dsRNA binding properties of RDE-4 and TRBP reflect their distinct roles in RNAi

Double-stranded RNA (dsRNA)-binding proteins facilitate Dicer functions in RNA interference. Caenorhabditis elegans RDE-4 facilitates cleavage of long dsRNA to small interfering RNA (siRNA), while human trans-activation response RNA-binding protein (TRBP) functions downstream to pass siRNA to the RNA-induced silencing complex. We show that these distinct in vivo roles are reflected in in vitro binding properties. RDE-4 preferentially binds long dsRNA, while TRBP binds siRNA with an affinity that is independent of dsRNA length. These properties are mechanistically based on the fact that RDE-4 binds cooperatively, via contributions from multiple domains, while TRBP binds noncooperatively. Our studies offer a paradigm for how dsRNA-binding proteins, which are not sequence specific, discern dsRNA length. Additionally, analyses of the ability of RDE-4 deletion constructs and RDE-4/TRBP chimeras to reconstitute Dicer activity suggest RDE-4 promotes activity using its dsRNA-binding motif 2 to bind dsRNA, its linker region to interact with Dicer, and its C-terminus for Dicer activation.     

Anti-cooperative assembly of the SRP19 and SRP68/72 components of the signal recognition particle

The mammalian SRP (signal recognition particle) represents an important model for the assembly and role of inter-domain interactions in complex RNPs (ribonucleoproteins). In the present study we analysed the interdependent interactions between the SRP19, SRP68 and SRP72 proteins and the SRP RNA. SRP72 binds the SRP RNA largely via non-specific electrostatic interactions and enhances the affinity of SRP68 for the RNA. SRP19 and SRP68 both bind directly and specifically to the same two RNA helices, but on opposite faces and at opposite ends. SRP19 binds at the apices of helices 6 and 8, whereas the SRP68/72 heterodimer binds at the three-way junction involving RNA helices 5, 6 and 8. Even though both SRP19 and SRP68/72 stabilize a similar parallel orientation for RNA helices 6 and 8, these two proteins bind to the RNA with moderate anti-cooperativity. Long-range anti-cooperative binding by SRP19 and SRP68/72 appears to arise from stabilization of distinct conformations in the stiff intervening RNA scaffold. Assembly of large RNPs is generally thought to involve either co-operative or energetically neutral interactions among components. By contrast, our findings emphasize that antagonistic interactions can play significant roles in assembly of multi-subunit RNPs.     

Determination of Heavy Metals and Their Distribution In Different Size Fractionated Sediment Samples Using Different Analytical Techniques

Distribution of heavy metals (Pb, Cu and Cd) in different size-fractionated sediment samples was studied using different analytical techniques such as flame atomic absorption spectrometry (FAAS), inductively coupled plasma atomic emission spectrometry (ICP-AES) and differential pulse anodic stripping voltammetry (DPASV). Pb and Cu concentrations were found to have respective variations of 6.58% and 9.45% from FAAS, ICP-AES and DPASV analysis. Cadmium was detectable only by DPASV because of its lower abundance in different size fractions. The percentage distribution of total organic carbon (TOC) and heavy metals increased with decrease in particle size. Metal concentrations increase with increasing TOC content in different size-fractionated sediment samples studied. Although the smallest fractions (< 53 μm) of sediment contributed only 3.4–17.8%, they had the highest mean distribution factor of 1.08 for Pb, 1.04 for Cu and 1.06 for Cd, respectively. Pb, Cu and Cd were correlated positively with organic carbon content in the sediment samples.