Volume 15 Issue 8, August 2008

Transcriptional termination by RNA polymerase II in yeast occurs by two different pathways: stable or cryptic unstable transcripts use the Nrd1 complex, whereas mRNA uses 3′ cleavage and polyadenylation factors together with Rat1 exonuclease. How RNA polymerase II selects which pathway to use is discussed.

The exact mechanism by which cellular RNA polymerases translocate and maintain exceptionally high fidelity during transcription remains an important unresolved issue. Two recent structural studies of yeast RNA polymerase II in complex with its potent inhibitor, the fungal toxin α-amanitin, address this matter by describing crucial and surprising details about the dynamic organization of the enzyme catalytic center.

A new study reveals that the serine/arginine-rich splicing factor SC35 is necessary to promote RNA polymerase II elongation in a subset of genes, confirming a bidirectional coupling between transcription and splicing.

All CLC proteins transport Cl⁻ across membranes. However, the family includes both Cl⁻ channels and Cl⁻/H⁺ antiporters, proteins once thought to operate by dramatically different mechanisms. An apparent evolutionary relic, a proton-transport apparatus in a CLC channel, reveals deep intertwinings between channel and transporter mechanisms.

New work shows that a toxin that normally kills the yeast Saccharomyces cerevisiae by cleavage of tRNA substrates can be neutralized by RNA ligases that repair the damage, suggesting that these ligases may have a more general role in tRNA repair in the cell.

The Nrd1 pathway is involved in turnover of cryptic untranslated transcripts. The recruitment of Nrd1 is now shown to be dependent upon the phosphorylation status of the RNA polymerase II C-terminal domain and the distance from the 5′ end of the gene, suggesting a model where this distance determines the termination pathway used.

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 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.

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.

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.

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.

Type II chaperonins, such as CCT, and Hsp70 class chaperones, such as Hsc70, have crucial roles in protein folding and share some substrate overlap. Structural data now indicate that a complex forms between the β subunit of CCT and Hsc70, suggesting a coordinated hand-off mechanism for substrate interactions.

PPARγ is a nuclear receptor that regulates metabolic homeostasis. It is activated by nitrated and oxidized fatty acids. The crystal structure of the ligand binding domain of PPARγ in complex with a physiological ligand, nitrated linoleic acid, is now described, showing differences with synthetic agonists that may have physiological relevance.

The NMR structure of the H2A.Z-H2B histone chaperone, Chz1, reveals electrostatic interactions between Chz1 and the histone pair via a long, irregular chain with two capping helices, and, based on a model, the possibility that Chz1 has a more active role in histone replacement is suggested.

Repeat-addition processivity (RAP), that is, generating multiple DNA repeats from a single template without primer dissociation, is a key property of telomerase. In the Tetrahymena reverse-transcriptase component of telomerase, a single amino acid mutation causes a profound and specific defect in RAP without altering enzymatic activity.

The Schizosaccharomyces pombe SWI/SNF family of ATP-dependent chromatin-remodeling complexes is now comprehensively analyzed, through composition, phenotypic and microarray analyses, thus broadly setting the stage for S. pombe as a new model organism for examining the SWI/SNF family remodelers. The S. pombe complexes are more akin to the metazoan SWI/SNF remodelers and have specific roles in repression of iron-transport genes.

A comprehensive library encompassing alanine scanning mutations across yeast histones is presented as a Resource that will facilitate screening of chromatin processes. The utility of the library is indicated by screening in cis and in trans for residues that affect histone H3K4 trimethylation, a modification that is associated with actively transcribed genes and known to be mediated by the Set1-COMPASS complex.