Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids

Previous work has shown that molecular phylogenies of plastids, cyanobacteria, and proteobacteria based on the rubisco (ribulose-1,5- bisphosphate carboxylase/oxygenase) genes rbcL and rbcS are incongruent with molecular phylogenies based on other genes and are also incompatible with structural and biochemical information. Although it has been much speculated that this is the consequence of a single horizontal gene transfer (of a proteobacterial or mitochondrial rubisco operon into plastids of rhodophytic and chromophytic algae), neither this hypothesis nor the alternative hypothesis of ancient gene duplication have been examined in detail. We have conducted phylogenetic analyses of all available bacterial rbcL sequences, and representative plastid sequences, in order to explore these alternative hypothesis and fully examine the complexity of rubisco gene evolution. The rbcL phylogeny reveals a surprising number of gene relationships that are fundamentally incongruent with organismal relationships as inferred from multiple lines of other molecular evidence. On the order of six horizontal gene transfers are implied by the form I (L8S8) rbcL phylogeny, two between cyanobacteria and proteobacteria, one between proteobacteria and plastids, and three within proteobacteria. Alternatively, a single ancient duplication of the form I rubisco operon, followed by repeated and pervasive differential loss of one operon or the other, would account for much of this incongruity. In all probability, the rubisco operon has undergone multiple events of both horizontal gene transfer and gene duplication in different lineages.      

Retrospective analysis of a secondary structure prediction: the catalytic domain of matrix metalloproteinases.

Secondary structure prediction of the catalytic domain of matrix metalloproteinases is evaluated in the light of recently published experimentally determined structures. The prediction was made by combining conformational propensity, surface probability, and residue conservation calculated for an alignment of 19 sequences. The position of each observed secondary structure element was correctly predicted with a high degree of accuracy, with a single beta-strand falsely predicted. The domain fold was also anticipated from the prediction by analogy with the structural elements found in the distantly related metalloproteinases thermolysin, astacin, and adamalysin.     

Environmental significance of the potential for mer(Tn21)-mediated reduction of Hg2+ to Hg0 in natural waters.

The role of mer(Tn21) in the adaptation of aquatic microbial communities to Hg2+ was investigated. Elemental mercury was the sole product of Hg2+ volatilization by freshwater and saline water microbial communities. Bacterial activity was responsible for biotransformation because most microeucaryotes did not survive the exposure conditions, and removal of larger microbes (greater than 1 micromole) from adapted communities did not significantly (P greater than 0.01) reduce Hg2+ volatilization rates. DNA sequences homologous to mer(Tn21) were found in 50% of Hg2+-resistant bacterial strains representing two freshwater communities, but in only 12% of strains representing two saline communities (the difference was highly significant; P less than 0.001). Thus, mer(Tn21) played a significant role in Hg2+ resistance among strains isolated from fresh waters, in which microbial activity had a limited role in Hg2+ volatilization. In saline water environments in which microbially mediated volatilization was the major mechanism of Hg2+ loss, other bacterial genes coded for this biotransformation.     

Evolutionary speed limited by water in arid Australia

The covariation of biodiversity with climate is a fundamental pattern in nature. However, despite the ubiquity of this relationship, a consensus on the ultimate cause remains elusive. The evolutionary speed hypothesis posits direct mechanistic links between ambient temperature, the tempo of micro-evolution and, ultimately, species richness. Previous research has demonstrated faster rates of molecular evolution in warmer climates for a broad range of poikilothermic and homeothermic organisms, in both terrestrial and aquatic environments. In terrestrial systems, species richness increases with both temperature and water availability and the interaction of those terms: productivity. However, the influence of water availability as an independent variable on micro-evolutionary processes has not been examined previously. Here, using methodology that limits the potentially confounding role of cladogenetic and demographic processes, we report, to our knowledge, the first evidence that woody plants living in the arid Australian Outback are evolving more slowly than related species growing at similar latitudes in moist habitats on the mesic continental margins. These results support a modified evolutionary speed explanation for the relationship between the water-energy balance and plant diversity patterns.     

Tree population studies in low-diversity forests,Guyana. I. Floristic composition and stand structure

Studies were undertaken on the floristic composition and stand structure of four 1 hectare plots in the lowland forests of Kurupukari, Guyana. A total of 3897 trees, covering 153 species and 31 plant families were recorded at greater than 5 cm diameter at breast height (dbh). The number of species per hectare ranged from 61 to 84 (>5.0 cm dbh) and 50–71 (>10.0 cm dbh). The total number of trees per hectare varied two-fold between study plots, with 45–50% of the trees within the 5–10 cm size-class. Mean total basal area varied from 32.39–34.63 m² per 100 m². The four most dominant plant families represented 43.8% of the total number of trees, while representing only 11.2% of the species. No one plant family dominated in more than one of the four study plots, and all four plots held at least one plant family with more than 20% of the total number of trees. Although 14 tree species were common to all four plots, only 26%–35% of the species were represented by a single tree. Between three and seven species represented 50% of the trees within all size-classes, with species dominance occurring within the highest density plot.These tropical forest types of central Guyana may represent some of the lowest diversity forests in the neotropics, whereby the total number of tree species is relatively limited, typically with six dominant canopy species, but the relative abundance of these species is highly variable between the forest types. Mechanisms influencing the competitive interactions associated with species dominance are discussed in relation to the importance of mycorrhizae and the persistence of species dominance.