Gloeobacter Genome

Ken Kinman kinman2 at YAHOO.COM
Mon Aug 16 22:48:32 CDT 2004

Dear All,
     Has anyone read this recent article?  I wonder if it might confirm or deny the presence of the kaiC gene in the Gloeobacter genome (see my December 2003 TAXACOM query on that subject below):

Mol. Biol. Evol. 21(8):1468-1476. 2004
Structure and Molecular Phylogeny of sasA Genes in Cyanobacteria: Insights into Evolution of the Prokaryotic Circadian System
Volodymyr Dvornyk*, Hong-Wen Deng* and Eviatar Nevo

     Part of abstract:  "The results of the phylogenetic analyses suggest that sasA emerged before the kaiA gene, about 3,000–2,500 MYA, and has evolved in parallel with the evolution of the kaiBC cluster. The observed concordant patterns of the sasA and kaiBC evolution suggest that these genes might compose an ancient KaiBC–SasA-based circadian system, without the kaiA gene, and that such a system still exists in some unicellular cyanobacteria."

On Wed, 24 Dec 2003 15:59:35 -0600, Ken Kinman <kinman2 at YAHOO.COM> wrote:
>Dear All,
>      Because I have believed for some years that the cyanobacterium Gloeobacter could be the most primitive known extant organism on Earth, I am quite happy that its complete genome was recently sequenced and released.  It could have a profound effect, not only on microbial systematics, but also systematics in general in the way we root trees and design computer algorithms for systematic work in general.
>      However, I was rather astonished when the abstract (to the Gloeobacter genome paper) emphasized that in spite of a intense search, no "kai" proteins were found in the completed genome.  Given my belief that Gloeobacter is extremely primitive, the purported absence of "kai" genes was music to my ears.  But what are we to make of AF239755 in the NCBI database, submitted three years ago (2000) as being a kaiC protein from Gloeobacter?  The "kai" proteins are very important, and the 2000 paper expresses the belief that ALL cyanobacteria possess the primitive "kaiC" protein.
>     Well, somebody is wrong here.  Is it more probable that the complete genome of Gloeobacter is not totally complete afterall, or is it more probable that AF239755 (clearly a "kaiC" sequence) is not actually from Gloeobacter?   What would be the best way to figure out who is wrong?
>        ----Thanks, and Merry Christmas,
>                      Ken Kinman
>P.S.  By the way, whatever the answer to the above question is, I believe Gloeobacter should definitely be removed from Order Chroococcales, and I heartily applaud Thomas Cavalier-Smith for proposing a new Order Gloeobacterales in his paper last year (International Journal of Systematic and Evolutionary Microbiology, 52:7-76).  Although he apparently only regards Gloeobacter as a primitive cyanobacterium (rather than as the most primitive organism of all), it is clearly distinctive, and I would hope NCBI would follow him in recognizing Order Gloeobacterales.

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