Table of Contents

VOLUME 1

Preface, xiii

Acknowledgements, xiv

List of contributors, xv

1 Introduction, 1
Frans J. de Bruijn

Section 2: Key overview chapters, 3

2.1 Stress-induced changes in transcript stability, 5
Dvora Biran and Eliora Z. Ron

2.2 StressChip for monitoring microbial stress response in the environment, 9
Joy D. Van Nostrand, Aifen Zhou and Jizhong Zhou

2.3 A revolutionary paradigm of bacterial genome regulation, 23
Akira Ishihama

2.4 Role of changes in σ70-driven transcription in adaptation of E. coli to conditions of stress or starvation, 37
Umender K. Sharma

2.5 The distribution and spatial organization of RNA polymerase in Escherichia coli: growth rate regulation and stress responses, 48
Ding Jun Jin, Cedric Cagliero, Jerome Izard, Carmen Mata Martin, and Yan Ning Zhou

2.6 The ECF classification: a phylogenetic reflection of the regulatory diversity in the extracytoplasmic function σ factor protein family, 64
Daniela Pinto andThorsten Mascher

2.7 Toxin–antitoxin systems in bacteria and archaea, 97
Yoshihiro Yamaguchi and Masayori Inouye

2.8 Bacterial sRNAs: regulation in stress, 108
Marimuthu Citartan, Carsten A. Raabe, Chee-Hock Hoe, Timofey S. Rozhdestvensky, andThean-Hock Tang

2.9 Bacterial stress responses as determinants of antimicrobial resistance, 115
Michael Fruci and Keith Poole

2.10 Transposable elements: a toolkit for stress and environmental adaptation in bacteria, 137
Anna Ullastres, Miriam Merenciano, Lain Guio, and Josefa González

2.11 CRISPR–Cas system: a new paradigm for bacterial stress response through genome rearrangement, 146
Joseph A. Hakim, Hyunmin Koo, Jan D. van Elsas, Jack T. Trevors, and Asim K. Bej

2.12 The copper metallome in prokaryotic cells, 161
Christopher Rensing, Hend A. Alwathnani, and Sylvia F. McDevitt

2.13 Ribonucleases as modulators of bacterial stress response, 174
Cátia Bárria, Vánia Pobre, Afonso M. Bravo, and Cecília M. Arraiano

2.14 Double-strand-break repair, mutagenesis, and stress, 185
Elizabeth Rogers, Raul Correa, Brittany Barreto, María Angélica Bravo Núñez, P.J. Minnick, Diana Vera Cruz, Jun Xia, P.J. Hastings, and Susan M. Rosenberg

2.15 Sigma factor competition in Escherichia coli: kinetic and thermodynamic perspectives, 196
Kuldeepkumar Ramnaresh Gupta and Dipankar Chatterji

2.16 Iron homeostasis and iron–sulfur cluster assembly in Escherichia coli, 203
Huangen Ding

2.17 Mechanisms underlying the antimicrobial capacity of metals, 215
Joe A. Lemire and Raymond J. Turner

2.18 Acyl-homoserine lactone-based quorum sensing in members of the marine bacterial Roseobacter clade: complex cell-to-cell communication controls multiple physiologies, 225
Alison Buchan, April Mitchell,W. Nathan Cude, and Shawn Campagna

2.19 Native and synthetic gene regulation to nitrogen limitation stress, 234
J örg Schumacher

Section 3: One-, two-, and three-component regulatory systems and stress responses, 247

3.1 Two-component systems that control the expression of aromatic hydrocarbon degradation pathways, 249
Tino Krell

3.2 Cross-talk of global regulators in Streptomyces, 257
Juan F. Martín, Fernando Santos-Beneit, Alberto Sola-Landa, and Paloma Liras

