Contributors
Preface
I. GENOMES, GENOMICS, AND GENETIC EXCHANGE
1. Gene Transfer in Mycobacterium tuberculosis: Shuttle Phasmids to Enlightenment
William R. Jacobs, Jr.
2. Mycobacterial Pathogenomics and Evolution
Daria Bottai, Timothy P. Stinear, Philip Supply, and Roland Brosch
3. BCG Vaccines
Vanessa Tran, Jun Liu, and Marcel A. Behr
4. Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria
Keith M. Derbyshire and Todd A. Gray
5. Molecular Genetics of Mycobacteriophages
Graham F. Hatfull
6. Genetics of Phage Lysis
Madalena Pimentel
II. GENE EXPRESSION AND REGULATION
7. Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence
Riccardo Manganelli
8. Transcription Factor Binding Site Mapping Using ChIP-Seq
Suma Jaini, Anna Lyubetskaya, Antonio Gomes, Matthew Peterson, Sang Tae Park, Sahadevan Raman, Gary Schoolnik, and James Galagan
9. Noncoding RNA in Mycobacteria
Kristine B. Arnvig, Teresa Cortes, and Douglas B. Young
10. Two-Component Regulatory Systems of Mycobacteria
Tanya Parish
11. Regulated Expression Systems for Mycobacteria and Their Applications
Dirk Schnappinger and Sabine Ehrt
III. THE MYCOBACTERIAL PROTEOME
12. Mycobacterium tuberculosis in the Proteomics Era
Martin Gengenbacher, Jeppe Mouritsen, Olga T. Schubert, Ruedi Aebersold, and Stefan H. E. Kaufmann
13. Structural Annotation of the Mycobacterium tuberculosis Proteome
Nagasuma Chandra, Sankaran Sandhya, and Praveen Anand
14. Cyclic AMP Signaling in Mycobacteria
Gwendowlyn S. Knapp and Kathleen A. McDonough
IV. METABOLISM
15. The Physiology and Genetics of Oxidative Stress in Mycobacteria
Bridgette M. Cumming, Dirk Lamprecht, Ryan M. Wells, Vikram Saini, James H. Mazorodze, and Adrie J. C. Steyn
16. Metabolomics of Central Carbon Metabolism in Mycobacterium tuberculosis
Anthony D. Baughn and Kyu Y. Rhee
17. Mycobacterial Lipidomics
Emilie Layre, Reem Al-Mubarak, John T. Belisle, and D. Branch Moody
18. Genetics of Mycobacterial Trehalose Metabolism
Rainer Kalscheuer and Hendrik Koliwer-Brandl
19. Metallobiology of Tuberculosis
G. Marcela Rodriguez and Olivier Neyrolles
20. Energetics of Respiration and Oxidative Phosphorylation in Mycobacteria
Gregory M. Cook, Kiel Hards, Catherine Vilchèze, Travis Hartman, and Michael Berney
V. GENETICS OF DRUG RESISTANCE
21. Molecular Basis of Drug Resistance in Mycobacterium tuberculosis
Keira A. Cohen, William R. Bishai, and Alexander S. Pym
22. Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis: Genes, Mutations, and Causalities
Catherine Vilchèze and William R. Jacobs, Jr.
23. The Molecular Genetics of Fluoroquinolone Resistance in Mycobacterium tuberculosis
Claudine Mayer and Howard Takiff
24. Mechanisms of Pyrazinamide Action and Resistance
Ying Zhang, Wanliang Shi, Wenhong Zhang, and Denis Mitchison
25. Genetic Strategies for Identifying New Drug Targets
Andrej Trauner, Christopher M. Sassetti, and Eric J. Rubin
VI. GENETICS OF MEMBRANE AND CELL WALL BIOSYNTHESIS
26. Genetics of Peptidoglycan Biosynthesis
Martin S. Pavelka, Jr., Sebabrata Mahapatra, and Dean C. Crick
27. Genetics of Mycobacterial Arabinogalactan and Lipoarabinomannan Assembly
Monika Jankute, Shipra Grover, Helen L. Birch, and Gurdyal S. Besra
28. Genetics of Capsular Polysaccharides and Cell Envelope (Glyco)lipids
Mamadou Daffé, Dean C. Crick, and Mary Jackson
29. The Molecular Genetics of Mycolic Acid Biosynthesis
Jakub Pawełstrok;czyk and Laurent Kremer
VII. GENETICS OF MACROMOLECULAR BIOSYNTHESIS
30. Nucleotide Metabolism and DNA Replication
Digby F. Warner, Joanna C. Evans, and Valerie Mizrahi
31. Double-Strand DNA Break Repair in Mycobacteria
Michael S. Glickman
32. The Pup-Proteasome System of Mycobacteria
Nadine J. Bode and K. Heran Darwin
33. Mycobacterium tuberculosis Serine/Threonine Protein Kinases
Sladjana Prisic and Robert N. Husson
VIII. THE MYCOBACTERIAL LIFESTYLE, PERSISTENCE, AND MACROPHAGE SURVIVAL
34. The Spectrum of Drug Susceptibility in Mycobacteria
Bree B. Aldridge, Iris Keren, and Sarah M. Fortune
35. The Sculpting of the Mycobacterium tuberculosis Genome by Host Cell–Derived Pressures
David G. Russell, Wonsik Lee, Shumin Tan, Neelima Sukumar, Maria Podinovskaia, Ruth J. Fahey, and Brian C. VanderVen
36. Evasion of Innate and Adaptive Immunity by Mycobacterium tuberculosis
Michael F. Goldberg, Neeraj K. Saini, and Steven A. Porcelli
37. Mycobacterial Biofilms
Jacobs P. Richards and Anil K. Ojha
Index
RUEDI AEBERSOLD
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, and Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
BREE B. ALDRIDGE
Department of Molecular Biology & Microbiology and Department of Biomedical Engineering, Tufts University, Boston, MA 02111, and Medford, MA 02155
REEM AL-MUBARAK
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
PRAVEEN ANAND
Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
KRISTINE B. ARNVIG
Mycobacterial Research Division, National Institute for Medical Research, London NW7 1AA, United Kingdom
ANTHONY D. BAUGHN
Department of Microbiology, University of Minnesota, 420 Delaware St. SE, MMC196, Mayo Building Room 1020, Minneapolis, MN 55455
MARCEL A. BEHR
McGill International TB Centre, Montreal, Quebec, Canada, H3G 1A4
JOHN T. BELISLE
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
MICHAEL BERNEY
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
GURDYAL S. BESRA
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
HELEN L. BIRCH
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
WILLIAM R. BISHAI
Johns Hopkins School of Medicine, The Center for TB Research, 1550 Orleans St., CRBII, Room 103, Baltimore, MD 21287
NADINE J. BODE
