the common mode of bacterial motility

David Faguy faguyd at methanogenone.microbio.queensu.ca
Wed Apr 20 10:47:52 EST 1994

In <1994Apr20.102015.23283 at dal1>, arlin at ac.dal.ca writes:

>I didn't know there was a method for showing that two proteins are not
>homologous, nor was I aware that enough diverse archaebacteria and
>eubacteria had been studied to warrant claims that ALL motility
>organelles were uniform within each group.  In fact, I am not aware that
>ANY archaebacterial motor protein/gene has been characterized.  Can you
>please provide references for these claims?  You must be summarizing

A recent review states that there are sequences available for 29 eubacterial
flagellins (Wilson And Beveridge. Can. J. Microbiol. 39:451), The complete 
gene sequences for for the five flagellins from Halobium and four flagellins 
from Methanococcus have been published. We have published the N-terminal 
(the most conserved region) amino acid sequences of 12 flagellins from five 
different methanogens and have the (unpublished) N-terminal sequence from 
another three organisms - including Sulfolobus. I think this is enough of a 
dataset to start drawing conclusions. (references are summarized at the end)

>alot of new data, since published work (e.g., see Oesterholt and Marwan,
>1993, and references therein) would yield a different set of
>1.  Known eubacterial and archaebacterial flagella are passively rotated
>by a membrane-embedded motor, while the analogous eukaryotic motility
>organelles (variously called "cilia" "flagella" or "undulipodia")
>produce longitudinal waves that are generated *within* the organelle by
>microtubule-based sliding-filament motors; rotary motors have not been
>observed in eukaryotes; repeated attempts to find micro-tubule based
>motility in bacteria (e.g., by Lynn Margulis) have failed.
That is one of my points - functionally the flagella from eu and archaeas 
are very similar.

>2.  The rotary motors studied in archaebacteria and eubacteria are
>driven by ion gradients accross the cell membrane; eukaryotic flagella

I could be wrong (I'll double check) but to my knowledge nobody has shown
that archaebacterial flagella are driven by ion gradients.
>are powered by cleavage of energy-rich substrates (I think its GTP, but
>don't quote me on this); eubacteria are not "all the same" in this
>regard: some use a proton gradient, others use sodium or unknown
>3.  Known eubacterial and archaebacterial flagella are external
>polymeric filaments composed of one or a few subunits, located outside
>the plasma membrane, whereas eukaryotic "flagella" are composed of
>hundreds of proteins within the plasma membrane; eubacterial flagellar
>filaments may be either left-handed or right-handed;

Again this is one of my points structurally and functionally they are similar.
(Halobacterium has a right handed helix- just as a point of info)

>4.  H. halobium (a halophilic archaebacterium) has methyl-accepting
>chemotaxis receptor domains that are demonstrably homologous to those of
>E. coli and other eubacteria;

This is one of the strongest points in your favour - but it could also be 
interpreted as evidence that a chemo sensing apparatus is more ancestral 
than the flagellar appartus.  

>Evidence of the uniqueness and distinctiveness of archaebacterial
>motility is not readily apparent, yet David Faguy is not the first to
>make such claims.  Zillig, et al., 1993 refer to motility just once
>in their most recent table comparing features of the three "domains":
>			eucarya	        bacteria	archaea
>flagellins 		eucaryal	bacterial	archaeal
>That is, they tell us that there are 3 states for the character
>"flagellins"!  And nothing else is said about motility!  By "eucaryal

Based on the molecular sequence data available there are three states for
the character "flagellin" . I agree that in terms of chemotaxis there may be
similarities between archaea and bacteria- this should be included.

>flagellins" they are presumably referring to proteins that are not
>flagellins at all but are called "tubulin," "spoke protein XXX", and so
>on. The very limited sense in which this statement is correct is that
>archaebacterial and eubacterial flagellins have not been demonstrated to
>be homologous, and neither type of flagellin has any demonstrable (or
>even suspected) relationship with a eukaryotic protein.  This is a 

Eukaryotes don't have flagellins (ie a protein (or a few closely related 
proteins) that assemble to form a helical filament responsible for motility).
I may be on thin ice here, but to me absence of a character is still a vaild 
character state for phylogenetic purposes.

>biased, superficial, and unsatisfactory account of the evidence.
>Why deny all of the obvious similarities?  Does anyone really believe
>that gradient-powered rotary flagellar motors and methyl-accepting
>chemotaxis proteins evolved twice?  

No one is saying methyl accepting chemotaxis evolved twice. As for flagella 
themselves - there a number of motility mechanisms that cleary evolved separately
 - eukaryotic, twitching motility, gliding motility. Why is it so impossible that two 
independant mechanisms for flagellar motility evolved.

>Does it hurt so much to admit 
>that archaebacteria and eubacteria have a common bacterial heritage?

Bacteria and archaea are both prokaryotes (no nucleus). They share a negative 
characteristic this implies nothing about their phylogenetic relationship. The shear 
mass of data - cell walls, lipids, protein translation, rRNA, and yes flagellins- that
supports the distinct nature of each domain makes it clear that archaea are not bacteria.

Sincerly (and combatively),
David Faguy

Kalmokoff et al, 1991. J. Bacteriol. 173:7113.
Faguy et al, 1994. Can. J. Microbiol. 40: 67.
Kalmokoff et al, 1990. Biochem. Biophys. Res. Commun. 167:154.
Gerl et al, 1989. FEBS Lett. 244:137-140.
Kalmokoff et al, 1992. Arch. Microbiol. 157:481.

PS I am on my way now to see if our library has the book you referenced.

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