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Table of Contents DECEMBER 2012 • VOLUME 194 • NO. 24 TABLE OF CONTENTS EDITORIAL Acknowledgment of Ad Hoc Reviewers Thomas J. Silhavy 6701–6705 COMMENTARY Training the Biofilm Generation—a Tribute to J. W. Costerton Robert J. C. McLean, Joseph S. Lam, 6706–6711 and Lori L. Graham ARTICLES Gene Cluster Encoding Cholate Catabolism in Rhodococcus spp. William W. Mohn, Maarten H. 6712–6719 Wilbrink, Israël Casabon, Gordon R. Stewart, Jie Liu, Robert van der Geize, and Lindsay D. Eltis Two Transporters Essential for Reassimilation of Novel Cholate Kendra Swain, Israël Casabon, Lindsay 6720–6727 Metabolites by Rhodococcus jostii RHA1 D. Eltis, and William W. Mohn Intragenic Suppressor of a Plug Deletion Nonmotility Mutation Shiwei Zhu, Michio Homma, and Seiji 6728–6735 in PotB, a Chimeric Stator Protein of Sodium-Driven Flagella Kojima Roles of the Structural Symbiosis Polysaccharide (syp) Genes in Satoshi Shibata, Emily S. Yip, Kevin P. 6736–6747 Host Colonization, Biofilm Formation, and Polysaccharide Quirke, Jakob M. Ondrey, and Karen L. Biosynthesis in Vibrio fischeri Visick AhpC Is Required for Optimal Production of Enterobactin by Li Ma and Shelley M. Payne 6748–6757 Escherichia coli Reexamining Transcriptional Regulation of the Bacillus subtilis Ta-Hui Lin, Shih-Chien Huang, and 6758–6765 htpX Gene and the ykrK Gene, Encoding a Novel Type of Gwo-Chyuan Shaw Transcriptional Regulator, and Redefining the YkrK Operator New Substrates on the Block: Clinically Relevant Resistances for Iris Nasie, Sonia Steiner-Mordoch, and 6766–6770 EmrE and Homologues Shimon Schuldiner Biophysical and Bioinformatic Analyses Implicate the Chad A. Brautigam, Ranjit K. Deka, 6771–6781 Treponema pallidum Tp34 Lipoprotein (Tp0971) in Transition Zhiming Ouyang, Mischa Machius, Metal Homeostasis Gregory Knutsen, Diana R. Tomchick, and Michael V. Norgard Calcium Causes Multimerization of the Large Adhesin LapF and Marta Martínez-Gil, Diego Romero, 6782–6789 Modulates Biofilm Formation by Pseudomonas putida Roberto Kolter, and Manuel Espinosa-Urgel Conjugal Transfer of a Virulence Plasmid in the Opportunistic V. N. Tripathi, W. C. Harding, J. M. 6790–6801 Intracellular Actinomycete Rhodococcus equi Willingham-Lane, and M. K. Hondalus Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ella Rotman, Elena Kouzminova, Guy 6802–6817 Ability To Spread in the Laboratory Environment Plunkett III, and Andrei Kuzminov Genome Sequence of the Bacterium Streptomyces davawensis Frank Jankowitsch, Julia Schwarz, 6818–6827 JCM 4913 and Heterologous Production of the Unique Christian Rückert, Bertolt Gust, Rafael Antibiotic Roseoflavin Szczepanowski, Jochen Blom, Stefan Pelzer, Jörn Kalinowski, and Matthias Mack Continued on following page Continued from preceding page DECEMBER 2012 • VOLUME 194 • NUMBER 24 Aquaporin AqpZ Is Involved in Cell Volume Regulation and Masaro Akai, Kiyoshi Onai, Megumi 6828–6836 Sensitivity to Osmotic Stress in Synechocystis sp. Strain PCC Morishita, Hiroyuki Mino, Toshiaki 6803 Shijuku, Hisataka Maruyama, Fumihito Arai, Shigeru Itoh, Akihiro Hazama, Vanessa Checchetto, Ildikò Szabò, Yoshinori Yukutake, Makoto Suematsu, Masato Yasui, Masahiro