Comprehensively Surveying Structure and Function of RING Domains from Drosophila melanogaster

Using a complete set of RING domains from Drosophila melanogaster, all the solved RING domains and cocrystal structures of RING-containing ubiquitin-ligases (RING-E3) and ubiquitin-conjugating enzyme (E2) pairs, we analyzed RING domains structures from their primary to quarternary structures. The results showed that: i) putative orthologs of RING domains between Drosophila melanogaster and the human largely occur (118/139, 84.9%); ii) of the 118 orthologous pairs from Drosophila melanogaster and the human, 117 pairs (117/118, 99.2%) were found to retain entirely uniform domain architectures, only Iap2/Diap2 experienced evolutionary expansion of domain architecture; iii) 4 evolutionary structurally conserved regions (SCRs) are responsible for homologous folding of RING domains at the superfamily level; iv) besides the conserved Cys/His chelating zinc ions, 6 equivalent residues (4 hydrophobic and 2 polar residues) in the SCRs possess good-consensus and conservation- these 4 SCRs function in the structural positioning of 6 equivalent residues as determinants for RING-E3 catalysis; v) members of these RING proteins located nucleus, multiple subcellular compartments, membrane protein and mitochondrion are respectively 42 (42/139, 30.2%), 71 (71/139, 51.1%), 22 (22/139, 15.8%) and 4 (4/139, 2.9%); vi) CG15104 (Topors) and CG1134 (Mul1) in C3HC4, and CG3929 (Deltex) in C3H2C3 seem to display broader E2s binding profiles than other RING-E3s; vii) analyzing intermolecular interfaces of E2/RING-E3 complexes indicate that residues directly interacting with E2s are all from the SCRs in RING domains. Of the 6 residues, 2 hydrophobic ones contribute to constructing the conserved hydrophobic core, while the 2 hydrophobic and 2 polar residues directly participate in E2/RING-E3 interactions. Based on sequence and structural data, SCRs, conserved equivalent residues and features of intermolecular interfaces were extracted, highlighting the presence of a nucleus for RING domain fold and formation of catalytic core in which related residues and regions exhibit preferential evolutionary conservation

Elevated CO2 reduces field decomposition rates of betula-pendula (roth) leaf-litter.

The effect of elevated atmospheric CO2 and nutrient supply on elemental composition and decomposition rates of tree leaf litter was studied using litters derived from birch (Betula pendula Roth.) plants grown under two levels of atmospheric CO2 (ambient and ambient +250 ppm) and two nutrient regimes in solar domes. CO2 and nutrient treatments affected the chemical composition of leaves, both independently and interactively. The elevated CO2 and unfertilized soil regime significantly enhanced lignin/N and C/N ratios of birch leaves. Decomposition was studied using field litter-bags, and marked differences were observed in the decomposition rates of litters derived from the two treatments, with the highest weight remaining being associated with litter derived from the enhanced CO2 and unfertilized regime. Highly significant correlations were shown between birch litter decomposition rates and lignin/N and C/N ratios. It can be concluded, from this study, that at levels of atmospheric CO2 predicted for the middle of the next century a deterioration of litter quality will result in decreased decomposition rates, leading to reduction of nutrient mineralization and increased C storage in forest ecosystems. However, such conclusions are difficult to generalize, since tree responses to elevated CO2 depend on soil nutritional status

Effects of terrestrial isopods on the decomposition of woodland leaf litter

The indirect contribution terrestrial isopods make to decomposition processes by stimulating microbial activites has been quantified in laboratory experiments. The extent to which microbial metabolism is enhanced as a result of the passage of Betula pendula leaf litter through the alimentary system of isopods was measured for both freshly fallen and decayed leaves. Faeces derived from 1 g freshly fallen litter lost 75 mg g-1 D.W. more than did intact leaves, as a result of enhanced microbial metabolism. Faeces derived from 1 g of previously decayed leaves, which were shown to be the preferred food of isopods, lost only 17.5 mg g-1 D.W. more than intact decaying leaves. The isopod's direct contribution to soil metabolism was calculated to be 151 mg and 138 mg g-1 litter ingested when fed on freshly fallen and decayed leaves respectively. It is concluded that the physical and chemical changes in the leaf substrate which result from fragmentation and digestion by isopods do not necessarily accelerate the subsequent decomposition of the litter very significantly. Fungal propagule density was 3.2x and 3.6x higher in faeces derived from freshly fallen and decayed leaves respectively than in the intact litter. Numbers of viable bacteria were correspondingly 126x and 34x higher in faeces than in the freshly fallen and the decayed leaves. Levels of microbial inhibitors were lower in the faeces than in the leaves but levels of free amino acids stayed higher for longer in the faeces than they did in intact litter. In the field the physical removal of litter by the soil macrofauna from surface to deeper and moister microsites may be the most important indirect contribution that they make to decomposition processes