RSS 2.0 Feed

» Welcome Guest Log In :: Register

    
  Topic: Evolution of eukaryotic cilia/flagella, Links to refs, discussions, etc.< Next Oldest | Next Newest >  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Jan. 27 2003,19:39   

Reposting from:

Topic: List of IC systems
http://www.arn.org/cgi-bin....#000096

First off,

An awful lot of entries in the NCBI protein database listing MotA, ExbB, and TolQ as being a "family", in opposition to what Mike Gene has been suggesting

 
Quote
Originally posted by Mike Gene:
Nic: Hey, I'm just following the peer-reviewed lit., man. Take it up in the pages of Biochemistry if you like...

The authors never claim MTH1022 is a homolog of motA. And even if they did, the claim would be unsupported.  
People can read the quote I posted and decide for themselves exactly what the authors meant.  Mentioning significant sequence similarity in the middle of a discussion of homologs seems like a strong indication to me that they meant homolog or at least "likely homolog".  And see below for what some of those proteins are labeled as in the NCBI database.

 
Quote

Actually, running a PSI-BLAST of ExbB gets me four hits on archaeabacteria, but whatever.

With e values of 0.005 and higher.  That's not very impressive.  Furthermore, even if there is a non-convergent and real relationship here, note that it is not widely distributed and would thus seem to have evolved long after archaea appeared.  

A much stronger point is that the ExbB homologs are very widely distributed in eubacteria, in very basal lineages.

Think so?  What groups did you have in mind?[/qb]


Hmm, well a standard protein BLAST  on E coli ExbB gives me this taxonomy report:

An E. coli "biopolymer transport exbB protein"

Here is the link

Here are some of the results *outside* the proteobacteria:

Code Sample
 Chlamydophila pneumoniae CWL029 [chlamydias] taxid 115713
gi|15618694|ref|NP_224980.1| Macromolecule transporter [Ch...      61  1e-08

 Cytophaga hutchinsonii [CFB group bacteria] taxid 985
gi|23136461|gb|ZP_00118181.1| hypothetical protein [Cytoph...      60  1e-08
gi|23136843|gb|ZP_00118557.1| hypothetical protein [Cytoph...      36  0.35

 Chlamydia trachomatis [chlamydias] taxid 813
gi|15605326|ref|NP_220112.1| polysaccharide transporter [C...      59  4e-08

 Chlamydia muridarum (agent of mouse pneumonitis) [chlamydias] taxid 83560
gi|15835499|ref|NP_297258.1| MotA/TolQ/ExbB proton channel...      58  8e-08

 Aquifex aeolicus [aquificales] taxid 63363
gi|15606982|ref|NP_214364.1| TolQ homolog [Aquifex aeolicu...      55  5e-07
gi|15606823|ref|NP_214203.1| biopolymer transport exbB [Aq...      42  0.005

[...]

 Deinococcus radiodurans [eubacteria] taxid 1299
gi|15805483|ref|NP_294179.1| biopolymer transport protein,...      47  1e-04

 Methanothermobacter thermautotrophicus str. Delta H [euryarchaeotes] taxid 187420
gi|15679040|ref|NP_276157.1| biopolymer transport protein ...      43  0.002

 Synechocystis sp. PCC 6803 [cyanobacteria] taxid 1148
gi|16329196|ref|NP_439924.1| biopolymer transport ExbB pro...      41  0.013
gi|16329550|ref|NP_440278.1| biopolymer transport ExbB pro...      40  0.018

[...]
Note below that *even* some proteobacteria ExbB proteins have "unimpressive" similarity scores and yet are still called ExbB proteins (as are some **archaeabacteria** ExbB-family proteins):

Code Sample
Photobacterium damselae subsp. piscicida [g-proteobacteria] taxid 38294
gi|19577341|emb|CAD27898.1| ExbB protein [Photobacterium d...      33  1.9

 Plesiomonas shigelloides [enterobacteria] taxid 703
gi|13774064|gb|AAG23397.1| ExbB [Plesiomonas shigelloides]         33  2.0

 Sulfolobus solfataricus [crenarchaeotes] taxid 2287
gi|15899059|ref|NP_343664.1| Amino acid transporter, putat...      33  2.6

[...]

 Methanosarcina acetivorans C2A [euryarchaeotes] taxid 188937
gi|20089242|ref|NP_615317.1| MotA/TolQ/ExbB proton channel...      33  3.4
gi|20093212|ref|NP_619287.1| MotA/TolQ/ExbB proton channel...      33  3.8
gi|20093420|ref|NP_619495.1| MotA/TolQ/ExbB proton channel...      32  6.7
MotA and ExbB appear to have equally wide distributions

The distribution taxonomy report for ExbB is, in fact, rather like the taxonomy report for standard protein blast of E. coli's MotA protein: lots and lots of enterobacteria and proteobacteria, and a few hits out in spirochetes and other various deeply divergent bacteria.

