Calmodulin triggers activity-dependent rRNA biogenesis via interaction with DDX21.

Protein synthesis in response to neuronal activity, known as activity-dependent translation, is critical for synaptic plasticity and memory formation. However, the signaling cascades that couple neuronal activity to the translational events remains elusive. In this study, we identified the role of calmodulin (CaM), a conserved Ca2+-binding protein, in rRNA biogenesis in neurons. We found the CaM-regulated rRNA synthesis is Ca2+-dependent and necessary for nascent protein synthesis and axon growth in hippocampal neurons. Mechanistically, CaM interacts with nucleolar DDX21 in a Ca2+-dependent manner to regulate nascent rRNA transcription within nucleoli. We further found CaM alters the conformation of DDX21 to liberate the DDX21-sequestered RPA194, the catalytic subunit of RNA polymerase I, to facilitate transcription of rDNA. Using high-throughput screening, we identified the small molecules Batefenterol and Indacaterol that attenuate the CaM-DDX21 interaction and suppress nascent rRNA synthesis and axon growth in hippocampal neurons. These results unveiled the previously unrecognized role of CaM as a messenger to link the activity-induced Ca2+ influx to the nucleolar events essential for protein synthesis. We thus identified the ability of CaM to transmit information to the nucleoli of neurons in response to stimulation.Significance statement Protein synthesis in response to neuronal activity, known as activity-dependent translation, is critical for synaptic plasticity and long-term memory formation. In this study, we identify the novel role of calmodulin (CaM), a highly conserved Ca2+-binding protein, which is well-known by regulating myriad vital biological processes, in activity-dependent translation by regulating rRNA synthesis in neurons. We find that CaM can shuttle into the nucleolus upon depolarization and modulate the activity-induced de novo rRNA biogenesis, which is associated with ribosome assembly and protein synthesis in neurons. Mechanistically, CaM interacts with DDX21, an RNA helicase directly associated with Pol I subunit, to regulate the transcription of rDNA. Our study demonstrates CaM as a messenger linking neuronal activity to ribosome-dependent protein biosynthesis.

Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA.

The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.

Crystal structures of human caspase 6 reveal a new mechanism for intramolecular cleavage self-activation.

Dimeric effectors caspase 3 and caspase 7 are activated by initiator caspase processing. In this study, we report the crystal structures of effector caspase 6 (CASP6) zymogen and N-Acetyl-Val-Glu-Ile-Asp-al-inhibited CASP6. Both of these forms of CASP6 have a dimeric structure, and in CASP6 zymogen the intersubunit cleavage site (190)TEVD(193) is well structured and inserts into the active site. This positions residue Asp 193 to be easily attacked by the catalytic residue Cys 163. We demonstrate biochemically that intramolecular cleavage at Asp 193 is a prerequisite for CASP6 self-activation and that this activation mechanism is dependent on the length of the L2 loop. Our results indicate that CASP6 can be activated and regulated through intramolecular self-cleavage.

Crystallization and preliminary X-ray analysis of argininosuccinate lyase from Streptococcus mutans.

Argininosuccinate lyase (ASL) is an important enzyme in arginine synthesis and the urea cycle, which are highly conserved from bacteria to eukaryotes. The gene encoding Streptococcus mutans ASL (smASL) was amplified and cloned into expression vector pET28a. The recombinant smASL protein was expressed in a soluble form in Escherichia coli strain BL21 (DE3) and purified to homogeneity by two-step column chromatography. Crystals suitable for X-ray analysis were obtained and X-ray diffraction data were collected to a resolution of 2.5 Å. The crystals belonged to space group R3, with unit-cell parameters a = b = 254.5, c = 78.3 Å.

Purification, crystallization and preliminary X-ray crystallographic analysis of 23S RNA m(2)G2445 methyltransferase RlmL from Escherichia coli.

