The genome of the social amoeba Dictyostelium discoideum

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.     

Reduced calcification of marine plankton in response to increased atmospheric CO2

The formation of calcareous skeletons by marine planktonic organisms and their subsequent sinking to depth generates a continuous rain of calcium carbonate to the deep ocean and underlying sediments. This is important in regulating marine carbon cycling and ocean-atmosphere CO2 exchange. The present rise in atmospheric CO2 levels causes significant changes in surface ocean pH and carbonate chemistry. Such changes have been shown to slow down calcification in corals and coralline macroalgae, but the majority of marine calcification occurs in planktonic organisms. Here we report reduced calcite production at increased CO2 concentrations in monospecific cultures of two dominant marine calcifying phytoplankton species, the coccolithophorids Emiliania huxleyi and Gephyrocapsa oceanica. This was accompanied by an increased proportion of malformed coccoliths and incomplete coccospheres. Diminished calcification led to a reduction in the ratio of calcite precipitation to organic matter production. Similar results were obtained in incubations of natural plankton assemblages from the north Pacific ocean when exposed to experimentally elevated CO2 levels. We suggest that the progressive increase in atmospheric CO2 concentrations may therefore slow down the production of calcium carbonate in the surface ocean. As the process of calcification releases CO2 to the atmosphere, the response observed here could potentially act as a negative feedback on atmospheric CO2 levels.     

Sensitivity of coccolithophores to carbonate chemistry and ocean acidification

About one-third of the carbon dioxide (CO(2)) released into the atmosphere as a result of human activity has been absorbed by the oceans, where it partitions into the constituent ions of carbonic acid. This leads to ocean acidification, one of the major threats to marine ecosystems and particularly to calcifying organisms such as corals, foraminifera and coccolithophores. Coccolithophores are abundant phytoplankton that are responsible for a large part of modern oceanic carbonate production. Culture experiments investigating the physiological response of coccolithophore calcification to increased CO(2) have yielded contradictory results between and even within species. Here we quantified the calcite mass of dominant coccolithophores in the present ocean and over the past forty thousand years, and found a marked pattern of decreasing calcification with increasing partial pressure of CO(2) and concomitant decreasing concentrations of CO(3)(2-). Our analyses revealed that differentially calcified species and morphotypes are distributed in the ocean according to carbonate chemistry. A substantial impact on the marine carbon cycle might be expected upon extrapolation of this correlation to predicted ocean acidification in the future. However, our discovery of a heavily calcified Emiliania huxleyi morphotype in modern waters with low pH highlights the complexity of assemblage-level responses to environmental forcing factors.     

Seismological constraints on a possible plume root at the core-mantle boundary

Recent seismological discoveries have indicated that the Earth's core-mantle boundary is far more complex than a simple boundary between the molten outer core and the silicate mantle. Instead, its structural complexities probably rival those of the Earth's crust. Some regions of the lowermost mantle have been observed to have seismic wave speed reductions of at least 10 per cent, which appear not to be global in extent. Here we present robust evidence for an 8.5-km-thick and approximately 50-km-wide pocket of dense, partially molten material at the core-mantle boundary east of Australia. Array analyses of an anomalous precursor to the reflected seismic wave ScP reveal compressional and shear-wave velocity reductions of 8 and 25 per cent, respectively, and a 10 per cent increase in density of the partially molten aggregate. Seismological data are incompatible with a basal layer composed of pure melt, and thus require a mechanism to prevent downward percolation of dense melt within the layer. This may be possible by trapping of melt by cumulus crystal growth following melt drainage from an anomalously hot overlying region of the lowermost mantle. This magmatic evolution and the resulting cumulate structure seem to be associated with overlying thermal instabilities, and thus may mark a root zone of an upwelling plume.     

Melting of the Earth's inner core

The Earth's magnetic field is generated by a dynamo in the liquid iron core, which convects in response to cooling of the overlying rocky mantle. The core freezes from the innermost surface outward, growing the solid inner core and releasing light elements that drive compositional convection. Mantle convection extracts heat from the core at a rate that has enormous lateral variations. Here we use geodynamo simulations to show that these variations are transferred to the inner-core boundary and can be large enough to cause heat to flow into the inner core. If this were to occur in the Earth, it would cause localized melting. Melting releases heavy liquid that could form the variable-composition layer suggested by an anomaly in seismic velocity in the 150 kilometres immediately above the inner-core boundary. This provides a very simple explanation of the existence of this layer, which otherwise requires additional assumptions such as locking of the inner core to the mantle, translation from its geopotential centre or convection with temperature equal to the solidus but with composition varying from the outer to the inner core. The predominantly narrow downwellings associated with freezing and broad upwellings associated with melting mean that the area of melting could be quite large despite the average dominance of freezing necessary to keep the dynamo going. Localized melting and freezing also provides a strong mechanism for creating seismic anomalies in the inner core itself, much stronger than the effects of variations in heat flow so far considered.     

Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes

The sub-cellular localization of a native protein constitutes one coarse-grained aspect of its function. Transport between compartments is often regulated through short sequence motifs. Here, we analyzed experimentally characterized endoplasmic reticulum (ER)/ Golgi retrieval motifs and investigated the accuracy of homology-transfer. Only the C-terminal ER retrieval motifs KDEL, HDEL and AIAKE were sufficiently specific. However, even unspecific motifs may help, provided we know the probability for localization given the motif. We provided such estimates. We also rigorously estimated the accuracy and coverage for inferring ER and Golgi localization through homology-transfer by sequence similarity. In entire proteomes, we could thereby annotate 3304 ER (3182 membrane) and 1853 Golgi (759 membrane) proteins. We identified another putative 5157 globular and 3941 membrane ER or Golgi proteins. Each experimental annotation yielded, on average, one to three high-accuracy and five to six low-accuracy homology-transfers in the six proteomes. These numbers will increase with each new experimental annotation.Received 6 January 2004; received after revision 10 March 2004; accepted 29 March 2004     

Homologue structure of the SLAC1 anion channel for closing stomata in leaves

The plant SLAC1 anion channel controls turgor pressure in the aperture-defining guard cells of plant stomata, thereby regulating the exchange of water vapour and photosynthetic gases in response to environmental signals such as drought or high levels of carbon dioxide. Here we determine the crystal structure of a bacterial homologue (Haemophilus influenzae) of SLAC1 at 1.20 ? resolution, and use structure-inspired mutagenesis to analyse the conductance properties of SLAC1 channels. SLAC1 is a symmetrical trimer composed from quasi-symmetrical subunits, each having ten transmembrane helices arranged from helical hairpin pairs to form a central five-helix transmembrane pore that is gated by an extremely conserved phenylalanine residue. Conformational features indicate a mechanism for control of gating by kinase activation, and electrostatic features of the pore coupled with electrophysiological characteristics indicate that selectivity among different anions is largely a function of the energetic cost of ion dehydration.     

Crystal structure of a potassium ion transporter, TrkH

The TrkH/TrkG/KtrB proteins mediate K(+) uptake in bacteria and probably evolved from simple K(+) channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K(+) channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K(+) and Rb(+) over smaller ions such as Na(+) or Li(+). Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K(+) flux. These results reveal the molecular basis of K(+) selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.