Table of Contents

Biological Sciences

• Biochemistry

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    DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3

    Grace Ee-Lu Siaw, I-Fen Liu, Po-Yen Lin, Michael D. Been, and Tao-shih Hsieh

    PNAS September 20, 2016 113 (38) E5544-E5551; first published August 31, 2016. https://doi.org/10.1073/pnas.1605517113
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    Kinetic barriers to SNAREpin assembly in the regulation of membrane docking/priming and fusion

    Feng Li, Neeraj Tiwari, James E. Rothman, and Frederic Pincet

    PNAS September 20, 2016 113 (38) 10536-10541; first published September 6, 2016. https://doi.org/10.1073/pnas.1604000113
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    Structure of Bor1 supports an elevator transport mechanism for SLC4 anion exchangers

    Bryan H. Thurtle-Schmidt and Robert M. Stroud

    PNAS September 20, 2016 113 (38) 10542-10546; first published September 6, 2016. https://doi.org/10.1073/pnas.1612603113
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    WD40 domain of Apc1 is critical for the coactivator-induced allosteric transition that stimulates APC/C catalytic activity

    Qiuhong Li, Leifu Chang, Shintaro Aibara, Jing Yang, Ziguo Zhang, and David Barford

    PNAS September 20, 2016 113 (38) 10547-10552; first published September 6, 2016. https://doi.org/10.1073/pnas.1607147113
  • Open Access

    Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6–Bre1

    Laura D. Gallego, Medini Ghodgaonkar Steger, Anton A. Polyansky, Tobias Schubert, Bojan Zagrovic, Ning Zheng, Tim Clausen, Franz Herzog, and Alwin Köhler

    PNAS September 20, 2016 113 (38) 10553-10558; first published September 6, 2016. https://doi.org/10.1073/pnas.1606863113
  • Open Access

    Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids

    Karin Öjemalm, Takashi Higuchi, Patricia Lara, Erik Lindahl, Hiroaki Suga, and Gunnar von Heijne

    PNAS September 20, 2016 113 (38) 10559-10564; first published September 6, 2016. https://doi.org/10.1073/pnas.1606776113

• Biophysics and Computational Biology

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    Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

    Levin U. L. Brinkmann and Jochen S. Hub

    PNAS September 20, 2016 113 (38) 10565-10570; first published September 6, 2016. https://doi.org/10.1073/pnas.1603539113

• Cell Biology

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    Coordinated autoinhibition of F-BAR domain membrane binding and WASp activation by Nervous Wreck

    Tatiana B. Stanishneva-Konovalova, Charlotte F. Kelley, Tania L. Eskin, Emily M. Messelaar, Steven A. Wasserman, Olga S. Sokolova, and Avital A. Rodal

    PNAS September 20, 2016 113 (38) E5552-E5561; first published September 6, 2016. https://doi.org/10.1073/pnas.1524412113
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    In B cells, phosphatidylinositol 5-phosphate 4-kinase–α synthesizes PI(4,5)P₂ to impact mTORC2 and Akt signaling

    Simon J. Bulley, Alaa Droubi, Jonathan H. Clarke, Karen E. Anderson, Len R. Stephens, Phillip T. Hawkins, and Robin F. Irvine

    PNAS September 20, 2016 113 (38) 10571-10576; first published September 6, 2016. https://doi.org/10.1073/pnas.1522478113
  • Open Access

    P31^comet, a member of the synaptonemal complex, participates in meiotic DSB formation in rice

    Jianhui Ji, Ding Tang, Yi Shen, Zhihui Xue, Hongjun Wang, Wenqing Shi, Chao Zhang, Guijie Du, Yafei Li, and Zhukuan Cheng

    PNAS September 20, 2016 113 (38) 10577-10582; first published September 6, 2016. https://doi.org/10.1073/pnas.1607334113

• Developmental Biology

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    Selenoprotein H is an essential regulator of redox homeostasis that cooperates with p53 in development and tumorigenesis

