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Moreau PL. Regulation of phosphate starvation-specific responses in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972330 DOI: 10.1099/mic.0.001312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Toxic agents added into the medium of rapidly growing Escherichia coli induce specific stress responses through the activation of specialized transcription factors. Each transcription factor and downstream regulon (e.g. SoxR) are linked to a unique stress (e.g. superoxide stress). Cells starved of phosphate induce several specific stress regulons during the transition to stationary phase when the growth rate is steadily declining. Whereas the regulatory cascades leading to the expression of specific stress regulons are well known in rapidly growing cells stressed by toxic products, they are poorly understood in cells starved of phosphate. The intent of this review is to both describe the unique mechanisms of activation of specialized transcription factors and discuss signalling cascades leading to the induction of specific stress regulons in phosphate-starved cells. Finally, I discuss unique defence mechanisms that could be induced in cells starved of ammonium and glucose.
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Affiliation(s)
- Patrice L Moreau
- Laboratoire Chimie Bactérienne, LCB-UMR 7283, Institut Microbiologie Méditerranée, CNRS/Université Aix-Marseille, Marseille, France
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Mikuła-Pietrasik J, Pakuła M, Markowska M, Uruski P, Szczepaniak-Chicheł L, Tykarski A, Książek K. Nontraditional systems in aging research: an update. Cell Mol Life Sci 2020; 78:1275-1304. [PMID: 33034696 PMCID: PMC7904725 DOI: 10.1007/s00018-020-03658-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/15/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022]
Abstract
Research on the evolutionary and mechanistic aspects of aging and longevity has a reductionist nature, as the majority of knowledge originates from experiments on a relatively small number of systems and species. Good examples are the studies on the cellular, molecular, and genetic attributes of aging (senescence) that are primarily based on a narrow group of somatic cells, especially fibroblasts. Research on aging and/or longevity at the organismal level is dominated, in turn, by experiments on Drosophila melanogaster, worms (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), and higher organisms such as mice and humans. Other systems of aging, though numerous, constitute the minority. In this review, we collected and discussed a plethora of up-to-date findings about studies of aging, longevity, and sometimes even immortality in several valuable but less frequently used systems, including bacteria (Caulobacter crescentus, Escherichia coli), invertebrates (Turritopsis dohrnii, Hydra sp., Arctica islandica), fishes (Nothobranchius sp., Greenland shark), reptiles (giant tortoise), mammals (blind mole rats, naked mole rats, bats, elephants, killer whale), and even 3D organoids, to prove that they offer biogerontologists as much as the more conventional tools. At the same time, the diversified knowledge gained owing to research on those species may help to reconsider aging from a broader perspective, which should translate into a better understanding of this tremendously complex and clearly system-specific phenomenon.
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Affiliation(s)
- Justyna Mikuła-Pietrasik
- Department of Pathophysiology of Ageing and Civilization Diseases, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Martyna Pakuła
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Małgorzata Markowska
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Paweł Uruski
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | | | - Andrzej Tykarski
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Krzysztof Książek
- Department of Pathophysiology of Ageing and Civilization Diseases, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
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Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M. Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling. Nat Commun 2020; 11:2905. [PMID: 32518228 PMCID: PMC7283360 DOI: 10.1038/s41467-020-16724-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/19/2020] [Indexed: 01/26/2023] Open
Abstract
Bacterial nucleoid remodeling dependent on conserved histone-like protein, HU is one of the determining factors in global gene regulation. By imaging of near-native, unlabeled E. coli cells by soft X-ray tomography, we show that HU remodels nucleoids by promoting the formation of a dense condensed core surrounded by less condensed isolated domains. Nucleoid remodeling during cell growth and environmental adaptation correlate with pH and ionic strength controlled molecular switch that regulated HUαα dependent intermolecular DNA bundling. Through crystallographic and solution-based studies we show that these effects mechanistically rely on HUαα promiscuity in forming multiple electrostatically driven multimerization interfaces. Changes in DNA bundling consequently affects gene expression globally, likely by constrained DNA supercoiling. Taken together our findings unveil a critical function of HU–DNA interaction in nucleoid remodeling that may serve as a general microbial mechanism for transcriptional regulation to synchronize genetic responses during the cell cycle and adapt to changing environments. HU is among the most conserved and abundant nucleoid-associated proteins in eubacteria. Here the authors investigate the role of histone-like proteins (HU) in the 3D organization of the bacteria DNA and show via soft X-ray tomography the process of nucleoid remodeling.
