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Nrd1 is involved in termination of small nuclear and small nucleolar RNAs, and contains an RNA polymerase II CTD interaction domain (CID). The structure of the Nrd1 CID is presented, and further functional analyses reveal that it interacts with RNA polymerase II phosphorylated at Ser5 of the CTD, suggesting a model for how the Nrd1 complex is recruited to its targets.
The NMR structure of the Notch binding region of one of its ligands, Jagged, gives insight into the binding surface. Subsequent in vivo analysis of mutants indicates that the same surface is likely to be active in signaling within cells as well as to different cells, and modeling indicates how this surface might interact to participate in such distinct functions.
The CLC protein family consists of chloride-selective ion channels and Cl−/H+ antiporters. Functional studies on the ClC-0 chloride channel, the founding member of the CLC family, reveals that channel gating is coupled to proton-transport events, providing a mechanistic connection between channels and transporters in this family of proteins.
It is known that components of the splicing machinery are guided to nascent transcripts through interactions with the Pol II transcriptional complex. Data now indicate that depletion of SC35, a splicing factor, leads to defective elongation as well as reduced Pol II phosphorylation and association with elongation factors. This leads to a model where components of the splicing machinery have a role in promoting elongation of the transcriptional machinery.
Synaptotagmin is generally accepted as being the calcium sensor in SNARE-mediated calcium-triggered synaptic vesicle fusion. New data now indicate that synaptotagmin may negatively regulate the SNARE complex in the absence of calcium, and that interactions with target SNARE proteins may help steer synaptotagmin to the target membrane in a calcium-independent manner.
Viruses have found mechanisms to translate their RNAs in the face of antiviral responses. Data now indicate that the hepatitis C virus internal ribosome entry site can use eIF5B to initiate translation in a bacterial-like mode when eIF2 is inactivated under stress.
The manner in which antigene RNAs (agRNAs) are complementary to the progesterone receptor promoter is further examined, and the presence of an antisense transcript overlapping the promoter detected. Presence of the transcript correlates with the ability of agRNAs to activate expression and physically interact with it. Argonaute, hnRNP-k and HP1 association with the promoter DNA or antisense RNA are detected to alter upon agRNA application.
Rtt109 is a relatively recently identified yeast histone acetyltransferase that forms distinct complexes with two histone chaperones. The structure of Rtt109 now reveals that while functionally distinct, it is structurally homologous to mammalian p300/CBP, which previously appeared to not contain a counterpart in yeast.
The cooperative action of multiple trans SNARE complexes are a likely requirement for successful membrane fusion. New in vitro analyses reveal the kinetic timescales of the sequential steps of the fusion process, beginning with trans SNARE pairing and clustering of vesicle SNARE proteins, proceeding to hemifusion of outer bilayer leaflets, and ending with full fusion.
Both genomic and antigenomic hepatitis delta virus (HDV) RNAs have hairpin-shaped ends. Small capped RNAs have now been identified from both genomic and antigenomic RNAs, and the human homolog of the Arabidopsis RNA amplification factor (SDE3) has been implicated in the replication of HDV.
Complexin is one of several regulatory molecules known to be important for SNARE-mediated fusion that occurs during neurotransmitter release. In vitro data now suggest that complexin plays inhibitory and Ca2+- dependent stimulatory roles that may be correlated to changing interactions with the SNARE complex.
The crystal structure of the yeast RNA Pol II elongation complex bound to the inhibitor α-amanitin is solved, revealing that two functional elements, the trigger loop and the bridge helix, are trapped in a position different from their pre- and post-translocation states. This is proposed to be a translocation intermediate, lending support to a Brownian ratchet mechanism for RNA Pol II translocation during elongation.
The origin of replication located at the human DBF4 promoter is finely characterized. Two initiation zones are on opposite strands and 400 bp apart, being fired in a sequential way, in a manner similar to replication at bacterial oriC.
Polysulfides are chains of sulfur atoms abundant in extreme environments. Some organisms reduce polysulfides, and this reaction may be coupled to respiratory processes. Now the structure of the multicomponent membrane complex that catalyzes this reaction is solved, revealing a potential proton channel that could have a role in energy conservation.
Group II chaperonins, such as TriC/CCT, have a build-in lid that can cover the folding chamber and functions in an analogous way to the GroES-like proteins used by their Group I counterparts. Structural and modeling data suggest an allosteric mechanism of TriC lid closure that differs from GroES–GroEL systems.