Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 2 Volume Set
Herausgeber: de Bruijn, Frans J
Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 2 Volume Set
Herausgeber: de Bruijn, Frans J
- Gebundenes Buch
- Merkliste
- Auf die Merkliste
- Bewerten Bewerten
- Teilen
- Produkt teilen
- Produkterinnerung
- Produkterinnerung
Bacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving…mehr
Andere Kunden interessierten sich auch für
- David N. Cooper (ed.)Encyclopedia of the Human Genome, 5 Volume Set2.347,99 €
- Translational Genomics for Crop Breeding, Volume 2270,99 €
- Tzvi Tzfira / Vitaly Citovsky (eds.)Agrobacterium: From Biology to Biotechnology239,99 €
- Dunn, Michael J.Jorde, Lynn B. / Peter F. R. Little / Shankar Subramaniam (Hgg.)Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 8 Volume Set3.214,99 €
- Physical Chemistry Research for Engineering and Applied Sciences, Volume Three210,99 €
- Physical Chemistry Research for Engineering and Applied Sciences, Volume One210,99 €
- Translational Genomics for Crop Breeding, Volume 1247,99 €
-
-
-
Bacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA's, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent response, efflux pumps, alarmones, and modulation of the cell envelope or membranes, to name a few. Many regulatory elements are conserved in different bacteria; however there are endless variations on the theme and novel elements of gene regulation in bacteria inhabiting particular environments are constantly being discovered. Especially in (pathogenic) bacteria colonizing the human body a plethora of bacterial responses to innate stresses such as pH, reactive nitrogen and oxygen species and antibiotic stress are being described. An attempt is made to not only cover model systems but give a broad overview of the stress-responsive regulatory systems in a variety of bacteria, including medically important bacteria, where elucidation of certain aspects of these systems could lead to treatment strategies of the pathogens. Many of the regulatory systems being uncovered are specific, but there is also considerable "cross-talk" between different circuits. Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria is a comprehensive two-volume work bringing together both review and original research articles on key topics in stress and environmental control of gene expression in bacteria. Volume One contains key overview chapters, as well as content on one/two/three component regulatory systems and stress responses, sigma factors and stress responses, small non-coding RNAs and stress responses, toxin-antitoxin systems and stress responses, stringent response to stress, responses to UV irradiation, SOS and double stranded systems repair systems and stress, adaptation to both oxidative and osmotic stress, and desiccation tolerance and drought stress. Volume Two covers heat shock responses, chaperonins and stress, cold shock responses, adaptation to acid stress, nitrosative stress, and envelope stress, as well as iron homeostasis, metal resistance, quorum sensing, chemotaxis and biofilm formation, and viable but not culturable (VBNC) cells. Covering the full breadth of current stress and environmental control of gene expression studies and expanding it towards future advances in the field, these two volumes are a one-stop reference for (non) medical molecular geneticists interested in gene regulation under stress.
Produktdetails
- Produktdetails
- Verlag: John Wiley & Sons / Wiley
- Artikelnr. des Verlages: 1W119004880
- Seitenzahl: 1472
- Erscheinungstermin: 6. September 2016
- Englisch
- Abmessung: 287mm x 220mm x 68mm
- Gewicht: 4023g
- ISBN-13: 9781119004882
- ISBN-10: 1119004888
- Artikelnr.: 42458097
- Verlag: John Wiley & Sons / Wiley
- Artikelnr. des Verlages: 1W119004880
- Seitenzahl: 1472
- Erscheinungstermin: 6. September 2016
- Englisch
- Abmessung: 287mm x 220mm x 68mm
- Gewicht: 4023g
- ISBN-13: 9781119004882
- ISBN-10: 1119004888
- Artikelnr.: 42458097
Frans J. de Bruijn is a Director of Research at the INRA/CNRS Laboratory of Plant-Microbe Interactions in Toulouse, France.
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 sigma70-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 sigma 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) sigma 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 sigma 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) sigma factors
344 JessicaL. Hastie and Craig D. Ellermeier 4.6 The ECF family sigma factor sigmaH 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 Kedzierska 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 (sigma38)
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(c)¥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
i
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 sigma70-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 sigma 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) sigma 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 sigma 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) sigma factors
344 JessicaL. Hastie and Craig D. Ellermeier 4.6 The ECF family sigma factor sigmaH 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 Kedzierska 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 (sigma38)
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(c)¥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
i
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 sigma70-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 sigma 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) sigma 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 sigma 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) sigma factors
344 JessicaL. Hastie and Craig D. Ellermeier 4.6 The ECF family sigma factor sigmaH 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 Kedzierska 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 (sigma38)
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(c)¥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
i
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 sigma70-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 sigma 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) sigma 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 sigma 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) sigma factors
344 JessicaL. Hastie and Craig D. Ellermeier 4.6 The ECF family sigma factor sigmaH 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 Kedzierska 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 (sigma38)
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(c)¥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
i