Animal Evolution: When Did the ‘Hox System’ Arise?

The origins of the Hox gene clusters and their coordinated activities during development have long been of considerable interest to biologists. In a recent paper in Current Biology, the Hox-like genes of two cnidarians are interpreted as evidence that the 'Hox system', sensu stricto, originated after the split from the lineage leading to bilaterian animals and that it was not requisite for complex axial patterning.     

Gibberellin Biosynthesis in Plants and Fungi: A Case of Convergent Evolution?

As well as being phytohormones, gibberellins (GAs) are present in some fungi and bacteria. Indeed, GAs were first discovered in the fungus Gibberella fujikuroi, from which gibberellic acid (GA3) and other GAs are produced commercially. Although higher plants and the fungus produce structurally identical GAs, there are important differences in the pathways and enzymes involved. This has become particularly apparent with the identification of almost all of the genes for GA-biosynthesis in Arabidopsis thaliana and G. fujikuroi, following the sequencing of the Arabidopsis genome and the detection of a GA-biosynthesis gene cluster in the fungus. For example, 3b-hydroxylation occurs early in the pathway in G. fujikuroi and is catalyzed by a cytochrome P450 monooxygenase, whereas it is usually the final step in plants and is catalyzed by 2-oxoglutarate-dependent dioxygenases. Similarly, 20-oxidation is catalyzed by dioxygenases in plants and a cytochrome P450 in the fungus. Even where cytochrome P450s have equivalent functions in plants and Gibberella, they are unrelated in terms of amino acid sequence. These profound differences indicate that higher plants and fungi have evolved their complex biosynthetic pathways to GAs independently and not by horizontal gene transfer.     

Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution

For over 100 years, molluscan eyes have been used as an example of convergent evolution and, more recently, as a textbook example of stepwise evolution of a complex lens eye via natural selection. Yet, little is known about the underlying mechanisms that create the eye and generate different morphologies. Assessing molluscan eye diversity and understanding how this diversity came about will be important to developing meaningful interpretations of evolutionary processes. This paper provides an introduction to the myriad of eye types found in molluscs, focusing on some of the more unusual structures. We discuss how molluscan eyes can be applied to the study of evolution by examining patterns of convergent and parallel evolution and provide several examples, including the putative convergence of the camera-type eyes of cephalopods and vertebrates.     

What Amino Acid Properties Affect Protein Evolution?

We studied 10 protein-coding mitochondrial genes from 19 mammalian species to evaluate the effects of 10 amino acid properties on the evolution of the genetic code, the amino acid composition of proteins, and the pattern of nonsynonymous substitutions. The 10 amino acid properties studied are the chemical composition of the side chain, two polarity measures, hydropathy, isoelectric point, volume, aromaticity, aliphaticity, hydrogenation, and hydroxythiolation. The genetic code appears to have evolved toward minimizing polarity and hydropathy but not the other seven properties. This can be explained by our finding that the presumably primitive amino acids differed much only in polarity and hydropathy, but little in the other properties. Only the chemical composition (C) and isoelectric point (IE) appear to have affected the amino acid composition of the proteins studied, that is, these proteins tend to have more amino acids with typical C and IE values, so that nonsynonymous mutations tend to result in small differences in C and IE. All properties, except for hydroxythiolation, affect the rate of nonsynonymous substitution, with the observed amino acid changes having only small differences in these properties, relative to the spectrum of all possible nonsynonymous mutations. Received: 2 January 1998 / Accepted: 25 April 1998     

The Specificity of Controlled Protein Disorder in the Photoprotection of?Plants

Light-harvesting pigment-protein complexes of photosystem II of plants have a dual function: they efficiently use absorbed energy for photosynthesis at limiting sunlight intensity and dissipate the excess energy at saturating intensity for photoprotection. Recent single-molecule spectroscopy studies on the trimeric LHCII complex showed that environmental control of the intrinsic protein disorder could in principle explain the switch between their light-harvesting and photoprotective conformations in vivo. However, the validity of this proposal depends strongly on the specificity of the protein dynamics. Here, a similar study has been performed on the minor monomeric antenna complexes of photosystem II (CP29, CP26, and CP24). Despite their high structural homology, similar pigment content and organization compared to LHCII trimers, the environmental response of these proteins was found to be rather distinct. A much larger proportion of the minor antenna complexes were present in permanently weakly fluorescent states under most conditions used; however, unlike LHCII trimers the distribution of the single-molecule population between the strongly and weakly fluorescent states showed no significant sensitivity to low pH, zeaxanthin, or low detergent conditions. The results support a unique role for LHCII trimers in the regulation of light harvesting by controlled fluorescence blinking and suggest that any contribution of the minor antenna complexes to photoprotection would probably involve a distinct mechanism.     

Origin and Evolution of GALA-LRR,a New Member of the CC-LRR Subfamily: From Plants to Bacteria?

The phytopathogenic bacterium Ralstonia solanacearum encodes type III effectors, called GALA proteins, which contain F-box and LRR domains. The GALA LRRs do not perfectly fit any of the previously described LRR subfamilies. By applying protein sequence analysis and structural prediction, we clarify this ambiguous case of LRR classification and assign GALA-LRRs to CC-LRR subfamily. We demonstrate that side-by-side packing of LRRs in the 3D structures may control the limits of repeat variability within the LRR subfamilies during evolution. The LRR packing can be used as a criterion, complementing the repeat sequences, to classify newly identified LRR domains. Our phylogenetic analysis of F-box domains proposes the lateral gene transfer of bacterial GALA proteins from host plants. We also present an evolutionary scenario which can explain the transformation of the original plant LRRs into slightly different bacterial LRRs. The examination of the selective evolutionary pressure acting on GALA proteins suggests that the convex side of their horse-shoe shaped LRR domains is more prone to positive selection than the concave side, and we therefore hypothesize that the convex surface might be the site of protein binding relevant to the adaptor function of the F-box GALA proteins. This conclusion provides a strong background for further functional studies aimed at determining the role of these type III effectors in the virulence of R. solanacearum.     

Do β-Cells Generate Peroxynitrite in Response to Cytokine Treatment?

The purpose of this study was to determine the reactive species that is responsible for cytokine-mediated β-cell death. Inhibitors of inducible nitric oxide synthase prevent this death, and addition of exogenous nitric oxide using donors induces β-cell death. The reaction of nitric oxide with superoxide results in the generation of peroxynitrite, and this powerful oxidant has been suggested to be the mediator of β-cell death in response to cytokine treatment. Recently, coumarin-7-boronate has been developed as a probe for the selective detection of peroxynitrite. Using this reagent, we show that addition of the NADPH oxidase activator phorbol 12-myristate 13-acetate to nitric oxide-producing macrophages results in peroxynitrite generation. Using a similar approach, we demonstrate that cytokines fail to stimulate peroxynitrite generation by rat islets and insulinoma cells, either with or without phorbol 12-myristate 13-acetate treatment. When forced to produce superoxide using redox cyclers, this generation is associated with protection from nitric oxide toxicity. These findings indicate that: (i) nitric oxide is the likely mediator of the toxic effects of cytokines, (ii) β-cells do not produce peroxynitrite in response to cytokines, and (iii) when forced to produce superoxide, the scavenging of nitric oxide by superoxide is associated with protection of β-cells from nitric oxide-mediated toxicity.