Bacterial Longevity Requires Protein Synthesis and a Stringent Response

Yin, Liang; Ma, Hongyu; Nakayasu, Ernesto S.; Payne, Samuel H.; Morris, David R.; Harwood, Caroline S.; Newman, ed., Dianne K.

doi:10.1128/mBio.02189-19

Bacterial Longevity Requires Protein Synthesis and a Stringent Response

Journal Article · Tue Oct 15 00:00:00 EDT 2019 · mBio (Online)

DOI:https://doi.org/10.1128/mBio.02189-19· OSTI ID:1607528

Yin, Liang; Ma, Hongyu; ; Payne, Samuel H.; Morris, David R.; ; Newman, ed., Dianne K.

ABSTRACT

Gram-negative bacteria in infections, biofilms, and industrial settings often stop growing due to nutrient depletion, immune responses, or environmental stresses. Bacteria in this state tend to be tolerant to antibiotics and are often referred to as dormant. Rhodopseudomonas palustris , a phototrophic alphaproteobacterium, can remain fully viable for more than 4 months when its growth is arrested. Here, we show that protein synthesis, specific proteins involved in translation, and a stringent response are required for this remarkable longevity. Because it can generate ATP from light during growth arrest, R. palustris is an extreme example of a bacterial species that will stay alive for long periods of time as a relatively homogeneous population of cells and it is thus an excellent model organism for studies of bacterial longevity. There is evidence that other Gram-negative species also continue to synthesize proteins during growth arrest and that a stringent response is required for their longevity as well. Our observations challenge the notion that growth-arrested cells are necessarily dormant and metabolically inactive and suggest that such bacteria may have a level of metabolic activity that is higher than many would have assumed. Our results also expand our mechanistic understanding of a crucial but understudied phase of the bacterial life cycle.

IMPORTANCE We are surrounded by bacteria, but they do not completely dominate our planet despite the ability of many to grow extremely rapidly in the laboratory. This has been interpreted to mean that bacteria in nature are often in a dormant state. We investigated life in growth arrest of Rhodopseudomonas palustris , a proteobacterium that stays alive for months when it is not growing. We found that cells were metabolically active, and they continued to synthesize proteins and mounted a stringent response, both of which were required for their longevity. Our results suggest that long-lived bacteria are not necessarily inactive but have an active metabolism that is well adjusted to life without growth.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1607528

Alternate ID(s):: OSTI ID: 1608785

Report Number(s):: PNNL-SA--143448; e02189-19

Journal Information:: mBio (Online), Journal Name: mBio (Online) Journal Issue: 5 Vol. 10; ISSN 2150-7511

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (72)