Department of Microbiology, New York University School of Medicine, 550 First Avenue, MSB 236, New York, NY 10016
DARIA BOTTAI
Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia Università di Pisa, Pisa, Italy
ROLAND BROSCH
Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
NAGASUMA CHANDRA
Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
KEIRA A. COHEN
KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Nelson R. Mandela School of Medicine, 719 Umbilo Road, Durban, South Africa, and Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115
GREGORY M. COOK
University of Otago, Department of Microbiology and Immunology, Dunedin, New Zealand
TERESA CORTES
Mycobacterial Research Division, National Institute for Medical Research, London NW7 1AA, United Kingdom
DEAN C. CRICK
Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682
BRIDGETTE M. CUMMING
KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa
MAMADOU DAFFé
CNRS, Institut de Pharmacologie et de Biologie Structurale, Département Mécanismes Moléculaires des Infections Mycobactériennes, and the Université de Toulouse Paul Sabatier, F-31077 Toulouse, France
K. HERAN DARWIN
Department of Microbiology, New York University School of Medicine, 550 First Avenue, MSB 236, New York, NY 10016
KEITH M. DERBYSHIRE
Division of Genetics, Wadsworth Center, New York State Department of Health, and Department of Biomedical Sciences, University at Albany, Albany, NY 12201
SABINE EHRT
Department of Microbiology and Immunology, Weill Medical College, and Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065
JOANNA C. EVANS
Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, P/Bag X3, Rondebosch 7700, South Africa
RUTH J. FAHEY
Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
SARAH M. FORTUNE
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
JAMES GALAGAN
Department of Biomedical Engineering, Bioinformatics Program, and National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA 02215, and Broad Institute of MIT and Harvard, Cambridge, MA 02142
MARTIN GENGENBACHER
Max Planck Institute for Infection Biology, Department of Immunology, Charitéplatz 1, 10117 Berlin, Germany
MICHAEL S. GLICKMAN
Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY 10803
MICHAEL F. GOLDBERG
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
ANTONIO GOMES
Bioinformatics Program, Boston University, Boston, MA 02215
TODD A. GRAY
Division of Genetics, Wadsworth Center, New York State Department of Health, and Department of Biomedical Sciences, University at Albany, Albany, NY 12201
SHIPRA GROVER
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
KIEL HARDS
University of Otago, Department of Microbiology and Immunology, Dunedin, New Zealand
TRAVIS HARTMAN
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
GRAHAM F. HATFULL
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
ROBERT N. HUSSON
Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115
MARY JACKSON
Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682
WILLIAM R. JACOBS, JR.
Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
SUMA JAINI
Department of Biomedical Engineering and National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA 02115
MONIKA JANKUTE
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
RAINER KALSCHEUER
Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
STEFAN H. E. KAUFMANN
Max Planck Institute for Infection Biology, Department of Immunology, Charitéplatz 1, 10117 Berlin, Germany
IRIS KEREN
Antimicrobial Discovery Center and Department of Biology, Northeastern University, Boston, MA 02115
GWENDOWLYN S. KNAPP
Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002
HENDRIK KOLIWER-BRANDL
Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
LAURENT KREMER
Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier 2 et 1, CNRS; UMR 5235, case 107; and INSERM, DIMNP, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
DIRK LAMPRECHT
KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa
EMILIE LAYRE
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
WONSIK LEE
Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
JUN LIU
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
ANNA LYUBETSKAYA
Bioinformatics Program, Boston University, Boston, MA 02215
SEBABRATA MAHAPATRA
Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523
RICCARDO MANGANELLI
Department of Molecular Medicine, University of Padova, Italy
CLAUDINE MAYER
Unité de Microbiologie Structurale, Institut Pasteur; UMR 3528 du CNRS; and Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, 75015, Paris, France
JAMES H. MAZORODZE
KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa
KATHLEEN A. MCDONOUGH
Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, and Department of Biomedical Sciences, University at Albany, Albany, NY 12222
DENIS MITCHISON
Centre for Infection, St. George's, University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
VALERIE MIZRAHI
Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, P/Bag X3, Rondebosch 7700, South Africa
D. BRANCH MOODY
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
JEPPE MOURITSEN
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland
OLIVIER NEYROLLES
Centre National de la Recherche Scientifique & Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
ANIL K. OJHA
Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
TANYA PARISH
Infectious Disease Research Institute, Seattle, WA 98102, and Queen Mary University of London, London, United Kingdom
SANG TAE PARK
Macrogen Clinical Laboratory, Macrogen Corp, Rockville, MD 20850
MARTIN S. PAVELKA, JR.
Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642
JAKUB PAWEŁCZYK
Institute for Medical Biology, Polish Academy of Sciences, Lodz, Poland
MATTHEW PETERSON
Department of Biomedical Engineering, Boston University, Boston, MA 02215
MADALENA PIMENTEL
Centro de Patogénese Molecular, Unidade dos Retrovirus e Infecções Associadas, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
MARIA PODINOVSKAIA
Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
STEVEN A. PORCELLI
Department of Microbiology and Immunology and Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461
SLADJANA PRISIC
Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115
ALEXANDER S. PYM
KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Nelson R. Mandela School of Medicine, 719 Umbilo Road, Durban, South Africa
SAHADEVAN RAMAN
National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA 02215
KYU Y. RHEE
Department of Medicine, Weill Cornell Medical College, 1300 York Avenue A-431A, New York, NY 10065
JACOBS P. RICHARDS
Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
G. MARCELA RODRIGUEZ
Public Health Research Institute Center & Department of Medicine, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
ERIC J. RUBIN
Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115
DAVID G. RUSSELL
Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
VIKRAM SAINI
Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
NEERAJ K. SAINI
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
SANKARAN SANDHYA
Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
CHRISTOPHER M. SASSETTI
University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655
DIRK SCHNAPPINGER
Department of Microbiology and Immunology, Weill Medical College, and Program in Molecular Biology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065
GARY SCHOOLNIK
Department of Medicine and Department of Microbiology and Immunology, Stanford Medical School, Stanford, CA 94305
OLGA T. SCHUBERT
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland
WANLIANG SHI
Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
ADRIE J. C. STEYN
KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa, and Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
TIMOTHY P. STINEAR
Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
NEELIMA SUKUMAR
Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
PHILIP SUPPLY
CNRS UMR 8204; INSERM, U1019; Center for Infection and Immunity of Lille, Institut Pasteur de Lille; and Université Lille Nord de France, Lille, France
HOWARD TAKIFF
Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela
SHUMIN TAN
Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
VANESSA TRAN
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
ANDREJ TRAUNER
Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115
BRIAN C. VANDERVEN
Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
CATHERINE VILCHÈZE
Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
DIGBY F. WARNER
Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, P/Bag X3, Rondebosch 7700, South Africa
RYAN M. WELLS
KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa, and Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
DOUGLAS B. YOUNG
Mycobacterial Research Division, National Institute for Medical Research, London NW7 1AA, United Kingdom
YING ZHANG
Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, and Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
WENHONG ZHANG
Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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Library of Congress Cataloging-in-Publication Data
Molecular genetics of mycobacteria / edited by Graham F. Hatfull, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, and William R. Jacobs, Jr., Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, NY. – Second edition.
pages cm
Includes index.
ISBN 978-1-55581-883-8 (print) – ISBN 978-1-68367-342-2 (electronic) 1. Mycobacteria. 2. Bacterial genetics. 3. Tuberculosis--Genetic aspects. I. Hatfull, Graham F., editor. II. Jacobs, William R., Jr, editor.
QR82.M8M64 2014
579.3′74–dc23
2014016666
doi:10.1128/9781555818845
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
Address editorial correspondence to: ASM Press, 1752 N St., N.W., Washington, DC 20036-2904, USA.
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Online: http://www.asmscience.org
A
ABC transporter, in trehalose transport, 365, 369
Abrahams, G. L., 503
Acadian phage, 128
acc genes, 615–616
Accelerator, in asymmetric growth, 716
Accurate-mass retention time values, 342
aceA gene, 146
Acetamidase system, switches, 225, 228
