Publications

Phylogenetic analysis of small and large subunits of rDNA genes suggested that Foraminifera originated early in the evolution of eukaryotes, preceding the origin of other rhizopodial protists. This view was recently challenged by the analysis of actin and ubiquitin protein sequences, which revealed a close relationship between Foraminifera and Cercozoa, an assemblage of various filose amoebae and amoeboflagellates that branch in the so-called crown of the SSU rDNA tree of eukaryotes. To further test this hypothesis, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1) from five foraminiferans, two cercozoans and the testate filosean Gromia oviformis. Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to Gromia as the closest relative of Foraminifera.

The sterol regulatory element-binding protein 2 (SREBP-2), a nuclear transcription factor that is essential for cholesterol metabolism, enters the nucleus through a direct interaction of its helix-loop-helix leucine zipper domain with importin-beta. We show the crystal structure of importin-beta complexed with the active form of SREBP-2. Importin-beta uses characteristic long helices like a pair of chopsticks to interact with an SREBP-2 dimer. Importin-beta changes its conformation to reveal a pseudo-twofold symmetry on its surface structure so that it can accommodate a symmetric dimer molecule. Importin-beta may use a similar strategy to recognize other dimeric cargoes.

Tousled-like kinases (TLKs) constitute a family of serine/threonine kinases conserved in plants and animals that act in a cell cycle-dependent manner. In mammals, their activity peaks during S phase, when they phosphorylate the antisilencing function protein 1 (ASF1), a histone chaperone involved in replication-dependent chromatin assembly. Here, we show that Drosophila ASF1 is also a phosphorylation target of TLK, and that the two components cooperate to control chromatin replication in vivo. By altering TLK activity through loss-of-function mutations, we show that nuclear divisions are arrested at interphase, followed by apoptosis. Overexpression of TLK alters the chromatin structure, suggesting that TLK mediates the activity of chromatin proteins. These results suggest that TLK coordinates cell cycle progression through the regulation of chromatin dynamics.

In 1926, Cushman described Rotalia beccarii var. tepida from San Juan Harbor, Puerto Rico. His publication illustrates a strew slide with many individuals, and no holotype was designated. Consequently, over the years, researchers have assumed that no holotype exists. A search of the Cushman Collection, however, discovered a slide labeled as holotype and it is so recorded in the Cushman Catalog of 1929. Here, this specimen is re-described and designated as a lectotype. All nine of the other surviving syntypes from the original collection in San Juan Harbor, Puerto Rico, now become paralectotypes. Hopefully, the designation of formal types for Ammonia tepida (Cushman) will help stabilize the taxonomy of this important species. Our study shows that the lectotype is morphologically distinguishable from other Ammonia types and that the distribution of Ammonia tepida is restricted to tropical shallow-water environments.

Nummulitidae are the largest extant calcareous Foraminifera, and are widely distributed in tropical and subtropical shallow-water seas. Classical morphology-based taxonomy divides the Nummulitidae in two subfamilies, the Nummulitinae and Heterostegininae, according to the presence or absence of secondary septa. To test the evolutionary importance of this morphological feature, phylogenetic relationships of five Recent nummulitid genera were investigated by sequencing fragments of the SSU and LSU rRNA gene. According to our results, species characterized by septate chambers (Heterostegina depressa, Planostegina operculinoides, and Cycloclypeus carpenteri) either group with species lacking septate chambers (Operculina ammonoides, Nummulites venosus) or branch separately. This suggests that chamber subdivisions developed several times independently in the evolutionary history of the Nummulitidae, providing an example of parallel evolution in Foraminifera.

Fossil Foraminifera appear in the Early Cambrian, at about the same time as the first skeletonized metazoans. However, due to the inadequate preservation of early unilocular (single-chambered) foraminiferal tests and difficulties in their identification, the evolution of early foraminifers is poorly understood. By using molecular data from a wide range of extant naked and testate unilocular species, we demonstrate that a large radiation of nonfossilized unilocular Foraminifera preceded the diversification of multilocular lineages during the Carboniferous. Within this radiation, similar test morphologies and wall types developed several times independently. Our findings indicate that the early Foraminifera were an important component of Neoproterozoic protistan community, whose ecological complexity was probably much higher than has been generally accepted.

The nuclear-transport protein importin-beta mediates the nuclear import of the transcription factor SREBP-2 without requiring adaptor proteins such as importin-alpha. An importin-beta-SREBP-2 HLHZ domain complex was purified and crystallized. The crystals belong to space group P2(1)2(1)2(1) and show diffraction to at least 3.0 A resolution. The unit-cell parameters are a = 101.0, b = 113.2, c = 240.0 A. Structure determination using the MAD or SAD method is under way.

Lobose amoebae are abundant free-living protists and important pathogenic agents, yet their evolutionary history and position in the universal tree of life are poorly known. Molecular data for lobose amoebae are limited to a few species, and all phylogenetic studies published so far lacked representatives of many of their taxonomic groups. Here we analyze actin and small-subunit ribosomal RNA (SSU rRNA) gene sequences of a broad taxon sampling of naked, lobose amoebae. Our results support the existence of a monophyletic Amoebozoa clade, which comprises all lobose amoebae examined so far, the amitochondriate pelobionts and entamoebids, and the slime molds. Both actin and SSU rRNA phylogenies distinguish two well-defined clades of amoebae, the "Gymnamoebia sensu stricto" and the Archamoebae (pelobionts + entamoebids), and one weakly supported and ill-resolved group comprising some naked, lobose amoebae and the Mycetozoa.

Progressive algorithms are widely used heuristics for the production of alignments among multiple nucleic-acid or protein sequences. Probabilistic approaches providing measures of global and/or local reliability of individual solutions would constitute valuable developments.