Rapid evolution buffers ecosystem impacts of viruses in a microbial food web

Predation and parasitism often regulate population dynamics, community interactions, and ecosystem functioning. The strength of these top-down pressures is variable, however, and may be influenced by both ecological and evolutionary processes. We conducted a chemostat experiment to assess the direct and indirect effects of viruses on a marine microbial food web comprised of an autotrophic host (Synechococcus) and non-target heterotrophic bacteria. Viruses dramatically altered the host population dynamics, which in turn influenced phosphorus resource availability and the stoichiometric allocation of nutrients into microbial biomass. These virus effects diminished with time, but could not be attributed to changes in the abundance or composition of heterotrophic bacteria. Instead, attenuation of the virus effects coincided with the detection of resistant host phenotypes, suggesting that rapid evolution buffered the effect of viruses on nutrient cycling. Our results demonstrate that evolutionary processes are important for community dynamics and ecosystem processes on ecologically relevant time scales.     

Engineering of complex polyketide biosynthesis — insights from sequencing of the monensin biosynthetic gene cluster

The biosynthesis of complex reduced polyketides is catalysed in actinomycetes by large multifunctional enzymes, the modular Type I polyketide synthases (PKSs). Most of our current knowledge of such systems stems from the study of a restricted number of macrolide-synthesising enzymes. The sequencing of the genes for the biosynthesis of monensin A, a typical polyether ionophore polyketide, provided the first genetic evidence for the mechanism of oxidative cyclisation through which polyethers such as monensin are formed from the uncyclised products of the PKS. Two intriguing genes associated with the monensin PKS cluster code for proteins, which show strong homology with enzymes that trigger double bond migrations in steroid biosynthesis by generation of an extended enolate of an unsaturated ketone residue. A similar mechanism operating at the stage of an enoyl ester intermediate during chain extension on a PKS could allow isomerisation of an E double bond to the Z isomer. This process, together with epoxidations and cyclisations, form the basis of a revised proposal for monensin formation. The monensin PKS has also provided fresh insight into general features of catalysis by modular PKSs, in particular into the mechanism of chain initiation. Journal of Industrial Microbiology & Biotechnology (2001) 27, 360–367. Received 18 March 2001/ Accepted in revised form 09 July 2001     

Fractal species distributions do not produce power-law species-area relationships

We derive the species-area relationship (SAR) expected from an assemblage of fractally distributed species. If species have truly fractal spatial distributions with different fractal dimensions, we show that the expected SAR is not the classical power-law function, as suggested recently in the literature. This analytically derived SAR has a distinctive shape that is not commonly observed in nature: upward-accelerating richness with increasing area (when plotted on log-log axes). This suggests that, in reality, most species depart from true fractal spatial structure. We demonstrate the fitting of a fractal SAR using two plant assemblages (Alaskan trees and British grasses). We show that in both cases, when modelled as fractal patterns, the modelled SAR departs from the observed SAR in the same way, in accord with the theory developed here. The challenge is to identify how species depart from fractality, either individually or within assemblages, and more importantly to suggest reasons why species distributions are not self-similar and what, if anything, this can tell us about the spatial processes involved in their generation.     

Domain alternation switches B(12)-dependent methionine synthase to the activation conformation.

B(12)-dependent methionine synthase (MetH) from Escherichia coli is a large modular protein that uses bound cobalamin as an intermediate methyl carrier. Major domain rearrangements have been postulated to explain how cobalamin reacts with three different substrates: homocysteine, methyltetrahydrofolate and S-adenosylmethionine (AdoMet). Here we describe the 3.0 A structure of a 65 kDa C-terminal fragment of MetH that spans the cobalamin- and AdoMet-binding domains, arranged in a conformation suitable for the methyl transfer from AdoMet to cobalamin that occurs during activation. In the conversion to the activation conformation, a helical domain that capped the cofactor moves 26 A and rotates by 63 degrees, allowing formation of a new interface between cobalamin and the AdoMet-binding (activation) domain. Interactions with the MetH activation domain drive the cobalamin away from its binding domain in a way that requires dissociation of the axial cobalt ligand and, thereby, provide a mechanism for control of the distribution of enzyme conformations.     

A CD36-dependent signaling cascade is necessary for macrophage foam cell formation

Accumulation of macrophage foam cells in atherosclerotic blood vessel intima is a critical component of atherogenesis mediated by scavenger receptor-dependent internalization of oxidized LDL. We demonstrated by coimmunoprecipitation and pull-down assays that the macrophage scavenger receptor CD36 associates with a signaling complex containing Lyn and MEKK2. The MAP kinases JNK1 and JNK2 were specifically phosphorylated in macrophages exposed to oxLDL. Using cells isolated from SRA, TLR2, or CD36 null mice, and phospholipid ligands specific for either SRA or CD36, we showed that JNK activation was mediated by CD36. Both foam cell formation and activation of JNK2 in hyperlipidemic mice were diminished in the absence of CD36. Furthermore, inhibition of Src or JNK blocked oxLDL uptake and inhibited foam cell formation in vitro and in vivo. These findings show that a specific CD36-dependent signaling pathway initiated by oxLDL is necessary for foam cell formation and identify potential targets for antiatherosclerosis therapy.     