Cold shock and adaptation Thieringer, Heather A.; Jones, Pamela G.; Inouye, Masayori BioEssays, Vol. 20, Issue 1 https://doi.org/10.1002/(SICI)1521-1878(199801)20:1<49::AID-BIES8>3.3.CO;2-A	journal	January 1998
Progress toward a biomimetic leaf: 4,000 h of hydrogen production by coating-stabilized nongrowing photosynthetic Rhodopseudomonas palustris Gosse, Jimmy L.; Engel, Brian J.; Hui, Jeremy C. -H. Biotechnology Progress https://doi.org/10.1002/btpr.406	journal	January 2010
The 100S ribosome: ribosomal hibernation induced by stress: 100S ribosome Yoshida, Hideji; Wada, Akira Wiley Interdisciplinary Reviews: RNA, Vol. 5, Issue 5 https://doi.org/10.1002/wrna.1242	journal	June 2014
Turnover of protein and nucleic acid in soluble and ribosome fractions of non-growing Escherichia coli Mandelstam, Joel; Halvorson, Harlyn Biochimica et Biophysica Acta, Vol. 40 https://doi.org/10.1016/0006-3002(60)91313-5	journal	January 1960
Versatile suicide vectors which allow direct selection for gene replacement in Gram-negative bacteria Quandt, Jürgen; Hynes, Michael F. Gene, Vol. 127, Issue 1 https://doi.org/10.1016/0378-1119(93)90611-6	journal	May 1993
Absence of accumulation of ppGpp and RNA during amino acid starvation in Rhizobium meliloti. Belitsky, B.; Kari, C. Journal of Biological Chemistry, Vol. 257, Issue 9 https://doi.org/10.1016/S0021-9258(18)34574-5	journal	May 1982
The fate of ribosomes in Escherichia coli cells starved for a carbon source. Kaplan, R.; Apirion, D. Journal of Biological Chemistry, Vol. 250, Issue 5 https://doi.org/10.1016/S0021-9258(19)41773-0	journal	March 1975
DksA Paul, Brian J.; Barker, Melanie M.; Ross, Wilma Cell, Vol. 118, Issue 3 https://doi.org/10.1016/j.cell.2004.07.009	journal	August 2004
Stress and Host Immunity Amplify Mycobacterium tuberculosis Phenotypic Heterogeneity and Induce Nongrowing Metabolically Active Forms Manina, Giulia; Dhar, Neeraj; McKinney, John D. Cell Host & Microbe, Vol. 17, Issue 1 https://doi.org/10.1016/j.chom.2014.11.016	journal	January 2015
Ribosome heterogeneity: another level of complexity in bacterial translation regulation Byrgazov, Konstantin; Vesper, Oliver; Moll, Isabella Current Opinion in Microbiology, Vol. 16, Issue 2 https://doi.org/10.1016/j.mib.2013.01.009	journal	April 2013
Analysis of a long term starved Pseudomonas aeruginosa ATCC27853 in seawater microcosms Machreki, Yasmine; Kouidhi, Bochra; Machreki, Sawsen Microbial Pathogenesis, Vol. 134 https://doi.org/10.1016/j.micpath.2019.103595	journal	September 2019
Conserved Bacterial RNase YbeY Plays Key Roles in 70S Ribosome Quality Control and 16S rRNA Maturation Jacob, Asha Ivy; Köhrer, Caroline; Davies, Bryan William Molecular Cell, Vol. 49, Issue 3 https://doi.org/10.1016/j.molcel.2012.11.025	journal	February 2013
Escherichia coli evolution during stationary phase Zinser, Erik R.; Kolter, Roberto Research in Microbiology, Vol. 155, Issue 5 https://doi.org/10.1016/j.resmic.2004.01.014	journal	June 2004
Bacterial lifestyle shapes stringent response activation Boutte, Cara C.; Crosson, Sean Trends in Microbiology, Vol. 21, Issue 4 https://doi.org/10.1016/j.tim.2013.01.002	journal	April 2013
Updates on the risk factors for latent tuberculosis reactivation and their managements Ai, Jing-Wen; Ruan, Qiao-Ling; Liu, Qi-Hui Emerging Microbes & Infections, Vol. 5, Issue 1 https://doi.org/10.1038/emi.2016.10	journal	January 2016
Global quantification of mammalian gene expression control Schwanhäusser, Björn; Busse, Dorothea; Li, Na Nature, Vol. 473, Issue 7347 https://doi.org/10.1038/nature10098	journal	May 2011
Phosphotransferase-dependent accumulation of (p)ppGpp in response to glutamine deprivation in Caulobacter crescentus Ronneau, Séverin; Petit, Kenny; De Bolle, Xavier Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11423	journal	April 2016
A replication clock for Mycobacterium tuberculosis Gill, Wendy P.; Harik, Nada S.; Whiddon, Molly R. Nature Medicine, Vol. 15, Issue 2 https://doi.org/10.1038/nm.1915	journal	February 2009
Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth Dai, Xiongfeng; Zhu, Manlu; Warren, Mya Nature Microbiology, Vol. 2, Issue 2 https://doi.org/10.1038/nmicrobiol.2016.231	journal	December 2016
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics Tyanova, Stefka; Temu, Tikira; Cox, Juergen Nature Protocols, Vol. 11, Issue 12 https://doi.org/10.1038/nprot.2016.136	journal	October 2016
The physiology of growth arrest: uniting molecular and environmental microbiology Bergkessel, Megan; Basta, David W.; Newman, Dianne K. Nature Reviews Microbiology, Vol. 14, Issue 9 https://doi.org/10.1038/nrmicro.2016.107	journal	August 2016
Long-term survival during stationary phase: evolution and the GASP phenotype Finkel, Steven E. Nature Reviews Microbiology, Vol. 4, Issue 2 https://doi.org/10.1038/nrmicro1340	journal	February 2006
Bacterial competition: surviving and thriving in the microbial jungle Hibbing, Michael E.; Fuqua, Clay; Parsek, Matthew R. Nature Reviews Microbiology, Vol. 8, Issue 1 https://doi.org/10.1038/nrmicro2259	journal	November 2009
Recent functional insights into the role of (p)ppGpp in bacterial physiology Hauryliuk, Vasili; Atkinson, Gemma C.; Murakami, Katsuhiko S. Nature Reviews Microbiology, Vol. 13, Issue 5 https://doi.org/10.1038/nrmicro3448	journal	April 2015
Publisher Correction: Definitions and guidelines for research on antibiotic persistence Balaban, Nathalie Q.; Helaine, Sophie; Lewis, Kim Nature Reviews Microbiology, Vol. 17, Issue 7 https://doi.org/10.1038/s41579-019-0207-4	journal	April 2019
Affinity-based capture and identification of protein effectors of the growth regulator ppGpp Wang, Boyuan; Dai, Peng; Ding, David Nature Chemical Biology, Vol. 15, Issue 2 https://doi.org/10.1038/s41589-018-0183-4	journal	December 2018
An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation Krásný, Libor; Gourse, Richard L. The EMBO Journal, Vol. 23, Issue 22 https://doi.org/10.1038/sj.emboj.7600423	journal	October 2004
Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era, an essential GTPase in Escherichia coli: Suppression of defective ribosome assembly by Era Inoue, Koichi; Alsina, Janivette; Chen, Jingqiu Molecular Microbiology, Vol. 48, Issue 4 https://doi.org/10.1046/j.1365-2958.2003.03475.x	journal	May 2003
Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria Gefen, O.; Gabay, C.; Mumcuoglu, M. Proceedings of the National Academy of Sciences, Vol. 105, Issue 16 https://doi.org/10.1073/pnas.0711712105	journal	April 2008
Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria McKinlay, J. B.; Harwood, C. S. Proceedings of the National Academy of Sciences, Vol. 107, Issue 26 https://doi.org/10.1073/pnas.1006175107	journal	June 2010
Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity Gefen, O.; Fridman, O.; Ronin, I. Proceedings of the National Academy of Sciences, Vol. 111, Issue 1 https://doi.org/10.1073/pnas.1314114111	journal	December 2013
ppGpp negatively impacts ribosome assembly affecting growth and antimicrobial tolerance in Gram-positive bacteria Corrigan, Rebecca M.; Bellows, Lauren E.; Wood, Alison Proceedings of the National Academy of Sciences, Vol. 113, Issue 12 https://doi.org/10.1073/pnas.1522179113	journal	March 2016
Translation quality control is critical for bacterial responses to amino acid stress Bullwinkle, Tammy J.; Ibba, Michael Proceedings of the National Academy of Sciences, Vol. 113, Issue 8 https://doi.org/10.1073/pnas.1525206113	journal	February 2016
Regulation of stringent factor by branched-chain amino acids Fang, Mingxu; Bauer, Carl E. Proceedings of the National Academy of Sciences, Vol. 115, Issue 25 https://doi.org/10.1073/pnas.1803220115	journal	June 2018
An aryl-homoserine lactone quorum-sensing signal produced by a dimorphic prosthecate bacterium Liao, Lisheng; Schaefer, Amy L.; Coutinho, Bruna G. Proceedings of the National Academy of Sciences, Vol. 115, Issue 29 https://doi.org/10.1073/pnas.1808351115	journal	July 2018
Evolution of microbial diversity during prolonged starvation Finkel, S. E.; Kolter, R. Proceedings of the National Academy of Sciences, Vol. 96, Issue 7 https://doi.org/10.1073/pnas.96.7.4023	journal	March 1999
