Molecular phylogeny of theatpB andatpE genes of the brown algaPylaiella littoralis

Abstract

Recent phylogenetic studies suggest that plastid ribosomal RNA genes from Pylaiella liltoralis have a cyanobacterial origin, whereas their Rubisco genes are related to the homologous 0¢-and fl-purple eubacterial genes. We have constructed a phylogenetic tree based upon the atpB and atpE sequences, including the same range of taxa (chlorophytes, chromophytes, cyanobacteria, c~-and 7-purple eubacteria) and using the same methods as previously described for rbcL genes. This phylogenetic tree clearly shows that the atpB and atpE genes of this brown alga are more closely related to their cyanobacterial homologues than to those of c¢-or ~-purple eubacteria. Different hypotheses that could explain the apparently composite origin of red-chromophyte plastomes are discussed. Key words:Chromophyte algae, plastidial genome, phylogeny. IntroductionThe atpB and the atpE genes encode, respectively, for the fi and ~ subunits of the CF1/ATPase complex. In the plastid genome of the brown alga Pylaiella ]ittoralis (L.) Kjellm., these two genes are organised in a cluster and separated by a I4-nucleotide spacer region (Jouannic et al., 1992).Comparison of the atpB gene sequences in organisms from eubacteria to land plants shows that this gene is highly conserved. Given its presence in all organisms and its large size, we predicted that it could be a good model for phylogenetic studies. In trees inferred from ribosomal RNA gene sequences all plastid lineages appear as descendants of the cyanobacterial lineage (Markowicz & Loiseaux-de Go6r, 1991;Douglas & Turner, 1991; Somerville eta]., 1993). However, in trees inferred from Rubisco gene sequences the red-chromophyte plastid lineage emerges from the ~-(type 1) and fl-purple eubacterial lineage while, in contrast, the green plastid lineage emerges from the cyanobacterial lineage (Assali et al., 1990(Assali et al., , 1991Martin et al., 1992). Thus, we constructed a phylogenetic tree based upon the atpB/E sequences to determine whether these protein-coding genes in redchromophyte plastids have a different origin from that of ribosomal RNA genes. Materials and methodsAligned amino acid sequences for the atpB and atpE genes were taken from Jouannic et al. (1992). Corresponding codon insertions were introduced into the nucleotide sequences. Amino-and carboxyterminal regions of length heterogeneity were deleted from the alignment, yielding * To whom correspondence should be addressed.for comparison 1914 nucleotide positions in each set of sequences (atpB+atpE). Divergence at non-synonymous sites between aligned nucleotide sequences (alignment available upon request from the authors) was measured as K~ with the weighted pathway method (Li et aI., 1985). The matrix of distance values was analysed with the neighbour-joining method (Saitou & Nei, 1987). Parsimony bootstrap analysis (Felsenstein, 1985) (Woessner el al., 1986(Woessner el al., , 1987, Marchanlia polymorpfla (Umesono et al., 1988), Nicotiana tabacum (Kazuo el al., 1983) and Spinacia oleracea (Zurawski et aL 1982). . Schemat...

Cloning of the amphibolic Calvin cycle/OPPP enzyme d-ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) from spinach chloroplasts: functional and evolutionary aspects

“…Firstly, it is quite clear that the duplication events which gave rise to the three E. coli genes (the encoded proteins of which share only 30~o identity) took place long prior to the diversification of purple bacteria. Ancient gene dupli- cations of this type are also known to have occurred for other genes for enzymes of primary metabolism such as GAPDH [14], Rubisco [25,26] and glutamine synthase [21]. Secondly, spinach chloroplast R5P3E is more similar to Calvin cycle homologues of eubacteria than to the R5P3E-like sequence from yeast.…”