Path: utzoo!utgpu!news-server.csri.toronto.edu!rpi!usc!ucselx!bionet!osucc.bitnet!BIOCUKM From: BIOCUKM@osucc.bitnet Newsgroups: bionet.genome.arabidopsis Subject: Arabidopsis evolution Message-ID: <9104301606.AA21111@genbank.bio.net> Date: 29 Apr 91 19:41:00 GMT Sender: daemon@genbank.bio.net Lines: 73 Arabidopsis molecular biologists and geneticists should look at the recent paper by Kemmerer, Lei and Wu (J. Mol. Evol. 32:227-237, 1991). The paper reports the isolation and nucleotide sequencing of the cytochrome c gene of Arabidopsis. The unusual aspect of the paper is that the predicted amino acid sequence is much more closely related to those of the cytochromes c of Neurospora and yeasts than it is to the cytochrome c sequences of another member of the crucifer family, cauliflower, and, indeed, of all flowering plants whose cytochrome c sequences are known. When I first saw the abstract, I thought that this would be another example of grand conclusions from uncertain trees. Calculated phylogenetic trees have uncertainties associated with the placement of branches. Those uncertainties are rarely included in diagrams and are often ignored when drawing conclusions. On reading the paper, I found the authors well aware of these difficulties. They analyzed the sequence data in many different ways. Each way produced the same highly significant conclusion. A visual examination of the amino acid sequences leads to the same conclusion, that the cytochrome c of the sequenced gene is more similar to Neurosopora and yeast sequences than it is to those of higher plants. What's going on? Several explanations come to mind. 1. The sequenced gene could encode a minor cytochrome c of plants, one not detected by protein sequencing. A S. cerevisiae probe was used to screen an Arabidopsis library. All 4 hybridizing library clones were the same. Thus, the gene is the only Arabidopsis cytochrome c gene recognized by the yeast probe. Perhaps the genes for the major cytochromes c of plants are not recognized by the S. cerevisiae probe. A difficulty with this and other technical explanations is that similar conclusions about ancestry were reached with histone H3 comparisons (though these are less certain). 2. The sequenced gene was from a contaminant in the DNA preparation. This is unlikely since a fragment of the cloned gene recognizes a fragment of the same size in blots of Arabidopsis DNA. 3. Lateral transfer of the cytochrome c gene (either from yeast to Arabidopsis or, I suppose, vice versa). This possibility, raised in the paper, seems unlikely since the transferred gene would have to have completely replaced an ancestral gene. 4. My off-the-cuff favorite hypothesis is that in studying molecular evolution over such large distances we are really not studying the evolution of the molecules themselves. We are really studying the evolution of the fitness landscape. Each of the cytochromes c has evolved to be optimally suited for its particular ecological niche. Perhaps the relevant features of the Arabidopsis cytochrome c ecological niche are smallness and rapid growth. Those properties seem more like those of the yeasts than of cotton, mung bean, cauliflower, sesame, sunflower, wheat, buckwheat and Gingko. Against this view is the presence of Chlamydomonas on the higher plant branch. 5. A synthesis of explanations 3 and 4 would be that somewhere in Arabidopsis' ancestry it was in close association (symbiosis?) with a fungus. The association was so close that heterokaryons formed. With time one of the copies of genes that were pesent in both the plant and the fungal progenitor was lost. Selection may have favored the fungal cytochrome c. What do the rest of you think? This is a question of economic, as well as scientific, importance. The paper makes the suggestion that Arabidopsis may not be a good model for higher plants. If this view takes hold, there goes the funding! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Ulrich Melcher !!! !!! Department of Biochemistry !!! !!! Oklahoma State University !!! !!! Stillwater OK 74078 USA !!! !!! BIOCUKM@OSUCC (Bitnet) 405-744-6210 !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!