127
Parti RPS, Shrivastava R, Srivastava S, Subramanian AR, Roy R, Srivastava BS, Srivastava R
(2008) A transposon insertion mutant of Mycobacterium fortuitum attenuated in virulence and
persistence in a murine infection model that is complemented by Rv3291c of Mycobacterium
tuberculosis. Microb Pathog 45(5–6):370–376. https://doi.org/10.1016/j.micpath.2008.08.008
Pedelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS (2006) Engineering and characterization of a superfolder green fluorescent protein (vol 24, pg 79, 2005). Nat Biotechnol
24(9):1170–1170. https://doi.org/10.1038/nbt0906-1170d
Prax M, Bertram R (2014) Metabolic aspects of bacterial persisters. Front Cell Infect Microbiol 4.
https://doi.org/10.3389/fcimb.2014.00148
Pu YY, Li YX, Jin X, Tian T, Ma Q, Zhao ZY, Lin SY, Chen ZH, Li BH, Yao G, Leake MC, Lo
CJ, Bai F (2019) ATP-dependent dynamic protein aggregation regulates bacterial dormancy
depth critical for antibiotic tolerance. Mol Cell 73(1):143–156. https://doi.org/10.1016/j.
molcel.2018.10.022
Roostalu J, Joers A, Luidalepp H, Kaldalu N, Tenson T (2008) Cell division in Escherichia
coli cultures monitored at single cell resolution. BMC Microbiol 8. https://doi.
org/10.1186/1471-2180-8-68
Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J (2016)
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.
Nat Microbiol 2:16206. https://doi.org/10.1038/nmicrobiol.2016.206
Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet
LC, Collins BC, Rost HL, Kaufmann SHE, Sauer U, Aebersold R (2015) Absolute proteome
composition and dynamics during dormancy and resuscitation of Mycobacterium tuberculosis.
Cell Host Microbe 18(1):96–108. https://doi.org/10.1016/j.chom.2015.06.001
Shah D, Zhang ZG, Khodursky A, Kaldalu N, Kurg K, Lewis K (2006) Persisters: a distinct physiological state of E-coli. BMC Microbiol 6. https://doi.org/10.1186/1471-2180-6-53
Shan Y, Lazinski D, Rowe S, Camilli A, Lewis K (2015) Genetic basis of persister tolerance to
aminoglycosides in Escherichia coli. MBio 6(2). https://doi.org/10.1128/mBio.00078-15
Shan Y, Gandt AB, Rowe SE, Deisinger JP, Conlon BP, Lewis K (2017) ATP-dependent persister
formation in Escherichia coli. MBio 8(1). https://doi.org/10.1128/mBio.02267-16
Shi WL, Zhang Y (2010) PhoY2 but not PhoY1 is the PhoU homologue involved in persisters in Mycobacterium tuberculosis. J Antimicrob Chemother 65(6):1237–1242. https://doi.
org/10.1093/jac/dkq103
Spanka DT, Konzer A, Edelmann D, Berghoff BA (2019) High-throughput proteomics identifies proteins with importance to postantibiotic recovery in depolarized persister cells. Front
Microbiol 10:378. https://doi.org/10.3389/fmicb.2019.00378
Spoering AL, Lewis K (2001) Biofilms and planktonic cells of Pseudomonas aeruginosa have
similar resistance to killing by antimicrobials. J Bacteriol 183(23):6746–6751. https://doi.
org/10.1128/Jb.183.23.6746-6751.2001
Spoering AL, Vulic M, Lewis K (2006) GlpD and PlsB participate in persister cell formation in
Eschetichia coli. J Bacteriol 188(14):5136–5144. https://doi.org/10.1128/Jb.00369-06
Stapels DAC, Hill PWS, Westermann AJ, Fisher RA, Thurston TL, Saliba AE, Blommestein I,
Vogel J, Helaine S (2018) Salmonella persisters undermine host immune defenses during antibiotic treatment. Science 362(6419):1156. https://doi.org/10.1126/science.aat7148
Starck J, Kallenius G, Marklund BI, Andersson DI, Akerlund T (2004) Comparative proteome
analysis of Mycobacterium tuberculosis grown under aerobic and anaerobic conditions.
