Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 2 Volume Set

Angélica Bravo Núñez, P.J. Minnick, Diana Vera Cruz, Jun Xia, P.J. Hastings, and Susan M. Rosenberg2.15 Sigma factor competition in Escherichia coli: kinetic and thermodynamic perspectives, 196Kuldeepkumar Ramnaresh Gupta and Dipankar Chatterji2.16 Iron homeostasis and iron-sulfur cluster assembly in Escherichia coli, 203Huangen Ding2.17 Mechanisms underlying the antimicrobial capacity of metals, 215Joe A. Lemire and Raymond J. Turner2.18 Acyl-homoserine lactone-based quorum sensing in members of the marine bacterial Roseobacter clade: complex cell-to-cell communication controls multiple physiologies, 225Alison Buchan, April Mitchell,W. Nathan Cude, and Shawn Campagna2.19 Native and synthetic gene regulation to nitrogen limitation stress, 234J örg SchumacherSection 3: One-, two-, and three-component regulatory systems and stress responses, 2473.1 Two-component systems that control the expression of aromatic hydrocarbon degradation pathways, 249\Tino Krell3.2 Cross-talk of global regulators in Streptomyces, 257Juan F. Martín, Fernando Santos-Beneit, Alberto Sola-Landa, and Paloma Liras3.3 NO-H-NOX-regulated two-component signaling, 268Dhruv P. Arora, Sandhya Muralidharan, and Elizabeth M. Boon3.4 The two-component CheY system in the chemotaxis of Sinorhizobium meliloti, 277Martin Haslbeck3.5 Stimulus perception by histidine kinases, 282Hannah Schramke, Yang Wang, Ralf Heermann, and Kirsten JungSection 4: Sigma factors and stress responses, 3014.1 The extracytoplasmic function sigma factor EcfO protects Bacteroides fragilis against oxidative stress, 303Ivan C. Ndamukong, Samantha Palethorpe, Michael Betteken, and C. Jeffrey Smith4.2 Regulation of energy metabolism by the extracytoplasmic function (ECF) sigma factors of Arcobacter butzleri, 311Irati Martinez-Malaxetxebarria, Rudy Muts, Linda van Dijk, Craig T. Parker, William G. Miller, Steven Huynh,Wim Gaastra, Jos P.M. van Putten, Aurora Fernandez-Astorga, and Marc M.S.M Wösten4.3 Extracytoplasmic function sigma factors and stress responses in Corynebacterium pseudotuberculosis, 321Thiago L.P. Castro, Nubia Seyffert, Anne C. Pinto, Artur Silva, Vasco Azevedo, and Luis G.C. Pacheco4.4 The complex roles and regulation of stress response sigma factors in Streptomyces coelicolor, 328Jan Kormanec, Beatrica Sevcikova, Renata Novakova, Dagmar Homerova, Bronislava Rezuchova, and Erik Mingyar4.5 Proteolytic activation of extra cytoplasmic function (ECF) sigma factors, 344JessicaL. Hastie and Craig D. Ellermeier4.6 The ECF family sigma factor sigmaH in Corynebacterium glutamicum controls the thiol-oxidative stress response, 352Tobias Busche and Jörn Kalinowski4.7 Posttranslational regulation of antisigma factors of RpoE: a comparison between the Escherichia coli and Pseudomonas aeruginosa systems, 361Sundar Pandey, Kyle L. Martins, and Kalai MatheeSection 5: Small noncoding RNAs and stress responses, 3695.1 Bacterial small RNAs in mixed regulatory circuits, 371Jonathan Jagodnik, DenisThieffry, and Maude Guillier5.2 Role of small RNAs in Pseudomonas aeruginosa virulence and adaptation, 383Hansi Kumari, Deepak Balasubramanian, and Kalai Mathee5.3 Physiological effects of posttranscriptional regulation by the small RNA SgrS during metabolic stress inEscherichia coli, 393Gregory R. Richards5.4 Three rpoS-activating small RNAs in pathways contributing to acid resistance of Escherichia coli, 402Geunu Bak, Kook Han, Daun Kim, Kwang-sun Kim, and Younghoon Lee5.5 Thermal stress noncoding RNAs in prokaryotes and eukaryotes: a comparative approach, 412Mercedes de la Fuente and José Luis Martínez-GuitarteSection 