Please List Attempts to Explain Flagellum

[swamidass (S. Joshua Swamidass)]

Continuing the discussion from Tickets for Swamidass & Behe event are all gone. Every seat filled:

@Timothy_Horton

The exact words on Behe’s slide which he read were

“The Bacterial Flagellum: More than 20 years after Darwin’s Black Box there has not been even an attempt to explain it in Darwinian terms. It remains at utter mystery”

That is a flat out lie, no two ways about it. Beside the well known Nic Matzke paper in Nature From The Origin of Species to the origin of bacterial flagella there have been around 600 published papers on the evolution of all parts of the flagellum.

Please list out all the attempts you can. It does not matter if the attempt is judged successful. I’d just like to see an attempt at listing the best attempts.

Though notice the word “Darwinian,” with this qualifier he may be correct. Does anyone explain things by exclusively “Darwinian” terms?

[T_aquaticus]

One of the classics.

Stepwise formation of the bacterial flagellar system

Renyi Liu and Howard Ochman

PNAS April 24, 2007 104 (17) 7116-7121

Abstract

Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.
https://www.pnas.org/content/104/17/7116

[Rumraket (Mikkel R.)]

The most extensive and detailed account is still Nick Matzke’s 2003 article:

EVOLUTION IN (BROWNIAN) SPACE:

a model for the origin of the bacterial flagellum

By Nicholas Joseph Matzke

Here’s one on the evolution of different types of extant flagella motors from a simpler ancestral motor:
Rossmann FM, Beeby M. Insights into the evolution of bacterial flagellar motors from high-throughput in situ electron cryotomography and subtomogram averaging. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):585-594. doi: 10.1107/S2059798318007945

This one is more about the evolution of various types of membrane protein secretion systems, but also talks about the evolution of structures related to the flagellum:
https://www.sciencedirect.com/science/article/abs/pii/S0966842X2030007X

I know there are more, which you can probably find most easily just by looking in the set of articles citing Pallen & Matzke 2006.¨

Edit: Updated the link to Matzke’s 2003 article to an article that contains some updates and reader background pages later written by Matzke.

[Timothy_Horton]

He’s a 2014 overview of flagellum knowledge with several dozen research papers on the evolution of various components referenced.

From molecular evolution to biobricks and synthetic modules: a lesson by the bacterial flagellum
Bange et al
Biotechnology and Genetic Engineering Reviews, Volume 30, 2014 - Issue 1

Abstract: The bacterial flagellum is a motility structure and represents one of the most sophisticated nanomachines in the biosphere. Here, we review the current knowledge on the flagellum, its architecture with respect to differences between Gram-negative and Gram-positive bacteria and other species-specific variations (e.g. the flagellar filament protein, Flagellin). We further focus on the mechanism by which the two nucleotide-binding proteins FlhF and FlhG ensure the correct reproduction of flagella place and number (the flagellation pattern). We will finish the review with an overview of current biotechnological applications, and a perspective of how understanding flagella can contribute to developing modules for synthetic approaches.

Not sure what the point of this thread is. Anyone can use PubMed or GoogleScholar and find plenty of papers on the topic. Anyone except Michael Behe it seems.

[Rumraket (Mikkel R.)]

Anyway, here’s some more:

Wong, Tim; Amidi, Arezou; Dodds, Alexandra; Siddiqi, Sara; Wang, Jing; Yep, Tracy; Tamang, Dorjee G.; Saier, Milton H. (2007). Evolution of the Bacterial Flagellum: Cumulative evidence indicates that flagella developed as modular systems, with many components deriving from other systems.(Archived here : PDF). Microbe . 2 (7): 335–40.

Pallen MJ, Gophna U. Bacterial flagella and Type III secretion: case studies in the evolution of complexity. Genome Dyn. 2007;3:30-47. https://doi.org/10.1159/000107602

Snyder LA, Loman NJ, Fütterer K, Pallen MJ. Bacterial flagellar diversity and evolution: seek simplicity and distrust it? Trends Microbiol. 2009 Jan;17(1):1-5. doi: 10.1016/j.tim.2008.10.002

These at least seem to deal directly with the evolutionary origin of the flagellum.

There are many more articles on the evolution of many different types of flagella from some common ancestral flagellum. It’s important to understand there is no one THE bacterial flagellum. There are many thousand types of flagella having evolved in different lineages from some common ancestral structure that only had a subset of the many different components seen in these different versions:

Rossmann FM, Beeby M. Insights into the evolution of bacterial flagellar motors from high-throughput in situ electron cryotomography and subtomogram averaging. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):585-594. doi: 10.1107/S2059798318007945

Terashima H, Kawamoto A, Morimoto YV, Imada K, Minamino T. Structural differences in the bacterial flagellar motor among bacterial species. Biophys Physicobiol. 2017 Dec 19;14:191-198. doi: 10.2142/biophysico.14.0_191.

Denise R, Abby SS, Rocha EPC. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biol. 2019 Jul 19;17(7):e3000390. doi:10.1371/journal.pbio.3000390.

… and on and on it goes.

[T.j_Runyon]

@Rumraket

Matzke’s 2003 article:

I know @Agauger hates that one. I need to track down where she discusses it

[T.j_Runyon]

@Timothy_Horton

Not sure what the point of this thread is.

Now we have em all in one easy to find place.

[sfmatheson]

Two really interesting and related papers from about a year ago showing existence of a toolkit of proteins (they call it CORE, but it’s previously known as set of proteins making up the T3SS export apparatus) that is shared by both flagella and the deliciously named injectisome. It’s deeply conserved but just as interesting is the fact that it also supports nanotube formation, which implies ancient, broad, conserved functions in molecular traffic between bacterial cells.

Does this “explain” the flagellum? That question is incoherent, which is to be expected from a “question” raised by the ID movement. What this means, IMO, is that the flagellum (more accurately, flagella) is one specialized reuse of a core machinery that can be repurposed extensively and effectively. That is the theme of the Trends in Genetics review posted above, and of Nick Matzke’s writing all those years ago.

Pathogenic E. coli Extracts Nutrients from Infected Host Cells Utilizing Injectisome Components

A Ubiquitous Platform for Bacterial Nanotube Biogenesis