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Table of Contents: March 2009

COVER

Genome and proteome analysis of Sahara bacterium Deinococcus deserti.

Image Credit: Photo of rocks and sand in the Sahara by Suzanne Sommer (Université Paris Sud, France).
Issue Image

Genome annotation of Deinococcus deserti, a species isolated from Sahara surface sand, was performed in parallel with proteome analysis. Proteomics and comparative genomics allowed for the correction of several gene prediction errors, which were also present in previously sequenced Deinococcus species. This work demonstrates that accurate primary genome annotation is obtained when a combination of high-throughput proteomic and genomic techniques is used (see de Groot et al., doi:10.1371/journal.pgen.1000434). Remarkably, D. deserti has three recA genes and three lesion-bypass DNA polymerases, which probably contribute to survival in its dry and ultraviolet-exposed extreme environment.

Perspectives

Mitotic Recombination: Why? When? How? Where?

Matthew C. LaFave, Jeff Sekelsky

Neocentromeres Come of Age

Owen J. Marshall, K. H. Andy Choo

Review

Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities?

Laurence Van Melderen, Manuel Saavedra De Bast

Research Articles

Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti

Arjan de Groot, Rémi Dulermo, Philippe Ortet, Laurence Blanchard, Philippe Guérin, Bernard Fernandez, Benoit Vacherie, Carole Dossat, Edmond Jolivet, Patricia Siguier, Michael Chandler, Mohamed Barakat, Alain Dedieu, Valérie Barbe, Thierry Heulin, Suzanne Sommer, Wafa Achouak, Jean Armengaud

A Common Variant Associated with Dyslexia Reduces Expression of the KIAA0319 Gene

Megan Y. Dennis, Silvia Paracchini, Thomas S. Scerri, Ludmila Prokunina-Olsson, Julian C. Knight, Richard Wade-Martins, Penny Coggill, Stephan Beck, Eric D. Green, Anthony P. Monaco

DNA Methylation Analysis of Chromosome 21 Gene Promoters at Single Base Pair and Single Allele Resolution

Yingying Zhang, Christian Rohde, Sascha Tierling, Tomasz P. Jurkowski, Christoph Bock, Diana Santacruz, Sergey Ragozin, Richard Reinhardt, Marco Groth, Jörn Walter, Albert Jeltsch

Gibberellin Acts through Jasmonate to Control the Expression of MYB21, MYB24, and MYB57 to Promote Stamen Filament Growth in Arabidopsis

Hui Cheng, Susheng Song, Langtao Xiao, Hui Meng Soo, Zhiwei Cheng, Daoxin Xie, Jinrong Peng

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

David C. Hess, Chad L. Myers, Curtis Huttenhower, Matthew A. Hibbs, Alicia P. Hayes, Jadine Paw, John J. Clore, Rosa M. Mendoza, Bryan San Luis, Corey Nislow, Guri Giaever, Michael Costanzo, Olga G. Troyanskaya, Amy A. Caudy

A Genome-Wide Association Study in Chronic Obstructive Pulmonary Disease (COPD): Identification of Two Major Susceptibility Loci

Sreekumar G. Pillai, Dongliang Ge, Guohua Zhu, Xiangyang Kong, Kevin V. Shianna, Anna C. Need, Sheng Feng, Craig P. Hersh, Per Bakke, Amund Gulsvik, Andreas Ruppert, Karin C. Lødrup Carlsen, Allen Roses, Wayne Anderson, Stephen I. Rennard, David A. Lomas, Edwin K. Silverman, David B. Goldstein , ICGN Investigators

Ciliary Beating Recovery in Deficient Human Airway Epithelial Cells after Lentivirus Ex Vivo Gene Therapy

Brigitte Chhin, Didier Negre, Olivier Merrot, Jacqueline Pham, Yves Tourneur, Denis Ressnikoff, Martine Jaspers, Mark Jorissen, François-Loïc Cosset, Patrice Bouvagnet

Germline Mutation in NLRP2 (NALP2) in a Familial Imprinting Disorder (Beckwith-Wiedemann Syndrome)