Non-growing Rhodopseudomonas palustris Increases the Hydrogen Gas Yield from Acetate by Shifting from the Glyoxylate Shunt to the Tricarboxylic Acid Cycle McKinlay, James B.; Oda, Yasuhiro; Rühl, Martin Journal of Biological Chemistry, Vol. 289, Issue 4 https://doi.org/10.1074/jbc.M113.527515	journal	December 2013
Degradation of Stable RNA in Bacteria Deutscher, Murray P. Journal of Biological Chemistry, Vol. 278, Issue 46 https://doi.org/10.1074/jbc.R300031200	journal	August 2003
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ Cox, Jürgen; Hein, Marco Y.; Luber, Christian A. Molecular & Cellular Proteomics, Vol. 13, Issue 9 https://doi.org/10.1074/mcp.M113.031591	journal	June 2014
Comparative analysis of the survival and gene expression of pathogenic strains Vibrio harveyi after starvation Sun, Jingjing; Gao, Xiaojian; Qun, Jiang FEMS Microbiology Letters, Vol. 363, Issue 22 https://doi.org/10.1093/femsle/fnw250	journal	November 2016
Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations Lever, Mark A.; Rogers, Karyn L.; Lloyd, Karen G. FEMS Microbiology Reviews, Vol. 39, Issue 5 https://doi.org/10.1093/femsre/fuv020	journal	May 2015
Ribosome hibernation factor promotes Staphylococcal survival and differentially represses translation Basu, Arnab; Yap, Mee-Ngan F. Nucleic Acids Research, Vol. 44, Issue 10 https://doi.org/10.1093/nar/gkw180	journal	March 2016
The extended loops of ribosomal proteins uL4 and uL22 of Escherichia coli contribute to ribosome assembly and protein translation Lawrence, Marlon G.; Shamsuzzaman, Md; Kondopaka, Maithri Nucleic Acids Research, Vol. 44, Issue 12 https://doi.org/10.1093/nar/gkw493	journal	June 2016
Regulation of (p)ppGpp hydrolysis by a conserved archetypal regulatory domain Ronneau, Séverin; Caballero-Montes, Julien; Coppine, Jérôme Nucleic Acids Research, Vol. 47, Issue 2 https://doi.org/10.1093/nar/gky1201	journal	November 2018
Genes essential for phototrophic growth by a purple alphaproteobacterium: Genes for phototrophic growth Yang, Jianming; Yin, Liang; Lessner, Faith H. Environmental Microbiology, Vol. 19, Issue 9 https://doi.org/10.1111/1462-2920.13852	journal	July 2017
Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing: YbeY is important for rRNA maturation Davies, Bryan W.; Köhrer, Caroline; Jacob, Asha I. Molecular Microbiology, Vol. 78, Issue 2 https://doi.org/10.1111/j.1365-2958.2010.07351.x	journal	September 2010
The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment: Characterization of the stringent response in a freshwater oligotroph Boutte, Cara C.; Crosson, Sean Molecular Microbiology, Vol. 80, Issue 3 https://doi.org/10.1111/j.1365-2958.2011.07602.x	journal	March 2011
ppGpp in Sinorhizobium meliloti: biosynthesis in response to sudden nutritional downshifts and modulation of the transcriptome: Stringent response in S. meliloti Krol, Elizaveta; Becker, Anke Molecular Microbiology, Vol. 81, Issue 5 https://doi.org/10.1111/j.1365-2958.2011.07752.x	journal	July 2011
Regulation of benzoate-CoA ligase in Rhodopseudomonas palustris Kim, Min-Kyung; Harwood, Caroline S. FEMS Microbiology Letters, Vol. 83, Issue 2 https://doi.org/10.1111/j.1574-6968.1991.tb04440.x-i1	journal	October 1991
Inhibiting the stringent response blocks Mycobacterium tuberculosis entry into quiescence and reduces persistence Dutta, Noton K.; Klinkenberg, Lee G.; Vazquez, Maria-Jesus Science Advances, Vol. 5, Issue 3 https://doi.org/10.1126/sciadv.aav2104	journal	March 2019
Bacterial Persistence as a Phenotypic Switch Balaban, Nathalie Q.; Merrin, Jack; Chait, Remy Science, Vol. 305, Issue 5690, p. 1622-1625 https://doi.org/10.1126/science.1099390	journal	September 2004
Active Starvation Responses Mediate Antibiotic Tolerance in Biofilms and Nutrient-Limited Bacteria Nguyen, D.; Joshi-Datar, A.; Lepine, F. Science, Vol. 334, Issue 6058, p. 982-986 https://doi.org/10.1126/science.1211037	journal	November 2011
Microbial competition: Escherichia coli mutants that take over stationary phase cultures Zambrano, M.; Siegele, D.; Almiron, M. Science, Vol. 259, Issue 5102 https://doi.org/10.1126/science.7681219	journal	March 1993
