Evolution of Cyanobacteria by Exchange of Genetic Material among Phyletically Related Strains

The cyanobacterial radiation consists of several lineages of phyletically (morphologically and genetically) related organisms. Several of these organisms show a striking resemblance to fossil counterparts. To investigate the molecular mechanisms responsible for stabilizing or homogenizing cyanobacterial characters, we compared the evolutionary rates and phylogenetic origins of the small-subunit rRNA-encoding DNA (16S rDNA), the conserved gene rbcL (encoding d-ribulose 1,5-bisphosphate carboxylase-oxygenase large subunit), and the less conserved gene rbcX. This survey includes four categories of phyletically related organisms: 16 strains of Microcystis, 6 strains of Tychonema, 10 strains of Planktothrix, and 12 strains of Nostoc. Both rbcL and rbcX can be regarded as neutrally evolving genes, with 95 to 100% and 50 to 80% synonymous nucleotide substitutions, respectively. There is generally low sequence divergence within the Microcystis, Tychonema, and Planktothrix categories both for rbcLX and 16S rDNA. The Nostoc category, on the other hand, consists of three genetically clustered lineages for these loci. The 16S rDNA and rbcLX phylogenies are not congruent for strains within the clustered groups. Furthermore, analysis of the phyletic structure for rbcLX indicates recombinational events between the informative sites within this locus. Thus, our results are best explained by a model involving both intergenic and intragenic recombinations. This evolutionary model explains the DNA sequence clustering for the modern species as a result of sequence homogenization (concerted evolution) caused by exchange of genetic material for neutrally evolving genes. The morphological clustering, on the other hand, is explained by structural and functional stability of these characters. We also suggest that exchange of genetic material for neutrally evolving genes may explain the apparent stability of cyanobacterial morphological characters, perhaps over billions of years.The current species diversity of the cyanobacterial radiation comprises several lineages of phyletically (morphologically and genetically) related organisms (26). An intriguing question is whether this reflects stability of cyanobacterial characters or whether the phyletic similarities originate from relatively recent common ancestors. Analyses of precambrian microfossils (superficially, hardly distinguishable from recent cyanobacteria) support the view of retention of cyanobacterial properties (1, 11, 28). However, on the basis of molecular data, a 2-billion-year-old mutual ancestor for prokaryotes has been suggested (5), implying that the similarities between the earliest records of cyanobacteria and present-day species do not reflect homologies but rather indicate analogies. In this context, the phyletically clustered groups may reflect a relatively recent divergence of the modern species.In this work we have addressed, by molecular evolutionary studies, the mechanisms responsible for conserving or homogenizing phyletical characters within groups of cyanobacteria. We investigated the evolutionary rates and origins for two genomic regions, by analyzing strains both within and among groups of phyletically related organisms. This was done by comparative analysis of the small-subunit rRNA-encoding DNA (16S rDNA), which is conserved by the RNA function (37), and the rbcLX region with both conserved and less conserved elements. The rbcLX region contains an intergenic spacer (with no identified functional units), the gene rbcX with a possible chaperonin-like function (18), and the 3′ end of rbcL (encoding the highly conserved d-ribulose 1,5-bisphosphate carboxylase-oxygenase large subunit [LSU]) (23). We analyzed a data set consisting of four phyletically clustered cyanobacterial strain categories, as inferred from microscopic observations and 16S rDNA analysis (26, 31). The data set includes the Microcystis category (16 strains), consisting of unicellular organisms, the Tychonema (6 strains) and Planktothrix (10 strains) categories, which contain multicellular, filamentous organisms, and the Nostoc category (12 strains), which includes both morphologically and genetically slightly divergent organisms (26, 34). The strains in this last category share among other features the ability of cellular differentiation to produce heterocysts with nitrogenase activity.Our sequence data suggest an evolutionary model involving several events of gene transfer between phyletically closely related organisms but not between less related organisms. We propose that this gene transfer has led to the observed sequence homogeneity for the groups of related organisms and that exchange of genetic material stabilizes the function and structure of proteins encoded by neutrally evolving genes. Our gene transfer model may explain the similarity between the fossil and the recent species.