Effects of light on respiration and oxygen isotope fractionation in soybean cotyledons

Light effects on electron flow through the cyanide-resistant respiratory pathway, oxygen isotope fractionation and total respiration were studied in soybean (Glycine max L.) cotyledons. During the first 12 h of illumination there was an increase in both electron partitioning through the alternative pathway and oxygen isotope fractionation by the alternative oxidase. The latter probably indicates a change in the properties of the alternative oxidase. There was no engagement of the alternative oxidase in darkness and its fractionation was 27‰. In green cotyledons 60% of the respiration flux was through the alternative pathway and the alternative oxidase fractionation was 32‰. Exposing previously illuminated tissue to continuous darkness induced a decrease in the electron partitioning through the alternative pathway. However, this decrease was not directly linked with the low cellular sugar concentration resulting from the lack of light because 5 min of light every 12 h was sufficient to keep the alternative pathway engaged to the same extent as plants grown under control conditions.     

Are Alaskan trees found in locally more favourable sites in marginal areas?

Aim Species generally become rarer and more patchily distributed as the margins of their ranges are approached. We predicted that in such marginal sites, tree species would tend to occur where some key environmental factors are at particularly favourable levels, compensating in part for the low overall suitability of marginal sites. Location The article considers the spatial distributions of trees in Southeast Alaska (the Alaskan ‘panhandle’). Methods We quantified range marginality using spatial distributions of eight tree species across more than one thousand surveyed sites in Southeast Alaska. For each species we derived a site core/margin index using a three‐dimensional trend surface generated from logistic regression on site coordinates. For each species, the relationships between the environmental factors slope, aspect and site marginality were then compared for occupied and unoccupied sets of sites. Results We found that site slope is important for more Alaskan tree species than aspect. Three out of eight had a significant core/margin by occupied/unoccupied interaction, tending to be present in significantly shallower‐sloped (more favourable) sites in the marginal areas than the simple core/margin trend predicted. For site aspect, one species had a significant interaction, selecting potentially more favourable northerly aspects in marginal areas. A finer‐scale analysis based on the same data came to the same overall conclusions. Conclusions There is evidence that several tree species in Alaska tend to occur in especially favourable sites in marginal areas. In these marginal areas, these species amplify habitat preferences shown in core areas.     

Nine Residues Influence the Binding of α-Bungarotoxin in α-Subunit Region 185–200 of Human Muscle Acetylcholine Receptor

Abstract: Identification of residues in the skeletal muscle nicotinic acetylcholine receptor (AChR) that bind snake venom a-neurotoxin antagonists of acetylcholine [e.g., α-bungarotoxin (α-BTx)] provides structural information about the neurotransmitter binding region of the receptor. Using synthetic peptides of the human AChR α-subunit region 177–208, we previously localized a pharmacologically specific binding site for α-BTx in segment 185–199. To define in more detail the residues that influence the binding of α-BTx to this region, we prepared 16 peptide analogues of the α-subunit segment 185–200, with the amino acid Lalanine sequentially replacing each native amino acid. Circular dichroism spectroscopy did not reveal changes in the secondary structure of the peptides except for the analogue in which Pro¹⁹⁴ was substituted with alanine. This implies that any change in α-BTx binding could be attributed to replacement of the native residue's side chain by alanine's methyl group, rather than to a change in the structure of the peptide. The influence of each substitution with alanine was determined by comparing the analogue to the parental sequence α 185–200 in solution-phase competition with native human AChR for binding of ¹²⁵I-labeled α-BTx. The binding of α-BTx by analogue peptides with alanine substituted for Tyr¹⁹⁰, Cys¹⁹², or Cys¹⁹³ was greatly diminished. Binding of α-BTx to peptides containing alanine replacements at Val¹⁸⁸, Thr¹⁸⁹, Pro¹⁹⁴, Asp¹⁹⁵, or Tyr¹⁹⁸ was also reduced significantly (p < 0.003). An unanticipated finding was that substitution of alanine for Ser¹⁹¹ significantly increased α-BTx binding (p < 0.003). The data imply that these nine amino acids influence the binding of the antagonist, α-BTx, to the nicotinic acetylcholine receptor of human skeletal muscle, and confirm previous reports for certain contact residues for α-BTX that were found in region α181-200 of the Torpedo AChR.