    Andrew G. Cox, Allison Tsomides, Andrew J. Kim, Diane Saunders, Katie L. Hwang, Kimberley J. Evason, Jerry Heidel, Kristin K. Brown, Min Yuan, Evan C. Lien, Byung Cheon Lee, Sahar Nissim, Bryan Dickinson, Sagar Chhangawala, Christopher J. Chang, John M. Asara, Yariv Houvras, Vadim N. Gladyshev, and Wolfram Goessling

    PNAS September 20, 2016 113 (38) E5562-E5571; first published September 1, 2016. https://doi.org/10.1073/pnas.1600204113
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    Minibrain and Wings apart control organ growth and tissue patterning through down-regulation of Capicua

    Liu Yang, Sayantanee Paul, Kenneth G. Trieu, Lucas G. Dent, Francesca Froldi, Marta Forés, Kaitlyn Webster, Kellee R. Siegfried, Shu Kondo, Kieran Harvey, Louise Cheng, Gerardo Jiménez, Stanislav Y. Shvartsman, and Alexey Veraksa

    PNAS September 20, 2016 113 (38) 10583-10588; first published September 6, 2016. https://doi.org/10.1073/pnas.1609417113

• Ecology

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    Spiny plants, mammal browsers, and the origin of African savannas

    • From the Cover

    Tristan Charles-Dominique, T. Jonathan Davies, Gareth P. Hempson, Bezeng S. Bezeng, Barnabas H. Daru, Ronny M. Kabongo, Olivier Maurin, A. Muthama Muasya, Michelle van der Bank, and William J. Bond

    PNAS September 20, 2016 113 (38) E5572-E5579; first published September 6, 2016. https://doi.org/10.1073/pnas.1607493113
  • Open Access

    Nonlinear, interacting responses to climate limit grassland production under global change

    • From the Cover

    Kai Zhu, Nona R. Chiariello, Todd Tobeck, Tadashi Fukami, and Christopher B. Field

    PNAS September 20, 2016 113 (38) 10589-10594; first published September 6, 2016. https://doi.org/10.1073/pnas.1606734113
  • Open Access

    Configuration of the thermal landscape determines thermoregulatory performance of ectotherms

    Michael W. Sears, Michael J. Angilletta Jr., Matthew S. Schuler, Jason Borchert, Katherine F. Dilliplane, Monica Stegman, Travis W. Rusch, and William A. Mitchell

    PNAS September 20, 2016 113 (38) 10595-10600; first published September 6, 2016. https://doi.org/10.1073/pnas.1604824113

• Environmental Sciences

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    Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters

    Laura A. Bristow, Tage Dalsgaard, Laura Tiano, Daniel B. Mills, Anthony D. Bertagnolli, Jody J. Wright, Steven J. Hallam, Osvaldo Ulloa, Donald E. Canfield, Niels Peter Revsbech, and Bo Thamdrup

    PNAS September 20, 2016 113 (38) 10601-10606; first published September 6, 2016. https://doi.org/10.1073/pnas.1600359113

• Evolution

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    Explosive ice age diversification of kiwi

    • From the Cover

    Jason T. Weir, Oliver Haddrath, Hugh A. Robertson, Rogan M. Colbourne, and Allan J. Baker

    PNAS September 20, 2016 113 (38) E5580-E5587; first published August 29, 2016. https://doi.org/10.1073/pnas.1603795113
  • Open Access

    Variation in the molecular clock of primates

    Priya Moorjani, Carlos Eduardo G. Amorim, Peter F. Arndt, and Molly Przeworski

    PNAS September 20, 2016 113 (38) 10607-10612; first published September 6, 2016. https://doi.org/10.1073/pnas.1600374113
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    Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

    Ruiqi Huang, Andrew J. O’Donnell, Jessica J. Barboline, and Todd J. Barkman

    PNAS September 20, 2016 113 (38) 10613-10618; first published September 20, 2016. https://doi.org/10.1073/pnas.1602575113