3.3 NO–H-NOX-regulated two-component signaling, 268
Dhruv P. Arora, Sandhya Muralidharan, and Elizabeth M. Boon

3.4 The two-component CheY system in the chemotaxis of Sinorhizobium meliloti, 277
Martin Haslbeck

3.5 Stimulus perception by histidine kinases, 282
Hannah Schramke, Yang Wang, Ralf Heermann, and Kirsten Jung

Section 4: Sigma factors and stress responses, 301

4.1 The extracytoplasmic function sigma factor EcfO protects Bacteroides fragilis against oxidative stress, 303
Ivan C. Ndamukong, Samantha Palethorpe, Michael Betteken, and C. Jeffrey Smith

4.2 Regulation of energy metabolism by the extracytoplasmic function (ECF) σ factors of Arcobacter butzleri, 311
Irati 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 Wösten

4.3 Extracytoplasmic function sigma factors and stress responses in Corynebacterium pseudotuberculosis, 321
Thiago L.P. Castro, Nubia Seyffert, Anne C. Pinto, Artur Silva, Vasco Azevedo, and Luis G.C. Pacheco

4.4 The complex roles and regulation of stress response σ factors in Streptomyces coelicolor, 328
Jan Kormanec, Beatrica Sevcikova, Renata Novakova, Dagmar Homerova, Bronislava Rezuchova, and Erik Mingyar

4.5 Proteolytic activation of extra cytoplasmic function (ECF) σ factors, 344
JessicaL. Hastie and Craig D. Ellermeier

4.6 The ECF family sigma factor σH in Corynebacterium glutamicum controls the thiol-oxidative stress response, 352
Tobias Busche and Jörn Kalinowski

4.7 Posttranslational regulation of antisigma factors of RpoE: a comparison between the Escherichia coli and Pseudomonas aeruginosa systems, 361
Sundar Pandey, Kyle L. Martins, and Kalai Mathee

Section 5: Small noncoding RNAs and stress responses, 369

5.1 Bacterial small RNAs in mixed regulatory circuits, 371
Jonathan Jagodnik, DenisThieffry, and Maude Guillier

5.2 Role of small RNAs in Pseudomonas aeruginosa virulence and adaptation, 383
Hansi Kumari, Deepak Balasubramanian, and Kalai Mathee

5.3 Physiological effects of posttranscriptional regulation by the small RNA SgrS during metabolic stress in
Escherichia coli, 393
Gregory R. Richards

5.4 Three rpoS-activating small RNAs in pathways contributing to acid resistance of Escherichia coli, 402
Geunu Bak, Kook Han, Daun Kim, Kwang-sun Kim, and Younghoon Lee

5.5 Thermal stress noncoding RNAs in prokaryotes and eukaryotes: a comparative approach, 412
Mercedes de la Fuente and José Luis Martínez-Guitarte

Section 6: Toxin-antitoxin systems and stress responses, 423

6.1 Epigenetics mediated by restriction modification systems, 425
Iwona Mruk and Ichizo Kobayashi

6.2 Toxin–antitoxin systems as regulators of bacterial fitness and virulence, 437
Brittany A. Fleming and Matthew A. Mulvey

6.3 Mechanisms of stress-activated persister formation in Escherichia coli, 446
Stephanie M. Amato and Mark P. Brynildsen

6.4 Identification and characterization of type II toxin–antitoxin systems in the opportunistic pathogen
Acinetobacter baumannii, 454
Edita Sûziedéliené, Milda Jurénaité, and Julija Armalyté

6.5 Transcriptional control of toxin–antitoxin expression: keeping toxins under wraps until the time is right, 463
Barbara Kℷedzierska and Finbarr Hayes

6.6 Opposite effects of GraT toxin on stress tolerance of Pseudomonas putida, 473
Rita Hõrak and Hedvig Tamman

Section 7: Stringent response to stress, 479

7.1 Preferential cellular accumulation of ppGpp or pppGpp in Escherichia coli, 481
K. Potrykus and M. Cashel

7.2 Global Rsh-dependent transcription profile of Brucella suis during stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses, 489
Stephan Köhler, Nabil Hanna, Safia Ouahrani-Bettache, Kenneth L. Drake, L. Garry Adams, and Alessandra Occhialini

