March 2018

Colonization of Arabidopsis seedlings at the root-shoot junction by a new beneficial bacterium Enterobacter sp. SA187 (in green) as visualized by confocal microscopy. This new strain was isolated from nodules of Indigofera, a desert plant living in the Arabian Peninsula. In field and laboratory experiments on alfalfa and Arabidopsis, respectively, it shows significant growth promotion under salt stress conditions. The mechanism of such a salt tolerance induction relies on modulation of the ethylene hormonal pathway and improved sodium to potassium ion ratio. The results reveal a part of the molecular communication process during the beneficial plant-microbe interactions. Red — cells walls; blue — chloroplasts; green — bacteria (SA187). See de Zélicourt et al.

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Image Credit: Lukas Synek

Editorial

PLOS Genetics 2017 Reviewer and Editorial Board Thank You

PLOS Genetics: published March 15, 2018 | https://doi.org/10.1371/journal.pgen.1007265

Perspective

Maternal or zygotic: Unveiling the secrets of the Pancrustacea transcription factor zelda

Rodrigo Nunes da Fonseca, Thiago M. Venancio

PLOS Genetics: published March 1, 2018 | https://doi.org/10.1371/journal.pgen.1007201

Research Articles

ZMYND10 stabilizes intermediate chain proteins in the cytoplasmic pre-assembly of dynein arms

Kyeong Jee Cho, Shin Hye Noh, Soo Min Han, Won-Il Choi, Hye-Youn Kim, Seyoung Yu, Joon Suk Lee, John Hoon Rim, Min Goo Lee, Friedhelm Hildebrandt, Heon Yung Gee

PLOS Genetics: published March 30, 2018 | https://doi.org/10.1371/journal.pgen.1007316

The presence of rNTPs decreases the speed of mitochondrial DNA replication

Josefin M. E. Forslund, Annika Pfeiffer, Gorazd Stojkovič, Paulina H. Wanrooij, Sjoerd Wanrooij

PLOS Genetics: published March 30, 2018 | https://doi.org/10.1371/journal.pgen.1007315

Cell polarity protein Spa2 coordinates Chs2 incorporation at the division site in budding yeast

Magdalena Foltman, Yasmina Filali-Mouncef, Damaso Crespo, Alberto Sanchez-Diaz

PLOS Genetics: published March 30, 2018 | https://doi.org/10.1371/journal.pgen.1007299

Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway

Lu Han, Michael P. Guy, Yoshiko Kon, Eric M. Phizicky

PLOS Genetics: published March 29, 2018 | https://doi.org/10.1371/journal.pgen.1007288

Germ cells in the teleost fish medaka have an inherent feminizing effect

Toshiya Nishimura, Kazuki Yamada, Chika Fujimori, Mariko Kikuchi, Toshihiro Kawasaki, Kellee R. Siegfried, Noriyoshi Sakai, Minoru Tanaka

PLOS Genetics: published March 29, 2018 | https://doi.org/10.1371/journal.pgen.1007259

A chitinase with two catalytic domains is required for organization of the cuticular extracellular matrix of a beetle

Mi Young Noh, Subbaratnam Muthukrishnan, Karl J. Kramer, Yasuyuki Arakane

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007307

Mutations in Diphosphoinositol-Pentakisphosphate Kinase PPIP5K2 are associated with hearing loss in human and mouse

Rizwan Yousaf, Chunfang Gu, Zubair M. Ahmed, Shaheen N. Khan, Thomas B. Friedman, Sheikh Riazuddin, Stephen B. Shears, Saima Riazuddin

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007297

Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease

Laura M. Raffield, Jacob C. Ulirsch, Rakhi P. Naik, Samuel Lessard, Robert E. Handsaker, Deepti Jain, Hyun M. Kang, Nathan Pankratz, Paul L. Auer, Erik L. Bao, Joshua D. Smith, Leslie A. Lange, Ethan M. Lange, Yun Li, Timothy A. Thornton, Bessie A. Young, Goncalo R. Abecasis, Cathy C. Laurie, Deborah A. Nickerson, Steven A. McCarroll, Adolfo Correa, James G. Wilson, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hematology & Hemostasis, Diabetes, and Structural Variation TOPMed Working Groups, Guillaume Lettre, Vijay G. Sankaran, Alex P. Reiner