6: Toxin-antitoxin systems and stress responses, 4236.1 Epigenetics mediated by restriction modification systems, 425Iwona Mruk and Ichizo Kobayashi6.2 Toxin-antitoxin systems as regulators of bacterial fitness and virulence, 437Brittany A. Fleming and Matthew A. Mulvey6.3 Mechanisms of stress-activated persister formation in Escherichia coli, 446Stephanie M. Amato and Mark P. Brynildsen6.4 Identification and characterization of type II toxin-antitoxin systems in the opportunistic pathogenAcinetobacter baumannii, 454Edita Sûziedéliené, Milda Jurénaité, and Julija Armalyté6.5 Transcriptional control of toxin-antitoxin expression: keeping toxins under wraps until the time is right, 463Barbara Kedzierska and Finbarr Hayes6.6 Opposite effects of GraT toxin on stress tolerance of Pseudomonas putida, 473Rita Hõrak and Hedvig TammanSection 7: Stringent response to stress, 4797.1 Preferential cellular accumulation of ppGpp or pppGpp in Escherichia coli, 481K. Potrykus and M. Cashel7.2 Global Rsh-dependent transcription profile of Brucella suis during stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses, 489Stephan Köhler, Nabil Hanna, Safia Ouahrani-Bettache, Kenneth L. Drake, L. Garry Adams, and Alessandra Occhialini7.3 The stringent response and antioxidant defences in Pseudomonas aeruginosa, 500Gowthami Sampathkumar, Malika Khakimova, Tevy Chan, and Dao Nguyen7.4 Molecular basis of the stringent response in Vibrio cholerae, 507Shreya Dasgupta, Bhabatosh Das, Pallabi Basu, and Rupak K. BhadraSection 8: Responses to UV irradiation, 5178.1 UV stress-responsive genes associated with ICE SXT/R391 group, 519Patricia Armshaw and J. Tony Pembroke8.2 Altered outer membrane proteins in response to UVC radiation in Vibrio parahaemolyticus and Vibrio alginolyticus, 528Fethi Ben Abdallah8.3 Ultraviolet-B radiation effects on the community, physiology, and mineralization of magnetotactic bacteria, 532Yingzhao Wang and Yongxin Pan8.4 Nucleotide excision repair system and gene expression in Mycobacterium smegmatis, 545Angelina CordoneSection 9: SOS and double stranded repair systems and stress, 5519.1 The SOS response modulates bacterial pathogenesis, 553Darja ¢§Zgur Bertok9.2 RNAP secondary-channel interactors in Escherichia coli: makers and breakers of genome stability, 561Priya Sivaramakrishnan and Christophe Herman9.3 How a large gene network couples mutagenic DNA break repair to stress in Escherichia coli, 570Elizabeth Rogers, P.J. Hastings, María Angélica Bravo Núñez, and Susan M. Rosenberg9.4 Double-strand DNA break repair in mycobacteria, 577Richa Gupta and Michael S. GlickmanSection 10: Adaptation to oxidative stress, 58710.1 Peroxide-sensing transcriptional regulators in bacteria, 58James M. Dubbs and Skorn Mongkolsuk10.2 Regulation of oxidative stress-related genes implicated in the establishment of opportunistic infections by Bacteroides fragilis, 603Felipe Lopes Teixeira, Regina Maria Cavalcanti Pilotto Domingues, and Leandro Araujo Lobo10.3 Investigation into oxidative stress response of Shewanella oneidensis reveals a distinct mechanism, 609Jie Yuan, Fen Wan, and Haichun Gao10.4 An omics view on the response to singlet oxygen, 619Bork A. Berghoff and Gabriele Klug10.5 Regulators of oxidative stress response genes in Escherichia coli and their conservation in bacteria, 632Herb E. Schellhorn, Mohammad Mohiuddin, Sarah M. Hammond, and Steven Botts10.6 Hydrogen peroxide resistance in Bifidobacterium animalis subsp. lactis and Bifidobacterium longum, 638Taylor S. Oberg and Jeff R. BroadbentSection 11: Adaptation to osmotic stress, 64711.1 Interstrain variation in the physiological and transcriptional