Table of Contents (PDF)

November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ 17581–18026

Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org Cover image: The 24 human chromosomes showing all of the SVA mobile element-mediated sequence transduction events mapped to individual chromosomes (shown as light lines and dots). SVA is a composite retrotransposon named for its main components: SINE, VNTR, and Alu. Gene duplication and transduction events for the acyl-malonyl condensing enzyme (AMAC) gene are shown as red lines; AMAC is an enzyme involved in fatty acid synthesis. See the article by Xing et al. on pages 17608–17613. Image courtesy of Bang Wong (ClearScience, Cambridge, MA), Jinchuan Xing, and Mark A. Batzer; the single copies of each chromosome are adapted from a human male karyotype image (Copyright 2003, Howard Hughes Medical Institute). From the Cover

17608 Retrotransposon-mediated gene transduction 17661 Sperm structure and fertilization 17736 Modes of microtubule sliding 18002 RNA interference in plant immunity

Contents INAUGURAL ARTICLE 17595 Life-history evolution under a production constraint THIS WEEK IN PNAS James H. Brown and Richard M. Sibly

EUKARYOTIC TRANSPOSABLE ELEMENTS AND 17581 In This Issue GENOME EVOLUTION SPECIAL FEATURE

COMMENTARIES INTRODUCTION 17600 Transposable elements and the evolution 17583 Timeless genes and jetlag of eukaryotic genomes Russell N. Van Gelder Susan R. Wessler ➜ See companion article on page 17313 in issue 46 of volume 103 RESEARCH ARTICLES RNA from the 5؅ end of the R2 retrotransposon 17602 17585 Better intracytoplasmic sperm injection controls R2 protein binding to and cleavage without sperm membranes of its DNA target site Eduardo R. S. Roldan Shawn M. Christensen, Junqiang Ye, ➜ See companion article on page 17661 and Thomas H. Eickbush

17587 Dynein shifts into second gear 17608 Emergence of primate genes by retrotransposon- mediated sequence transduction Michael P. Koonce ➜ See companion article on page 17736 Jinchuan Xing, Hui Wang, Victoria P. Belancio, Richard Cordaux, Prescott L. Deininger, and Mark A. Batzer PERSPECTIVE 17614 Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis 17589 Low micronutrient intake may accelerate the Sara L. Sawyer and Harmit S. Malik degenerative diseases of aging through allocation of scarce micronutrients by triage 17620 Dramatic amplification of a rice transposable Bruce N. Ames element during recent domestication Ken Naito, Eunyoung Cho, Guojun Yang, Matthew A. Campbell, Kentaro Yano, Yutaka Okumoto, Takatoshi Tanisaka, Freely available online through the PNAS open access option. and Susan R. Wessler

