003). How bacteria assemble flagella. Annual Review of Microbiology 57:77–100. doi:10.1146/annurev.micro.57.030502.090832
  14. Miller KR (2004). The flagellum unspun: the collapse of 'irreducible complexity'. In Dembski WA, Ruse M (eds) Debating Design, pp. 81–97, Cambridge University Press. doi:10.1017/cbo9780511804823.006 Book chapter, not a peer-reviewed journal article.
  15. Minamino T, Imada K (2015). The bacterial flagellar motor and its structural diversity. Trends in Microbiology 23:267–274. doi:10.1016/j.tim.2014.12.011
  16. Minamino T, Namba K (2008). Distinct roles of the FliI ATPase and proton motive force in bacterial flagellar protein export. Nature 451:485–488. doi:10.1038/nature06449
  17. Pallen MJ, Gophna U (2007). Bacterial flagella and type III secretion: case studies in the evolution of complexity. Genome Dynamics 3:30–47. doi:10.1159/000107602
  18. Pallen MJ, Matzke NJ (2006). From The Origin of Species to the origin of bacterial flagella. Nature Reviews Microbiology 4:784–790. doi:10.1038/nrmicro1493
  19. Paul K, Erhardt M, Hirano T, Blair DF, Hughes KT (2008). Energy source of flagellar type III secretion. Nature 451:489–492. doi:10.1038/nature06497
  20. Reid SW, Leake MC, Chandler JH, et al. (2006). The maximum number of torque-generating units in the flagellar motor of Escherichia coli is at least 11. PNAS 103:8066–8071. doi:10.1073/pnas.0509932103
  21. Santiveri M, Roa-Eguiara A, Kühne C, et al. (2020). Structure and function of stator units of the bacterial flagellar motor. Cell 183:244–257. doi:10.1016/j.cell.2020.08.016
  22. Wagner S, Grin I, Malmsheimer S, et al. (2018). Bacterial type III secretion systems: a complex device for the delivery of bacterial effector proteins into eukaryotic host cells. FEMS Microbiology Letters 365:fny201. doi:10.1093/femsle/fny201