• Genetics

  • Open Access

    Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli

    Michael G. Napolitano, Matthieu Landon, Christopher J. Gregg, Marc J. Lajoie, Lakshmi Govindarajan, Joshua A. Mosberg, Gleb Kuznetsov, Daniel B. Goodman, Oscar Vargas-Rodriguez, Farren J. Isaacs, Dieter Söll, and George M. Church

    PNAS September 20, 2016 113 (38) E5588-E5597; first published September 6, 2016. https://doi.org/10.1073/pnas.1605856113
  • Open Access

    Mutations in mitochondrial enzyme GPT2 cause metabolic dysfunction and neurological disease with developmental and progressive features

    Qing Ouyang, Tojo Nakayama, Ozan Baytas, Shawn M. Davidson, Chendong Yang, Michael Schmidt, Sofia B. Lizarraga, Sasmita Mishra, Malak EI-Quessny, Saima Niaz, Mirrat Gul Butt, Syed Imran Murtaza, Afzal Javed, Haroon Rashid Chaudhry, Dylan J. Vaughan, R. Sean Hill, Jennifer N. Partlow, Seung-Yun Yoo, Anh-Thu N. Lam, Ramzi Nasir, Muna Al-Saffar, A. James Barkovich, Matthew Schwede, Shailender Nagpal, Anna Rajab, Ralph J. DeBerardinis, David E. Housman, Ganeshwaran H. Mochida, and Eric M. Morrow

    PNAS September 20, 2016 113 (38) E5598-E5607; first published September 6, 2016. https://doi.org/10.1073/pnas.1609221113
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    eIF4B stimulates translation of long mRNAs with structured 5′ UTRs and low closed-loop potential but weak dependence on eIF4G

    • Inaugural Article

    Neelam Dabas Sen, Fujun Zhou, Michael S. Harris, Nicholas T. Ingolia, and Alan G. Hinnebusch

    PNAS September 20, 2016 113 (38) 10464-10472; first published September 6, 2016. https://doi.org/10.1073/pnas.1612398113

    See companion article:

    • QnAs with Alan G. Hinnebusch

      - Oct 03, 2016
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    PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line

    Vipul Kumar, Frederick W. Alt, and Richard L. Frock

    PNAS September 20, 2016 113 (38) 10619-10624; first published September 6, 2016. https://doi.org/10.1073/pnas.1611882113

• Immunology and Inflammation

  • Open Access

    Class II major histocompatibility complex mutant mice to study the germ-line bias of T-cell antigen receptors

    Daniel Silberman, Sai Harsha Krovi, Kathryn D. Tuttle, James Crooks, Richard Reisdorph, Janice White, James Gross, Jennifer L. Matsuda, Laurent Gapin, Philippa Marrack, and John W. Kappler

    PNAS September 20, 2016 113 (38) E5608-E5617; first published September 1, 2016. https://doi.org/10.1073/pnas.1609717113
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    Rabex-5 is a lenalidomide target molecule that negatively regulates TLR-induced type 1 IFN production

    David Millrine, Mami Tei, Yohannes Gemechu, and Tadamitsu Kishimoto

    PNAS September 20, 2016 113 (38) 10625-10630; first published September 6, 2016. https://doi.org/10.1073/pnas.1611751113
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    De novo DNA methylation by DNA methyltransferase 3a controls early effector CD8⁺ T-cell fate decisions following activation

    Brian H. Ladle, Kun-Po Li, Maggie J. Phillips, Alexandra B. Pucsek, Azeb Haile, Jonathan D. Powell, Elizabeth M. Jaffee, David A. Hildeman, and Christopher J. Gamper

    PNAS September 20, 2016 113 (38) 10631-10636; first published August 31, 2016. https://doi.org/10.1073/pnas.1524490113
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    Leptin promotes systemic lupus erythematosus by increasing autoantibody production and inhibiting immune regulation