PNAS ͉ November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ iii–x Downloaded by guest on October 4, 2021 17626 Recurrent duplication-driven transposition of DNA 17672 Genetically modified pigs produced with a nonviral during hominoid evolution episomal vector Matthew E. Johnson, NISC Comparative Sequencing Stefano Manzini, Alessia Vargiolu, Isa M. Stehle, Program, Ze Cheng, V. Anne Morrison, Steven Maria Laura Bacci, Maria Grazia Cerrito, Roberto Scherer, Mario Ventura, Richard A. Gibbs, Giovannoni, Augusta Zannoni, Maria Rosaria Eric D. Green, and Evan E. Eichler Bianco, Monica Forni, Pierluigi Donini, Michele Papa, Hans J. Lipps, and Marialuisa Lavitrano 17632 Transposon insertion site profiling chip (TIP-chip) Sarah J. Wheelan, Lisa Z. Scheifele, Francisco 17678 Immunoabsorbent nanoparticles based Marti´nez-Murillo, Rafael A. Irizarry, on a tobamovirus displaying protein A and Jef D. Boeke Stefan Werner, Sylvestre Marillonnet, Gerd Hause, Victor Klimyuk, and Yuri Gleba 17638 Analysis of retrotransposon structural diversity 17684 Lentiviral vectors with a defective integrase allow uncovers properties and propensities in efficient and sustained transgene expression angiosperm genome evolution in vitro and in vivo Cle´mentine Vitte and Jeffrey L. Bennetzen Ste´phanie Philippe, Chamsy Sarkis, Martine Barkats, Hamid Mammeri, Charline Ladroue, Caroline Petit, 17644 Remarkable variation in maize genome structure Jacques Mallet, and Che Serguera inferred from haplotype diversity at the bz locus Qinghua Wang and Hugo K. Dooner BIOCHEMISTRY ؅ PHYSICAL SCIENCES 17602 RNA from the 5 end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site APPLIED PHYSICAL SCIENCES Shawn M. Christensen, Junqiang Ye, and Thomas H. Eickbush 17741 Cooperative deformation of mineral and collagen in bone at the nanoscale 17690 Chromatin structure can strongly facilitate Himadri S. Gupta, Jong Seto, Wolfgang Wagermaier, enhancer action over a distance Paul Zaslansky, Peter Boesecke, and Peter Fratzl Mikhail A. Rubtsov, Yury S. Polikanov, Vladimir A. Bondarenko, Yuh-Hwa Wang, and Vasily M. Studitsky CHEMISTRY 17696 A cryptochrome͞photolyase class of enzymes with 17650 Self-organization of nano-lines and dots triggered single-stranded DNA-specific photolyase activity by a local mechanical stimulus Christopher P. Selby and Aziz Sancar Fabio Biscarini, Massimiliano Cavallini, Rajendra Kshirsagar, Giovanni Bottari, David A. Leigh, 17701 Crystal structure of cryptochrome 3 from Arabidopsis Salvador Leo´n, and Francesco Zerbetto thaliana and its implications for photolyase activity Yihua Huang, Richard Baxter, Barbara S. Smith, 17655 Synthetic selectivity through avoidance Carrie L. Partch, Christopher L. Colbert, of valence frustration and Johann Deisenhofer Marie Hutin, Ge´rald Bernardinelli, 17707 Designer short peptide surfactants stabilize G and Jonathan R. Nitschke protein-coupled receptor bovine rhodopsin 17667 Polymeric coatings that inactivate both influenza Xiaojun Zhao, Yusuke Nagai, Philip J. Reeves, Patrick virus and pathogenic bacteria Kiley, H. Gobind Khorana, and Shuguang Zhang ´ Jayanta Haldar, Deqiang An, Luis Alvarez de Cienfuegos, 17713 Crystal structures of human cardiac ␤-myosin II Jianzhu Chen, and Alexander M. Klibanov S2-⌬ provide insight into the functional role of the S2 subfragment COMPUTER SCIENCES Wulf Blankenfeldt, Nicolas H. Thoma¨, John S. Wray, 18014 Bayesian estimation of the shape skeleton Mathias Gautel, and Ilme Schlichting Jacob Feldman and Manish Singh 17718 Oligozoospermia with normal fertility in male mice lacking the androgen receptor in testis peritubular BIOLOGICAL SCIENCES myoid cells Caixia Zhang, Shuyuan Yeh, Yen-Ta Chen, Cheng-Chia Wu, Kuang-Hsiang Chuang, Hung-Yun Lin, Ruey-Sheng APPLIED BIOLOGICAL SCIENCES Wang, Yu-Jia Chang, Chamindrani Mendis-Handagama, 17661 Simultaneous removal of sperm plasma membrane Liquan Hu, Henry Lardy, and Chawnshang Chang and acrosome before intracytoplasmic sperm injection 17724 Specificity in substrate and cofactor recognition ͞ improves oocyte activation embryonic development by the N-terminal domain of the chaperone ClpX Kazuto Morozumi, Tomohide Shikano, Shunichi Guillaume Thibault, Jovana Yudin, Philip Wong, Miyazaki, and Ryuzo Yanagimachi Vladimir Tsitrin, Remco Sprangers, Rongmin Zhao, ➜ See Commentary on page 17585 and Walid A. Houry