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Affiliation(s)
- Soumya G Remesh
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Subhash C Verma
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Axel A Ekman
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Carolyn A Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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4
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Hamill PG, Stevenson A, McMullan PE, Williams JP, Lewis ADR, S S, Stevenson KE, Farnsworth KD, Khroustalyova G, Takemoto JY, Quinn JP, Rapoport A, Hallsworth JE. Microbial lag phase can be indicative of, or independent from, cellular stress. Sci Rep 2020; 10:5948. [PMID: 32246056 PMCID: PMC7125082 DOI: 10.1038/s41598-020-62552-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/16/2020] [Indexed: 01/01/2023] Open
Abstract
Measures of microbial growth, used as indicators of cellular stress, are sometimes quantified at a single time-point. In reality, these measurements are compound representations of length of lag, exponential growth-rate, and other factors. Here, we investigate whether length of lag phase can act as a proxy for stress, using a number of model systems (Aspergillus penicillioides; Bacillus subtilis; Escherichia coli; Eurotium amstelodami, E. echinulatum, E. halophilicum, and E. repens; Mrakia frigida; Saccharomyces cerevisiae; Xerochrysium xerophilum; Xeromyces bisporus) exposed to mechanistically distinct types of cellular stress including low water activity, other solute-induced stresses, and dehydration-rehydration cycles. Lag phase was neither proportional to germination rate for X. bisporus (FRR3443) in glycerol-supplemented media (r2 = 0.012), nor to exponential growth-rates for other microbes. In some cases, growth-rates varied greatly with stressor concentration even when lag remained constant. By contrast, there were strong correlations for B. subtilis in media supplemented with polyethylene-glycol 6000 or 600 (r2 = 0.925 and 0.961), and for other microbial species. We also analysed data from independent studies of food-spoilage fungi under glycerol stress (Aspergillus aculeatinus and A. sclerotiicarbonarius); mesophilic/psychrotolerant bacteria under diverse, solute-induced stresses (Brochothrix thermosphacta, Enterococcus faecalis, Pseudomonas fluorescens, Salmonella typhimurium, Staphylococcus aureus); and fungal enzymes under acid-stress (Terfezia claveryi lipoxygenase and Agaricus bisporus tyrosinase). These datasets also exhibited diversity, with some strong- and moderate correlations between length of lag and exponential growth-rates; and sometimes none. In conclusion, lag phase is not a reliable measure of stress because length of lag and growth-rate inhibition are sometimes highly correlated, and sometimes not at all.
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Affiliation(s)
- Philip G Hamill
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Phillip E McMullan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - James P Williams
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Abiann D R Lewis
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Sudharsan S
- Department of Chemistry, PGP College of Arts and Science, NH-7, Karur Main Road, Paramathi, Namakkal, Tamil Nadu, 637 207, India
| | - Kath E Stevenson
- Special Collections and Archives, McClay Library, Queen's University Belfast, 10 College Park Avenue, Belfast, BT7 1LP, Northern Ireland
| | - Keith D Farnsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Galina Khroustalyova
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, LV-1004, Riga, Latvia
| | - Jon Y Takemoto
- Utah State University, Department of Biology, 5305 Old Main Hill, Logan, UT, 84322, USA
| | - John P Quinn
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, LV-1004, Riga, Latvia
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland.
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Very rapid flow cytometric assessment of antimicrobial susceptibility during the apparent lag phase of microbial (re)growth. Microbiology (Reading) 2019; 165:439-454. [DOI: 10.1099/mic.0.000777] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Lag Phase Is a Dynamic, Organized, Adaptive, and Evolvable Period That Prepares Bacteria for Cell Division. J Bacteriol 2019; 201:JB.00697-18. [PMID: 30642990 DOI: 10.1128/jb.00697-18] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Lag is a temporary period of nonreplication seen in bacteria that are introduced to new media. Despite latency being described by Müller in 1895, only recently have we gained insights into the cellular processes characterizing lag phase. This review covers literature to date on the transcriptomic, proteomic, metabolomic, physiological, biochemical, and evolutionary features of prokaryotic lag. Though lag is commonly described as a preparative phase that allows bacteria to harvest nutrients and adapt to new environments, the implications of recent studies indicate that a refinement of this view is well deserved. As shown, lag is a dynamic, organized, adaptive, and evolvable process that protects bacteria from threats, promotes reproductive fitness, and is broadly relevant to the study of bacterial evolution, host-pathogen interactions, antibiotic tolerance, environmental biology, molecular microbiology, and food safety.