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007293

Novel function of HATs and HDACs in homologous recombination through acetylation of human RAD52 at double-strand break sites

Takeshi Yasuda, Wataru Kagawa, Tomoo Ogi, Takamitsu A. Kato, Takehiro Suzuki, Naoshi Dohmae, Kazuya Takizawa, Yuka Nakazawa, Matthew D. Genet, Mika Saotome, Michio Hama, Teruaki Konishi, Nakako Izumi Nakajima, Masaharu Hazawa, Masanori Tomita, Manabu Koike, Katsuko Noshiro, Kenichi Tomiyama, Chizuka Obara, Takaya Gotoh, Ayako Ui, Akira Fujimori, Fumiaki Nakayama, Fumio Hanaoka, Kaoru Sugasawa, Ryuichi Okayasu, Penny A. Jeggo, Katsushi Tajima

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007277

Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space

Amanda O. Veri, Zhengqiang Miao, Rebecca S. Shapiro, Faiza Tebbji, Teresa R. O’Meara, Sang Hu Kim, Juan Colazo, Kaeling Tan, Valmik K. Vyas, Malcolm Whiteway, Nicole Robbins, Koon Ho Wong, Leah E. Cowen

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007270

Glial loss of the metallo β-lactamase domain containing protein, SWIP-10, induces age- and glutamate-signaling dependent, dopamine neuron degeneration

Chelsea L. Gibson, Joseph T. Balbona, Ashlin Niedzwiecki, Peter Rodriguez, Ken C. Q. Nguyen, David H. Hall, Randy D. Blakely

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007269

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization

Marianne Emery, M. Madeline S. Willis, Yue Hao, Kerrie Barry, Khouanchy Oakgrove, Yi Peng, Jeremy Schmutz, Eric Lyons, J. Chris Pires, Patrick P. Edger, Gavin C. Conant

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007267

Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans

Thomas C. A. Smith, Peter F. Arndt, Adam Eyre-Walker

PLOS Genetics: published March 28, 2018 | https://doi.org/10.1371/journal.pgen.1007254

PIKfyve regulates melanosome biogenesis

Marc C. Liggins, Jessica L. Flesher, Sohail Jahid, Priya Vasudeva, Victoria Eby, Shunsuke Takasuga, Junko Sasaki, Takehiko Sasaki, Raymond E. Boissy, Anand K. Ganesan

PLOS Genetics: published March 27, 2018 | https://doi.org/10.1371/journal.pgen.1007290

Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate

Thomas P. Wytock, Aretha Fiebig, Jonathan W. Willett, Julien Herrou, Aleksandra Fergin, Adilson E. Motter, Sean Crosson

PLOS Genetics: published March 27, 2018 | https://doi.org/10.1371/journal.pgen.1007284

Oxygen-sensing neurons reciprocally regulate peripheral lipid metabolism via neuropeptide signaling in Caenorhabditis elegans

Rosalind Hussey, Nicole K. Littlejohn, Emily Witham, Erik Vanstrum, Jaleh Mesgarzadeh, Harkaranveer Ratanpal, Supriya Srinivasan

PLOS Genetics: published March 26, 2018 | https://doi.org/10.1371/journal.pgen.1007305

DNA strand-exchange patterns associated with double-strand break-induced and spontaneous mitotic crossovers in Saccharomyces cerevisiae

Yee Fang Hum, Sue Jinks-Robertson

PLOS Genetics: published March 26, 2018 | https://doi.org/10.1371/journal.pgen.1007302

The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans

Christina Fassnacht, Cristina Tocchini, Pooja Kumari, Dimos Gaidatzis, Michael B. Stadler, Rafal Ciosk

PLOS Genetics: published March 26, 2018 | https://doi.org/10.1371/journal.pgen.1007252

The TIE1 transcriptional repressor controls shoot branching by directly repressing BRANCHED1 in Arabidopsis

Yan Yang, Michael Nicolas, Jinzhe Zhang, Hao Yu, Dongshu Guo, Rongrong Yuan, Tiantian Zhang, Jianzhao Yang, Pilar Cubas, Genji Qin