7.3 The stringent response and antioxidant defences in Pseudomonas aeruginosa, 500
Gowthami Sampathkumar, Malika Khakimova, Tevy Chan, and Dao Nguyen

7.4 Molecular basis of the stringent response in Vibrio cholerae, 507
Shreya Dasgupta, Bhabatosh Das, Pallabi Basu, and Rupak K. Bhadra

Section 8: Responses to UV irradiation, 517

8.1 UV stress-responsive genes associated with ICE SXT/R391 group, 519
Patricia Armshaw and J. Tony Pembroke

8.2 Altered outer membrane proteins in response to UVC radiation in Vibrio parahaemolyticus and Vibrio alginolyticus, 528
Fethi Ben Abdallah

8.3 Ultraviolet-B radiation effects on the community, physiology, and mineralization of magnetotactic bacteria, 532
Yingzhao Wang and Yongxin Pan

8.4 Nucleotide excision repair system and gene expression in Mycobacterium smegmatis, 545
Angelina Cordone

Section 9: SOS and double stranded repair systems and stress, 551

9.1 The SOS response modulates bacterial pathogenesis, 553
Darja ¢§Zgur Bertok

9.2 RNAP secondary-channel interactors in Escherichia coli: makers and breakers of genome stability, 561
Priya Sivaramakrishnan and Christophe Herman

9.3 How a large gene network couples mutagenic DNA break repair to stress in Escherichia coli, 570
Elizabeth Rogers, P.J. Hastings, María Angélica Bravo Núñez, and Susan M. Rosenberg

9.4 Double-strand DNA break repair in mycobacteria, 577
Richa Gupta and Michael S. Glickman

Section 10: Adaptation to oxidative stress, 587

10.1 Peroxide-sensing transcriptional regulators in bacteria, 58
James M. Dubbs and Skorn Mongkolsuk

10.2 Regulation of oxidative stress–related genes implicated in the establishment of opportunistic infections by Bacteroides fragilis, 603
Felipe Lopes Teixeira, Regina Maria Cavalcanti Pilotto Domingues, and Leandro Araujo Lobo

10.3 Investigation into oxidative stress response of Shewanella oneidensis reveals a distinct mechanism, 609
Jie Yuan, Fen Wan, and Haichun Gao

10.4 An omics view on the response to singlet oxygen, 619
Bork A. Berghoff and Gabriele Klug

10.5 Regulators of oxidative stress response genes in Escherichia coli and their conservation in bacteria, 632
Herb E. Schellhorn, Mohammad Mohiuddin, Sarah M. Hammond, and Steven Botts

10.6 Hydrogen peroxide resistance in Bifidobacterium animalis subsp. lactis and Bifidobacterium longum, 638
Taylor S. Oberg and Jeff R. Broadbent

Section 11: Adaptation to osmotic stress, 647

11.1 Interstrain variation in the physiological and transcriptional responses of Pseudomonas syringae to osmotic stress, 649
Gwyn A. Beattie, Chiliang Chen, Lindsey Nielsen, and Brian C. Freeman

11.2 Management of osmotic stress by Bacillus subtilis: genetics and physiology, 657
Tamara Hoffmann and Erhard Bremer

11.3 Hyperosmotic response of Streptococcus mutans: from microscopic physiology to transcriptomic profile, 677
Lu Wang and Xin Xu

11.4 Defective ribosome maturation or function makes Escherichia coli cells salt-resistant, 687
Hyouta Himeno, Takefusa Tarusawa, Shion Ito, and Simon Goto

Section 12: Dessication tolerance and drought stress, 693

12.1 Consequences of elevated salt concentrations on expression profiles in the rhizobium S. meliloti 1021 likely involved in heat and desiccation stress, 695
Jan A.C. Vriezen, Caroline M. Finn, and Klaus Nüsslein