Acetylated PIMs, 545–546
Acetylation, 247, 289
Acetyl-CoA carboxylase, 615–616
N-Acetylglucosamine, in lysis, 122
N-Acetylglucosamine rhamnose linker, in peptidoglycan synthesis, 520
N-Acetylglycosylases, in lysis, 122
N-Acetylmuramidases, in lysis, 122
N-Acetyl-muramyl-l-alanine amidases, in lysis, 122, 124
Acetyltransferase, 307
Acid stress, 193
genome changes due to, 732
PZA activity and, 484
Acidobacteria, STPKs of, 682
Acidothermus cellulolyticus, Pup-proteasome system of, 669
Acinetobacter baumannii, drug susceptibility in, 714
Acinetoferrin, 378
Aconitase, 330–331
AcpM protein, 443
Acr2 protein, 213
Actinobacteria, 27
energetics of, 396
STPKs of, 682
stress response of, 193
Actinomycetales, 310
Activation loops, in STPKs, 685–687
Active site pockets, 269–270
N-Acylated glucosamine (GlcNAc), in peptidoglycan, 513, 515–517
Acyltransferases, 563, 574
Acyltrehaloses, 572–579
Adams, K. N., 715
Adaptive immunity, evasion of, 756–762
Adaptive response, in signal transduction, 681
AddAB protein, 658
Adenosine deaminase, 639
Adenosine kinase, 639–640
S-Adenosylmethionine, 311
S-Adenosylmethionine-dependent methyltransferase, 619
Adenylate cyclases, in cyclic AMP signaling, 281, 283–285
Adenylosuccinate synthase, 637
Adephagia phage, 106
AdnAB protein, 658, 660
Ag85 antigens, 755–756
ahp genes and Ahp proteins, 151, 232, 304, 417, 436, 733
Airborne pathogens, biosafety requirements for, 4–5
Akhter, Y., 188
Alanine dehydrogenase, 245–246
Alanine ligase, 515
Alanine racemase, 232, 500, 515
l-Alanyl-d-glutamine-meso-diaminopimelyl-d-alanine, 513
Alber, M., 365
AlbG protein, 469
Albicidin, 469
Aldridge, B. B., 716
Alkyl hydroperoxidase, 304
Alkyl hydroperoxide reductase, 733
Allelic exchange reactions, 17–18
Alma phage, 97
Almeida, D., 418
Alonso, S., 735
Alpha/beta hydrolases, 268
Alpha-glucans, 362, 370–372
Alpha-mycolic acids, 613
alr gene, 414
Alternative sigma factor density, 138
Alternator, in asymmetric growth, 716
Alveolar surface area, 301
Amidophosphoribosyltransferase, 636
Amikacin, resistance to, 419–420
Aminoglycosides, resistance to, 414, 419–420
5-Aminoimdazole-4-carboxyamide ribonucleotide transformylase, 637
Aminoimidazole moiety, in dNTP synthesis, 641–642
Amplification, in ChIP-Seq, 163
Amurin, 121
Anaerobic conditions, PZA activity and, 483
Anaplerosis, 333–334
Andersen, S. J., 647
Anderson, R. J., 611
Annotation, structural, 261–280
Anoosheh, S., 139
Anti-anti-sigma factors, 138, 681
Antigen 85, 245, 366
Antigen(s), as immunological decoys, 755–756
Antigen presenting cells, infection of, 752–753
Antigenic peptides, for vaccines, 252–253
Antiholins, 122
Antimicrobial peptides, 735–736
Antimycobacterial agents, see Drug(s); specific agents
Antioxidants
ergothioneine as, 312
in lung, 301
Antisense RNAs, 189–192, 232
Anti-sigma factors, 303
Apa protein, 247
aph gene, 4
Apoptosis, blocking of, 762
aprABC gene, 212, 732
Arabinase, 536
d-Arabino-d-mannan, 590
Arabinofuranosyl (Araf) residues, 536, 540–541
Arabinofuranosyltransferase, 539–540
Arabinogalactan, 350, 535–541, 614
Arabinose, in arabinogalactan, 536
Arabinosyltransferases, 418–419
AraC protein, 226, 229
Araf (arabinofuranosyl) residues, 536, 540–541, 547–548
Araucaria, 83
Aravind, A., 671
ARC (AAA ATP forming ring-shaped complexes), 667
ArcB, 214
ArcBA proteins, 399
Argaman, L., 198
Arginase, 304
Arginine, nitric oxide generation from, 301
Arnvig, K. B., 193, 198, 199
Ars proteins, 212, 402
Artemis genome browser, 184
Artifacts, in ChIP-Seq, 164
Arylamine N-acetyltransferase, 442
asd gene, 515
asino1 gene, 190
Aspartate carbamoyltransferase, 638
Aspartate semialdehyde dehydrogenase, 5
Aspartokinase, 5
ASpks protein, 191
asRNAs
detection of, 199
function of, 189–190, 200
Assembly genes, of phages, 93–95
Atc protein, in ChIP-Seq, 166–167
Atmospheric pressure chemical ionization, 342, 344
ATP7 transporters, 734
atp genes, 640
ATP, synthesis of, 390–391, 402–403
ATPase, in virulence, 36
atpBEFHAGDC operon, 402
atpE gene, 414, 423
att sites, 4, 101, 104, 106–107
Attachment, in biofilm formation, 774
Attenuation indicator lipid, 581, 585
Autoinducers, in biofilm formation, 774
Autophagy, 735–736, 748, 751
Autoregulation, 214, 217
Auxotrophic mutants, 4–5
Auxotrophy, amino acid, 395
Avery, Oswald, 7
Av-Gay, Y., 306
Azides, 482, 483
B
Babitzke, P., 189
Babsiella phage, 83
Bach, H., 699
Bacillus
energetics of, 401
sigma factors of, 138
Bacillus anthracis
cAMP signaling in, 281, 290
noncoding RNAs of, 199
Bacillus subtilis
in biofilms, 775
buffers of, 311
cell envelope composition of, 569
defenses against reactive species, 305
DNA replication in, 642, 644, 649
