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ISSUE

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August 2008, Volume 15 No 8 pp767-888

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Editorial

Getting resourceful p767

doi:10.1038/nsmb0808-767

A new section in Nature Structural & Molecular Biology will house articles that serve primarily as Resources and also lead to novel molecular insights, adding a new flavor to our pages.

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Review

Visualizing one-dimensional diffusion of proteins along DNA pp768 - 774

Jason Gorman & Eric C Greene

doi:10.1038/nsmb.1441

Abstract | Full Text | PDF (663 KB)

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News and Views

Terminating transcription in yeast: whether to be a 'nerd' or a 'rat' pp775 - 776

Ana G Rondon, Hannah E Mischo & Nick J Proudfoot

doi:10.1038/nsmb0808-775

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.

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See also: Article by Gudipati et al. | Article by Vasiljeva et al.

Jamming the ratchet of transcription pp777 - 779

Vladimir Svetlov & Evgeny Nudler

doi:10.1038/nsmb0808-777

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 alpha-amanitin, address this matter by describing crucial and surprising details about the dynamic organization of the enzyme catalytic center.

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See also: Article by Brueckner & Cramer

A splicing regulator promotes transcriptional elongation pp779 - 781

Juan Pablo Fededa & Alberto R Kornblihtt

doi:10.1038/nsmb0808-779

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.

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See also: Article by Lin et al.

The chloride channel's appendix pp781 - 783

Joseph A Mindell

doi:10.1038/nsmb0808-781

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.

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See also: Article by Lísal & Maduke

Waste not, want not: a case for tRNA repair pp783 - 784

Eric M Phizicky

doi:10.1038/nsmb0808-783

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.

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Research Highlights

Research highlights p785

doi:10.1038/nsmb0808-785

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Articles

Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice pp786 - 794

Rajani Kanth Gudipati, Tommaso Villa, Jocelyne Boulay & Domenico Libri

doi:10.1038/nsmb.1460

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.

Abstract | Full Text | PDF (581 KB) | Supplementary information

See also: News and Views by Rondon et al.

The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain pp795 - 804

Lidia Vasiljeva, Minkyu Kim, Hannes Mutschler, Stephen Buratowski & Anton Meinhart

doi:10.1038/nsmb.1468

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.

Abstract | Full Text | PDF (848 KB) | Supplementary information

See also: News and Views by Rondon et al.

The ClC-0 chloride channel is a 'broken' Cl-/H+ antiporter pp805 - 810

Jiří Lísal & Merritt Maduke

doi:10.1038/nsmb.1466

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.

Abstract | Full Text | PDF (491 KB) | Supplementary information

See also: News and Views by Mindell

Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation pp811 - 818

Florian Brueckner & Patrick Cramer

doi:10.1038/nsmb.1458

The crystal structure of the yeast RNA Pol II elongation complex bound to the inhibitor alpha-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.

Abstract | Full Text | PDF (1,702 KB)

See also: News and Views by Svetlov & Nudler

The splicing factor SC35 has an active role in transcriptional elongation pp819 - 826

Shengrong Lin, Gabriela Coutinho-Mansfield, Dong Wang, Shatakshi Pandit & Xiang-Dong Fu

doi:10.1038/nsmb.1461

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.

Abstract | Full Text | PDF (666 KB) | Supplementary information

See also: News and Views by Fededa & Kornblihtt

Synaptotagmin arrests the SNARE complex before triggering fast, efficient membrane fusion in response to Ca2+ pp827 - 835

Michael C Chicka, Enfu Hui, Huisheng Liu & Edwin R Chapman

doi:10.1038/nsmb.1463

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.

Abstract | Full Text | PDF (754 KB) | Supplementary information

Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2 pp836 - 841

Ilya M Terenin, Sergey E Dmitriev, Dmitry E Andreev & Ivan N Shatsky

doi:10.1038/nsmb.1445

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.

Abstract | Full Text | PDF (547 KB)

Antisense transcripts are targets for activating small RNAs pp842 - 848

Jacob C Schwartz, Scott T Younger, Ngoc-Bich Nguyen, Daniel B Hardy, Brett P Monia, David R Corey & Bethany A Janowski

doi:10.1038/nsmb.1444

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.

Abstract | Full Text | PDF (471 KB) | Supplementary information

A conserved face of the Jagged/Serrate DSL domain is involved in Notch trans-activation and cis-inhibition pp849 - 857

Jemima Cordle, Steven Johnson, Joyce Zi Yan Tay, Pietro Roversi, Marian B Wilkin, Beatriz Hernández de Madrid, Hideyuki Shimizu, Sacha Jensen, Pat Whiteman, Boquan Jin, Christina Redfield, Martin Baron, Susan M Lea & Penny A Handford

doi:10.1038/nsmb.1457

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.

Abstract | Full Text | PDF (864 KB) | Supplementary information

The structure of CCT–Hsc70NBD suggests a mechanism for Hsp70 delivery of substrates to the chaperonin pp858 - 864

Jorge Cuéllar, Jaime Martín-Benito, Sjors H W Scheres, Rui Sousa, Fernando Moro, Eduardo López-Viñas, Paulino Gómez-Puertas, Arturo Muga, José L Carrascosa & José M Valpuesta

doi:10.1038/nsmb.1464

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 beta subunit of CCT and Hsc70, suggesting a coordinated hand-off mechanism for substrate interactions.

Abstract | Full Text | PDF (651 KB) | Supplementary information

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Brief Communications

Molecular recognition of nitrated fatty acids by PPARbold gamma pp865 - 867

Yong Li, Jifeng Zhang, Francisco J Schopfer, Dariusz Martynowski, Minerva T Garcia-Barrio, Amanda Kovach, Kelly Suino-Powell, Paul R S Baker, Bruce A Freeman, Y Eugene Chen & H Eric Xu

doi:10.1038/nsmb.1447

PPARgamma 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 PPARgamma in complex with a physiological ligand, nitrated linoleic acid, is now described, showing differences with synthetic agonists that may have physiological relevance.

Abstract | Full Text | PDF (480 KB) | Supplementary information

NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B pp868 - 869

Zheng Zhou, Hanqiao Feng, D Flemming Hansen, Hidenori Kato, Ed Luk, Daron I Freedberg, Lewis E Kay, Carl Wu & Yawen Bai

doi:10.1038/nsmb.1465

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.

Abstract | Full Text | PDF (404 KB) | Supplementary information

Mutation in TERT separates processivity from anchor-site function pp870 - 872

Arthur J Zaug, Elaine R Podell & Thomas R Cech

doi:10.1038/nsmb.1462

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.

Abstract | Full Text | PDF (311 KB) | Supplementary information

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Resources

Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast pp873 - 880

Brendon J Monahan, Judit Villén, Samuel Marguerat, Jürg Bähler, Steven P Gygi & Fred Winston

doi:10.1038/nsmb.1452

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.

Abstract | Full Text | PDF (615 KB) | Supplementary information

A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation pp881 - 888

Shima Nakanishi, Brian W Sanderson, Kym M Delventhal, William D Bradford, Karen Staehling-Hampton & Ali Shilatifard

doi:10.1038/nsmb.1454

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.

Abstract | Full Text | PDF (820 KB)

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