Ishiura, and Nobuyuki Uozumi NdgR, a Common Transcriptional Activator for Methionine and Songhee H. Kim, Bo-Rahm Lee, Ji-Nu 6837–6846 Leucine Biosynthesis in Streptomyces coelicolor Kim, and Byung-Gee Kim Enzymatic Characterization of AMP Phosphorylase and Ribose- Riku Aono, Takaaki Sato, Ayumu Yano, 6847–6855 1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Shosuke Yoshida, Yuichi Nishitani, Metabolic Pathway Kunio Miki, Tadayuki Imanaka, and Haruyuki Atomi Metal Resistance and Lithoautotrophy in the Extreme Yukari Maezato, Tyler Johnson, Samuel 6856–6863 Thermoacidophile Metallosphaera sedula McCarthy, Karl Dana, and Paul Blum An Archaeal Histone Is Required for Transformation of Lubomira Cˇ ubonˇová, Masahiro 6864–6874 Thermococcus kodakarensis Katano, Tamotsu Kanai, Haruyuki Atomi, John N. Reeve, and Thomas J. Santangelo Gateway Role for rRNA Precursors in Ribosome Assembly Nancy S. Gutgsell and Chaitanya Jain 6875–6882 Transcriptional Regulation of the CmeABC Multidrug Efflux Sunyoung Hwang, Qijing Zhang, 6883–6891 Pump and the KatA Catalase by CosR in Campylobacter jejuni Sangryeol Ryu, and Byeonghwa Jeon ArcA and AppY Antagonize IscR Repression of Hydrogenase-1 A. D. Nesbit, A. S. Fleischhacker, S. J. 6892–6899 Expression under Anaerobic Conditions, Revealing a Novel Teter, and P. J. Kiley Mode of O2 Regulation of Gene Expression in Escherichia coli CspR, a Cold Shock RNA-Binding Protein Involved in the Long- Charlotte Michaux, Cecilia Martini, 6900–6908 Term Survival and the Virulence of Enterococcus faecalis Koki Shioya, Sandra Ahmed Lecheheb, Aurélie Budin-Verneuil, Pascal Cosette, Maurizio Sanguinetti, Axel Hartke, Nicolas Verneuil, and Jean-Christophe Giard AglS, a Novel Component of the Haloferax volcanii N- Chen Cohen-Rosenzweig, Sophie 6909–6916 Glycosylation Pathway, Is a Dolichol Phosphate-Mannose Yurist-Doutsch, and Jerry Eichler Mannosyltransferase Identification and Characterization of a Highly Conserved Yindi Chu, Zhenfeng Zhang, Qian 6917–6926 Crenarchaeal Protein Lysine Methyltransferase with Broad Wang, Yuanming Luo, and Li Huang Substrate Specificity GENOME ANNOUNCEMENTS Genome Sequences of Burkholderia sp. Strains CCGE1002 and Ernesto Ormeño-Orrillo, Marco A. 6927 H160, Isolated from Legume Nodules in Mexico and Brazil Rogel, Ligia Maria Oliveira Chueire, James M. Tiedje, Esperanza Martínez- Romero, and Mariangela Hungria Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Yue Yan, Chuan-Wu Zhao, Yi-Zheng 6928–6929 Strain 08XA1, a Fecal Bacterium of Giant Pandas Zhang, Zhi-He Zhang, Guang-Lin Pan, Wen-Wang Liu, Qing-Yi Ma, Rong Hou, and Xue-Mei Tan Full Genome Sequences of All Nine Chlamydia psittaci Sarah Van Lent, Jurgen R. Piet, 6930–6931 Genotype Reference Strains Delphine Beeckman, Arie van der Ende, Filip Van Nieuwerburgh, Patrik Bavoil, Garry Myers, Daisy Vanrompay, and Yvonne Pannekoek Continued on following page Continued from preceding page DECEMBER 2012 • VOLUME 194 • NUMBER 24 Complete Genome Sequence of Brucella melitensis 133, an Yuehua Ke, Qing Zhen, Tiefeng Li, 6932 Isolate of Biovar 1 of Sequence Type 32 Yufei Wang, Xitong Yuan, Jie Xu, Liuyu Huang, Dali Wang, Hongbin Song, and Zeliang Chen Genome Sequence and Comparative