Microbiology 150:3821–3829. https://doi.org/10.1099/mic.0.27284-0
Strack RL, Strongin DE, Mets L, Glick BS, Keenan RJ (2010) Chromophore formation in DsRed
occurs by a branched pathway. J Am Chem Soc 132(24):8496–8505. https://doi.org/10.1021/
ja1030084
Sulaiman JE, Hao CL, Lam H (2018) Specific enrichment and proteomics analysis of Escherichia
coli persisters from rifampin pretreatment. J Proteome Res 17(11):3984–3996. https://doi.
org/10.1021/acs.jproteome.8b00625
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…
Parti RPS, Shrivastava R, Srivastava S, Subramanian AR, Roy R, Srivastava BS, Srivastava R
(2008) A transposon insertion mutant of Mycobacterium fortuitum attenuated in virulence and
persistence in a murine infection model that is complemented by Rv3291c of Mycobacterium
tuberculosis. Microb Pathog 45(5–6):370–376. https://doi.org/10.1016/j.micpath.2008.08.008
Pedelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS (2006) Engineering and characterization of a superfolder green fluorescent protein (vol 24, pg 79, 2005). Nat Biotechnol
24(9):1170–1170. https://doi.org/10.1038/nbt0906-1170d
Prax M, Bertram R (2014) Metabolic aspects of bacterial persisters. Front Cell Infect Microbiol 4.
https://doi.org/10.3389/fcimb.2014.00148
Pu YY, Li YX, Jin X, Tian T, Ma Q, Zhao ZY, Lin SY, Chen ZH, Li BH, Yao G, Leake MC, Lo
CJ, Bai F (2019) ATP-dependent dynamic protein aggregation regulates bacterial dormancy
depth critical for antibiotic tolerance. Mol Cell 73(1):143–156. https://doi.org/10.1016/j.
molcel.2018.10.022
Roostalu J, Joers A, Luidalepp H, Kaldalu N, Tenson T (2008) Cell division in Escherichia
coli cultures monitored at single cell resolution. BMC Microbiol 8. https://doi.
org/10.1186/1471-2180-8-68
Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J (2016)
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.
Nat Microbiol 2:16206. https://doi.org/10.1038/nmicrobiol.2016.206
Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet
LC, Collins BC, Rost HL, Kaufmann SHE, Sauer U, Aebersold R (2015) Absolute proteome
composition and dynamics during dormancy and resuscitation of Mycobacterium tuberculosis.
Cell Host Microbe 18(1):96–108. https://doi.org/10.1016/j.chom.2015.06.001
Shah D, Zhang ZG, Khodursky A, Kaldalu N, Kurg K, Lewis K (2006) Persisters: a distinct physiological state of E-coli. BMC Microbiol 6. https://doi.org/10.1186/1471-2180-6-53
Shan Y, Lazinski D, Rowe S, Camilli A, Lewis K (2015) Genetic basis of persister tolerance to
aminoglycosides in Escherichia coli. MBio 6(2). https://doi.org/10.1128/mBio.00078-15
Shan Y, Gandt AB, Rowe SE, Deisinger JP, Conlon BP, Lewis K (2017) ATP-dependent persister
formation in Escherichia coli. MBio 8(1). https://doi.org/10.1128/mBio.02267-16
Shi WL, Zhang Y (2010) PhoY2 but not PhoY1 is the PhoU homologue involved in persisters in Mycobacterium tuberculosis. J Antimicrob Chemother 65(6):1237–1242. https://doi.
org/10.1093/jac/dkq103
Spanka DT, Konzer A, Edelmann D, Berghoff BA (2019) High-throughput proteomics identifies proteins with importance to postantibiotic recovery in depolarized persister cells. Front
Microbiol 10:378. https://doi.org/10.3389/fmicb.2019.00378
Spoering AL, Lewis K (2001) Biofilms and planktonic cells of Pseudomonas aeruginosa have
similar resistance to killing by antimicrobials. J Bacteriol 183(23):6746–6751. https://doi.
org/10.1128/Jb.183.23.6746-6751.2001
Spoering AL, Vulic M, Lewis K (2006) GlpD and PlsB participate in persister cell formation in
Eschetichia coli. J Bacteriol 188(14):5136–5144. https://doi.org/10.1128/Jb.00369-06
Stapels DAC, Hill PWS, Westermann AJ, Fisher RA, Thurston TL, Saliba AE, Blommestein I,
Vogel J, Helaine S (2018) Salmonella persisters undermine host immune defenses during antibiotic treatment. Science 362(6419):1156. https://doi.org/10.1126/science.aat7148
Starck J, Kallenius G, Marklund BI, Andersson DI, Akerlund T (2004) Comparative proteome
analysis of Mycobacterium tuberculosis grown under aerobic and anaerobic conditions.
Microbiology 150:3821–3829. https://doi.org/10.1099/mic.0.27284-0
Strack RL, Strongin DE, Mets L, Glick BS, Keenan RJ (2010) Chromophore formation in DsRed
occurs by a branched pathway. J Am Chem Soc 132(24):8496–8505. https://doi.org/10.1021/
ja1030084
Sulaiman JE, Hao CL, Lam H (2018) Specific enrichment and proteomics analysis of Escherichia
coli persisters from rifampin pretreatment. J Proteome Res 17(11):3984–3996. https://doi.
org/10.1021/acs.jproteome.8b00625
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…