Nature Structural & Molecular Biology Contents: September 2012 Volume #19 pp 853 - 971

TABLE OF CONTENTS September 2012 Volume 19, Issue 9 Editorial Feature News and Views Research Highlights Obituary Articles Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Online-only personal subscriptions now available to Nature Cell Biology and Nature Structural Molecular Biology For only 49 USD/29 GBP/29 EUR Subscribe now!   Editorial Top The BMRB matters   p853 doi:10.1038/nsmb.2387 In this issue of NSMB, we have opened our pages to the research community to express their thoughts about the importance of the Biological Magnetic Resonance Bank as it copes with budget cuts and faces the termination of its funding from the National Library of Medicine in 2014. Feature Top In support of the BMRB   pp854 - 860 doi:10.1038/nsmb.2371 The Biological Magnetic Resonance Bank (BMRB) is facing the threat of having its funding discontinued. Concerned about this situation, the editors of Nature Structural & Molecular Biology have asked the community why it is important to continue to support the BMRB. We have also asked John Markley, head of the BMRB, to present his case. News and Views Top Getting ready to commit: ribosomes rehearse translation   pp861 - 862 Sabina Schutz and Vikram Govind Panse doi:10.1038/nsmb.2368 Eukaryotic ribosomal subunits are assembled in the nucleus and exported in a functionally inactive state to the cytoplasm, where they undergo final maturation steps before initiating translation. In the case of pre-40S subunits, these steps involve cleavage of the 20S pre-rRNA to the mature 18S rRNA. Two recent studies have surprisingly revealed that mature 60S subunits, aided by the translation initiation factor eIF5b (known as Fun12 in yeast), bind pre-40S subunits to assess their translation 'potential' before triggering cleavage of 20S pre-rRNA. Chromatin 'resetting' during transcription elongation: a central role for methylated H3K36   pp863 - 864 Jill S Butler and Sharon Y R Dent doi:10.1038/nsmb.2370 A number of events must occur to preserve the integrity of the chromatin template during gene transcription. A study in this issue reveals a novel mechanism whereby chromatin remodelers are recruited to histone modifications within gene bodies to prevent aberrant histone exchange during transcriptional elongation. Pinpointing a puzzling polymerase   pp865 - 866 Rebecca A Mosher doi:10.1038/nsmb.2374 One of the surprising discoveries in the genomic age was the presence in plant genomes of two noncanonical DNA-dependent RNA polymerases involved in small RNA-mediated gene silencing. Two recent studies map the binding sites of RNA polymerase V, uncovering new mysteries concerning the targeting and function of this enigmatic enzyme. Research Highlights Targeting ion channels | DNA methylation caste-ing call | Competing for survival Obituary Ivano Bertini 1940-2012   pp868 - 869 Harry Barkus Gray, Lucia Banci, Claudio Luchinat and Paola Turano doi:10.1038/nsmb.2369 Structural & Molecular Biology JOBS of the week Beamline scientist (m / f) on ID30 in the Structural Biology Group ESRF Associate Professorship (Tenure Position W2) in Structural Biology Johannes Gutenberg-Universitat Mainz Research Center for Strategic Materials, Structural Materials Unit, Strength Design Group [R08-07] National Institue for Materials Science (NIMS) Postdoctoral and PhD Fellowships in Structural Biology / Biochemistry and Molecular Biology / Cellular Biology Max Planck Institute for Developmental Biology Structural Cellular Biology Postdoc Okinawa Institute of Science and Technology Graduate University More Science jobs from Structural & Molecular Biology EVENT X-Ray Methods in Structural Biology 15th - 30th October 2012 US More science events from Articles Top DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons   pp870 - 875 Xuehua Zhong, Christopher J Hale, Julie A Law, Lianna M Johnson, Suhua