Esther Meyer, Derek Lim, Shanaz Pasha, Louise J. Tee, Fatimah Rahman, John R. W. Yates, C. Geoffrey Woods, Wolf Reik, Eamonn R. Maher

An African Ancestry-Specific Allele of CTLA4 Confers Protection against Rheumatoid Arthritis in African Americans

James M. Kelley, Laura B. Hughes, Jeffrey D. Faggard, Maria I. Danila, Monica H. Crawford, Yuanqing Edberg, Miguel A. Padilla, Hemant K. Tiwari, Andrew O. Westfall, Graciela S. Alarcón, Doyt L. Conn, Beth L. Jonas, Leigh F. Callahan, Edwin A. Smith, Richard D. Brasington Jr, David B. Allison, Robert P. Kimberly, Larry W. Moreland, Jeffrey C. Edberg, S. Louis Bridges Jr

Parallel Germline Infiltration of a Lentivirus in Two Malagasy Lemurs

Clément Gilbert, David G. Maxfield, Steven M. Goodman, Cédric Feschotte

Independent S-Locus Mutations Caused Self-Fertility in Arabidopsis thaliana

Nathan A. Boggs, June B. Nasrallah, Mikhail E. Nasrallah

Evolution of a Bacterial Regulon Controlling Virulence and Mg2+ Homeostasis

J. Christian Perez, Dongwoo Shin, Igor Zwir, Tammy Latifi, Tricia J. Hadley, Eduardo A. Groisman

A Genome-Wide Association Study of Pulmonary Function Measures in the Framingham Heart Study

Jemma B. Wilk, Ting-hsu Chen, Daniel J. Gottlieb, Robert E. Walter, Michael W. Nagle, Brian J. Brandler, Richard H. Myers, Ingrid B. Borecki, Edwin K. Silverman, Scott T. Weiss, George T. O'Connor

A Plant Germline-Specific Integrator of Sperm Specification and Cell Cycle Progression

Lynette Brownfield, Said Hafidh, Michael Borg, Anna Sidorova, Toshiyuki Mori, David Twell

Genetic Drift of HIV Populations in Culture

Yegor Voronin, Sarah Holte, Julie Overbaugh, Michael Emerman

A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose

Fumihiko Takeuchi, Ralph McGinnis, Stephane Bourgeois, Chris Barnes, Niclas Eriksson, Nicole Soranzo, Pamela Whittaker, Venkatesh Ranganath, Vasudev Kumanduri, William McLaren, Lennart Holm, Jonatan Lindh, Anders Rane, Mia Wadelius, Panos Deloukas

Escherichia coli MazF Leads to the Simultaneous Selective Synthesis of Both “Death Proteins” and “Survival Proteins”

Shahar Amitai, Ilana Kolodkin-Gal, Mirit Hananya-Meltabashi, Ayelet Sacher, Hanna Engelberg-Kulka

A Fine-Structure Map of Spontaneous Mitotic Crossovers in the Yeast Saccharomyces cerevisiae

Phoebe S. Lee, Patricia W. Greenwell, Margaret Dominska, Malgorzata Gawel, Monica Hamilton, Thomas D. Petes

Multifactorial Regulation of a Hox Target Gene

Petra Stöbe, Sokrates M. A. Stein, Anette Habring-Müller, Daniela Bezdan, Aurelia L. Fuchs, Stefanie D. Hueber, Haijia Wu, Ingrid Lohmann

A Novel Role for MAPKAPK2 in Morphogenesis during Zebrafish Development

Beth A. Holloway, Sol Gomez de la Torre Canny, Ying Ye, Diane C. Slusarski, Christina M. Freisinger, Roland Dosch, Margaret M. Chou, Daniel S. Wagner, Mary C. Mullins

A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species

Russell Bell, Alan Hubbard, Rakesh Chettier, Di Chen, John P. Miller, Pankaj Kapahi, Mark Tarnopolsky, Sudhir Sahasrabuhde, Simon Melov, Robert E. Hughes

Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics

Michael A. Nalls, Javier Simon-Sanchez, J. Raphael Gibbs, Coro Paisan-Ruiz, Jose Tomas Bras, Toshiko Tanaka, Mar Matarin, Sonja Scholz, Charles Weitz, Tamara B. Harris, Luigi Ferrucci, John Hardy, Andrew B. Singleton

The Complete Genome and Proteome of Laribacter hongkongensis Reveal Potential Mechanisms for Adaptations to Different Temperatures and Habitats

Patrick C. Y. Woo, Susanna K. P. Lau, Herman Tse, Jade L. L. Teng, Shirly O. T. Curreem, Alan K. L. Tsang, Rachel Y. Y. Fan, Gilman K. M. Wong, Yi Huang, Nicholas J. Loman, Lori A. S. Snyder, James J. Cai, Jian-Dong Huang, William Mak, Mark J. Pallen, Si Lok, Kwok-Yung Yuen

Sequential Assembly of Centromeric Proteins in Male Mouse Meiosis

María Teresa Parra, Rocío Gómez, Alberto Viera, Elena Llano, Alberto M. Pendás, Julio S. Rufas, José A. Suja

Genome-Wide Association Analyses Identify SPOCK as a Key Novel Gene Underlying Age at Menarche

Yao-Zhong Liu, Yan-Fang Guo, Liang Wang, Li-Jun Tan, Xiao-Gang Liu, Yu-Fang Pei, Han Yan, Dong-Hai Xiong, Fei-Yan Deng, Na Yu, Yin-Ping Zhang, Lei Zhang, Shu-Feng Lei, Xiang-Ding Chen, Hong-Bin Liu, Xue-Zhen Zhu, Shawn Levy, Christopher J. Papasian, Betty M. Drees, James J. Hamilton, Robert R. Recker, Hong-Wen Deng

Uncoupling Time and Space in the Collinear Regulation of Hox Genes

Patrick Tschopp, Basile Tarchini, François Spitz, Jozsef Zakany, Denis Duboule

Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans

Carrie Ketel, Helen S. W. Wang, Mark McClellan, Kelly Bouchonville, Anna Selmecki, Tamar Lahav, Maryam Gerami-Nejad, Judith Berman

Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers

Karine Van Doninck, Morgan L. Mandigo, Jae H. Hur, Peter Wang, Julien Guglielmini, Michel C. Milinkovitch, William S. Lane, Matthew Meselson

Death and Resurrection of the Human IRGM Gene

Cemalettin Bekpen, Tomas Marques-Bonet, Can Alkan, Francesca Antonacci, Maria Bruna Leogrande, Mario Ventura, Jeffrey M. Kidd, Priscillia Siswara, Jonathan C. Howard, Evan E. Eichler

Selection at a Single Locus Leads to Widespread Expansion of Toxoplasma gondii Lineages That Are Virulent in Mice

Asis Khan, Sonya Taylor, James W. Ajioka, Benjamin M. Rosenthal, L. David Sibley

Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli

T. Sabari Sankar, Girish Neelakanta, Vartul Sangal, Georg Plum, Mark Achtman, Karin Schnetz

Pro-Aging Effects of Glucose Signaling through a G Protein-Coupled Glucose Receptor in Fission Yeast

Antoine E. Roux, Alexandre Leroux, Manal A. Alaamery, Charles S. Hoffman, Pascal Chartrand, Gerardo Ferbeyre, Luis A. Rokeach

Genetic Determinants of Height Growth Assessed Longitudinally from Infancy to Adulthood in the Northern Finland Birth Cohort 1966

Ulla Sovio, Amanda J. Bennett, Iona Y. Millwood, John Molitor, Paul F. O'Reilly, Nicholas J. Timpson, Marika Kaakinen, Jaana Laitinen, Jari Haukka, Demetris Pillas, Ioanna Tzoulaki, Jassy Molitor, Clive Hoggart, Lachlan J. M. Coin, John Whittaker, Anneli Pouta, Anna-Liisa Hartikainen, Nelson B. Freimer, Elisabeth Widen, Leena Peltonen, Paul Elliott, Mark I. McCarthy, Marjo-Riitta Jarvelin