Studies on the Assembly Characteristics of Large Subunit Ribosomal Proteins in S. cerevisae

During the assembly process of ribosomal subunits, their structural components, the ribosomal RNAs (rRNAs) and the ribosomal proteins (r-proteins) have to join together in a highly dynamic and defined manner to enable the efficient formation of functional ribosomes. In this work, the assembly of large ribosomal subunit (LSU) r-proteins from the eukaryote S. cerevisiae was systematically investigated. Groups of LSU r-proteins with specific assembly characteristics were detected by comparing the protein composition of affinity purified early, middle, late or mature LSU (precursor) particles by semi-quantitative mass spectrometry. The impact of yeast LSU r-proteins rpL25, rpL2, rpL43, and rpL21 on the composition of intermediate to late nuclear LSU precursors was analyzed in more detail. Effects of these proteins on the assembly states of other r-proteins and on the transient LSU precursor association of several ribosome biogenesis factors, including Nog2, Rsa4 and Nop53, are discussed.     

Escherichia coli S-adenosylmethionine decarboxylase. Subunit structure, reductive amination, and NH2-terminal sequences

S-Adenosylmethionine decarboxylase is one of a small group of enzymes that use a pyruvoyl residue as a cofactor. Histidine decarboxylase from Lactobacillus 30a, the best studied pyruvoyl-containing enzyme, has an (alpha beta)6 subunit structure with the pyruvoyl moiety linked through an amide bond to the NH2-terminal of the larger alpha subunit (Recsei, P. A., Huynh, Q. K., and Snell, E. E. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 973-977). To examine potential structural analogies between the two enzymes, we have isolated and partially characterized S-adenosylmethionine decarboxylase. The purified enzyme comprises equimolar amounts of two subunits of Mr = 14,000 and 19,000 (by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and has a native molecular weight of 136,000 (by gel filtration). Approximately 4 mol of [methyl-3H] adenosylmethionine are incorporated per mol of enzyme (Mr = 136,000) when the enzyme is inactivated with this substrate and NaCNBH3. These data suggest an (alpha beta)4 structure with 1 pyruvoyl residue for each alpha beta pair. The two subunits have been separated by reversed-phase high performance liquid chromatography after reduction and carboxymethylation. The smaller subunit (beta) has a free amino terminus. The amino terminus of the larger subunit (alpha) appears to be blocked by a pyruvoyl group; this subunit can be sequenced only after this group is converted to an alanyl residue by reduction with sodium cyanoborohydride in the presence of ammonium acetate. This work suggests that S-adenosylmethionine decarboxylase is structurally much more similar to histidine decarboxylase than previously thought.     

Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land

Plants provide resources and shape the habitat of soil organisms thereby affecting the composition and functioning of soil communities. Effects of plants on soil communities are largely taxon‐dependent, but how different functional groups of herbaceous plants affect trophic niches of individual animal species in soil needs further investigation. Here, we studied the use of basal resources and trophic levels of dominating soil meso‐ and macrofauna using stable isotope ratios of carbon and nitrogen in arable fallow systems 3 and 14–16 years after abandonment. Animals were sampled from the rhizosphere of three plant species of different functional groups: a legume (Medicaco sativa), a nonlegume herb (Taraxacum officinale), and a grass (Bromus sterilis). We found virtually no consistent effects of plant identity on stable isotope composition of soil animals and on thirteen isotopic metrics that reflect general food‐web structure. However, in old fallows, the carbon isotope composition of some predatory macrofauna taxa had shifted closer to that of co‐occurring plants, which was particularly evident for Lasius, an aphid‐associated ant genus. Trophic levels and trophic‐chain lengths in food webs were similar across plant species and fallow ages. Overall, the results suggest that variations in local plant diversity of grassland communities may little affect the basal resources and the trophic level of prey consumed by individual species of meso‐ and macrofauna belowground. By contrast, successional changes in grassland communities are associated with shifts in the trophic niches of certain species, reflecting establishment of trophic interactions with time, which shapes the functioning and stability of soil food webs.     

Multi-proxy analysis of waterlogged preserved Late Neolithic canine excrements

Vegetation History and Archaeobotany - Multi-proxy analysis of the coprolites which were found during excavations at two Late Neolithic (fourth millennium bc) pile-dwelling sites (Črnelnik and...     

Geographical vs. ecological diversification in Carex section Phacocystis (Cyperaceae): Patterns hidden behind a twisted taxonomy

Carex section Phacocystis (Cyperaceae) is one of the most diverse and taxonomically complex groups of sedges (between 116 and 147 species), with a worldwide distribution in a wide array of biomes. It has a very complicated taxonomic history, with numerous disagreements among different treatments. We studied the biogeography and niche evolution in a phylogenetic framework to unveil the relative contribution of geographical and ecological drivers to diversification of the group. We used a large species sampling of the section (82% of extant species) to build a phylogeny based on four DNA regions, constrained with a phylogenomic HybSeq tree and dated with six fossil calibrations. Our phylogenetic results recovered section Phacocystis s.s. (core Phacocystis) as sister to section Praelongae. Ancestral area reconstruction points toward the N Pacific as the cradle for the crown diversification of section Phacocystis during the Middle Miocene. Wide distributions were recurrently inferred across deep nodes. Large Northern Hemisphere lineages with geographical congruence were retrieved, pointing toward the importance of allopatric divergence at deep phylogenetic levels, whereas within-area speciation emerges as the predominant pattern at shallow phylogenetic level. The Southern Hemisphere (Neotropics, SW Pacific) was colonized several times from the Northern Hemisphere. The global expansion of Carex section Phacocystis did not entail major ecological changes along the inner branches of the phylogeny. Nevertheless, ecological differentiation seems to gain importance toward recent times.