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Söderholm H, Derman Y, Lindström M, Korkeala H. Functional csdA is needed for effective adaptation and initiation of growth of Clostridium botulinum ATCC 3502 at suboptimal temperature. Int J Food Microbiol 2015; 208:51-7. [DOI: 10.1016/j.ijfoodmicro.2015.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 02/20/2015] [Accepted: 05/23/2015] [Indexed: 11/29/2022]
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Kocharunchitt C, King T, Gobius K, Bowman JP, Ross T. Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity. PLoS One 2014; 9:e90422. [PMID: 24594867 PMCID: PMC3940904 DOI: 10.1371/journal.pone.0090422] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/30/2014] [Indexed: 01/10/2023] Open
Abstract
The present study was undertaken to investigate growth kinetics and time-dependent change in global expression of Escherichia coli O157∶H7 Sakai upon an abrupt downshift in water activity (aw). Based on viable count data, shifting E. coli from aw 0.993 to aw 0.985 or less caused an apparent loss, then recovery, of culturability. Exponential growth then resumed at a rate characteristic for the aw imposed. To understand the responses of this pathogen to abrupt osmotic stress, we employed an integrated genomic and proteomic approach to characterize its cellular response during exposure to a rapid downshift but still within the growth range from aw 0.993 to aw 0.967. Of particular interest, genes and proteins with cell envelope-related functions were induced during the initial loss and subsequent recovery of culturability. This implies that cells undergo remodeling of their envelope composition, enabling them to adapt to osmotic stress. Growth at low aw, however, involved up-regulating additional genes and proteins, which are involved in the biosynthesis of specific amino acids, and carbohydrate catabolism and energy generation. This suggests their important role in facilitating growth under such stress. Finally, we highlighted the ability of E. coli to activate multiple stress responses by transiently inducing the RpoE and RpoH regulons to control protein misfolding, while simultaneously activating the master stress regulator RpoS to mediate long-term adaptation to hyperosmolality. This investigation extends our understanding of the potential mechanisms used by pathogenic E. coli to adapt, survive and grow under osmotic stress, which could potentially be exploited to aid the selection and/or development of novel strategies to inactivate this pathogen.
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Affiliation(s)
- Chawalit Kocharunchitt
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
- * E-mail:
| | - Thea King
- Commonwealth Scientific and Industrial Research Organisation Animal, Food and Health Sciences, North Ryde, New South Wales, Australia
| | - Kari Gobius
- Commonwealth Scientific and Industrial Research Organisation Animal, Food and Health Sciences, Werribee, Victoria, Australia
| | - John P. Bowman
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Tom Ross
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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Rosenkrantz JT, Aarts H, Abee T, Rolfe MD, Knudsen GM, Nielsen MB, Thomsen LE, Zwietering MH, Olsen JE, Pin C. Non-essential genes form the hubs of genome scale protein function and environmental gene expression networks in Salmonella enterica serovar Typhimurium. BMC Microbiol 2013; 13:294. [PMID: 24345035 PMCID: PMC3878590 DOI: 10.1186/1471-2180-13-294] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/10/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Salmonella Typhimurium is an important pathogen of human and animals. It shows a broad growth range and survives in harsh conditions. The aim of this study was to analyze transcriptional responses to a number of growth and stress conditions as well as the relationship of metabolic pathways and/or cell functions at the genome-scale-level by network analysis, and further to explore whether highly connected genes (hubs) in these networks were essential for growth, stress adaptation and virulence. RESULTS De novo generated as well as published transcriptional data for 425 selected genes under a number of growth and stress conditions were used to construct a bipartite network connecting culture conditions and significantly regulated genes (transcriptional network). Also, a genome scale network was constructed for strain LT2. The latter connected genes with metabolic pathways and cellular functions. Both networks were shown to belong to the family of scale-free networks characterized by the presence of highly connected nodes or hubs which are genes whose transcription is regulated when responding to many of the assayed culture conditions or genes encoding products involved in a high number of metabolic pathways and cell functions.The five genes with most connections in the transcriptional network (wraB, ygaU, uspA, cbpA and osmC) and in the genome scale network (ychN, siiF (STM4262), yajD, ybeB and dcoC) were selected for mutations, however mutagenesis of ygaU and ybeB proved unsuccessful. No difference between mutants and the wild type strain was observed during growth at unfavorable temperatures, pH values, NaCl concentrations and in the presence of H2O2. Eight mutants were evaluated for virulence in C57/BL6 mice and none differed from the wild type strain. Notably, however, deviations of phenotypes with respect to the wild type were observed when combinations of these genes were deleted. CONCLUSION Network analysis revealed the presence of hubs in both transcriptional and functional networks of S. Typhimurium. Hubs theoretically confer higher resistance to random mutation but a greater susceptibility to directed attacks, however, we found that genes that formed hubs were dispensable for growth, stress adaptation and virulence, suggesting that evolution favors non-essential genes as main connectors in cellular networks.