double-strand DNA break repair in, 658, 660–661
drug susceptibility in, 715
genetic switches in, 226
metallobiology of, 383
noncoding RNAs of, 188, 192, 196, 199
nucleotide metabolism in, 638
prophage of, 126
Pup-proteasome system of, 676
sigma factors of, 148
STPKs of, 690
BACTEC-MGIT, 463
Bacterioferritin, 245–246, 380
Bacteriophage(s), see also Mycobacteriophage(s)
lysis of, 121–133
Bacteriophage lambda, 10–11, 15–17, 105–106, 121
Bacteriophage recombineering of electroporated DNA (BRED) technique, 104–105
Bacteroides, alternative sigma factor-density of, 138
BAKA phage, 83, 97
Banerjee, S. K., 144
Banfield, J. F., 668
Bar codes, for transposons, 18–19
Bardarov, Stoyan, 13–14
Barnyard phage, 99
Battesti, A., 191
Bcp proteins, 304
BDM31343, 495, 497
Beadle, George, 6
Beaucher, J., 148
Beckman, E. M., 614
Beclin-1, 736
Bedaquiline, 4, 414, 423, 487, 493, 498, 501
Benzoic acid, for PZA enhancement, 483–484
Beresford, N. J., 699, 701
Berney, M., 403
Berthelot, M., 361
Beste, D. J., 334, 494
Bet DNA pairing enzyme, 107–108
Beta-lactams, resistance to, 423, 498, 525–526
Bethlehem phage, 98, 128
bfr genes and Bfr proteins, 380–381, 729, 734
BglII, 14
Bibb, Mervyn, 11
Bigger, Joseph, 716, 718
BigNuz phage, 104
Billman-Jacobe, H., 589
Binding sites, for transcription factors, ChIP-Seq mapping of, 161–181
bioA gene, 232
Biocyc Pathway/Genome databases, 177
Biofilm-associated proteins, 774
Biofilms, 19–20, 773–784
changes induced by, 715
characteristics of, 774–775
drug efficacy and, 715–716
formation of, 777, 779–780
genetics of, 777–779
history of hypothesis, 773–774
mycolic acids in, 614
as persistence strategy, 775–777
phenotype resistance of, 779
population-level studies of, 721
single-cell studies of, 721
Bioinformatics
for lipidomics, 353–354
structural, 263
Biological validation, of target, 500
Bioluminescence gene, 14
Biomarkers
mycobacterial lipids as, 356
for Mycobacterium tuberculosis, 254
Biosignatures, 254
Biotin carboxylase, 615
Bishai, W. R., 106–107, 674
blaC gene and BlaC protein, 423, 526
Blanchard, J. S., 306, 325
Blasco, B., 168
BLAST, 262
BLASTN, 90, 101
Blind deconvolution, in ChIP-Seq, 166
Bloom, Barry, 10–11
BMHI, 14
bom sites, 65–68
Boomer phage, 128
Bordetella pertussis, cAMP signaling in, 281, 290
Botella, H., 735
Bott, M., 400
Bound sites, in ChIP-Seq, 168, 171
BP phage, 95, 97, 104–106
BRACIL algorithm, in ChIP-Seq, 166
Branched-chain keto acid dehydrogenase, 329
Braun's lipoprotein, 522
BRED (bacteriophage recombineering of electroporated DNA) technique, 104–105
Brennan, Patrick, 11
Brodie, A. F., 389, 569
“Bronx box,” 14
Broxmeyer, L., 130
Brujita phage, 104, 106
Bsz2 phage, 99
Buffers, for ChIP-Seq, 178
Burkholderia cenocepacia, noncoding RNAs of, 199
Burns, K. E., 670, 672
Buruli ulcers, 777
Bxb1 phage, 101, 103, 106, 107
Bxz1 phage, 105, 127, 129
Bxz2 phage, 101, 106
C
Calamita, H., 143
Calcium, in mycobacteria, 734
Caldwell, D. E., 774
Cali phage, 83
Calmette, Albert, 49–52
cAMP and macrophage regulator (Cmr), 285, 287–288
cAMP signaling, see Cyclic AMP signaling
Campbell, G. R., 736
cAMP-receptor protein (CRP), 282, 285–289
Campylobacter jejuni
drug susceptibility in, 714–715
noncoding RNAs of, 199
Candida albicans
cAMP signaling in, 282
drug susceptibility in, 718
drug targets in, 503
Canetti, Georges, 32–33, 779
Canonical endolysins, 122
Canonical holins, 122
Canonical promoter signal, in ChIP-Seq, 173
Capping motifs, 542–543, 548
Capreomycin, resistance to, 414, 420–421
Capsular polysaccharides, 590–592
Carbamoyltransferase, 638
Carbon metabolism, central, 323–339
Carbon monoxide dehydrogenase, 399
Carbonyl cyanide m-chlorophenylhydrazone, 482
N5-Carboxyaminoimdazole ribonucleotide (CAIR), 636–637
Carboxylic acids, short-chain, metabolism of, 329
Carboxymycobactin, 377–379, 592
Carboxy-mycolic acids, 613
Carboxypeptidases, 520, 521
Carboxytransferase, 615
CarD protein, 233, 637
Cardiolipids, 541
Cardiolipin, 561–562
Carotenes, 570–571
Carotenoids, 30, 570–571
Carriere, Christian, 13–14
Cas proteins, 197
Casonato, S., 144
CASP experiments, 262
Caspase activation and recruitment domain, 749–750
Catabolite activator protein, 227
Catalão, M. J., 124–125
Catalase-peroxidase enzymes, 304
Catalytic/ATP binding domain, of histidine kinase, 209
CATH database, 263
Cathelicidin, 736
Cathepsins, 759
Cation diffusion facilitator family, 381
CatS protein, 759
CD1 molecules, lipid antigen presentation by, 762
cdd genes, 641
cds genes, 562
Cell envelope, 28
acyltrihaloses in, 572–579
capsular polysaccharides in, 590–592
composition of, 559–561
glycolipids in, see Glycolipids
glycopeptidolipids in, 587–590
isoprenoids in, 563–572