17667 Polymeric coatings that inactivate both influenza 17730 Specific SNARE complex binding mode of the virus and pathogenic bacteria Sec1͞Munc-18 protein, Sec1p Jayanta Haldar, Deqiang An, Luis Alvarez´ de Cienfuegos, John Togneri, Yi-Shan Cheng, Mary Munson, Jianzhu Chen, and Alexander M. Klibanov Frederick M. Hughson, and Chavela M. Carr

PNAS ͉ November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ v Downloaded by guest on October 4, 2021 BIOPHYSICS 17813 An efficient promoter trap for detection of patterned 17736 Two modes of microtubule sliding driven gene expression and subsequent functional analysis by cytoplasmic dynein in Drosophila Tomohiro Shima, Takahide Kon, Kenji Imamula, Camilla Larsen, Xavier Franch-Marro, Volker Hartenstein, Reiko Ohkura, and Kazuo Sutoh Cyrille Alexandre, and Jean-Paul Vincent ➜ See Commentary on page 17587 ECOLOGY 17741 Cooperative deformation of mineral and collagen in bone at the nanoscale 17818 A common pumiliotoxin from poison frogs exhibits Himadri S. Gupta, Jong Seto, Wolfgang Wagermaier, enantioselective toxicity against mosquitoes Paul Zaslansky, Peter Boesecke, and Peter Fratzl Paul J. Weldon, Matthew Kramer, Scott Gordon, Thomas F. Spande, and John W. Daly 17747 Understanding ensemble protein folding at atomic detail Isaac A. Hubner, Eric J. Deeds, and Eugene I. Shakhnovich EVOLUTION 17753 Atomic structures of peptide self-assembly mimics 17595 Life-history evolution under a production constraint Koki Makabe, Dan McElheny, Valentia Tereshko, James H. Brown and Richard M. Sibly Aaron Hilyard, Grzegorz Gawlak, Shude Yan, Akiko Koide, and Shohei Koide 17608 Emergence of primate genes by retrotransposon- 17759 Viscoelastic properties of individual glial cells mediated sequence transduction and neurons in the CNS Jinchuan Xing, Hui Wang, Victoria P. Belancio, Yun-Bi Lu, Kristian Franze, Gerald Seifert, Christian Richard Cordaux, Prescott L. Deininger, Steinha¨user, Frank Kirchhoff, Hartwig Wolburg, and Mark A. Batzer Jochen Guck, Paul Janmey, Er-Qing Wei, Josef 17614 Positive selection of yeast nonhomologous end-joining Ka¨s, and Andreas Reichenbach genes and a retrotransposon conflict hypothesis 17765 Secondary structure provides a template Sara L. Sawyer and Harmit S. Malik for the folding of nearby polypeptides Tomoshi Kameda, and Shoji Takada 17822 Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry Structural changes in troponin in response to Ca2؉ 17771 Christopher L. Dupont, Song Yang, Brian Palenik, and myosin binding to thin filaments during and Philip E. Bourne activation of skeletal muscle Yin-Biao Sun, Birgit Brandmeier, and Malcolm Irving GENETICS CELL BIOLOGY 17620 Dramatic amplification of a rice transposable element during recent domestication 17777 Golgi twins in late mitosis revealed by genetically Ken Naito, Eunyoung Cho, Guojun Yang, Matthew A. encoded tags for live cell imaging and correlated Campbell, Kentaro Yano, Yutaka Okumoto, electron microscopy Takatoshi Tanisaka, and Susan R. Wessler Guido M. Gaietta, Ben N. G. Giepmans, Thomas J. Deerinck, W. Bryan Smith, Lucy Ngan, Juan 17626 Recurrent duplication-driven transposition of DNA Llopis, Stephen R. Adams, Roger Y. Tsien, during hominoid evolution and Mark H. Ellisman Matthew E. Johnson, NISC Comparative Sequencing 17783 Surface comparison of active and inactive Program, Ze Cheng, V. Anne Morrison, Steven protein kinases identifies a conserved Scherer, Mario Ventura, Richard A. Gibbs, activation mechanism Eric D. Green, and Evan E. Eichler Alexandr P. Kornev, Nina M. Haste, Susan S. 17632 Transposon insertion site profiling chip (TIP-chip) Taylor, and Lynn F. Ten Eyck Sarah J. Wheelan, Lisa Z. Scheifele, Francisco 17789 Some G protein heterotrimers physically Marti´nez-Murillo, Rafael A. Irizarry, dissociate in living cells and Jef D. Boeke Gregory J. Digby, Robert M. Lober, Pooja R. Sethi, and Nevin A. Lambert 17638 Analysis of retrotransposon structural diversity uncovers properties and propensities in 17795 Pleiotrophin disrupts calcium-dependent homophilic angiosperm genome evolution cell–cell adhesion and initiates an epithelial– Cle´mentine Vitte and Jeffrey L. Bennetzen mesenchymal transition P. Perez-Pinera, S. Alcantara, T. Dimitrov, J. A. Vega, 17828 Asymptotically increasing compliance of genomes and T. F. Deuel with Chargaff’s second parity rules through 17801 ELYS is a dual nucleoporin͞kinetochore protein required inversions and inverted transpositions for nuclear pore assembly and proper cell division Guenter Albrecht-Buehler Beth A. Rasala, Arturo V. Orjalo, Zhouxin Shen, 17834 Global mapping of c-Myc binding sites and target Steven Briggs, and Douglass J. Forbes gene networks in human B cells Karen I. Zeller, XiaoDong Zhao, Charlie W. H. Lee, DEVELOPMENTAL BIOLOGY Kuo Ping Chiu, Fei Yao, Jason T. Yustein, Hong Sain 17807 Transcription factor profiling in individual hematopoietic Ooi, Yuriy L. Orlov, Atif Shahab, How Choong Yong, progenitors by digital RT-PCR YuTao Fu, Zhiping Weng, Vladimir A. Kuznetsov, Luigi Warren, David Bryder, Irving L. Weissman, Wing-Kin Sung, Yijun Ruan, Chi V. Dang, and Stephen R. Quake and Chia-Lin Wei

