AUGUST 2012 • VOLUME 194 • NO. 15

TABLE OF CONTENTS

MINIREVIEW Expanded Roles for Multicargo and Class 1B Effector Nikhil A. Thomas, Irene Ma, 3767–3773 Chaperones in Type III Secretion Madhulika E. Prasad, and Cheryl Rafuse ARTICLES Development of Competence for Genetic Transformation of Kunal Desai, Lauren Mashburn- 3774–3780 Streptococcus mutans in a Chemically Defined Medium Warren, Michael J. Federle, and Donald A. Morrison Extracellular Identification of a Processed Type II ComR/ComS Rabia Khan, Håkon V. Rukke, Antonio 3781–3788 Pheromone of Streptococcus mutans Pedro Ricomini Filho, Gunnar Fimland, Magnus Ø. Arntzen, Bernd Thiede, and Fernanda C. Petersen Ligand-Binding Properties and Conformational Dynamics of Sebastian Zoll, Martin Schlag, 3789–3802 Autolysin Repeat Domains in Staphylococcal Cell Wall Alexander V. Shkumatov, Maren Recognition Rautenberg, Dmitri I. Svergun, Friedrich Götz, and Thilo Stehle FdhTU-Modulated Formate Dehydrogenase Expression and Mark Pryjma, Dmitry Apel, Steven 3803–3813 Electron Donor Availability Enhance Recovery of Huynh, Craig T. Parker, and Erin C. following Host Cell Infection Gaynor Selenium-Dependent Biogenesis of Formate Dehydrogenase in Frances L. Shaw, Francis Mulholland, 3814–3823 Campylobacter jejuni Is Controlled by the fdhTU Accessory Gwénaëlle Le Gall, Ida Porcelli, Dave J. Genes Hart, Bruce M. Pearson, and Arnoud H. M. van Vliet CcpA-Dependent Carbohydrate Catabolite Repression Jun Cai, Huichun Tong, Fengxia Qi, 3824–3832 Regulates Galactose Metabolism in Streptococcus and Xiuzhu Dong oligofermentans Surface-Layer (S-Layer) Proteins Sap and EA1 Govern the Valerie J. Kern, Justin W. Kern, Julie A. 3833–3840 Binding of the S-Layer-Associated Protein BslO at the Cell Septa Theriot, Olaf Schneewind, and of Bacillus anthracis Dominique Missiakas Secretion Genes as Determinants of Bacillus anthracis Chain Sao-Mai Nguyen-Mau, So-Young Oh, 3841–3850 Length Valerie J. Kern, Dominique M. Missiakas, and Olaf Schneewind Degradation of 2,3-Dihydroxybenzoate by a Novel meta- Macarena Marín, Iris Plumeier, and 3851–3860 Cleavage Pathway Dietmar H. Pieper Identification of a Third Osmoprotectant Transport System, the Stephen M. Frossard, Aftab A. Khan, 3861–3871 OsmU System, in Eric C. Warrick, Jonathan M. Gately, Andrew D. Hanson, Michael L. Oldham, David Avram Sanders, and Laszlo N. Csonka Delineation of the Caffeine C-8 Oxidation Pathway in Sujit Kumar Mohanty, Chi-Li Yu, 3872–3882 Pseudomonas sp. Strain CBB1 via Characterization of a New Shuvendu Das, Tai Man Louie, Lokesh Trimethyluric Acid Monooxygenase and Genes Involved in Gakhar, and Mani Subramanian Trimethyluric Acid Metabolism Novel Role for RNase PH in the Degradation of Structured RNA Chaitanya Jain 3883–3890 DprB Facilitates Inter- and Intragenomic Recombination in Xue-Song Zhang and Martin J. Blaser 3891–3903

