A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels

Proteins of the cradle-loop barrel metafold are formed by duplication of a conserved betaalphabeta-element, suggesting a common evolutionary origin from an ancestral group of nucleic acid-binding proteins. The basal fold within this metafold, the RIFT barrel, is also found in a wide range of enzymes, whose homologous relationship with the nucleic acid-binding group is unclear. We have characterized a protein family that is intermediate in sequence and structure between the basal group of cradle-loop barrels and one family of RIFT-barrel enzymes, the riboflavin kinases. We report the structure, substrate-binding mode, and catalytic activity for one of these proteins, Methanocaldococcus jannaschii Mj0056, which is an archaeal riboflavin kinase. Mj0056 is unusual in utilizing CTP rather than ATP as the donor nucleotide, and sequence conservation in the relevant residues suggests that this is a general feature of archaeal riboflavin kinases.     

Functional biodiversity of lipids in Antarctic zooplankton: Calanoides acutus, Calanus propinquus, Thysanoessa macrura and Euphausia crystallorophias

Zooplankton samples were collected in January 1993 off Dronning Maud Land along a transect from open waters to the marginal ice zone close to the Antarctic ice shelf. Thysanoessa macrura was caught in open waters while Calanoides acutus and Calanus propinquus were mainly sampled between ice floes in the marginal ice zone. The “ice-krill”Euphausia crystallorophias was found over the shelf directly associated with ice floes. T. macrura had a lipid content up to 36% of its dry weight with the dominant lipid class, wax ester, accounting for 45–50% of the total lipid. The predominance of 18:1 fatty alcohols is the striking characteristic of the wax esters. Small specimens of E. crystallorophias had lipid levels up to 26% of their dry weight with, unexpectedly, triacylglycerols being the dominant lipid (up to 41% of total lipid). The small levels of wax esters in these animals (3–6% of total lipid) had phytol as a major constituent. Large specimens of E. crystallorophias had up to 34% of their dry weight as lipid, with wax esters (47% of total lipid) dominated by 16:0 and 14:0 fatty alcohols as the major lipid. Calanus propinquus had lipid levels of up to 34% of their dry weight, with triacylglycerols (up to 63% of total lipid) being the dominant lipid. High levels of 22:1 (n-9) fatty acid were present in the triacylglycerols. Calanoides acutus had lipid levels up to 35% of the dry weight with wax esters accounting for up to 83% of total lipid. High levels of (n-3) polyunsaturated fatty acids were recorded with 20:5(n-3), 22:6(n-3) and 18:4(n-3) being the dominant moieties. On the basis of their lipid compositions we deduce that: (1) Calanoides acutus is the strictest herbivore among the four species studied, heavily utilizing the typical spring bloom; (2) T. macrura is essentially omnivorous, probably utilizing the less defined bloom situations found in oceanic waters; (3) E. crystallorophias is an omnivore well adapted to utilize both a bloom situation and to feed on ice algae and micro-zooplankton associated with the ice; (4) Calanus propinquus seems to be the most opportunistic feeder of the four species studied, probably grazing heavily on phytoplankton during a bloom and, during the rest of the year, feeding on whatever material is available, including particulates, flagellates and other ice-associated algae. We conclude that the different biochemical pathways generating large oil reserves of different compositions, enabling species to utilize different ecological niches, are major determinants of biodiversity in polar zooplankton. Accepted: 22 June 1998     

Non-native Species and Rates of Spread: Lessons from the Brackish Baltic Sea

The Baltic Sea, a semi-enclosed brackish water region, has been inoculated by non-indigenous species for centuries. Today, much of its biological diversity is of foreign origin (i.e. xenodiversity), intentionally or unintentionally moved by humans over ecological and geographical barriers. As many as 98 introduced species have been recorded in the Baltic Sea and Kattegat. The role and abundance of much of the unique native brackish water fauna of the Baltic Sea are threatened by these non-indigenous species. The rate of primary introductions into the Baltic has increased since the 1950s; the secondary rate of spread of non-indigenous species within the basin varies from 30–480 km/year. We review here the invasion histories of the brown alga Sargassum muticum (introduced in the early 1990s), the mud snail Potamopyrgus antipodarum (1887), the barnacle Balanus improvisus (1844), the polychaetes Marenzelleria viridis (1985) and Polydora redeki (1963), the cladoceran Cercopagis pengoi (1992) and the mysid shrimp Hemimysis anomala (1962). This revised version was published online in July 2006 with corrections to the Cover Date.     