PNAS ͉ November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ vii Downloaded by guest on October 4, 2021 ؉ ؉ 17840 Pmr1, a Golgi Ca2 ͞Mn2 -ATPase, is a regulator of the 17909 L,L-diaminopimelate aminotransferase, a trans-kingdom target of rapamycin (TOR) signaling pathway in yeast enzyme shared by Chlamydia and plants for synthesis Gina Devasahayam, Danilo Ritz, Stephen B. Helliwell, of diaminopimelate͞lysine Daniel J. Burke, and Thomas W. Sturgill Andrea J. McCoy, Nancy E. Adams, Andre´O. Hudson, Charles Gilvarg, Thomas Leustek, and Anthony T. Maurelli 17846 A large-scale full-length cDNA analysis to explore the budding yeast transcriptome 17915 Salmonella typhimurium disseminates within its host Fumihito Miura, Noriko Kawaguchi, Jun Sese, Atsushi by manipulating the motility of infected cells Toyoda, Masahira Hattori, Shinichi Morishita, Micah J. Worley, George S. Nieman, Kaoru Geddes, and Takashi Ito and Fred Heffron

17921 An unconventional pathway for reduction of CO2 IMMUNOLOGY to methane in CO-grown Methanosarcina 17852 Developmental switch of mouse hematopoietic acetivorans revealed by proteomics stem cells from fetal to adult type occurs Daniel J. Lessner, Lingyun Li, Qingbo Li, Tomas Rejtar, in bone marrow after birth Victor P. Andreev, Matthew Reichlen, Kevin Hill, Kazu Kikuchi and Motonari Kondo James J. Moran, Barry L. Karger, and James G. Ferry 17927 The twin-arginine translocation pathway is a major 17858 On the definition of a criterion of immunogenicity route of protein export in Streptomyces coelicolor Thomas Pradeu and Edgardo D. Carosella David A. Widdick, Kieran Dilks, Govind Chandra, Andrew Bottrill, Mike Naldrett, Mechthild Pohlschro¨der, MEDICAL SCIENCES and Tracy Palmer 17862 An immunocompetent mouse model for the tolerance 17933 Mapping the Sinorhizobium meliloti 1021 solute-binding of human chronic hepatitis B virus infection protein-dependent transportome Li-Rung Huang, Hui-Lin Wu, Pei-Jer Chen, T. H. Mauchline, J. E. Fowler, A. K. East, A. L. Sartor, and Ding-Shinn Chen R. Zaheer, A. H. F. Hosie, P. S. Poole, and T. M. Finan 17868 Oncogenic steroid receptor coactivator-3 is a key regulator of the white adipogenic program NEUROSCIENCE ` Jean-Francois Louet, Agnes Coste, Larbi Amazit, 17939 Construction of a mutated pro-nerve growth factor Mounia Tannour-Louet, Ray-Chang Wu, resistant to degradation and suitable for Sophia Y. Tsai, Ming-Jer J. Tsai, Johan biophysical and cellular utilization Auwerx, and Bert W. O’Malley Promila C. Pagadala, Laura A. Dvorak, and Kenneth E. Neet 17874 Radiation dose-rate effects, endogenous DNA damage, 17944 