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Affiliation(s)
- Jesper T Rosenkrantz
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
| | - Henk Aarts
- Centre for Infectious disease control, National Institute for Public Health, PO box 1, 3720 BA Bilthoven, The Netherlands
| | - Tjakko Abee
- Wageningen University and Research Centre, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, Netherlands
| | - Matthew D Rolfe
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Gitte M Knudsen
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
- National Food Institute, Danish Technical University, Soelvtofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Maj-Britt Nielsen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
- Present address: DANSTEM Laboratory, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, N, Denmark
| | - Line E Thomsen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
| | - Marcel H Zwietering
- Wageningen University and Research Centre, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, Netherlands
| | - John E Olsen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
| | - Carmen Pin
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
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Harcombe WR, Delaney NF, Leiby N, Klitgord N, Marx CJ. The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum. PLoS Comput Biol 2013; 9:e1003091. [PMID: 23818838 PMCID: PMC3688462 DOI: 10.1371/journal.pcbi.1003091] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 04/26/2013] [Indexed: 11/21/2022] Open
Abstract
The most powerful genome-scale framework to model metabolism, flux balance analysis (FBA), is an evolutionary optimality model. It hypothesizes selection upon a proposed optimality criterion in order to predict the set of internal fluxes that would maximize fitness. Here we present a direct test of the optimality assumption underlying FBA by comparing the central metabolic fluxes predicted by multiple criteria to changes measurable by a 13C-labeling method for experimentally-evolved strains. We considered datasets for three Escherichia coli evolution experiments that varied in their length, consistency of environment, and initial optimality. For ten populations that were evolved for 50,000 generations in glucose minimal medium, we observed modest changes in relative fluxes that led to small, but significant decreases in optimality and increased the distance to the predicted optimal flux distribution. In contrast, seven populations evolved on the poor substrate lactate for 900 generations collectively became more optimal and had flux distributions that moved toward predictions. For three pairs of central metabolic knockouts evolved on glucose for 600–800 generations, there was a balance between cases where optimality and flux patterns moved toward or away from FBA predictions. Despite this variation in predictability of changes in central metabolism, two generalities emerged. First, improved growth largely derived from evolved increases in the rate of substrate use. Second, FBA predictions bore out well for the two experiments initiated with ancestors with relatively sub-optimal yield, whereas those begun already quite optimal tended to move somewhat away from predictions. These findings suggest that the tradeoff between rate and yield is surprisingly modest. The observed positive correlation between rate and yield when adaptation initiated further from the optimum resulted in the ability of FBA to use stoichiometric constraints to predict the evolution of metabolism despite selection for rate. The most common method of modeling genome-scale metabolism, flux balance analysis, involves using known stoichiometry to define feasible metabolic states and then choosing between these states by proposing that evolution has selected a metabolic flux that optimizes fitness. But does evolution optimize metabolism, and if so, what component of metabolism equates to fitness? We directly tested the underlying assumption of stoichiometric optimality by comparing predicted flux distributions with changes in fluxes that occurred following experimental evolution. Across three experiments ranging in length from a few hundred to fifty thousand generations, we found that substrate uptake – an input to the model – always increased, but supposed optimality criteria such as yield only increased sometimes. Despite this, there was a clear trend. Highly optimal ancestors evolved slightly lower yield in the course of increasing the overall rate, whereas more sub-optimal strains were able to increase both. These results suggest that flux balance analysis is capable of predicting either the initial metabolic behavior of strains or how they will evolve, but not both.