Salmonella persisters undermine host immune defenses during antibiotic treatment Stapels, Daphne A. C.; Hill, Peter W. S.; Westermann, Alexander J. Science, Vol. 362, Issue 6419 https://doi.org/10.1126/science.aat7148	journal	December 2018
Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris Pechter, Kieran B.; Gallagher, Larry; Pyles, Harley Journal of Bacteriology, Vol. 198, Issue 5 https://doi.org/10.1128/JB.00771-15	journal	December 2015
The Stringent Response of Mycobacterium tuberculosis Is Required for Long-Term Survival Primm, Todd P.; Andersen, Susan J.; Mizrahi, Valerie Journal of Bacteriology, Vol. 182, Issue 17 https://doi.org/10.1128/JB.182.17.4889-4898.2000	journal	January 2000
The Universally Conserved Prokaryotic GTPases Verstraeten, N.; Fauvart, M.; Versees, W. Microbiology and Molecular Biology Reviews, Vol. 75, Issue 3 https://doi.org/10.1128/MMBR.00009-11	journal	September 2011
Starvation-Survival Patterns of Sixteen Freshly Isolated Open-Ocean Bacteria Amy, Penny S.; Morita, Richard Y. Applied and Environmental Microbiology, Vol. 45, Issue 3 https://doi.org/10.1128/aem.45.3.1109-1115.1983	journal	March 1983
Effect of nutrient deprivation on lipid, carbohydrate, DNA, RNA, and protein levels in Vibrio cholerae Hood, M. A.; Guckert, J. B.; White, D. C. Applied and Environmental Microbiology, Vol. 52, Issue 4 https://doi.org/10.1128/aem.52.4.788-793.1986	journal	October 1986
Role of ribosome degradation in the death of starved Escherichia coli cells. Davis, B. D.; Luger, S. M.; Tai, P. C. Journal of Bacteriology, Vol. 166, Issue 2 https://doi.org/10.1128/jb.166.2.439-445.1986	journal	January 1986
Stringency in the absence of ppGpp accumulation in Rhodobacter sphaeroides. Acosta, R.; Lueking, D. R. Journal of Bacteriology, Vol. 169, Issue 2 https://doi.org/10.1128/jb.169.2.908-912.1987	journal	January 1987
Molecular Basis of Bacterial Longevity Pechter, Kieran B.; Yin, Liang; Oda, Yasuhiro mBio, Vol. 8, Issue 6 https://doi.org/10.1128/mBio.01726-17	journal	November 2017
Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli Vercruysse, Maarten; Köhrer, Caroline; Shen, Yang mBio, Vol. 7, Issue 6 https://doi.org/10.1128/mBio.01785-16	journal	November 2016
Ancient Regulatory Role of Lysine Acetylation in Central Metabolism Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E. mBio, Vol. 8, Issue 6 https://doi.org/10.1128/mBio.01894-17	journal	November 2017
Novel (p)ppGpp Binding and Metabolizing Proteins of Escherichia coli Zhang, Yong; Zborníková, Eva; Rejman, Dominik mBio, Vol. 9, Issue 2 https://doi.org/10.1128/mBio.02188-17	journal	March 2018
ATP-Dependent Persister Formation in Escherichia coli Shan, Yue; Brown Gandt, Autumn; Rowe, Sarah E. mBio, Vol. 8, Issue 1 https://doi.org/10.1128/mBio.02267-16	journal	February 2017
Persister Cells Lewis, Kim Annual Review of Microbiology, Vol. 64, Issue 1, p. 357-372 https://doi.org/10.1146/annurev.micro.112408.134306	journal	October 2010
Microbiological Safety of Drinking Water Szewzyk, U.; Szewzyk, R.; Manz, W. Annual Review of Microbiology, Vol. 54, Issue 1 https://doi.org/10.1146/annurev.micro.54.1.81	journal	October 2000
Nonreplicating Persistence of Mycobacterium Tuberculosis Wayne, Lawrence G.; Sohaskey, Charles D. Annual Review of Microbiology, Vol. 55, Issue 1 https://doi.org/10.1146/annurev.micro.55.1.139	journal	October 2001
Survival of Burkholderia pseudomallei in Water Moore, Richard A.; Tuanyok, Apichai; Woods, Donald E. BMC Research Notes, Vol. 1, Issue 1 https://doi.org/10.1186/1756-0500-1-11	journal	January 2008
Pseudomonas aeruginosa displays a dormancy phenotype during long-term survival in water Lewenza, Shawn; Abboud, Jason; Poon, Karen PLOS ONE, Vol. 13, Issue 9 https://doi.org/10.1371/journal.pone.0198384	journal	September 2018
tRNAs as regulators of biological processes Raina, Medha; Ibba, Michael Frontiers in Genetics, Vol. 5 https://doi.org/10.3389/fgene.2014.00171	journal	June 2014

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