responses of Pseudomonas syringae to osmotic stress, 649Gwyn A. Beattie, Chiliang Chen, Lindsey Nielsen, and Brian C. Freeman11.2 Management of osmotic stress by Bacillus subtilis: genetics and physiology, 657Tamara Hoffmann and Erhard Bremer11.3 Hyperosmotic response of Streptococcus mutans: from microscopic physiology to transcriptomic profile, 677Lu Wang and Xin Xu11.4 Defective ribosome maturation or function makes Escherichia coli cells salt-resistant, 687Hyouta Himeno, Takefusa Tarusawa, Shion Ito, and Simon GotoSection 12: Dessication tolerance and drought stress, 69312.1 Consequences of elevated salt concentrations on expression profiles in the rhizobium S. meliloti 1021 likely involved in heat and desiccation stress, 695Jan A.C. Vriezen, Caroline M. Finn, and Klaus Nüsslein12.2 Genes involved in the formation of desiccationresistant cysts in Azotobacter vinelandii, 709Guadalupe Espín12.3 Osmotic and desiccation tolerance in Escherichia coli O157:H7 and Salmonella enterica requires rpoS (sigma38), 716Zach Pratt, Megan Shiroda, Andrew J. Stasic, Josh Lensmire, and C.W. Kaspar12.4 Desiccation of Salmonella enterica induces cross-tolerance to other stresses, 725Shlomo Sela (Saldinger) and Chellaiah Edward RajaIndex, i1VOLUME 2Preface, xiiiAcknowledgements, xivList of contributors, xvSection 13: Heat shock responses, 73713.1 Heat shock response in bacteria with large genomes: lessons from rhizobia, 739Ana Alexandre and Solange Oliveira13.2 Small heat shock proteins in bacteria, 747Martin Haslbeck13.3 Transcriptome analysis of bacterial response to heat shock using next-generation sequencing, 754Kok-Gan Chan13.4 Comparative analyses of bacterial transcriptome reorganisation in response to temperature increase, 757Bei-Wen Ying and Tetsuya Yomo13.5 Participation of Ser-Thr protein kinases in regulation of heat stress responses in Synechocystis, 766Anna A. Zorina, Galina V. Novikova, and Dmitry A. LosSection 14: Chaperonins and stress, 78114.1 GroEL/ES chaperonin: unfolding and refolding reactions, 783Victor V. Marchenkov, Nataliya A. Ryabova, Olga M. Selivanova, and Gennady V. Semisotnov14.2 Functional comparison between the DnaK chaperone systems of Streptococcus intermedius and Escherichia coli, 791Toshifumi Tomoyasu and Hideaki Nagamune14.3 Coevolution analysis illuminates the evolutionary plasticity of the chaperonin system GroES/L, 796Mario A. Fares14.4 ClpL ATPase: a novel chaperone in bacterial stress responses, 812Pratick Khara and Indranil Biswas14.5 Duplicated groEL genes inMyxococcus xanthus DK1622, 820Yan Wang, Xiao-jing Chen, and Yue-zhong LiSection 15: Cold shock responses, 82715.1 Gene regulation by cold shock proteins via transcription antitermination, 829Sangita Phadtare and Konstantin Severinov15.2 Metagenomic analysis of microbial cold stress proteins in polar lacustrine ecosystems, 837Hyunmin Koo, Joseph A. Hakim, and Asim K. Bej15.3 Role of two-component systems in cold tolerance of Clostridium botulinum, 845Yâgmur Derman, Elias Dahlsten, and Hannu Korkeala15.4 Cold shock CspA protein production during periodic temperature cycling in Escherichia coli, 854David Stopar and Tina Ivancic15.5 Cold shock response in Escherichia coli: a model system to study posttranscriptional regulation, 859Anna Maria Giuliodori15.6 New insight into cold shock proteins: RNA-binding proteins involved in stress response and virulence, 873Charlotte Michaux and Jean-Christophe Giard15.7 Light regulation of cold stress responses in Synechocystis, 881Kirill S. Mironov and Dmitry A. Los15.8 Escherichia coli cold shock gene profiles in response to overexpression or deletion of CsdA, RNase R, andPNPase and