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Pseudomonas aeruginosa Thiol Peroxidase Protects against Nawarat Somprasong, Thichakorn 3904–3912 Hydrogen Peroxide Toxicity and Displays Atypical Patterns of Jittawuttipoka, Jintana Duang-nkern, Gene Regulation Adisak Romsang, Pimchai Chaiyen, Herbert P. Schweizer, Paiboon Vattanaviboon, and Skorn Mongkolsuk Two Surfaces of a Conserved Interdomain Linker Differentially Tatiana A. Gaidenko, Xiaomei Bie, 3913–3921 Affect Output from the RST Sensing Module of the Bacillus Enoch P. Baldwin, and Chester W. subtilis Stressosome Price Comparative Genomic Analyses of 17 Clinical Isolates of Azad Ahmed, Josh Earl, Adam 3922–3937 Gardnerella vaginalis Provide Evidence of Multiple Genetically Retchless, Sharon L. Hillier, Lorna K. Isolated Clades Consistent with Subspeciation into Genovars Rabe, Thomas L. Cherpes, Evan Powell, Benjamin Janto, Rory Eutsey, N. Luisa Hiller, Robert Boissy, Margaret E. Dahlgren, Barry G. Hall, J. William Costerton, J. Christopher Post, Fen Z. Hu, and Garth D. Ehrlich Functional Analyses of Mycobacterial Lipoprotein Andreas Tschumi, Thomas Grau, Dirk 3938–3949 Diacylglyceryl Transferase and Comparative Secretome Analysis Albrecht, Mandana Rezwan, Haike of a Mycobacterial lgt Mutant Antelmann, and Peter Sander Identification of Ata, a Multifunctional Trimeric Leticia V. Bentancor, Ana Camacho- 3950–3960 Autotransporter of Peiro, Cagla Bozkurt-Guzel, Gerald B. Pier, and Tomás Maira-Litrán Growth Phase-Dependent Modulation of Rgg Binding Srivishnupriya Anbalagan, Alexander 3961–3971 Specificity in Streptococcus pyogenes Dmitriev, W. Michael McShan, Paul M. Dunman, and Michael S. Chaussee FeoB2 Functions in Magnetosome Formation and Oxidative Chengbo Rong, Chan Zhang, Yiting 3972–3976 Stress Protection in Magnetospirillum gryphiswaldense Strain Zhang, Lei Qi, Jing Yang, Guohua MSR-1 Guan, Ying Li, and Jilun Li Cellular Characterization of the Primosome and Rep Helicase in Charmain T. Courcelle, Allison J. 3977–3986 Processing and Restoration of Replication following Arrest by Landstrom, Brittany Anderson, and UV-Induced DNA Damage in Justin Courcelle

Novel L-Cysteine-Dependent Maleylpyruvate Isomerase in the Ting-Ting Liu and Ning-Yi Zhou 3987–3994 Gentisate Pathway of Paenibacillus sp. Strain NyZ101 Characterization of a Vibrio fischeri Aminopeptidase and Pat M. Fidopiastis, Bethany A. Rader, 3995–4002 Evidence for Its Influence on an Early Stage of Squid David G. Gerling, Nestor A. Gutierrez, Colonization Katherine H. Watkins, Michelle West Frey, Spencer V. Nyholm, and Cheryl A. Whistler MS_RHII-RSD, a Dual-Function RNase HII-(p)ppGpp Maya S. Murdeshwar and Dipankar 4003–4014 Synthetase from Mycobacterium smegmatis Chatterji Caldicellulosiruptor Core and Pangenomes Reveal Determinants Sara E. Blumer-Schuette, Richard J. 4015–4028 for Noncellulosomal Thermophilic Deconstruction of Plant Giannone, Jeffrey V. Zurawski, Inci Biomass Ozdemir, Qin Ma, Yanbin Yin, Ying Xu, Irina Kataeva, Farris L. Poole II, Michael W. W. Adams, Scott D. Hamilton-Brehm, James G. Elkins, Frank W. Larimer, Miriam L. Land, Loren J. Hauser, Robert W. Cottingham, Robert L. Hettich, and Robert M. Kelly Sinorhizobium meliloti ExoR Is the Target of Periplasmic Hai-Yang Lu, Li Luo, Meng-Hua Yang, 4029–4040 Proteolysis and Hai-Ping Cheng Enterococcus faecalis PrgJ, a VirB4-Like ATPase, Mediates Feng Li, Cristina Alvarez-Martinez, 4041–4051 pCF10 Conjugative Transfer through Substrate Binding Yuqing Chen, Kyoung-Jae Choi, Hye- Jeong Yeo, and Peter J. Christie