    Elaine V. Lourenço, Aijing Liu, Giuseppe Matarese, and Antonio La Cava

    PNAS September 20, 2016 113 (38) 10637-10642; first published September 1, 2016. https://doi.org/10.1073/pnas.1607101113
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    Gene-expression profiling of different arms of lymphatic vasculature identifies candidates for manipulation of cell traffic

    Imtiaz Iftakhar-E-Khuda, Ruth Fair-Mäkelä, Anu Kukkonen-Macchi, Kati Elima, Marika Karikoski, Pia Rantakari, Masayuki Miyasaka, Marko Salmi, and Sirpa Jalkanen

    PNAS September 20, 2016 113 (38) 10643-10648; first published September 6, 2016. https://doi.org/10.1073/pnas.1602357113
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    Mannose receptor induces T-cell tolerance via inhibition of CD45 and up-regulation of CTLA-4

    Verena Schuette, Maria Embgenbroich, Thomas Ulas, Meike Welz, Jonas Schulte-Schrepping, Astrid M. Draffehn, Thomas Quast, Katharina Koch, Melanie Nehring, Jessica König, Annegret Zweynert, Frederike L. Harms, Nancy Steiner, Andreas Limmer, Irmgard Förster, Friederike Berberich-Siebelt, Percy A. Knolle, Dirk Wohlleber, Waldemar Kolanus, Marc Beyer, Joachim L. Schultze, and Sven Burgdorf

    PNAS September 20, 2016 113 (38) 10649-10654; first published September 6, 2016. https://doi.org/10.1073/pnas.1605885113

• Medical Sciences

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    Pericyte–fibroblast transition promotes tumor growth and metastasis

    Kayoko Hosaka, Yunlong Yang, Takahiro Seki, Carina Fischer, Olivier Dubey, Erik Fredlund, Johan Hartman, Piotr Religa, Hiromasa Morikawa, Yoko Ishii, Masakiyo Sasahara, Ola Larsson, Giulio Cossu, Renhai Cao, Sharon Lim, and Yihai Cao

    PNAS September 20, 2016 113 (38) E5618-E5627; first published September 7, 2016. https://doi.org/10.1073/pnas.1608384113
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    Pathological Ace2-to-Ace enzyme switch in the stressed heart is transcriptionally controlled by the endothelial Brg1–FoxM1 complex

    Jin Yang, Xuhui Feng, Qiong Zhou, Wei Cheng, Ching Shang, Pei Han, Chiou-Hong Lin, Huei-Sheng Vincent Chen, Thomas Quertermous, and Ching-Pin Chang

    PNAS September 20, 2016 113 (38) E5628-E5635; first published September 6, 2016. https://doi.org/10.1073/pnas.1525078113
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    Sufficient trial size to inform clinical practice

    Charles F. Manski and Aleksey Tetenov

    PNAS September 20, 2016 113 (38) 10518-10523; first published September 6, 2016. https://doi.org/10.1073/pnas.1612174113
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    Circulating microRNA signature for the diagnosis of very high-risk prostate cancer

    Ali H. Alhasan, Alexander W. Scott, Jia J. Wu, Gang Feng, Joshua J. Meeks, C. Shad Thaxton, and Chad A. Mirkin

    PNAS September 20, 2016 113 (38) 10655-10660; first published September 6, 2016. https://doi.org/10.1073/pnas.1611596113
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    Genome editing using CRISPR-Cas9 to create the HPFH genotype in HSPCs: An approach for treating sickle cell disease and β-thalassemia

    Lin Ye, Jiaming Wang, Yuting Tan, Ashley I. Beyer, Fei Xie, Marcus O. Muench, and Yuet Wai Kan

    PNAS September 20, 2016 113 (38) 10661-10665; first published September 6, 2016. https://doi.org/10.1073/pnas.1612075113
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    Actinomycin D enhances killing of cancer cells by immunotoxin RG7787 through activation of the extrinsic pathway of apoptosis