12.2 Genes involved in the formation of desiccationresistant cysts in Azotobacter vinelandii, 709
Guadalupe Espín

12.3 Osmotic and desiccation tolerance in Escherichia coli O157:H7 and Salmonella enterica requires rpoS (σ38), 716
Zach Pratt, Megan Shiroda, Andrew J. Stasic, Josh Lensmire, and C.W. Kaspar

12.4 Desiccation of Salmonella enterica induces cross-tolerance to other stresses, 725
Shlomo Sela (Saldinger) and Chellaiah Edward Raja

Index, i1

VOLUME 2

Preface, xiii

Acknowledgements, xiv

List of contributors, xv

Section 13: Heat shock responses, 737

13.1 Heat shock response in bacteria with large genomes: lessons from rhizobia, 739
Ana Alexandre and Solange Oliveira

13.2 Small heat shock proteins in bacteria, 747
Martin Haslbeck

13.3 Transcriptome analysis of bacterial response to heat shock using next-generation sequencing, 754
Kok-Gan Chan

13.4 Comparative analyses of bacterial transcriptome reorganisation in response to temperature increase, 757
Bei-Wen Ying and Tetsuya Yomo

13.5 Participation of Ser–Thr protein kinases in regulation of heat stress responses in Synechocystis, 766
Anna A. Zorina, Galina V. Novikova, and Dmitry A. Los

Section 14: Chaperonins and stress, 781

14.1 GroEL/ES chaperonin: unfolding and refolding reactions, 783
Victor V. Marchenkov, Nataliya A. Ryabova, Olga M. Selivanova, and Gennady V. Semisotnov

14.2 Functional comparison between the DnaK chaperone systems of Streptococcus intermedius and Escherichia coli, 791
Toshifumi Tomoyasu and Hideaki Nagamune

14.3 Coevolution analysis illuminates the evolutionary plasticity of the chaperonin system GroES/L, 796
Mario A. Fares

14.4 ClpL ATPase: a novel chaperone in bacterial stress responses, 812
Pratick Khara and Indranil Biswas

14.5 Duplicated groEL genes inMyxococcus xanthus DK1622, 820
Yan Wang, Xiao-jing Chen, and Yue-zhong Li

Section 15: Cold shock responses, 827

15.1 Gene regulation by cold shock proteins via transcription antitermination, 829
Sangita Phadtare and Konstantin Severinov

15.2 Metagenomic analysis of microbial cold stress proteins in polar lacustrine ecosystems, 837
Hyunmin Koo, Joseph A. Hakim, and Asim K. Bej

15.3 Role of two-component systems in cold tolerance of Clostridium botulinum, 845
Yâgmur Derman, Elias Dahlsten, and Hannu Korkeala

15.4 Cold shock CspA protein production during periodic temperature cycling in Escherichia coli, 854
David Stopar and Tina Ivancic

15.5 Cold shock response in Escherichia coli: a model system to study posttranscriptional regulation, 859
Anna Maria Giuliodori

15.6 New insight into cold shock proteins: RNA-binding proteins involved in stress response and virulence, 873
Charlotte Michaux and Jean-Christophe Giard

15.7 Light regulation of cold stress responses in Synechocystis, 881
Kirill S. Mironov and Dmitry A. Los

15.8 Escherichia coli cold shock gene profiles in response to overexpression or deletion of CsdA, RNase R, and
PNPase and relevance to low-temperature RNA metabolism, 890
Sangita Phadtare

Section 16: Adaptation to acid stress, 897

16.1 Acid-adaptive responses of Streptococcus mutans, and mechanisms of integration with oxidative stress, 899
Robert G. Quivey Jr., Roberta C. Faustoferri, Brendaliz Santiago, Jonathon Baker, Benjamin Cross, and Jin Xiao

16.2 Acid survival mechanisms in neutralophilic bacteria, 911
Eugenia Pennacchietti, Fabio Giovannercole, and Daniela De Biase