layers of, 559–561
mannosyl phosphomycoketides in, 579–580
peptidoglycans in, 513–533
phenolic glycolipids in, 581–587
phospholipids in, 561–563
phthiocerol dimycocerosates in, 581–587
plasma membrane of, 349–353, 587
polysaccharides in, 590–592
triglycerides in, 561–563
Cell(s), septation of, 525
Cell wall
arabinogalactan in, 535–541
composition of, 212
lipidomics of, 341–360
phosphatidyl-myo-inositol glycolipids of, 541–550
proteomics of, 245
recycling of, 522
Cellular redox ratio, 313
Central carbon metabolism, 323–339
definition of, 323
Emden-Meyerhof-Parnas pathway in, 325–328
energy sources for, 324–325
glycoxylate shunt, 333–334
methylcitrate cycle in, 333–334
pentose phosphate pathway in, 328–329
pyruvate dehydrogenase complex in, 329
schematic representation of, 323
short-chain carboxylic acids in, 329
tricarboxylic acid cycle in, 330–334
CentroidFold program, 200
ceo genes, 443
CESTET (conditional expression-specialized transduction essentiality test), 535, 544
CFP-10 protein, 29, 35, 247
Chah phage, 128
Chao, J. D., 697
Chaperone-like proteins, 124
Chaperones, 189, 213
Charlie phage, 104, 106, 128, 130
Chatterjee, D., 589
Chauhan, R., 141, 144
Che8 phage, 99, 127, 129
Che9c phage, 104–105, 108
Che9d phage, 127, 128
Che12 phage, 130
Che92 phage, 84, 91–93
Chemical scaffolds, 501–503
Chemical tractability (druggability), 273–276
Chemoinformatic analysis, 501
Chen, S., 198
Chenodeoxycholate, 587
Chi site, 658
ChIP-on-chip analysis, 148
ChIP-Seq (chromatin immunoprecipitation followed by sequencing), 161–181
comprehensive mapping in, 166–168
control experiments in, 162–163
data analysis in, 163–166
data availability in, 176–178
diagram of, 162
extensive binding in, 175–176
nonpromoter binding in, 173–175
in prokaryotes, 171–173
protocol for, 162–163, 177–178
validation of, 168–171
Chiradia, L. D., 701
ChiZ protein, 525
Chloride
genome changes due to, 732
in mycobacteria, 734
5-Chloro pyrazinamide, 484
Chlorobium tepidum, carbon metabolism in, 330
Cholesterol metabolism, 495–497, 757–758
Chorismate, 582
Chp protein, 366–367, 574
Chromatin immunoprecipitation, followed by sequencing (ChIP-Seq), 161–181
Chromatography, for mycolic acids, 612–613
Chromosomal gene transfer, 62–68, 106
Ciprofloxacin, 421, 456, 461, 466, 469, 713
Cirello, Jeffrey, 15
cis-Encoded base pairing RNAs, 189–191
Citric synthase, 330
Cjw1 phage, 128
cKD mutants, 232
Clark-Curtiss, Josephine E., 9–10
Class II transcriptional transactivator, 757
Classroom Undergraduate Research Experience (CURE), 84
Clastogens, 658
Claviceps purpurea, 310
Clavulanate, 526
Cleaving peptides, 668
ClgR protein, 145–146
Clofazimine, resistance to, 423
Cloning, direct, 104–105
Cloning-based screen approach, for RNA, 198–199
Clostridium difficile, resistance in, 468
Clostridium perfringens, resistance in, 468
Clostridium, sigma factors of, 138
Clp proteases, 249, 774
ClpXP protease, 104, 230
Cluster(s), in mycobacteriophage organization, 82, 84–90
Cluster K family phages, 13
Clustered, regularly interspaced short palindromic repeats (CRISPRs), 33, 100, 196–197
cma genes and Cma proteins, 265, 620
cmk genes, 641
Cmr (cAMP and macrophage regulator), 285, 287–288
CmrR protein, 384
Cmt proteins, 381
C-mycosides, 587
cmyt genes, 541
Cobalamin riboswitch, 187–188
CobC protein, 638
Coimmunoprecipitation, of RNAs, 200
Cole, Stewart, 16–18
Collins, D. M., 140
Collins, P. B., 433
Colony-forming units, plating of, 251–252
Comparative genome analysis
of phages, 90–93
for RNA, 199–200
Comparative lipidomics, 345, 347
Comparative modeling, for structural information, 262–263
Comparative proteomics, 243–246
Complement receptor, 747
Complex I, Complex II, Complex III, and Complex IV enzymes
in electron transport chain, 400
in growth, 390–391
structures of, 391–396
Compound libraries, 500–501
Compound-driven target selection, 494
Computational methods, for RNA prediction, 197–198
Condition tree analysis, 729
Conditional expression-specialized transduction essentiality test (CESTET), 535, 544
Conjugation, 7
chromosomal transfer in, 62–68
classical (oriT-mediated), 62–63, 65
distributive conjugal transfer, 68–76
genetic requirements for, 67
paradoxes in, 67–68
plasmid transfer in, 62–64
Conservons, 468
Consumption, see Tuberculosis
Control experiments, in ChIP-Seq, 162–163
Controlled proteolysis, 230, 231
Cook, G. M., 403
Cooperative binding, in ChIP-Seq, 166
CopA protein, 383
Copper, in mycobacteria, 381–384, 734
Copurification, of sRNAs, 200
Cord factor (trehalose dimycolate), 127, 350, 353, 362
Core particle, of proteasomes, 668, 670, 675
Corndog phage, 125, 127–129
Coronin-1, 751