The RlmL (YcbY) protein in Escherichia coli is an rRNA methyltransferase that is specific for m(2)G2445 modification of 23S RNA. The rlmL gene was cloned into the expression vector pET28a and expressed in the host E. coli strain BL21 (DE3). Recombinant protein with a six-histidine tag was purified by Ni(2+)-affinity chromatography followed by gel filtration. Crystals were grown using the hanging-drop vapour-diffusion method and a detergent was used as an additive to improve diffraction quality. The final crystals diffracted to 2.2 Šresolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 73.6, b = 140.8, c = 102.9 Å, ß = 102.3°. The crystal has a most probable solvent content of 62.8% with two molecules in the asymmetric unit.

Superhydrophobic Coatings Prepared by the in Situ Growth of Silicone Nanofilaments on Alkali-Activated Geopolymers Surface.

As a highly hydrophobic and good environmental durable material, silicone nanofilaments have shown great advantages in the construction of superhydrophobic coatings. However, the synthesis of these materials has always been limited to the application of trifunctional organosilane monomers under the action of acidic catalysts. For the first time, long-chain polymeric hydrogenated siloxane-poly(methyl-hydrosiloxane) (PMHS) was used to synthesize rapidly silicone nanofilaments in situ under alkaline conditions. A dense silicone nanofilament coating was obtained by PMHS + geopolymer layer on a smooth iron sheet, and achieved by one-step brushing of PMHS on the surface of a just-solidified alkali-activated metakaolin-based geopolymer coating at 120 °C for an hour of sealed curing. This composite coating was followed by a superhydrophobic composite coating with a contact angle of approximately 161° and a rolling angle of 2°. Consistent with this, laser scanning confocal microscopy and field-emission scanning electron microscopy images show the presence of micro- and nanoscale features that enable the entrapment of air when exposed to water and endow excellent superhydrophobic properties. Because geopolymer material has good adhesion ability with metal, ceramic, or other materials, the composite superhydrophobic coating is expected to be widely used.

Development of near-zero water consumption cement materials via the geopolymerization of tektites and its implication for lunar construction.

The environment on the lunar surface poses some difficult challenges to building long-term lunar bases; therefore, scientists and engineers have proposed the creation of habitats using lunar building materials. These materials must meet the following conditions: be resistant to severe lunar temperature cycles, be stable in a vacuum environment, have minimal water requirements, and be sourced from local Moon materials. Therefore, the preparation of lunar building materials that use lunar resources is preferred. Here, we present a potential lunar cement material that was fabricated using tektite powder and a sodium hydroxide activator and is based on geopolymer technology. Geopolymer materials have the following properties: approximately zero water consumption, resistance to high- and low-temperature cycling, vacuum stability and good mechanical properties. Although the tektite powder is not equivalent to lunar soil, we speculate that the alkali activated activity of lunar soil will be higher than that of tektite because of its low Si/Al composition ratio. This assumption is based on the tektite geopolymerization research and associated references. In summary, this study provides a feasible approach for developing lunar cement materials using a possible water recycling system based on geopolymer technology.

Structural studies of P-type ATPase-ligand complexes using an X-ray free-electron laser.

Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein-ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

Crystal structures of catalytic intermediates of human selenophosphate synthetase 1.

Selenophosphate synthetase catalyzes the synthesis of the highly active selenium donor molecule selenophosphate, a key intermediate in selenium metabolism. We have determined the high-resolution crystal structure of human selenophosphate synthetase 1 (hSPS1). An unexpected reaction intermediate, with a tightly bound phosphate and ADP at the active site has been captured in the structure. An enzymatic assay revealed that hSPS1 possesses low ADP hydrolysis activity in the presence of phosphate. Our structural and enzymatic results suggest that consuming the second high-energy phosphoester bond of ATP could protect the labile product selenophosphate during catalytic reaction. We solved another hSPS1 structure with potassium ions at the active sites. Comparing the two structures, we were able to define the monovalent cation-binding site of the enzyme. The detailed mechanism of the ADP hydrolysis step and the exact function of the monovalent cation for hSPS1 catalytic reaction are proposed.