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The bhuQ Gene Encodes a Heme Oxygenase That Contributes to Jenifer F. Ojeda, David A. Martinson, 4052–4058 the Ability of 2308 To Use Heme as an Iron Evan A. Menscher, and R. Martin Roop Source and Is Regulated by Irr II Bacterium-Generated Nitric Oxide Hijacks Host Tumor Brian Mocca and Wei Wang 4059–4068 Necrosis Factor Alpha Signaling and Modulates the Host Cell Cycle In Vitro cis-Acting Elements That Control Expression of the Master Jennifer L. Dale, Malik J. Raynor, 4069–4079 Virulence Regulatory Gene atxA in Bacillus anthracis Prabhat Dwivedi, and Theresa M. Koehler Pathway and Enzyme Redundancy in Putrescine Catabolism in Barbara L. Schneider and Larry Reitzer 4080–4088 Escherichia coli OmpA Is the Principal Nonspecific Slow Porin of Acinetobacter Etsuko Sugawara and Hiroshi Nikaido 4089–4096 baumannii Genome Sequencing of a Genetically Tractable Pyrococcus Stephanie L. Bridger, W. Andrew 4097–4106 furiosus Strain Reveals a Highly Dynamic Genome Lancaster, Farris L. Poole II, Gerrit J. Schut, and Michael W. W. Adams

Characterization of the PIB-Type ATPases Present in Thermus Lici A. Schurig-Briccio and Robert B. 4107–4113 thermophilus Gennis GENOME ANNOUNCEMENTS Genome Sequence of a Novel Human Pathogen, Aeromonas Chi-Jung Wu, Hsuan-Chen Wang, 4114–4115 aquariorum Chang-Shi Chen, Hung-Yu Shu, Ai- Wen Kao, Po-Lin Chen, and Wen- Chien Ko Complete Genome Sequence of Bacillus anthracis H9401, an Jeong-Hoon Chun, Kee-Jong Hong, 4116–4117 Isolate from a Korean Patient with Anthrax Sun Ho Cha, Min-Hee Cho, Kwang Jun Lee, Duck Hee Jeong, Cheon-Kwon Yoo, and Gi-eun Rhie Complete Genome Sequence of Geobacillus thermoglucosidans Yu Zhao, Martien P. Caspers, Tjakko 4118 TNO-09.020, a Thermophilic Sporeformer Associated with a Abee, Roland J. Siezen, and Remco Dairy-Processing Environment Kort Draft Genome Sequence of the Antagonistic Rhizosphere P. Garbeva, J. D. van Elsas, and W. de 4119–4120 Bacterium Serratia plymuthica Strain PRI-2C Boer Draft Genome Sequence of High-Siderophore-Yielding Jingwei Gao, Xinyan Yu, and Zhixiong 4121 Pseudomonas sp. Strain HYS Xie Complete Genome Sequence of Leptospirillum ferrooxidans Reiko Fujimura, Yoshinori Sato, 4122–4123 Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Tomoyasu Nishizawa, Kenshiro Island of Miyake, Japan Oshima, Seok-Won Kim, Masahira Hattori, Takashi Kamijo, and Hiroyuki Ohta Whole-Genome Sequence of Staphylococcus aureus Strain Junfeng Wang, Yanhong Liu, Daiwei 4124 LCT-SA112 Wan, Xiangqun Fang, Tianzhi Li, Yinghua Guo, De Chang, Longxiang Su, Yajuan Wang, Jiao Zhao, and Changting Liu Genome Sequence of Mycobacterium massiliense M18, Isolated Yun Fong Ngeow, Yan Ling Wong, 4125 from a Lymph Node Biopsy Specimen Joon Liang Tan, Ramitha Arumugam, Guat Jah Wong, Chia Sui Ong, Kee Peng Ng, and Siew Woh Choo Complete Genome Sequences of Methylophaga sp. Strain JAM1 Céline Villeneuve, Christine Martineau, 4126–4127 and Methylophaga sp. Strain JAM7 Florian Mauffrey, and Richard Villemur

