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 70-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 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
Gonzalez
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
Catia Barria, Vania Pobre, Afonso M. Bravo, and Cecilia M.
Arraiano
2.14 Double-strand-break repair, mutagenesis, and stress,
185
Elizabeth Rogers, Raul Correa, Brittany Barreto, Maria Angelica
Bravo Nunez, 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 oerg 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. Martin, 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) 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 Woesten
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
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) factors, 344
JessicaL. Hastie and Craig D. Ellermeier
4.6 The ECF family sigma factor H in Corynebacterium
glutamicum controls the thiol-oxidative stress response, 352
Tobias Busche and Joern 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 Jose Luis Martinez-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 Suziedeliene, Milda Jurenaite, and Julija Armalyte
6.5 Transcriptional control of toxin-antitoxin expression:
keeping toxins under wraps until the time is right, 463
Barbara K edzierska and Finbarr Hayes
6.6 Opposite effects of GraT toxin on stress tolerance of
Pseudomonas putida, 473
Rita Horak 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 Koehler, 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 AcAZgur 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, Maria Angelica Bravo Nunez, 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 Nusslein
12.2 Genes involved in the formation of desiccationresistant
cysts in Azotobacter vinelandii, 709
Guadalupe Espin
12.3 Osmotic and desiccation tolerance in Escherichia coli
O157:H7 and Salmonella enterica requires rpoS ( 38), 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 2Preface, xiii
Acknowledgements, xiv
List of contributors, xv
Section 13: Heat shock responses, 73713.1 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
Yagmur 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 Andres
Vazquez-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
Ligia S. Nobre and LiA (c)AYgia 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
Maria Luisa Peleato, Maria Teresa Bes, and Maria 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
Jose 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
Rogerio 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 Celine M. Levesque
21.5 Quorum sensing in Bacillus cereus in relation to
cysteine metabolism and the oxidative stress response, 1242
Eugenie 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-Agnes Jacques, Jean-Francis 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 Winkelstroeter, 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, Ines N. Silva, Ana S. Ferreira, and Mario R.
Santos
22.7 Effect of environmental conditions present in the
fishery industry on the biofilm-forming ability of Staphylococcus
aureus, 1304
Daniel Vazquez-Sanchez
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
Frans J. de Bruijn is a Director of Research at the INRA/CNRS Laboratory of Plant-Microbe Interactions in Toulouse, France.
|
Ask a Question About this Product More... |
|
