The crystal structure of S. cerevisiae Sad1, a catalytically inactive deubiquitinase that is broadly required for pre-mRNA splicing

Sad1 is an essential splicing factor initially identified in a genetic screen in Saccharomyces cerevisiae for snRNP assembly defects. Based on sequence homology, Sad1, or USP39 in humans, is predicted to comprise two domains: a zinc finger ubiquitin binding domain (ZnF-UBP) and an inactive ubiquitin-specific protease (iUSP) domain, both of which are well conserved. The role of these domains in splicing and their interaction with ubiquitin are unknown. We first used splicing microarrays to analyze Sad1 function in vivo and found that Sad1 is critical for the splicing of nearly all yeast intron-containing genes. By using in vitro assays, we then showed that it is required for the assembly of the active spliceosome. To gain structural insights into Sad1 function, we determined the crystal structure of the full-length protein at 1.8 Å resolution. In the structure, the iUSP domain forms the characteristic ubiquitin binding pocket, though with an amino acid substitution in the active site that results in complete inactivation of the enzymatic activity of the domain. The ZnF-UBP domain of Sad1 shares high structural similarly to other ZnF-UBPs; however, Sad1''s ZnF-UBP does not possess the canonical ubiquitin binding motif. Given the precedents for ZnF-UBP domains to function as activators for their neighboring USP domains, we propose that Sad1''s ZnF-UBP acts in a ubiquitin-independent capacity to recruit and/or activate Sad1''s iUSP domain to interact with the spliceosome.     

Performance of two Picea abies (L.) Karst. stands at different stages of decline

Summary The water relations of Picea abies in a healthy stand with green trees only and a declining stand with trees showing different stages of needle yellowing were investigated in northern Bavaria. The present study is based on observations of trees differing in their nutritional status but apparently green on both sites in order to identify changes in the response pattern which might be caused by atmospheric concentrations of air pollutants and could lead to the phenomenon of decline. Transpiration was measured as water flow through the hydroactive xylem using an equilibrium mass-flow measurement system. Total tree transpiration was monitored diurnally, from July 1985 until October 1985 at both sites. The relationship between transpiration and meteorological measurements indicated that transpiration was a linear function of the vapor pressure deficit. No differences in transpiration of green trees were observed between the two sites. Canopy transpiration was 57%–68% of total throughfall and 41%–54% of total rainfall. Due to this positive water balance, soil water potential at 10 and 20 cm depths remained close to-0.02 MPa (max.-0.09 MPa) for most of the summer. Soil water potential was correlated with the difference between the weekly precipitation and transpiration. No differences in the water relations of apparently healthy trees in the two P. abies stands were observed. It is concluded that differences between green trees at the two sites in terms of nutrient relations or growth rate cannot be explained by changes in whole-tree transpiration or soil water status.     

Performance of two Picea abies (L.) Karst. stands at different stages of decline

Summary The annual replacement of tillers of Agropyron desertorum (Fisch. ex Link) Schult., a grazing-tolerant, Eurasian tussock grass, was examined in the field following cattle grazing. Heavy grazing before internode (culm) elongation seldom affected tiller replacement. Heavy grazing during or after internode elongation, which elevates apical meristems, increased overwinter mortality of fall-produced tillers and reduced the number and heights of these replacement tillers. Unexpectedly, tussocks grazed twice within the spring growing season tended to have lower overwinter tiller mortality, greater tiller replacement, and larger replacement tillers than tussocks grazed only once in late spring. These responses of twice-grazed tussocks, however, were still less than those of ungrazed tussocks or tussocks grazed moderately in early spring. The presence of ungrazed tillers on partially grazed tussoks did not increase the replacement of associated grazed tillers relative to tillers on uniformly grazed plants. This result indicates that resource sharing among tillers, if present, is short-lived or ecologically unimportant in this species. Although A. desertorum is considered grazing-tolerant, tiller replacement on heavily grazed tussocks, particularly those grazed during or after internode elongation when apical meristems were removed, was usually inadequate for tussock maintenance. These observations at the tiller (ramet) level of organization in individual tussocks (genet) may explain the often noted reduction in stand (population) longevity with consistent heavy grazing.     

Accumulation of Trehalose and Sucrose in Cyanobacteria Exposed to Matric Water Stress

The drought-resistant cyanobacteria Phormidium autumnale, strain LPP₄, and a Chroococcidiopsis sp. accumulated trehalose, sucrose, and both trehalose and sucrose, respectively, in response to matric water stress. Accumulated sugar concentrations reached values of up to 6.2 μg of trehalose per μg of chlorophyll in P. autumnale, 6.9 μg of sucrose per μg of chlorophyll in LPP₄, and 4.1 μg of sucrose and 3.2 μg of trehalose per μg of chlorophyll in the Chroococcidiopsis sp. The same sugars were accumulated by these cyanobacteria in similar concentrations under osmotic water stress. Cyanobacteria that did not show drought resistance (Plectonema boryanum and Synechococcus strain PCC 7942) did not accumulate significant amounts of sugars when matric water stress was applied.     

Reduction of nitrosubstituted aromatic compounds by the halophilic anaerobic eubacteria Haloanaerobium praevalens and Sporohalobacter marismortui.

The moderately halophilic, obligately anaerobic eubacteria Haloanaerobium praevalens DSM 2228 and Sporohalobacter marismortui ATCC 35420 are able to reduce a variety of nitrosubstituted aromatic compounds at a high rate to the corresponding amines. Compounds degraded included nitrobenzene, o-nitrophenol, m-nitrophenol, p-nitrophenol, nitroanilines, 2,4-dinitrophenol, and 2,4-dinitroaniline. Most of these compounds, when added at concentrations of 50 to 100 mg/liter, were completely transformed within 24 h, but at the highest concentrations growth rates were somewhat lowered. Growth of H. praevalens in the presence of 14C-labeled p-nitrophenol showed that the compound was not incorporated by the cells or degraded to acid-volatile compounds.     

Thermal affinity as the dominant factor changing Mediterranean fish abundances

Recent decades have seen profound changes in species abundance and community composition. In the marine environment, the major anthropogenic drivers of change comprise exploitation, invasion by nonindigenous species, and climate change. However, the magnitude of these stressors has been widely debated and we lack empirical estimates of their relative importance. In this study, we focused on Eastern Mediterranean, a region exposed to an invasion of species of Red Sea origin, extreme climate change, and high fishing pressure. We estimated changes in fish abundance using two fish trawl surveys spanning a 20‐year period, and correlated these changes with estimated sensitivity of species to the different stressors. We estimated sensitivity to invasion using the trait similarity between indigenous and nonindigenous species; sensitivity to fishing using a published composite index based on the species’ life‐history; and sensitivity to climate change using species climatic affinity based on occurrence data. Using both a meta‐analytical method and random forest analysis, we found that for shallow‐water species the most important driver of population size changes is sensitivity to climate change. Species with an affinity to warm climates increased in relative abundance and species with an affinity to cold climates decreased suggesting a strong response to warming local sea temperatures over recent decades. This decrease in the abundance of cold‐water‐associated species at the trailing “warm” end of their distribution has been rarely documented. Despite the immense biomass of nonindigenous species and the presumed high fishing pressure, these two latter factors seem to have only a minor role in explaining abundance changes. The decline in abundance of indigenous species of cold‐water origin indicates a future major restructuring of fish communities in the Mediterranean in response to the ongoing warming, with unknown impacts on ecosystem function.