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Affiliation(s)
- William R. Harcombe
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nigel F. Delaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nicholas Leiby
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Systems Biology Program, Harvard University, Cambridge, Massachusetts, United States of America
| | - Niels Klitgord
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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12
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Pin C, Hansen T, Muñoz-Cuevas M, de Jonge R, Rosenkrantz JT, Löfström C, Aarts H, Olsen JE. The transcriptional heat shock response of Salmonella typhimurium shows hysteresis and heated cells show increased resistance to heat and acid stress. PLoS One 2012; 7:e51196. [PMID: 23236453 PMCID: PMC3517412 DOI: 10.1371/journal.pone.0051196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 10/30/2012] [Indexed: 11/18/2022] Open
Abstract
We investigated if the transcriptional response of Salmonella Typhimurium to temperature and acid variations was hysteretic, i.e. whether the transcriptional regulation caused by environmental stimuli showed memory and remained after the stimuli ceased. The transcriptional activity of non-replicating stationary phase cells of S. Typhimurium caused by the exposure to 45 °C and to pH 5 for 30 min was monitored by microarray hybridizations at the end of the treatment period as well as immediately and 30 minutes after conditions were set back to their initial values, 25 °C and pH 7. One hundred and two out of 120 up-regulated genes during the heat shock remained up-regulated 30 minutes after the temperature was set back to 25 °C, while only 86 out of 293 down regulated genes remained down regulated 30 minutes after the heat shock ceased. Thus, the majority of the induced genes exhibited hysteresis, i.e., they remained up-regulated after the environmental stress ceased. At 25 °C the transcriptional regulation of genes encoding for heat shock proteins was determined by the previous environment. Gene networks constructed with up-regulated genes were significantly more modular than those of down-regulated genes, implying that down-regulation was significantly less synchronized than up-regulation. The hysteretic transcriptional response to heat shock was accompanied by higher resistance to inactivation at 50 °C as well as cross-resistance to inactivation at pH 3; however, growth rates and lag times at 43 °C and at pH 4.5 were not affected. The exposure to pH 5 only caused up-regulation of 12 genes and this response was neither hysteretic nor accompanied of increased resistance to inactivation conditions. Cellular memory at the transcriptional level may represent a mechanism of adaptation to the environment and a deterministic source of variability in gene regulation.
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Affiliation(s)
- Carmen Pin
- Institute of Food Research, Norwich, United Kingdom.
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13
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Pires-Santos G, Santana-Anjos K, Vannier-Santos M. Optimization of Entamoeba histolytica culturing in vitro. Exp Parasitol 2012; 132:561-5. [DOI: 10.1016/j.exppara.2012.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 06/15/2012] [Accepted: 09/21/2012] [Indexed: 01/15/2023]
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Kocharunchitt C, King T, Gobius K, Bowman JP, Ross T. Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress. Mol Cell Proteomics 2012; 11:M111.009019. [PMID: 22008207 PMCID: PMC3270098 DOI: 10.1074/mcp.m111.009019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An integrated transcriptomic and proteomic analysis was undertaken to determine the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcass chilling in cold air. The response of E. coli during exponential growth at 25 °C a(w) 0.985, 14 °C a(w) 0.985, 25 °C a(w) 0.967, and 14 °C a(w) 0.967 was compared with that of a reference culture (35 °C a(w) 0.993). Gene and protein expression profiles of E. coli were more strongly affected by low water activity (a(w) 0.967) than by low temperature (14 °C). Predefined group enrichment analysis revealed that a universal response of E. coli to all test conditions included activation of the master stress response regulator RpoS and the Rcs phosphorelay system involved in the biosynthesis of the exopolysaccharide colanic acid, as well as down-regulation of elements involved in chemotaxis and motility. However, colanic acid-deficient mutants were shown to achieve comparable growth rates to their wild-type parents under all conditions, indicating that colanic acid is not required for growth. In contrast to the transcriptomic data, the proteomic data revealed that several processes involved in protein synthesis were down-regulated in overall expression at 14 °C a(w) 0.985, 25 °C a(w) 0.967, and 14 °C a(w) 0.967. This result suggests that during growth under these conditions, E. coli, although able to transcribe the required mRNA, may lack the cellular resources required for translation. Elucidating the global adaptive response of E. coli O157:H7 during exposure to chilling and water activity stress has provided a baseline of knowledge of the physiology of this pathogen.