Neuroglobin-overexpressing transgenic mice are and signaling resonance resistant to cerebral and myocardial ischemia Michael M. Vilenchik and Alfred G. Knudson Adil A. Khan, Yaoming Wang, Yunjuan Sun, Xiao Ou Mao, 17880 Molecular mechanism for analgesia involving specific Lin Xie, Erin Miles, Justin Graboski, Sylvia Chen, antagonism of ␣9␣10 nicotinic acetylcholine receptors Lisa M. Ellerby, Kunlin Jin, and David A. Greenberg Michelle Vincler, Shannon Wittenauer, Renee Parker, 17949 Lipocalin-type prostaglandin D synthase produces Michael Ellison, B. M. Olivera, and J. Michael McIntosh prostaglandin D2 involved in regulation of physiological sleep 17885 Evolution and expression of chimeric POTE–actin Wei-Min Qu, Zhi-Li Huang, Xin-Hong Xu, genes in the human genome Kosuke Aritake, Naomi Eguchi, Fumio Yoomi Lee, Tomoko Ise, Duc Ha, Ashley Saint Fleur, Nambu, Shu Narumiya, Yoshihiro Yoonsoo Hahn, Xiu-Fen Liu, Satoshi Nagata, Urade, and Osamu Hayaishi Byungkook Lee, Tapan K. Bera, and Ira Pastan 17955 Inhibition of dynamin completely blocks compensatory 17891 Revertant mutants G550E and 4RK rescue cystic fibrosis synaptic vesicle endocytosis mutants in the first nucleotide-binding domain of CFTR A. Jamila Newton, Tom Kirchhausen, by different mechanisms and Venkatesh N. Murthy Mo´nica Roxo-Rosa, Zhe Xu, Andre´ Schmidt, Ma´rio Neto, Zhiwei Cai, Cla´udio M. Soares, David N. Sheppard, 17961 The spine neck filters membrane potentials and Margarida D. Amaral Roberto Araya, Jiang Jiang, Kenneth B. Eisenthal, and Rafael Yuste MICROBIOLOGY 17967 LRRTM3 promotes processing of amyloid-precursor 17897 Rationally designed small compounds inhibit pilus protein by BACE1 and is a positional candidate biogenesis in uropathogenic bacteria gene for late-onset Alzheimer’s disease Jerome S. Pinkner, Han Remaut, Floris Buelens, Eric John Majercak, William J. Ray, Amy Espeseth, Adam Miller, Veronica Åberg, Nils Pemberton, Mattias Simon, Xiao-Ping Shi, Carrie Wolffe, Krista Hedenstro¨m, Andreas Larsson, Patrick Seed, Getty, Shane Marine, Erica Stec, Marc Ferrer, Gabriel Waksman, Scott J. Hultgren, Berta Strulovici, Steven Bartz, Adam Gates, and Fredrik Almqvist Min Xu, Qian Huang, Lei Ma, Paul Shughrue, Julja Burchard, Dennis 17903 Refolding of a paramyxovirus F protein from prefusion Colussi, Beth Pietrak, Jason Kahana, to postfusion conformations observed by liposome Dirk Beher, Thomas Rosahl, Mark binding and electron microscopy Shearman, Daria Hazuda, Alan B. Sarah A. Connolly, George P. Leser, Hsien-Shen Yin, Sachs, Kenneth S. Koblan, Guy R. Theodore S. Jardetzky, and Robert A. Lamb Seabrook, and David J. Stone