Genomics Analysis of a Abdulrazak Osama, Han Ming Gan, 6933 Vibrio cholerae O1 Strain Isolated from a Cholera Patient in Cindy Shuan Ju Teh, Kien-Pong Yap, Malaysia and Kwai-Lin Thong Draft Genome Sequence of the Biocontrol Bacterium Bacillus Sang-Yeob Lee, Byung-Yong Kim, Jae- 6934–6935 amyloliquefaciens Strain M27 Hyung Ahn, Jaekyeong Song, Young- Joo Seol, Wan-Gyu Kim, and Hang- Yeon Weon Genome Sequence of an Alkane-Degrading Bacterium, Qiliang Lai and Zongze Shao 6936 Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment Genome Sequence of Gallaecimonas xiamenensis Type Strain Qiliang Lai, Liping Wang, Wanpeng 6937 3-C-1 Wang, and Zongze Shao Genome Sequence of Idiomarina xiamenensis Type Strain Qiliang Lai, Liping Wang, Wanpeng 6938 10-D-4 Wang, and Zongze Shao Genome Sequence of Coxiella burnetii 109, a Doxycycline- Laetitia Rouli, Jean-Marc Rolain, Adil 6939 Resistant Clinical Isolate El Filali, Catherine Robert, and Didier Raoult Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, Soo-Je Park, Jong-Geol Kim, Man- 6940–6941 “Candidatus Nitrosopumilus koreensis” AR1, from Marine Young Jung, So-Jeong Kim, In-Tae Sediment Cha, KaeKyoung Kwon, Jung-Hyun Lee, and Sung-Keun Rhee Genome Sequence of Oceanibaculum indicum Type Strain P24 Qiliang Lai and Zongze Shao 6942 Complete Genome Sequence of Brucella abortus Strain BCB034, Zhijun Zhong, Lulu Wang, Yanfen 6943 a Strain of Biovar 2 Isolated from Human Chen, Zhoujia Wang, Yufei Wang, Mingquan Cui, Tiefeng Li, Yuehua Ke, Xitong Yuan, Dali Wang, Zeliang Chen, and Guangneng Peng Genome Sequence of “Candidatus Methanomethylophilus Guillaume Borrel, Hugh M. B. Harris, 6944–6945 alvus” Mx1201, a Methanogenic Archaeon from the Human Gut William Tottey, Agnès Mihajlovski, Belonging to a Seventh Order of Methanogens Nicolas Parisot, Eric Peyretaillade, Pierre Peyret, Simonetta Gribaldo, Paul W. O’Toole, and Jean-François Brugère Draft Genome Sequence of Staphylococcus aureus ST672, an Supriya Khedkar, Sushma Prabhakara, 6946–6947 Emerging Disease Clone from India Ramya Malarini Loganathan, Chandana S, Malali Gowda, Gayathri Arakere, and Aswin Sai Narain Seshasayee Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, Soo-Je Park, Jong-Geol Kim, Man- 6948–6949 “Candidatus Nitrosopumilus sediminis” AR2, from Svalbard in Young Jung, So-Jeong Kim, In-Tae the Arctic Circle Cha, Rohit Ghai, Ana-Belén Martín- Cuadrado, Francisco Rodríguez-Valera, and Sung-Keun Rhee Genome Sequence of Clostridium tunisiense TJ, Isolated from Lili Sun, Yu Wang, Chunyan Yu, 6950–6951 Drain Sediment from a Pesticide Factory Yongqin Zhao, and Yinbo Gan Genome Sequence of Strain IMCC14465, Isolated from the East Seung-Jo Yang, Ilnam Kang, and Jang- 6952–6953 Sea, Belonging to the PS1 Clade of Alphaproteobacteria Cheon Cho Genome Sequence of the Human-Pathogenic Bacterium Vibrio Zhaoyun Li, Huihong Chen, Xianjun 6954–6955 vulnificus Type Strain ATCC 27562 Chen, Tieli Zhou, Lei Zhao, Chunling Zhang, and Wenyang Jin Continued on following page Continued from preceding page DECEMBER 2012 • VOLUME 194 • NUMBER 24 Genome Sequence of Thalassospira profundimaris Type Strain Qiliang Lai and Zongze Shao 6956
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