Advance online publication


The latest research papers, published online ahead of print. These online versions are definitive and may be cited using the digital object identifier (DOI).

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Articles

Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions

Anthony J Cesare, Zeenia Kaul, Scott B Cohen, Christine E Napier, Hilda A Pickett, Axel A Neumann & Roger R Reddel

Published online: 22 November 2009 | doi:10.1038/nsmb.1725

Telomeric DNA is protected by the shelterin complex, whose disruption triggers DNA-damage responses, checkpoint activation and chromosomal fusions. Now analysis of human cell lines reveals a spontaneously occurring intermediate state in which the DNA-damage response is activated at the telomeres without cell cycle arrest or chromosomal fusions, and with TRF2 playing a central role in determining such a state.


Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II

Olga I Kulaeva, Daria A Gaykalova, Nikolai A Pestov, Viktor V Golovastov, Dmitry G Vassylyev, Irina Artsimovitch & Vasily M Studitsky

Published online: 22 November 2009 | doi:10.1038/nsmb.1689

On specific DNA sequences in vitro, a nucleosome is a polar barrier to RNA polymerase II (Pol II). Further analyses of the sequences underlying this barrier effect now indicate the formation of a loop that would preserve the position of the nucleosome on the DNA, while allowing passage of Pol II.


Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components

Zbigniew Warkocki, Peter Odenwälder, Jana Schmitzová, Florian Platzmann, Holger Stark, Henning Urlaub, Ralf Ficner, Patrizia Fabrizio & Reinhard Lührmann

Published online: 22 November 2009 | doi:10.1038/nsmb.1729

Pre-mRNA splicing is catalyzed by the spliceosome in a two-step reaction. Both catalytic steps have now been reconstituted using purified, defined components. This system identifies a role for Cwc25 in the first step of splicing and allows future detailed mechanistic analyses of splicing.


An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe

Hyun-Soo Kim, Vincent Vanoosthuyse, Jeffrey Fillingham, Assen Roguev, Stephen Watt, Thomas Kislinger, Alex Treyer, Laura Rocco Carpenter, Christopher S Bennett, Andrew Emili, Jack F Greenblatt, Kevin G Hardwick, Nevan J Krogan, Jürg Bähler & Michael-Christopher Keogh

Published online: 15 November 2009 | doi:10.1038/nsmb.1688

H2A.Z is implicated in genome stability across species. Acetylation of this histone variant in S. pombe is now found to be involved in maintaining condensed chromosomes during mitosis, with premature dissociation of condensin occurring in its absence.


A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase

Annie Schwartz, Makhlouf Rabhi, Frédérique Jacquinot, Emmanuel Margeat, A Rachid Rahmouni & Marc Boudvillain

Published online: 15 November 2009 | doi:10.1038/nsmb.1711

The bacterial transcriptional termination factor Rho is a hexameric helicase that tracks along RNA and dissociates DNA-RNA hybrids. Here the activity of Rho is examined using nucleotide analog interference mapping, revealing that the helicase takes large, 7-nt steps, triggered by contacts with 2'OH in the tracked RNA substrate.


The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A

Ai Takemoto, Kazuhiro Maeshima, Tsuyoshi Ikehara, Kazumitsu Yamaguchi, Akiko Murayama, Shihoko Imamura, Naoko Imamoto, Shigeyuki Yokoyama, Tatsuya Hirano, Yoshinori Watanabe, Fumio Hanaoka, Junn Yanagisawa & Keiji Kimura

Published online: 15 November 2009 | doi:10.1038/nsmb.1708

Condensins are protein complexes essential for eukaryotic mitosis and whose chromosome association is regulated by phosphorylation and dephosphorylation events. Now protein phosphatase PP2A is important for association of condensin II to mitotic chromosomes, but its catalytic activity is not required.


The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation

Stephen Tam, Christoph Spiess, William Auyeung, Lukasz Joachimiak, Bryan Chen, Michelle A Poirier & Judith Frydman

Published online: 15 November 2009 | doi:10.1038/nsmb.1700

The eukaryotic group II chaperonin TRiC can block polyQ tract aggregation, present in proteins such as Htt. Here the TRiC-Htt interaction is examined using in vitro and in vivo experiments, revealing that TRiC does not physically block the polyQ tract, but rather sequesters a short N-terminal sequence that promotes the amyloidogenic conformation.


Physical determinants of strong voltage sensitivity of K+ channel block

Yanping Xu, Hyeon-Gyu Shin, Szilvia Szép & Zhe Lu

Published online: 15 November 2009 | doi:10.1038/nsmb.1717

Inward-rectifier K+ channels respond to voltage via blockage by intracellular polyamines. How these blockers work is not entirely clear. Now a crystal structure of the cytoplasmic portion of Kir3.1 reveals five ion sites, and functional analyses indicate these ions are displaced by spermine binding.