Feng, Andy Tu and Steven E Jacobsen doi:10.1038/nsmb.2354 Plant RNA Pol V is involved in the RNA-directed DNA-methylation pathway that leads to heterochromatic silencing at some endogenous loci. Now the genomic regions targeted by Pol V in Arabidopsis thaliana are determined by ChIP-seq analyses revealing Pol V's enrichment at evolutionarily recent transposons. BIRC7–E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer   pp876 - 883 Hao Dou, Lori Buetow, Gary J Sibbet, Kenneth Cameron and Danny T Huang doi:10.1038/nsmb.2379 RING domain–containing E3 ligases promote the transfer of ubiquitin from the active site of an E2 to acceptor lysine residues on substrates, but the mechanism by which this occurs was unclear. Structural and biochemical studies using the E3 BIRC7 and E2 UbcH5b indicate that the E3 properly orients and stabilizes the ubiquitin-charged E2 to promote an efficient transfer reaction. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange   pp884 - 892 Michaela Smolle, Swaminathan Venkatesh, Madelaine M Gogol, Hua Li, Ying Zhang, Laurence Florens, Michael P Washburn and Jerry L Workman doi:10.1038/nsmb.2312 The histone H3K36 methylation mark is associated with coding regions of actively transcribed genes, yet it plays a negative role during transcription elongation. In vitro and in vivo studies in budding yeast now reveal that the Isw1b chromatin remodeler is recruited by H3K36 methylation to open reading frames, where it acts in conjunction with a second remodeler to prevent histone exchange and maintain chromatin integrity during transcription elongation. Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer   pp893 - 899 Youdong Mao, Liping Wang, Christopher Gu, Alon Herschhorn, Shi-Hua Xiang, Hillel Haim, Xinzhen Yang and Joseph Sodroski doi:10.1038/nsmb.2351 HIV-1 virions interact with host-cell receptors via the trimeric envelope glycoprotein (Env) consisting of gp120 and gp41 polypeptides. Single-particle cryo-EM is now used to reconstruct the structure of membrane-bound Env trimer in its unliganded state, revealing a cage-like architecture and allowing the identification of interprotomer contacts. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis   pp900 - 905 Francesca Tuorto, Reinhard Liebers, Tanja Musch, Matthias Schaefer, Sarah Hofmann, Stefanie Kellner, Michaela Frye, Mark Helm, Georg Stoecklin and Frank Lyko doi:10.1038/nsmb.2357 Although cytosine-C5 methylation is a prominent modification of tRNAs, its functional significance has been unclear. Mice that lack both the Dnmt2 and NSun2 tRNA methyltransferases showed developmental and cellular differentiation defects, and loss of Dnmt2 and NSun2 was further associated with tRNA degradation and reduced rates of protein synthesis, suggesting that this modification promotes mouse development by supporting protein synthesis. Nectin ectodomain structures reveal a canonical adhesive interface   pp906 - 915 Oliver J Harrison, Jeremie Vendome, Julia Brasch, Xiangshu Jin, Soonjin Hong, Phinikoula S Katsamba, Goran Ahlsen, Regina B Troyanovsky, Sergey M Troyanovsky, Barry Honig and Lawrence Shapiro doi:10.1038/nsmb.2366 Nectins and nectin-like proteins promote intercellular adhesion and tissue patterning in vertebrates through homophilic or heterophilic interactions. Now the formation of all the possible nectin pairs is studied systematically in vitro, and crystal structures provide insight into the molecular basis for the adhesive binding specificity of nectins. PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53    pp916 - 924 Gaofeng Cui, Sungman Park, Aimee I Badeaux, Donghwa Kim, Joseph Lee, James R Thompson, Fei Yan, Satoshi Kaneko, Zengqiang Yuan, Maria Victoria Botuyan, Mark T Bedford, Jin Q Cheng and Georges Mer doi:10.1038/nsmb.2353 Tumor suppressor protein p53 interacts with and is acetylated by PHF20, but the consequences of this association were not clear. Now PHF20 is shown to