Here is said taxonomy report

Are we to conclude that MotA is just as likely to be of late origin and derived as ExbB?

...methinks the database may be a wee bit biased towards certain intensively-studied gram-negative bacteria groups and that therefore seeing many hits in those groups and few outside means very little in terms of relative significance.  As I showed, you have to put MotA and ExbB in the same distribution bucket regardless.

Regarding low e-values:

Based on your blanket skepticism of marginal e-values, you may want to argue that some MotA proteins are of independent origins and convergent on standard MotA's.  Many of these scores are non too impressive, yet some are MotAs (or PomA, a related motor) despite this:

Code Sample
 Treponema denticola [spirochetes] taxid 158
gi|4426945|gb|AAD20619.1| flagellar motor protein MotA [Tr...      53  3e-06

 Pseudomonas putida [g-proteobacteria] taxid 303
gi|2853602|gb|AAC08066.1| MotA [Pseudomonas putida]                53  5e-06

 Leptospira interrogans serovar lai str. 56601 [spirochetes] taxid 189518
gi|24213362|ref|NP_710843.1| Chemotaxis motA protein [Lept...      52  6e-06
gi|24216276|ref|NP_713757.1| motility protein A [Leptospir...      39  0.056

 Bacillus anthracis str. A2012 [eubacteria] taxid 191218
gi|21402555|ref|NP_658540.1| MotA_ExbB, MotA/TolQ/ExbB pro...      52  8e-06
gi|21399546|ref|NP_655531.1| MotA_ExbB, MotA/TolQ/ExbB pro...      51  1e-05

 Shewanella oneidensis MR-1 [g-proteobacteria] taxid 211586
gi|24375769|ref|NP_719812.1| chemotaxis motA protein [Shew...      51  1e-05
gi|24373102|ref|NP_717145.1| chemotaxis motA protein [Shew...      38  0.13

 Thermotoga maritima [thermotogales] taxid 2336
gi|15643440|ref|NP_228484.1| motility protein A [Thermotog...      50  3e-05

 Campylobacter jejuni [e-proteobacteria] taxid 197
gi|15791705|ref|NP_281528.1| putative flagellar motor prot...      48  9e-05

 Rhodopseudomonas palustris [a-proteobacteria] taxid 1076
gi|22963976|gb|ZP_00011582.1| hypothetical protein [Rhodop...      42  0.006

 Magnetococcus sp. MC-1 [proteobacteria] taxid 156889
gi|22999422|gb|ZP_00043404.1| hypothetical protein [Magnet...      41  0.011
gi|23000123|gb|ZP_00044067.1| hypothetical protein [Magnet...      33  3.5

 Vibrio alginolyticus [g-proteobacteria] taxid 663
gi|3024412|sp|O06873|POMA_VIBAL Chemotaxis pomA protein >g...      40  0.038

 Bacillus halodurans [eubacteria] taxid 86665
gi|15615802|ref|NP_244106.1| flagellar motor apparatus [Ba...      39  0.058

 Vibrio vulnificus CMCP6 [g-proteobacteria] taxid 216895
gi|27363787|ref|NP_759315.1| Flagellar motor component Mot...      37  0.18

 Clostridium thermocellum ATCC 27405 [eubacteria] taxid 203119
gi|23021959|gb|ZP_00061601.1| hypothetical protein [Clostr...      35  0.87

 Vibrio cholerae [g-proteobacteria] taxid 666
gi|15640908|ref|NP_230539.1| chemotaxis protein PomA [Vibr...      32  5.6
Regarding the e-values of archaeal ExbB homologs, PSI-BLAST on E. coli ExbB gives an archaeabacterial homolog with e-value of 2e-17, which ought to be good enough for Mike Gene:

PSI-BLAST search

 
Quote
 Methanothermobacter thermautotrophicus str. Delta H [euryarchaeotes] taxid 187420
gi|15679040|ref|NP_276157.1| biopolymer transport protein ...      90  2e-17
gi|15678698|ref|NP_275813.1| unknown [Methanothermobacter ...      43  0.003
gi|15678311|ref|NP_275426.1| protein kinase [Methanothermo...      33  3.4
My point

These kinds of things ought to at least be mentioned and discussed before reckless statements are made about absolutely no evidence for precursors to flagellar proteins, that's my only point.  For some reason you guys prefer to sweep it under the rug by unsupported arguments about ExbB's narrow distribution.  Just acknowledge that this little bit of the biological world is a bit disharmonious with the flagellum-was-specially-created thesis.  All I've been saying, and now documenting, is that ExbB homologs are at least as widely distributed as MotA, and possibly more widely distributed.

Edited by niiicholas on Jan. 27 2003,19:48

  
  5 replies since Nov. 28 2002,23:11 < Next Oldest | Next Newest >  

    


Track this topic Email this topic Print this topic

[ Read the Board Rules ] | [Useful Links] | [Evolving Designs]