PNAS ͉ November 21, 2006 ͉ vol. 103 ͉ no. 47 ͉ ix Downloaded by guest on October 4, 2021 17973 Conservation and evolution of gene coexpression 18008 Suppression of Arabidopsis vesicle-SNARE expression networks in human and chimpanzee brains inhibited fusion of H2O2-containing vesicles with Michael C. Oldham, Steve Horvath, tonoplast and increased salt tolerance and Daniel H. Geschwind Yehoram Leshem, Naomi Melamed-Book, Olivier Cagnac, Gil Ronen, Yossi Nishri, Mazal Solomon, Gil Cohen, PHARMACOLOGY and Alex Levine 17979 Human Opiorphin, a natural antinociceptive modulator of opioid-dependent pathways PSYCHOLOGY Anne Wisner, Evelyne Dufour, Michae¨l Messaoudi, 18014 Bayesian estimation of the shape skeleton Amine Nejdi, Audrey Marcel, Marie-Noelle Jacob Feldman and Manish Singh Ungeheuer, and Catherine Rougeot

18020 Recent fear is resistant to extinction PHYSIOLOGY Stephen Maren and Chun-hui Chang 17985 Angiotensin II causes hypertension and cardiac hypertrophy through its receptors in the kidney Steven D. Crowley, Susan B. Gurley, Maria J. CORRECTION Herrera, Phillip Ruiz, Robert Griffiths, Anil P. Kumar, Hyung-Suk Kim, Oliver Smithies, Thu H. Le, and Thomas M. Coffman PLANT BIOLOGY 17991 Na channel inactivation from open and closed states Clay M. Armstrong 18026 Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes PLANT BIOLOGY Steven B. Cannon, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung, Je´roˆme Gouzy, Xiaohong 17644 Remarkable variation in maize genome structure Wang, Joann Mudge, Jayprakash Vasdewani, inferred from haplotype diversity at the bz locus Thomas Schiex, Manuel Spannagl, Erin Monaghan, Qinghua Wang and Hugo K. Dooner Christine Nicholson, Sean J. Humphray, Heiko 17997 A single chromoprotein with triple chromophores Schoof, Klaus F. X. Mayer, Jane Rogers, Francis acts as both a phytochrome and a phototropin Que´tier, Giles E. Oldroyd, Fre´de´ric Debelle´, Takeshi Kanegae, Emi Hayashida, Chihiro Kuramoto, Douglas R. Cook, Ernest F. Retzel, Bruce A. Roe, and Masamitsu Wada Christopher D. Town, Satoshi Tabata, 18002 A pathogen-inducible endogenous siRNA Yves Van de Peer, and Nevin D. Young in plant immunity Surekha Katiyar-Agarwal, Rebekah Morgan, xi–xii Author Index Douglas Dahlbeck, Omar Borsani, Andy Villegas, Jr., Jian-Kang Zhu, Brian J. Staskawicz, and Hailing Jin xiii Subscription Form

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