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Draft Genome Sequence of the Sulfur-Oxidizing Bacterium Soo-Je Park, Rohit Ghai, Ana-Belén 4128–4129 “Candidatus Sulfurovum sediminum” AR, Which Belongs to the Martín-Cuadrado, Francisco Rodríguez-Valera, Man-Young Jung, Jong-Geol Kim, and Sung-Keun Rhee Draft Genome Sequence of Treponema sp. Strain JC4, a Novel Carly P. Rosewarne, Jane L. Cheung, 4130 Spirochete Isolated from the Bovine Rumen Wendy J. M. Smith, Paul N. Evans, Nigel W. Tomkins, Stuart E. Denman, Páraic Ó Cuív, and Mark Morrison Complete Genome Sequences of Probiotic Strains Buffy Stahl and Rodolphe Barrangou 4131–4132 Bifidobacterium animalis subsp. lactis B420 and Bi-07 Genome Sequences of Two Thermophilic Bacillus licheniformis Lixiang Li, Fei Su, Yu Wang, Lijie 4133–4134 Strains, Efficient Producers of Platform Chemical Zhang, Cuicui Liu, Jingwen Li, Cuiqing 2,3-Butanediol Ma, and Ping Xu Genome Sequence of Micromonospora lupini Lupac 08, Isolated Pablo Alonso-Vega, Philippe Normand, 4135 from Root Nodules of Lupinus angustifolius Rodrigo Bacigalupe, Petar Pujic, Aurelie Lajus, David Vallenet, Lorena Carro, Pedro Coll, and Martha E. Trujillo Draft Genome Sequence of Herbaspirillum lusitanum P6-12, an Vinícius Almir Weiss, Helisson Faoro, 4136–4137 Endophyte Isolated from Root Nodules of Phaseolus vulgaris Michelle Zibbetti Tadra-Sfeir, Roberto Tadeu Raittz, Emanuel Maltempi de Souza, Rose Adele Monteiro, Rodrigo Luis Alves Cardoso, Roseli Wassem, Leda Satie Chubatsu, Luciano Fernandes Huergo, Marcelo Müller- Santos, Maria Berenice Reynaud Steffens, Liu Un Rigo, Fábio de Oliveira Pedrosa, and Leonardo Magalhães Cruz Genome Annotation of Five Mycoplasma canis Strains D. R. Brown, M. May, D. L. Michaels, 4138–4139 and A. F. Barbet Draft Genome Sequence of Arctic Marine Bacterium Ha Ju Park, Seung Chul Shin, and 4140 Pseudoalteromonas issachenkonii PAMC 22718 Dockyu Kim Complete Genome Sequence of Mycobacterium intracellulare Byoung-Jun Kim, Beom-Soon Choi, 4141–4142 Clinical Strain MOTT-36Y, Belonging to the INT5 Genotype Ik-Young Choi, Je-Hee Lee, Jongsik Chun, Seok-Hyun Hong, Yoon-Hoh Kook, and Bum-Joon Kim Genome Sequence of Aerococcus viridans LL1 Nan Qin, Beiwen Zheng, Fengling 4143 Yang, Yanfei Chen, Jing Guo, Xinjun Hu, and Lanjuan Li Draft Genome Sequence of Streptomyces globisporus C-1027, Lifei Wang, Songmei Wang, Qing He, 4144 Which Produces an Antitumor Antibiotic Consisting of a Nine- Tengfei Yu, Qinglian Li, and Bin Hong Membered Enediyne with a Chromoprotein

Genomic Comparison of honei Strain RBT and Other Dong Xin, Khalid El Karkouri, 4145 Rickettsia Species Catherine Robert, Didier Raoult, and Pierre-Edouard Fournier Genome of Helicobacter pylori Strain XZ274, an Isolate from a Ying Guo, Haiying Wang, Yan Li, Yang 4146–4147 Tibetan Patient with Gastric Cancer in China Song, Chen Chen, Yaling Liao, Li Ren, Chunliang Guo, Wende Tong, Wei Shen, Ming Chen, Xuhu Mao, Gang Guo, and Quanming Zou

Draft Genome Sequence of the Plant Growth-Promoting Haeyoung Jeong, Da-Eun Jeong, Sun 4148–4149 Bacterium Bacillus siamensis KCTC 13613T Hong Kim, Geun Cheol Song, Soo- Young Park, Choong-Min Ryu, Seung- Hwan Park, and Soo-Keun Choi

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Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Gun Woong Lee, Kui-Jae Lee, and 4150 Growth-Promoting Bacterium Jong-Chan Chae

Cover photograph (Copyright © 2012, American Society for Microbiology. All Rights Reserved.): Spontaneous streptomycin-resistant mu- tants of Streptomyces coelicolor growing at the edge of the areas of streptomycin-induced growth inhibition on a lawn of the . (Image by Roberto Kolter.)