Nonspecifically bound proteins spin while diffusing along DNA

Paul C Blainey, Guobin Luo, S C Kou, Walter F Mangel, Gregory L Verdine, Biman Bagchi & X Sunney Xie

Published online: 08 November 2009 | doi:10.1038/nsmb.1716

Some proteins move along DNA, searching for a specific target. Now these proteins are shown to follow a helical path, i.e., they rotate while sliding, hence maintaining a specific orientation to the DNA helix. This is accomplished by tracking single molecules of labeled human oxoguanine DNA glycosylase 1, alone or bound to a bulky streptavidin moiety, and calculating their diffusion constants.


Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch

Nadia Kulshina, Nathan J Baird & Adrian R Ferré-D'Amaré

Published online: 08 November 2009 | doi:10.1038/nsmb.1701

c-di-GMP is a bacterial second messenger implicated in processes such as biofilm formation and switches between motile and sedentary lifestyles. The structure of the c-di-GMP–binding GEMM riboswitch is now presented with ligand and the large conformational changes between ligand-bound and unbound forms analyzed by small-angle X-ray scattering.


Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters

Alessandra Picollo, Mattia Malvezzi, Jon C D Houtman & Alessio Accardi

Published online: 08 November 2009 | doi:10.1038/nsmb.1704

The crucial ion-binding events that drive H+/Cl- exchange in the bacterial transporter CLC-ec1 are now probed by isothermal calorimetry and detergent-solubilized proteins. The results indicate that transport via CLC channels have an inherent directionality, rather than being driven by an electrochemical gradient.


Structural basis of ligand binding by a c-di-GMP riboswitch

Kathryn D Smith, Sarah V Lipchock, Tyler D Ames, Jimin Wang, Ronald R Breaker & Scott A Strobel

Published online: 08 November 2009 | doi:10.1038/nsmb.1702

The GEMM riboswitch is conserved in diverse bacteria and recognizes the second messenger c-di-GMP which mediates many processes, such as the transition between sedentary and motile behavior. The structure of the GEMM riboswitch with ligand now elucidates ligand recognition and specificity.


Solution structure and functional analysis of the influenza B proton channel

Junfeng Wang, Rafal M Pielak, Mark A McClintock & James J Chou

Published online: 08 November 2009 | doi:10.1038/nsmb.1707

Influenza B virus is responsible for about half of all the seasonal flu cases. The integral protein BM2 oligomerizes and forms a pH-activated proton channel that is essential for viral entry into host cells. The solution structures of the membrane-embedded chain domain and the C-terminal cytoplasmic domain reveal significant differences from the AM2 protein of influenza A virus and explain antiviral drug resistance.


Structural insights into the mechanism of abscisic acid signaling by PYL proteins

Ping Yin, He Fan, Qi Hao, Xiaoqiu Yuan, Di Wu, Yuxuan Pang, Chuangye Yan, Wenqi Li, Jiawei Wang & Nieng Yan

Published online: 05 November 2009 | doi:10.1038/nsmb.1730

PYL-PYR proteins were recently described as receptors for the plant hormone abscisic acid (ABA) and as inhibitors of the phosphatases ABI1 and ABI2 in the presence of ABA. The crystal structures of PYL2 in its apo and ABA-bound forms and of the ternary complex PYL1–ABA–ABI1 have now been solved, providing insight into ABA sensing and signaling.


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Brief Communications

Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain

Yogesh Kulathu, Masato Akutsu, Anja Bremm, Kay Hofmann & David Komander

Published online: 22 November 2009 | doi:10.1038/nsmb.1731

The TAK1 kinase binds K63-linked ubiquitin specifically via its TAB2 subunit. The structure of the TAB2 NZF domain in complex with K63-linked ubiquitins now indicates that this domain interacts with neighboring ubiquitins through distinct sites, explaining the basis of specific recognition.


IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana

Israel Ausin, Todd C Mockler, Joanne Chory & Steven E Jacobsen

Published online: 15 November 2009 | doi:10.1038/nsmb.1690

De novo methylation of DNA can affect the function of underlying genes and transposons in plants. Using a genetic screen, two factors required for de novo demethylation in Arabidopsis thaliana are identified and analyzed.


Until print versions of AOP papers are published, they should be cited in the style "Author(s) Nature Structural & Molecular Biology advance online publication, day month year (doi:10.1038/nsmbXXXXX)". Once the print version (identical to the AOP) is published, it should be cited as follows: "Author(s) Nature Structural & Molecular Biology volume, page (year); advance online publication, (doi:10.1038/nsmbXXXXX)".

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