be a direct regulator of p53, with its Tudor domain recognizing p53 modified with dimethyl groups at Lys370 or Lys382. This association promotes p53's stabilization and activation during the DNA-damage response, by inhibiting the association of Mdm2 with p53. The structure of purified kinetochores reveals multiple microtubule-attachment sites   pp925 - 929 Shane Gonen, Bungo Akiyoshi, Matthew G Iadanza, Dan Shi, Nicole Duggan, Sue Biggins and Tamir Gonen doi:10.1038/nsmb.2358 Kinetochores are large structures composed of hundreds of proteins that assemble onto centromeric DNA to form a microtubule-binding site that is essential for proper chromosomal segregation. The structure of budding-yeast kinetochore particles is now studied by EM and electron tomography, revealing a large central hub surrounded by multiple globular domains, and multiple attachment sites for microtubules. H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes   pp930 - 937 Kiran Mahajan, Bin Fang, John M Koomen and Nupam P Mahajan doi:10.1038/nsmb.2356 Histone gene transcription is downregulated after DNA synthesis is completed, but how cells terminate histone gene transcription has been unknown. A new study uncovers that phosphorylation of histone H2B at Tyr37 by WEE1 kinase leads to a coordinated transcriptional repression of replication-dependent core histone genes in the late S/G2 phase in yeast and mammalian cells. Allosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1    pp938 - 947 Jonathan Elegheert, Nathalie Bracke, Philippe Pouliot, Irina Gutsche, Alexander V Shkumatov, Nicolas Tarbouriech, Kenneth Verstraete, Anaïs Bekaert, Wim P Burmeister, Dmitri I Svergun, Bart N Lambrecht, Bjorn Vergauwen and Savvas N Savvides doi:10.1038/nsmb.2367 The human colony-stimulating factor (hCSF-1) cytokine is essential for innate and adaptive immune responses. The Epstein-Barr virus protein BARF1 binds to hCSF-1, preventing interferon-α secretion. Structural and functional data reveal a new mechanism for the antagonism of human but not mouse CSF-1 signaling by BARF1. Telomere length regulates TERRA levels through increased trimethylation of telomeric H3K9 and HP1α    pp948 - 956 Nausica Arnoult, Amandine Van Beneden and Anabelle Decottignies doi:10.1038/nsmb.2364 Telomeres have the ability to repress expression of nearby genes, a phenomenon known as telomere position effect (TPE). Telomeric RNA species called TERRA now allow assessment of whether TPE exists at human chromosome ends. Telomere elongation is found to repress TERRA expression, which is mediated by increased trimethylation of telomeric H3K9 and by heterochromatic protein HP1α. Allosteric control of the ribosome by small-molecule antibiotics   pp957 - 963 Leyi Wang, Arto Pulk, Michael R Wasserman, Michael B Feldman, Roger B Altman, Jamie H Doudna Cate and Scott C Blanchard doi:10.1038/nsmb.2360 Antibiotics target protein synthesis by binding and inhibiting key functional centers of the ribosome. Single-molecule imaging and X-ray crystallography studies now demonstrate that the aminoglycoside antibiotic neomycin binds to ribosomal RNA within the large subunit to allosterically control ribosomal subunit rotation and stabilize an inactive configuration of the ribosome. The Rad1-Rad10 nuclease promotes chromosome translocations between dispersed repeats   pp964 - 971 Gerard Mazón, Alicia F Lam, Chu Kwen Ho, Martin Kupiec and Lorraine S Symington doi:10.1038/nsmb.2359 The structure-specific endonucleases Mus81-Mms4 and Yen1 are involved in the resolution of Holliday junctions and in crossover formation in the budding yeast. Now genetic work implicates the nucleotide excision repair nuclease complex Rad1-Rad10 in the processing of recombination intermediates formed between substrates with limited homology. Top Advertisement Experimental & Molecular Medicine (EMM) Co-published with NPG from 2013! 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