relevance to low-temperature RNA metabolism, 890Sangita PhadtareSection 16: Adaptation to acid stress, 89716.1 Acid-adaptive responses of Streptococcus mutans, and mechanisms of integration with oxidative stress, 899Robert G. Quivey Jr., Roberta C. Faustoferri, Brendaliz Santiago, Jonathon Baker, Benjamin Cross, and Jin Xiao16.2 Acid survival mechanisms in neutralophilic bacteria, 911Eugenia Pennacchietti, Fabio Giovannercole, and Daniela De Biase16.3 Two-component systems in sensing and adapting to acid stress in Escherichia coli, 927Yoko Eguchi and Ryutaro Utsumi16.4 Slr1909, a novel two-component response regulator involved in acid tolerance in Synechocystis sp. PCC 6803, 935Lei Chen, Qiang Ren, Jiangxin Wang, and Weiwen Zhang16.5 Comparative mass spectrometry-based proteomics to elucidate the acid stress response in Lactobacillusplantarum, 944Tiaan Heunis, Shelly Deane, and Leon M.T. DicksSection 17: Adaptation to nitrosative stress, 95317.1 Transcriptional regulation by thiol-based sensors of oxidative and nitrosative stress, 955Timothy Tapscott, Matthew A. Crawford, and Andr¿es Vázquez-Torres17.2 Haemoglobins of Mycobacterium tuberculosis and their involvement in management of environmental stress, 967Kanak L. Dikshit17.3 What is it about NO that you don't understand? The role of heme and HcpR in Porphyromonas gingivalis's response to nitrate (NO3), nitrite (NO2), and nitric oxide (NO), 976Janina P. Lewis and Benjamin R. Belvin17.4 Di-iron RICs: players in nitrosative-oxidative stress defences, 989Lígia S. Nobre and Lí(c)¥gia M. Saraiva17.5 The Vibrio cholerae stress response: an elaborate system geared toward overcoming host defenses during infection, 997Karl-Gustav Rueggeberg and Jun Zhu17.6 Ensemble modeling enables quantitative exploration of bacterial nitric oxide stress networks, 1009Jonathan L. Robinson and Mark P. BrynildsenSection 18: Adaptation to cell envelope stress, 101518.1 The Cpx inner membrane stress response, 1017Randi L. Guest and Tracy L. Raivio18.2 New insights into stimulus detection and signal propagation by the Cpx-envelope stress system, 1025Patrick Hoernschemeyer and Sabine Hunke18.3 Promiscuous functions of cell envelope stress-sensing systems in Klebsiella pneumoniae and Acinetobacterbaumannii, 1031Vijaya Bharathi Srinivasan and Govindan Rajamohan18.4 Influence of BrpA and Psr on cell envelope homeostasis and virulence of Streptococcus mutans, 1043Zezhang T.Wen, Jacob P. Bitoun, Sumei Liao, and Jacqueline Abranches18.5 Modulators of the bacterial two-component systems involved in envelope stress, transport, and virulence, 1055Rajeev MisraSection 19: Iron homeostasis, 106519.1 Iron homeostasis and environmental responses in cyanobacteria: regulatory networks involving Fur, 1067María Luisa Peleato, María Teresa Bes, and María F. Fillat19.2 Interplay between O2 and iron in gene expression: environmental sensing by FNR, ArcA, and Fur in bacteria, 1079Bryan Troxell and Hosni M. Hassan19.3 The iron-sulfur cluster biosynthesis regulator IscR contributes to iron homeostasis and resistance tooxidants in Pseudomonas aeruginosa, 1090Adisak Romsang, James M. Dubbs, and Skorn Mongkolsuk19.4 Transcriptional analysis of iron-responsive regulatory networks in Caulobacter crescentus, 1103José F. da Silva Neto19.5 Protein-protein interactions regulate the release of iron stored in bacterioferritin, 1109Huili Yao, YanWang, and Mario Rivera19.6 Protein dynamics and ion traffic in bacterioferritin function: a molecular dynamics simulation study onwild-type and mutant Pseudomonas aeruginosa BfrB, 1118Huan Rui, Mario Rivera, and Wonpil ImSection 20: Metal resistance, 113120.1 Nickel