The energetics of rearrangement and water elimination reactions in the radiolysis of the DNA bases in aqueous solution (eaq- and *OH attack): DFT calculations

DFT calculations on the relative stability of various nucleobase radicals induced by e(aq)(-) and (*)OH have been carried out for assessing the energetics of rearrangements and water elimination reactions, taking the solvent effect of water into account. Uracil and thymine radical anions are protonated fast at O2 and O4, whereby the O2-protonated anions are higher in energy (50 kJ mol(-1), equivalent to a 9-unit lower pK(a)). The experimentally observed pK(a)=7 is thus that of the O4-protonated species. Thermodynamically favored protonation occurs slowly at C6 (driving force, thymine: 49 kJ mol(-1), uracil: 29 kJ mol(-1)). The cytosine radical anion is rapidly protonated by water at N3. Final protonation at C6 is disfavored here. The kinetically favored pyrimidine C5 (*)OH adducts rearrange into the thermodynamically favored C6 (*)OH adducts (driving force, thymine: 42 kJ mol(-1)). Very similar in energy is a water elimination that leads to the Ura-5-methyl radical. Purine (*)OH adducts at C4 and C5 (plus C2 in guanine) eliminate water in exothermic reactions, while water elimination from the C8 (*)OH adducts is endothermic. The latter open the ring en route to the FAPY products, an H transfer from the C8(*)OH to N9 being the most likely process.     

Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations

Membrane electroporation is the method to directly transfer bioactive substances such as drugs and genes into living cells, as well as preceding electrofusion. Although much information on the microscopic mechanism has been obtained both from experiment and simulation, the existence and nature of possible intermediates is still unclear. To elucidate intermediates of electropore formation by direct comparison with measured prepore formation kinetics, we have carried out 49 atomistic electroporation simulations on a palmitoyl-oleoyl-phosphatidylcholine bilayer for electric field strengths between 0.04 and 0.7 V/nm. A statistical theory is developed to facilitate direct comparison of experimental (macroscopic) prepore formation kinetics with the (single event) preporation times derived from the simulations, which also allows us to extract an effective number of lipids involved in each pore formation event. A linear dependency of the activation energy for prepore formation on the applied field is seen, with quantitative agreement between experiment and simulation. The distribution of preporation times suggests a four-state pore formation model. The model involves a first intermediate characterized by a differential tilt of the polar lipid headgroups on both leaflets, and a second intermediate (prepore), where a polar chain across the bilayer is formed by 3-4 lipid headgroups and several water molecules, thereby providing a microscopic explanation for the polarizable volume derived previously from the measured kinetics. An average pore radius of 0.47 ± 0.15 nm is seen, in favorable agreement with conductance measurements and electrooptical experiments of lipid vesicles.     

A spatially extended stochastic model of the bacterial chemotaxis signalling pathway

We have combined two distinct but related stochastic approaches to model the Escherichia coli chemotaxis pathway. Reactions involving cytosolic components of the pathway were assumed to obey the laws of conventional stochastic chemical kinetics, while the clustered membrane receptors were represented in two-dimensional arrays similar to the Ising model. Receptors were assumed to flip between an active and an inactive state with probabilities dependent upon three energy inputs: ligand binding, methylation level due to adaptation, and the activity of neighbouring receptors. Examination of models with different lattice size and geometry showed that the sensitivity to stimuli increases with lattice size and the nearest-neighbour coupling strength up to a critical point, but this amplification was also accompanied by a proportional increase in steady-state noise. Multiple methylation of receptors resulted in diminished signal-to-noise ratio, but showed improved stability to variation in the coupling strength and increased gain. Under the best conditions the simulated output of a coupled lattice of receptors closely matched the time-course and amplitude found experimentally in living bacteria. The model also has some of the properties of a cellular automaton and shows an unexpected emergence of spatial patterns of methylation within the receptor lattice.