    Xiu Fen Liu, Laiman Xiang, Qi Zhou, Jean-Philippe Carralot, Marco Prunotto, Gerhard Niederfellner, and Ira Pastan

    PNAS September 20, 2016 113 (38) 10666-10671; first published September 6, 2016. https://doi.org/10.1073/pnas.1611481113
  • Open Access

    Whole-exome sequencing identifies recurrent AKT1 mutations in sclerosing hemangioma of lung

    Seung-Hyun Jung, Min Sung Kim, Sung-Hak Lee, Hyun-Chun Park, Hyun Joo Choi, Leeso Maeng, Ki Ouk Min, Jeana Kim, Tae In Park, Ok Ran Shin, Tae-Jung Kim, Haidong Xu, Kyo Young Lee, Tae-Min Kim, Sang Yong Song, Charles Lee, Yeun-Jun Chung, and Sug Hyung Lee

    PNAS September 20, 2016 113 (38) 10672-10677; first published September 6, 2016. https://doi.org/10.1073/pnas.1606946113

• Microbiology

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    CD4⁺ T-cell–independent mechanisms suppress reactivation of latent tuberculosis in a macaque model of HIV coinfection

    • From the Cover

    Taylor W. Foreman, Smriti Mehra, Denae N. LoBato, Adel Malek, Xavier Alvarez, Nadia A. Golden, Allison N. Bucşan, Peter J. Didier, Lara A. Doyle-Meyers, Kasi E. Russell-Lodrigue, Chad J. Roy, James Blanchard, Marcelo J. Kuroda, Andrew A. Lackner, John Chan, Shabaana A. Khader, William R. Jacobs Jr., and Deepak Kaushal

    PNAS September 20, 2016 113 (38) E5636-E5644; first published September 6, 2016. https://doi.org/10.1073/pnas.1611987113
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    Prolonged activation of innate antiviral gene signature after childbirth is determined by IFNL3 genotype

    Aryn A. Price, Dana Tedesco, Mona R. Prasad, Kimberly A. Workowski, Christopher M. Walker, Mehul S. Suthar, Jonathan R. Honegger, and Arash Grakoui

    PNAS September 20, 2016 113 (38) 10678-10683; first published September 6, 2016. https://doi.org/10.1073/pnas.1602319113

    See companion article:

    • Genetic determinants of postpartum HCV control

      - Sep 06, 2016
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    Influence of IFNL3 and HLA-DPB1 genotype on postpartum control of hepatitis C virus replication and T-cell recovery

    Jonathan R. Honegger, Dana Tedesco, Jennifer A. Kohout, Mona R. Prasad, Aryn A. Price, Tera Lindquist, Samantha Ohmer, Melissa Moore-Clingenpeel, Arash Grakoui, and Christopher M. Walker

    PNAS September 20, 2016 113 (38) 10684-10689; first published September 6, 2016. https://doi.org/10.1073/pnas.1602337113

    See companion article:

    • Innate antiviral gene signature after childbirth

      - Sep 06, 2016
  • Open Access

    Point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone of Campylobacter jejuni

    Zuowei Wu, Balamurugan Periaswamy, Orhan Sahin, Michael Yaeger, Paul Plummer, Weiwei Zhai, Zhangqi Shen, Lei Dai, Swaine L. Chen, and Qijing Zhang

    PNAS September 20, 2016 113 (38) 10690-10695; first published September 6, 2016. https://doi.org/10.1073/pnas.1605869113

• Neuroscience

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    GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors

    Xue-Yan He, Yan-Jun Li, Chakrapani Kalyanaraman, Li-Li Qiu, Chen Chen, Qi Xiao, Wen-Xue Liu, Wei Zhang, Jian-Jun Yang, Guiquan Chen, Matthew P. Jacobson, and Yun Stone Shi

    PNAS September 20, 2016 113 (38) E5645-E5654; first published September 6, 2016. https://doi.org/10.1073/pnas.1524358113
  • Open Access