Corynebacteriaceae, nucleotide metabolism in, 636
Corynebacterium
mycolic acids of, 613
Pup-proteasome system of, 669
Corynebacterium diphtheriae, metallobiology of, 379
Corynebacterium glutamicum
arabinogalactan of, 536, 538–541
cAMP signaling in, 282
carbon metabolism in, 334
cell envelope composition of, 559
energetics of, 399–400, 403
genetic switches in, 226
mycolic acids of, 622
phosphatidyl-myo-inositol glycolipids of, 545–547
Pup-proteasome system of, 670
redox sensors in, 302
STPKs of, 683, 696
trehalose in, 364
Cosmids, 4, 11, 105–106
Costerton, J. W, 774
Courthouse gene, 99
Cowley, S., 696
Cox, J. S., 586
Cox, Jeffery, 15
Coxsackie virus, Pup-proteasome system of, 674
crgA gene, 525
Crick, Francis, 7
CRISPRs (clustered, regularly interspaced short palindromic repeats), 33, 100, 196–197
Cross-correlation function, in ChIP-Seq, 164
Cross-presentation, of antigens, 759
CRP (cAMP-receptor protein), 282, 285–289
crRNAs (CRISPRs), 33, 100, 196–197
crt genes and Crt proteins, 30, 570–571
Cryptococcus neoformans, cAMP signaling in, 282
CSDevonv method, 166
CsgD protein, 774
CsoR protein, 382, 384
Csr proteins, 189, 198, 200
Cta proteins, 400
ctaBCDE gene, 389–390, 400
ctp genes and Ctp proteins, 381–383, 734, 735
Ctr1 protein, 734–735
C-type leptin receptor (mincle), 353, 614, 647, 747, 750
CURE (Classroom Undergraduate Research Experience), 84
Curtiss, Roy, III, 7, 9–10
cwlM gene, 522–523
CwsA protein, 525
Cyanide, 482
cycA gene, 414
Cyclic AMP receptor protein, 52
Cyclic AMP signaling, 281–295
adenylate cyclases in, 281, 283–285
cAMP production and secretion in, 290–291
control of, 289–299
CRP regulon in, 288–289
in gene regulation, 286–287
host cell interactions in, 290–291
lysine acetylase in, 289
mechanisms of, 281–282
in metabolism, 286–287
organisms using, 281–282
overview of, 281–282
regulation of, 285–286
transcription factors in, 287–288
Cyclic AMP, synthesis of, 404
Cyclic monophosphate binding proteins, 285–286
Cyclopropanation, 621–622
Cyclopropane synthases, 265, 624
Cycloserine
resistance to, 414, 422, 515
target of, 500
cydA genes, 401
cydABCD gene, 389–390
Cystein ligase, 307
Cytidine deaminase, 641
Cytidylate kinase, 641
Cytochrome c oxidase, 400
aa 3-type, 389–390
bc 1-aa 3-type, 400
bd-type, 389–390, 400–401
Cytochrome oxidase, copper in, 381
Cytoplasmic membrane, lysis of, 122
Cytoprotectant, ergothioneine as, 312
Cytosol, proteomics of, 245
Cytotoxicity, of phages, 95
D
D4 phage, 99–100
D19 phage, 11
D29 phage, 95, 99, 108, 127–129
Dac proteins, 521–522
Dainese, E., 145, 152
Dallman, H. G., 648
DAP (meso-diaminopimelate), 513–516, 518
Darwin, K. H., 667, 670, 672, 674, 734
DAS+4 tag, Switches, 229–230
Dassie bacillus, 35, 37, 51
Data analysis, in lipidomics, 347–348
DATs (2,3-di-O-acyltrehaloses), 575–577
Davies, Julian, 8–9
Davis, Ron, 10
Davy, K.W., 714
dcd genes, 641
DD5 phage, 128
DDD (F1F0-ATP synthase), 391, 402–403, 482
ddl gene, 414
de Steenwinkel, J. E M., 713
DECAL (differential expression using customized amplification libraries), 442
Decaprenol-1-monophosphoryl-2-keto-β-erythro-pentofuranose (DPX), 539
Decaprenyl-5-phosphoribose (DPR), 539
Decaprenyl diphosphate (Dec-PP), 518–519
Decaprenyl phosphate (Dec-P), 349–350, 517–519, 567–568
Decaprenyl phosphoryl-4-phosphoribose (DPPR), 539
Decoys, immunological, 755–756
Dec-P (decaprenyl phosphate), 349–350, 517–519, 567–568
Dec-PP (decaprenyl diphosphate), 518–519
Degradation, of proteins, Pup-proteasome system in, 667–680
Degradosomes, 196
Dehydrolipoamide acyltransferase, 674
Dehydroquinase, 273
Delamanid, 487, 493
Deltaproteobacteria, STPKs of, 682
Demethylmenaquinone, 569
Dendritic cells, infection of, 753
1-Deoxy-d-xylulose-5-phosphate reductoisomerase, 565–566
1-Deoxy-d-xylulose-5-phosphate synthase, 563, 565
Deoxynucleotide triphosphates (dNTPs), biosynthesis of, 636–642
Depupylase, 672
Depupylation, 671–672
Dessication, double-strand DNA breaks in, 657
Detergents, for waxy cultures, 715
Detoxification
of copper, 734
of isoniazide, 442
mycothiol for, 309
truncated hemoglobins in, 305
Deubiquitylases, 669–672
DfrA protein, 503
Dhar, N., 401
D'Herelle, Felix, 108–109
Diacylglycerol, 544–545
2,3-Diacyltrehalose, 368
meso-Diaminopimelate (DAP), 513–516, 518
Diaminopimelic acid, 5, 9
Diarylquinolines, 403
Dibutyryl cAMP, 286–287
DiChiara, J. M, 198–199
Dietzia, mycolic acids of, 613
Differential expression using customized amplification libraries (DECAL), 442
Diglyceride acyltransferases, 562
Dihydrofolate reductase, 232, 273, 444, 500
Dihydrolipoamide transferase, 733
Dihydrolipoyl dehydrogenase, 331
Dihydrolipoyllysine-residue acetyltransferase, 329, 331
