Bulky Trichomonad Genomes: Encoding a Swiss Army Knife

The trichomonads are a remarkably successful lineage of ancient, predominantly parasitic protozoa. Recent molecular analyses have revealed extensive duplication of certain genetic loci in trichomonads. Consequently, their genomes are exceptionally large compared to other parasitic protozoa. Retention of these large gene expansions across different trichomonad families raises the question: do these duplications afford an advantage? Many duplicated genes are linked to the parasitic lifestyle and some are regulated differently to their paralogues, suggesting they have acquired new functions. It is proposed that these large genomes encode a Swiss army knife of sorts, packed with a multitude of tools for use in many different circumstances. This may have bestowed trichomonads with the extraordinary versatility that has undoubtedly contributed to their success.

Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell

The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation.

Diversification of SUMO-activating enzyme in Arabidopsis: implications in SUMO conjugation

Sumoylation is an essential posttranslational modification that participates in many biological processes including stress responses. However, little is known about the mechanisms that control Small Ubiquitin-like MOdifier (SUMO) conjugation in vivo. We have evaluated the regulatory role of the heterodimeric E1 activating enzyme, which catalyzes the first step in SUMO conjugation. We have established that the E1 large SAE2 and small SAE1 subunits are encoded by one and three genes, respectively, in the Arabidopsis genome. The three paralogs genes SAE1a, SAE1b1, and SAE1b2 are the result of two independent duplication events. Since SAE1b1 and SAE1b2 correspond to two identical copies, only two E1 small subunit isoforms are present in vivo: SAE1a and SAE1b. The E1 heterodimer nuclear localization is modulated by the C-terminal tail of the SAE2 subunit. In vitro, SUMO conjugation rate is dependent on the SAE1 isoform contained in the E1 holoenzyme and our results suggest that downstream steps to SUMO-E1 thioester bond formation are affected. In vivo, SAE1a isoform deletion in T-DNA insertion mutant plants conferred sumoylation defects upon abiotic stress, consistent with a sumoylation defective phenotype. Our results support previous data pointing to a regulatory role of the E1 activating enzyme during SUMO conjugation and provide a novel mechanism to control sumoylation in vivo by diversification of the E1 small subunit.

Evolution of multicopper oxidase genes in coprophilous and non-coprophilous members of the order sordariales

Multicopper oxidases (MCO) catalyze the biological oxidation of various aromatic substrates and have been identified in plants, insects, bacteria, and wood rotting fungi. In nature, they are involved in biodegradation of biopolymers such as lignin and humic compounds, but have also been tested for various industrial applications. In fungi, MCOs have been shown to play important roles during their life cycles, such as in fruiting body formation, pigment formation and pathogenicity. Coprophilous fungi, which grow on the dung of herbivores, appear to encode an unexpectedly high number of enzymes capable of at least partly degrading lignin. This study compared the MCO-coding capacity of the coprophilous filamentous ascomycetes Podospora anserina and Sordaria macrospora with closely related non-coprophilous members of the order Sordariales. An increase of MCO genes in coprophilic members of the Sordariales most probably occurred by gene duplication and horizontal gene transfer events.