    TRiC subunits enhance BDNF axonal transport and rescue striatal atrophy in Huntington’s disease

    Xiaobei Zhao, Xu-Qiao Chen, Eugene Han, Yue Hu, Paul Paik, Zhiyong Ding, Julia Overman, Alice L. Lau, Sarah H. Shahmoradian, Wah Chiu, Leslie M. Thompson, Chengbiao Wu, and William C. Mobley

    PNAS September 20, 2016 113 (38) E5655-E5664; first published September 6, 2016. https://doi.org/10.1073/pnas.1603020113
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    Infiltrating monocytes promote brain inflammation and exacerbate neuronal damage after status epilepticus

    Nicholas H. Varvel, Jonas J. Neher, Andrea Bosch, Wenyi Wang, Richard M. Ransohoff, Richard J. Miller, and Raymond Dingledine

    PNAS September 20, 2016 113 (38) E5665-E5674; first published September 6, 2016. https://doi.org/10.1073/pnas.1604263113
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    Episodic specificity induction impacts activity in a core brain network during construction of imagined future experiences

    Kevin P. Madore, Karl K. Szpunar, Donna Rose Addis, and Daniel L. Schacter

    PNAS September 20, 2016 113 (38) 10696-10701; first published September 6, 2016. https://doi.org/10.1073/pnas.1612278113
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    Unique pH dynamics in GABAergic synaptic vesicles illuminates the mechanism and kinetics of GABA loading

    Yoshihiro Egashira, Miki Takase, Shoji Watanabe, Junji Ishida, Akiyoshi Fukamizu, Ryosuke Kaneko, Yuchio Yanagawa, and Shigeo Takamori

    PNAS September 20, 2016 113 (38) 10702-10707; first published September 6, 2016. https://doi.org/10.1073/pnas.1604527113

• Pharmacology

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    Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor

    Yinglong Miao, Dahlia Anne Goldfeld, Ee Von Moo, Patrick M. Sexton, Arthur Christopoulos, J. Andrew McCammon, and Celine Valant

    PNAS September 20, 2016 113 (38) E5675-E5684; first published September 6, 2016. https://doi.org/10.1073/pnas.1612353113
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    SCAP/SREBP pathway is required for the full steroidogenic response to cyclic AMP

    Masami Shimizu-Albergine, Brian Van Yserloo, Martin G. Golkowski, Shao-En Ong, Joseph A. Beavo, and Karin E. Bornfeldt

    PNAS September 20, 2016 113 (38) E5685-E5693; first published September 6, 2016. https://doi.org/10.1073/pnas.1611424113

• Plant Biology

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    Chloroplast retrograde signal regulates flowering

    Peiqiang Feng, Hailong Guo, Wei Chi, Xin Chai, Xuwu Sun, Xiumei Xu, Jinfang Ma, Jean-David Rochaix, Dario Leister, Haiyang Wang, Congming Lu, and Lixin Zhang

    PNAS September 20, 2016 113 (38) 10708-10713; first published September 6, 2016. https://doi.org/10.1073/pnas.1521599113
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    Synthesis and transfer of galactolipids in the chloroplast envelope membranes of Arabidopsis thaliana

    Amélie A. Kelly, Barbara Kalisch, Georg Hölzl, Sandra Schulze, Juliane Thiele, Michael Melzer, Rebecca L. Roston, Christoph Benning, and Peter Dörmann

    PNAS September 20, 2016 113 (38) 10714-10719; first published September 6, 2016. https://doi.org/10.1073/pnas.1609184113
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    RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga Chlamydomonas reinhardtii

    Tomohito Yamasaki, Masayuki Onishi, Eun-Jeong Kim, Heriberto Cerutti, and Takeshi Ohama

    PNAS September 20, 2016 113 (38) 10720-10725; first published August 31, 2016. https://doi.org/10.1073/pnas.1523230113