Dihydroorotate, 638
1,4-Dihydroxy-2-naphthoate, 569
Dihydroxyacetone kinase, 327
Dimer and phosphotransferase domain, of histidine kinase, 209
Dimerization
of STPKs, 685–686
in two-component regulatory systems, 211, 216
Dimethylallyl diphosphate, 563, 565–566
Dimycolyl diarabinoglycerol, 614
din genes and Din proteins, 644–645
Dinitrobenzamide derivatives (DNBs), 539, 549–550
Dinitrophenol, 482
2,3-Di-O-acyltrehaloses (DATs), 575–577
Diphosphatidylglycerol, 561
4-Diphosphocytidyl-2C-methyl-d-erythritol, 565–566
4-Diphosphocytidyl-2C-methyl-d-erythritol phosphate, 566
dipZ gene, 151
Direct cloning, 104–105
Direct plating, for phage isolation, 82
Direct transcriptional silencing, 232
Direct transitional repression, 232
Dispersal, in biofilm formation, 774–775
Distributive conjugal transfer, 68–76
evolutionary effects of, 71–75
as genetic mapping tool, 75–76
indel formation in, 74–75
mating identity switch in, 75
mid genes in, 75–76
models for, 68–70
mosaicism in, 68, 72–74
in native mycobacterial species, 71–74
vs. oriT-mediated conjugation, 68
reproductive success and, 74
spontaneous mutation and, 74
unanswered questions about, 71
Disulfide bonding, 305
Disulfide reductases, 304
Disulfide stress, 303
DivIVA protein, 525, 527
DivIVC protein, 527
DlaT protein, 733
DNA
as active factor in gene transfer, 7
double-stranded, 82, 123
extracellular, 774
replication of, 642–649
DNA binding protein, 380
dna genes and Dna proteins, for replication, 642–649
DNA gyrases, 421, 457–463, 468
DNA ligases, 273
DNA microarrays, for sigma factors, 141–143, 145, 147–148, 151
DNA polymerases, 95, 642–645
DNA topoisomerases, fluoroquinolones targeting, 457–459
DnaA boxes, 645
DNA/RNA-binding 3-helical bundle, 268
dN/dS (nonsynonymous vs. synonymous) ratios, 33
DocB7 phage, 130
Domagk, G., 431
dop gene and Dop protein, 671–675
Dori phage, 101
Dormant infections, 713
DosR/S/T in, 302
electron transport in, 404
persisters in, 718
proteomics of, 245–246, 253
redox potential and, 300
Dorrestein, P. C., 674
Dos regulon, 213, 697, 729–730
Dose-responsiveness, in gene expression, 231
DosR protein, 166, 175–176, 193, 199, 212, 249
DosR/DevR proteins, 401–402
DosRS-DosT system, 402
DosR/S/T dormancy regulon, 302
DosRST system, 217
DosT/DosS/DosR system, 404
Double-strand DNA breaks
causes of, 657
repair of, 657–666
homologous recombination method for, 658–660
nonhomologous end joining in, 660–662
in pathogenesis, 663–664
single-strand annealing in, 662–663
dpr genes and Dpr proteins, 539, 549–550
Drr AB protein, 467, 586
Drug(s), development of, 253–254
structural considerations in, 273–276
targets for, 493–509
Drug resistance
aminoglycosides, 414, 419–420
bedaquiline, 4, 414, 423
beta-lactams, 423
capreomycin, 414, 420–421
ciprofloxacin, 713
cycloserine, 414, 422, 515
definitions of, 413, 712
detection of, 423
efflux pumps in, 714–715
ethambutol, 4, 414, 418–419, 548–549
ethionamide, 4, 395, 414, 421–422, 431–453
fluoroquinolones, 455–478
genomics and, 423–424
historical review of, 431
isoniazid, 4, 395–396, 414, 416–417, 431–453, 434–446
linezolid, 414
mechanisms of, 7–9, 19–20, 414
molecular basis of, 413–429
new drug development for, 253–254, 493–509
oxazolidinones, 422–423
para-aminosalicylic acid, 414, 422
proteomics for, 245
prothionamide, 421–422
pyrazinamide, 414, 417–418, 479–493
quinolones, 414, 421
redox environment and, 301–302
reversal of, 498
rifamycin, 414–416, 713
streptomycin, 7–9, 414
susceptibility testing for, 14
WhiB family and, 303
Drug sensitivity, definition of, 712
Drug susceptibility, 711–725; see also Drug resistance
definition of, 711
drug tolerance, 712–720, 723
persistence, see Persistence and persisters
testing for, 14
Drug targets, 273–276
BTZs, 549–550
DNBs, 549–550
ethambutol, 548–549
ethionamide, 434–435
fluoroquinolones, 457–458
isoniazid, 434–435
modification of, 414
multiple, single inhibitor for, 498
mycolic acids, 621
new, 493–509
current status of, 494–495
expanding screening for, 500–503
genetic approaches to, 494
relevant biology for, 495–498
replication properties and, 648–649
overexpression of, 499–500
pyrazinamide, 480–484
serine/threonine protein kinases as, 700–701
specificity of, 273, 495
SQ109, 549
Drug tolerance
asymmetric growth in, 716–717
in biofilms, 775, 779
definition of, 712
heritable, 716
persister population in, 716, 718–720
population-level, 712–714
Druggability, 273–276, 495
DS6A phage, 101
DsbE-like protein, 151
DtxR protein, 380, 383–384
DU1 and DU2, 55–56
Dubos, R. J., 572, 774
dUDP-Rha, 536–538
Duplication, tandem, 55
dut genes and Dut proteins, 640–641
dxs gene and Dxs protein, 563, 565