16.3 Two-component systems in sensing and adapting to acid stress in Escherichia coli, 927
Yoko Eguchi and Ryutaro Utsumi

16.4 Slr1909, a novel two-component response regulator involved in acid tolerance in Synechocystis sp. PCC 6803, 935
Lei Chen, Qiang Ren, Jiangxin Wang, and Weiwen Zhang

16.5 Comparative mass spectrometry–based proteomics to elucidate the acid stress response in Lactobacillus
plantarum, 944
Tiaan Heunis, Shelly Deane, and Leon M.T. Dicks

Section 17: Adaptation to nitrosative stress, 953

17.1 Transcriptional regulation by thiol-based sensors of oxidative and nitrosative stress, 955
Timothy Tapscott, Matthew A. Crawford, and Andr´es Vázquez-Torres

17.2 Haemoglobins of Mycobacterium tuberculosis and their involvement in management of environmental stress, 967
Kanak L. Dikshit

17.3 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), 976
Janina P. Lewis and Benjamin R. Belvin

17.4 Di-iron RICs: players in nitrosative-oxidative stress defences, 989
Lígia S. Nobre and Lí©¥gia M. Saraiva

17.5 The Vibrio cholerae stress response: an elaborate system geared toward overcoming host defenses during infection, 997
Karl-Gustav Rueggeberg and Jun Zhu

17.6 Ensemble modeling enables quantitative exploration of bacterial nitric oxide stress networks, 1009
Jonathan L. Robinson and Mark P. Brynildsen

Section 18: Adaptation to cell envelope stress, 1015

18.1 The Cpx inner membrane stress response, 1017
Randi L. Guest and Tracy L. Raivio

18.2 New insights into stimulus detection and signal propagation by the Cpx-envelope stress system, 1025
Patrick Hoernschemeyer and Sabine Hunke

18.3 Promiscuous functions of cell envelope stress-sensing systems in Klebsiella pneumoniae and Acinetobacter
baumannii, 1031
Vijaya Bharathi Srinivasan and Govindan Rajamohan

18.4 Influence of BrpA and Psr on cell envelope homeostasis and virulence of Streptococcus mutans, 1043
Zezhang T.Wen, Jacob P. Bitoun, Sumei Liao, and Jacqueline Abranches

18.5 Modulators of the bacterial two-component systems involved in envelope stress, transport, and virulence, 1055
Rajeev Misra

Section 19: Iron homeostasis, 1065

19.1 Iron homeostasis and environmental responses in cyanobacteria: regulatory networks involving Fur, 1067
María Luisa Peleato, María Teresa Bes, and María F. Fillat

19.2 Interplay between O2 and iron in gene expression: environmental sensing by FNR, ArcA, and Fur in bacteria, 1079
Bryan Troxell and Hosni M. Hassan

19.3 The iron–sulfur cluster biosynthesis regulator IscR contributes to iron homeostasis and resistance to
oxidants in Pseudomonas aeruginosa, 1090
Adisak Romsang, James M. Dubbs, and Skorn Mongkolsuk

19.4 Transcriptional analysis of iron-responsive regulatory networks in Caulobacter crescentus, 1103
José F. da Silva Neto

19.5 Protein–protein interactions regulate the release of iron stored in bacterioferritin, 1109
Huili Yao, YanWang, and Mario Rivera

19.6 Protein dynamics and ion traffic in bacterioferritin function: a molecular dynamics simulation study on
wild-type and mutant Pseudomonas aeruginosa BfrB, 1118
Huan Rui, Mario Rivera, and Wonpil Im

Section 20: Metal resistance, 1131

20.1 Nickel toxicity, regulation, and resistance in bacteria, 1133
Lee Macomber and Robert P. Hausinger

20.2 Metabolic networks to counter Al toxicity in Pseudomonas fluorescens: a holistic view, 1145
Christopher Auger, Nishma D. Appanna, and Vasu D. Appanna