toxicity, regulation, and resistance in bacteria, 1133Lee Macomber and Robert P. Hausinger20.2 Metabolic networks to counter Al toxicity in Pseudomonas fluorescens: a holistic view, 1145Christopher Auger, Nishma D. Appanna, and Vasu D. Appanna20.3 Genomics of the resistance to metal and oxidative stresses in cyanobacteria, 1154Corinne Cassier-Chauvat and Franck Chauvat20.4 Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria, 1165Jiangxin Wang, Gang Wu, Lei Chen, and Weiwen Zhang20.5 The extracytoplasmic function sigma factor-mediated response to heavy metal stress in Caulobacter crescentus, 1171Rogério F. Lourenco and Suely L. Gomes20.6 Metal ion toxicity and oxidative stress in Streptococcus pneumoniae, 1184Christopher A. McDevitt, Stephanie L. Begg, and James C. PatonSection 21: Quorum sensing, 119521.1 Quorum sensing and bacterial social interactions in biofilms: bacterial cooperation and competition, 1197Yung-Hua Li and Xiao-Lin Tian21.2 Recent advances in bacterial quorum quenching, 1206Kok-Gan Chan, Wai-Fong Yin, and Kar-Wai Hong21.3 LuxR-type quorum-sensing regulators that are antagonized by cognate pheromones, 1221Stephen C. Winans, Ching-Sung Tsai, Gina T. Ryan, Ana Lidia Flores-Mireles, Esther Costa, Kevin Y. Shih, Thomas C.Winans, Youngchang Kim, Robert Jedrzejczak, and Gekleng Chhor21.4 Adaptation to environmental stresses in Streptococcus mutans through the production of its quorum-sensing peptide pheromone, 1232Delphine Dufour, Vincent Leung, and Céline M. Lévesque21.5 Quorum sensing in Bacillus cereus in relation to cysteine metabolism and the oxidative stress response, 1242Eugénie Huillet and Michel GoharSection 22: Chemotaxis and biofilm formation, 125322.1 The flagellum as a sensor, 1255Rasika M. Harshey22.2 Flagellar motility and fitness in xanthomonads, 1265Marie-Agnès Jacques, Jean-Françis Guimbaud, Martial Briand, Arnaud Indiana, and Armelle Darrasse22.3 Understanding Listeriamonocytogenes biofilms: perspectives into mechanisms of adaptation and regulation under stress conditions, 1274Lizziane Kretli Winkelströter, Fernanda Barbosa dos Reis-Teixeira, Gabriela Satti Lameu, and Elaine Cristina Pereira De Martinis22.4 Biofilm formation and environmental signals in Bordetella, 1279Tomoko Hanawa22.5 Biofilm formation by rhizobacteria in response to water-limiting conditions, 1287Pablo Bogino, Fiorela Nievas, and Walter Giordano22.6 Stress conditions triggering mucoid-to-nonmucoid morphotype variation in Burkholderia, and effects onvirulence and biofilm formation, 1295Leonilde M. Moreira, Inês N. Silva, Ana S. Ferreira, and Mário R. Santos22.7 Effect of environmental conditions present in the fishery industry on the biofilm-forming ability of Staphylococcus aureus, 1304Daniel Vázquez-Sánchez22.8 Biofilm development and stress response in the cholera bacterium, 1310Anisia J. Silva and Jorge A. Benitez22.9 Outer membrane vesicle secretion: from envelope stress to biofilm formation, 1322Thomas Baumgarten and Hermann J. HeipieperSection 23: Viable but nonculturable (VBNC) cells, 132923.1 Resuscitation of Vibrios fromthe viable but nonculturable state is induced by quorum-sensing molecules, 1331Mesrop Ayrapetyan, Tiffany C. Williams, and James D. Oliver23.2 Differential resuscitative effects of pyruvate and its analogs on VBNC (viable but nonculturable)Salmonella, 1338Fumio Amano23.3 Environmental persistence of Shiga toxin-producing E. coli, 1346Philipp Aurass and Antje Flieger23.4 Of a tenacious and versatile relic: the role of inorganic polyphosphate (poly-P) metabolism in the survival, adaptation, and virulence of Campylobacter jejuni, 1354Issmat I. Kassem and Gireesh RajashekaraIndex, i