PLOS Genetics: published March 23, 2018 | https://doi.org/10.1371/journal.pgen.1007296

Long-lived rodents reveal signatures of positive selection in genes associated with lifespan

Arne Sahm, Martin Bens, Karol Szafranski, Susanne Holtze, Marco Groth, Matthias Görlach, Cornelis Calkhoven, Christine Müller, Matthias Schwab, Johann Kraus, Hans A. Kestler, Alessandro Cellerino, Hynek Burda, Thomas Hildebrandt, Philip Dammann, Matthias Platzer

PLOS Genetics: published March 23, 2018 | https://doi.org/10.1371/journal.pgen.1007272

The long-range interaction map of ribosomal DNA arrays

Shoukai Yu, Bernardo Lemos

PLOS Genetics: published March 23, 2018 | https://doi.org/10.1371/journal.pgen.1007258

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

Timothy L. Haskett, Jason J. Terpolilli, Vinoy K. Ramachandran, Callum J. Verdonk, Phillip S. Poole, Graham W. O’Hara, Joshua P. Ramsay

PLOS Genetics: published March 22, 2018 | https://doi.org/10.1371/journal.pgen.1007292

The RNA-binding protein Celf1 post-transcriptionally regulates p27^Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development

Archana D. Siddam, Carole Gautier-Courteille, Linette Perez-Campos, Deepti Anand, Atul Kakrana, Christine A. Dang, Vincent Legagneux, Agnès Méreau, Justine Viet, Jeffrey M. Gross, Luc Paillard, Salil A. Lachke

PLOS Genetics: published March 22, 2018 | https://doi.org/10.1371/journal.pgen.1007278

MKLN1 splicing defect in dogs with lethal acrodermatitis

Anina Bauer, Vidhya Jagannathan, Sandra Högler, Barbara Richter, Neil A. McEwan, Anne Thomas, Edouard Cadieu, Catherine André, Marjo K. Hytönen, Hannes Lohi, Monika M. Welle, Petra Roosje, Cathryn Mellersh, Margret L. Casal, Tosso Leeb

PLOS Genetics: published March 22, 2018 | https://doi.org/10.1371/journal.pgen.1007264

FIN219/JAR1 and cryptochrome1 antagonize each other to modulate photomorphogenesis under blue light in Arabidopsis

Huai-Ju Chen, Tsu-Yu Fu, Shao-Li Yang, Hsu-Liang Hsieh

PLOS Genetics: published March 21, 2018 | https://doi.org/10.1371/journal.pgen.1007248

Impaired proteoglycan glycosylation, elevated TGF-β signaling, and abnormal osteoblast differentiation as the basis for bone fragility in a mouse model for gerodermia osteodysplastica

Wing Lee Chan, Magdalena Steiner, Tomasz Witkos, Johannes Egerer, Björn Busse, Shuji Mizumoto, Jan M. Pestka, Haikuo Zhang, Ingrid Hausser, Layal Abo Khayal, Claus-Eric Ott, Mateusz Kolanczyk, Bettina Willie, Thorsten Schinke, Chiara Paganini, Antonio Rossi, Kazuyuki Sugahara, Michael Amling, Petra Knaus, Danny Chan, Martin Lowe, Stefan Mundlos, Uwe Kornak

PLOS Genetics: published March 21, 2018 | https://doi.org/10.1371/journal.pgen.1007242

Cdk1 phosphorylation of Esp1/Separase functions with PP2A and Slk19 to regulate pericentric Cohesin and anaphase onset

Noel Lianga, Carole Doré, Erin K. Kennedy, Elaine Yeh, Elizabeth C. Williams, Camille Marie Fortinez, Alick Wang, Kerry S. Bloom, Adam D. Rudner

PLOS Genetics: published March 21, 2018 | https://doi.org/10.1371/journal.pgen.1007029

Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2‐keto‐4‐methylthiobutyric acid production