20.3 Genomics of the resistance to metal and oxidative stresses in cyanobacteria, 1154
Corinne Cassier-Chauvat and Franck Chauvat

20.4 Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria, 1165
Jiangxin Wang, Gang Wu, Lei Chen, and Weiwen Zhang

20.5 The extracytoplasmic function sigma factor–mediated response to heavy metal stress in Caulobacter crescentus, 1171
Rogério F. Lourenco and Suely L. Gomes

20.6 Metal ion toxicity and oxidative stress in Streptococcus pneumoniae, 1184
Christopher A. McDevitt, Stephanie L. Begg, and James C. Paton

Section 21: Quorum sensing, 1195

21.1 Quorum sensing and bacterial social interactions in biofilms: bacterial cooperation and competition, 1197
Yung-Hua Li and Xiao-Lin Tian

21.2 Recent advances in bacterial quorum quenching, 1206
Kok-Gan Chan, Wai-Fong Yin, and Kar-Wai Hong

21.3 LuxR-type quorum-sensing regulators that are antagonized by cognate pheromones, 1221
Stephen 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 Chhor

21.4 Adaptation to environmental stresses in Streptococcus mutans through the production of its quorum-sensing peptide pheromone, 1232
Delphine Dufour, Vincent Leung, and Céline M. Lévesque

21.5 Quorum sensing in Bacillus cereus in relation to cysteine metabolism and the oxidative stress response, 1242
Eugénie Huillet and Michel Gohar

Section 22: Chemotaxis and biofilm formation, 1253

22.1 The flagellum as a sensor, 1255
Rasika M. Harshey

22.2 Flagellar motility and fitness in xanthomonads, 1265
Marie-Agnès Jacques, Jean-Françis Guimbaud, Martial Briand, Arnaud Indiana, and Armelle Darrasse

22.3 Understanding Listeriamonocytogenes biofilms: perspectives into mechanisms of adaptation and regulation under stress conditions, 1274
Lizziane Kretli Winkelströter, Fernanda Barbosa dos Reis-Teixeira, Gabriela Satti Lameu, and Elaine Cristina Pereira De Martinis

22.4 Biofilm formation and environmental signals in Bordetella, 1279
Tomoko Hanawa

22.5 Biofilm formation by rhizobacteria in response to water-limiting conditions, 1287
Pablo Bogino, Fiorela Nievas, and Walter Giordano

22.6 Stress conditions triggering mucoid-to-nonmucoid morphotype variation in Burkholderia, and effects on
virulence and biofilm formation, 1295
Leonilde M. Moreira, Inês N. Silva, Ana S. Ferreira, and Mário R. Santos

22.7 Effect of environmental conditions present in the fishery industry on the biofilm-forming ability of Staphylococcus aureus, 1304
Daniel Vázquez-Sánchez

22.8 Biofilm development and stress response in the cholera bacterium, 1310
Anisia J. Silva and Jorge A. Benitez

22.9 Outer membrane vesicle secretion: from envelope stress to biofilm formation, 1322
Thomas Baumgarten and Hermann J. Heipieper

Section 23: Viable but nonculturable (VBNC) cells, 1329

23.1 Resuscitation of Vibrios fromthe viable but nonculturable state is induced by quorum-sensing molecules, 1331
Mesrop Ayrapetyan, Tiffany C. Williams, and James D. Oliver

23.2 Differential resuscitative effects of pyruvate and its analogs on VBNC (viable but nonculturable)
Salmonella, 1338
Fumio Amano

23.3 Environmental persistence of Shiga toxin–producing E. coli, 1346
Philipp Aurass and Antje Flieger

23.4 Of a tenacious and versatile relic: the role of inorganic polyphosphate (poly-P) metabolism in the survival, adaptation, and virulence of Campylobacter jejuni, 1354
Issmat I. Kassem and Gireesh Rajashekara

Index, i1

About the Author

Frans J. de Bruijn is a Director of Research at the INRA/CNRS Laboratory of Plant-Microbe Interactions in Toulouse, France.