Axel de Zélicourt, Lukas Synek, Maged M. Saad, Hanin Alzubaidy, Rewaa Jalal, Yakun Xie, Cristina Andrés-Barrao, Eleonora Rolli, Florence Guerard, Kiruthiga G. Mariappan, Ihsanullah Daur, Jean Colcombet, Moussa Benhamed, Thomas Depaepe, Dominique Van Der Straeten, Heribert Hirt

PLOS Genetics: published March 19, 2018 | https://doi.org/10.1371/journal.pgen.1007273

POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana

Celine Tasset, Avilash Singh Yadav, Sridevi Sureshkumar, Rupali Singh, Lennard van der Woude, Maxim Nekrasov, David Tremethick, Martijn van Zanten, Sureshkumar Balasubramanian

PLOS Genetics: published March 16, 2018 | https://doi.org/10.1371/journal.pgen.1007280

Dek overexpression in murine epithelia increases overt esophageal squamous cell carcinoma incidence

Marie C. Matrka, Katherine A. Cimperman, Sarah R. Haas, Geraldine Guasch, Lisa A. Ehrman, Ronald R. Waclaw, Kakajan Komurov, Adam Lane, Kathryn A. Wikenheiser-Brokamp, Susanne I. Wells

PLOS Genetics: published March 14, 2018 | https://doi.org/10.1371/journal.pgen.1007227

Controlled branched-chain amino acids auxotrophy in Listeria monocytogenes allows isoleucine to serve as a host signal and virulence effector

Moran Brenner, Lior Lobel, Ilya Borovok, Nadejda Sigal, Anat A. Herskovits

PLOS Genetics: published March 12, 2018 | https://doi.org/10.1371/journal.pgen.1007283

Argonaute2 and LaminB modulate gene expression by controlling chromatin topology

Ezequiel Nazer, Ryan K. Dale, Madoka Chinen, Behram Radmanesh, Elissa P. Lei

PLOS Genetics: published March 12, 2018 | https://doi.org/10.1371/journal.pgen.1007276

Parallel roles of transcription factors dFOXO and FER2 in the development and maintenance of dopaminergic neurons

Damla Tas, Luca Stickley, Federico Miozzo, Rafael Koch, Nicolas Loncle, Virginie Sabado, Bettina Gnägi, Emi Nagoshi

PLOS Genetics: published March 12, 2018 | https://doi.org/10.1371/journal.pgen.1007271

The C-terminal of CASY-1/Calsyntenin regulates GABAergic synaptic transmission at the Caenorhabditis elegans neuromuscular junction

Shruti Thapliyal, Amruta Vasudevan, Yongming Dong, Jihong Bai, Sandhya P. Koushika, Kavita Babu

PLOS Genetics: published March 12, 2018 | https://doi.org/10.1371/journal.pgen.1007263

Zinc transporters belonging to the Cation Diffusion Facilitator (CDF) family have complementary roles in transporting zinc out of the cytosol

Sangyong Choi, Ya-Mei Hu, Mark E. Corkins, Amy E. Palmer, Amanda J. Bird

PLOS Genetics: published March 12, 2018 | https://doi.org/10.1371/journal.pgen.1007262

Large-scale profiling of noncoding RNA function in yeast

Steven Parker, Marcin G. Fraczek, Jian Wu, Sara Shamsah, Alkisti Manousaki, Kobchai Dungrattanalert, Rogerio Alves de Almeida, Edith Invernizzi, Tim Burgis, Walid Omara, Sam Griffiths-Jones, Daniela Delneri, Raymond T. O’Keefe

PLOS Genetics: published March 12, 2018 | https://doi.org/10.1371/journal.pgen.1007253

Müller glia-derived PRSS56 is required to sustain ocular axial growth and prevent refractive error

Seyyedhassan Paylakhi, Cassandre Labelle-Dumais, Nicholas G Tolman, Michael A. Sellarole, Yusef Seymens, Joseph Saunders, Hesham Lakosha, Wilhelmine N. deVries, Andrew C. Orr, Piotr Topilko, Simon WM. John, K. Saidas Nair

PLOS Genetics: published March 12, 2018 | https://doi.org/10.1371/journal.pgen.1007244

Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans

Megan M. Senchuk, Dylan J. Dues, Claire E. Schaar, Benjamin K. Johnson, Zachary B. Madaj, Megan J. Bowman, Mary E. Winn, Jeremy M. Van Raamsdonk

PLOS Genetics: published March 9, 2018 | https://doi.org/10.1371/journal.pgen.1007268

Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome

Anurag Kumar Sinha, Christophe Possoz, Adeline Durand, Jean-Michel Desfontaines, François-Xavier Barre, David R. F. Leach, Bénédicte Michel

PLOS Genetics: published March 9, 2018 | https://doi.org/10.1371/journal.pgen.1007256

Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4

Zhenfei Sun, Min Li, Ying Zhou, Tongtong Guo, Yin Liu, Hui Zhang, Yuda Fang

PLOS Genetics: published March 9, 2018 | https://doi.org/10.1371/journal.pgen.1007247

Morphogenetic defects underlie Superior Coloboma, a newly identified closure disorder of the dorsal eye

Jennifer C. Hocking, Jakub K. Famulski, Kevin H. Yoon, Sonya A. Widen, Cassidy S. Bernstein, Sophie Koch, Omri Weiss, FORGE Canada Consortium, Seema Agarwala, Adi Inbal, Ordan J. Lehmann, Andrew J. Waskiewicz

PLOS Genetics: published March 9, 2018 | https://doi.org/10.1371/journal.pgen.1007246

Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes

Christian Beck, Henning Knoop, Ralf Steuer

PLOS Genetics: published March 9, 2018 | https://doi.org/10.1371/journal.pgen.1007239

Exome-wide somatic mutation characterization of small bowel adenocarcinoma

Ulrika A. Hänninen, Riku Katainen, Tomas Tanskanen, Roosa-Maria Plaketti, Riku Laine, Jiri Hamberg, Ari Ristimäki, Eero Pukkala, Minna Taipale, Jukka-Pekka Mecklin, Linda M. Forsström, Esa Pitkänen, Kimmo Palin, Niko Välimäki, Netta Mäkinen, Lauri A. Aaltonen

PLOS Genetics: published March 9, 2018 | https://doi.org/10.1371/journal.pgen.1007200

RNA helicase, DDX27 regulates skeletal muscle growth and regeneration by modulation of translational processes

Alexis H. Bennett, Marie-Francoise O’Donohue, Stacey R. Gundry, Aye T. Chan, Jeffrey Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard I. Zon, Pierre-Emmanuel Gleizes, Alan H. Beggs, Vandana A. Gupta

PLOS Genetics: published March 8, 2018 | https://doi.org/10.1371/journal.pgen.1007226

Arabidopsis ICK/KRP cyclin-dependent kinase inhibitors function to ensure the formation of one megaspore mother cell and one functional megaspore per ovule

Ling Cao, Sheng Wang, Prakash Venglat, Lihua Zhao, Yan Cheng, Shengjian Ye, Yuan Qin, Raju Datla, Yongming Zhou, Hong Wang

PLOS Genetics: published March 7, 2018 | https://doi.org/10.1371/journal.pgen.1007230

BRDT is an essential epigenetic regulator for proper chromatin organization, silencing of sex chromosomes and crossover formation in male meiosis

Marcia Manterola, Taylor M. Brown, Min Young Oh, Corey Garyn, Bryan J. Gonzalez, Debra J. Wolgemuth

PLOS Genetics: published March 7, 2018 | https://doi.org/10.1371/journal.pgen.1007209

Formal Comments

Asgard archaea do not close the debate about the universal tree of life topology

Violette Da Cunha, Morgan Gaia, Arshan Nasir, Patrick Forterre

PLOS Genetics: published March 29, 2018 | https://doi.org/10.1371/journal.pgen.1007215

Asgard archaea are the closest prokaryotic relatives of eukaryotes

Anja Spang, Laura Eme, Jimmy H. Saw, Eva F. Caceres, Katarzyna Zaremba-Niedzwiedzka, Jonathan Lombard, Lionel Guy, Thijs J. G. Ettema

PLOS Genetics: published March 29, 2018 | https://doi.org/10.1371/journal.pgen.1007080

Cover

Arabidopsis seedling colonization by beneficial bacteria.

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