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Affiliation(s)
- Chawalit Kocharunchitt
- Food Safety Centre, Tasmanian Institute of Agricultural Research, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
| | - Thea King
- CSIRO Food and Nutritional Sciences, PO Box 52, North Ryde NSW 1670, Australia
| | - Kari Gobius
- CSIRO Food and Nutritional Sciences, PO Box 745, Archerfield BC QLD 4108, Australia
| | - John P Bowman
- Food Safety Centre, Tasmanian Institute of Agricultural Research, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
| | - Tom Ross
- Food Safety Centre, Tasmanian Institute of Agricultural Research, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia.
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15
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Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation. J Bacteriol 2011; 194:686-701. [PMID: 22139505 DOI: 10.1128/jb.06112-11] [Citation(s) in RCA: 339] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lag phase represents the earliest and most poorly understood stage of the bacterial growth cycle. We developed a reproducible experimental system and conducted functional genomic and physiological analyses of a 2-h lag phase in Salmonella enterica serovar Typhimurium. Adaptation began within 4 min of inoculation into fresh LB medium with the transient expression of genes involved in phosphate uptake. The main lag-phase transcriptional program initiated at 20 min with the upregulation of 945 genes encoding processes such as transcription, translation, iron-sulfur protein assembly, nucleotide metabolism, LPS biosynthesis, and aerobic respiration. ChIP-chip revealed that RNA polymerase was not "poised" upstream of the bacterial genes that are rapidly induced at the beginning of lag phase, suggesting a mechanism that involves de novo partitioning of RNA polymerase to transcribe 522 bacterial genes within 4 min of leaving stationary phase. We used inductively coupled plasma mass spectrometry (ICP-MS) to discover that iron, calcium, and manganese are accumulated by S. Typhimurium during lag phase, while levels of cobalt, nickel, and sodium showed distinct growth-phase-specific patterns. The high concentration of iron during lag phase was associated with transient sensitivity to oxidative stress. The study of lag phase promises to identify the physiological and regulatory processes responsible for adaptation to new environments.
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16
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Czechowska K, van der Meer JR. A flow cytometry based oligotrophic pollutant exposure test to detect bacterial growth inhibition and cell injury. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:5820-5827. [PMID: 21657560 DOI: 10.1021/es200591v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Toxicity of chemical pollutants in aquatic environments is often addressed by assays that inquire reproductive inhibition of test microorganisms, such as algae or bacteria. Those tests, however, assess growth of populations as a whole via macroscopic methods such as culture turbidity or colony-forming units. Here we use flow cytometry to interrogate the fate of individual cells in low-density populations of the bacterium Pseudomonas fluorescens SV3 exposed or not under oligotrophic conditions to a number of common pollutants, some of which derive from oil contamination. Cells were stained at regular time intervals during the exposure assay with fluorescent dyes that detect membrane injury (i.e., live-dead assay). Reduction of population growth rates was observed upon toxicant insult and depended on the type of toxicant. Modeling and cell staining indicate that population growth rate decrease is a combined effect of an increased number of injured cells that may or may not multiply, and live cells dividing at normal growth rates. The oligotrophic assay concept presented here could be a useful complement for existing biomarker assays in compliance with new regulations on chemical effect studies or, more specifically, for judging recovery after exposure to fluctuating toxicant conditions.
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Affiliation(s)
- Kamila Czechowska
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland
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17
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The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production. Appl Environ Microbiol 2011; 77:5294-306. [PMID: 21666015 DOI: 10.1128/aem.02976-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The organic acids lactate and diacetate are commonly used in combination in ready-to-eat foods because they show synergistic ability to inhibit the growth of Listeria monocytogenes. Full-genome microarrays were used to investigate the synergistic transcriptomic responses of two L. monocytogenes strains, H7858 (serotype 4b) and F6854 (serotype 1/2a), to these two organic acids under conditions representing osmotic and cold stress encountered in foods. Strains were exposed to brain heart infusion (BHI) broth at 7°C with 4.65% water-phase (w.p.) NaCl at pH 6.1 with (i) 2% w.p. potassium lactate, (ii) 0.14% w.p. sodium diacetate, (iii) the combination of both at the same levels, or (iv) no organic acids as a control. RNA was extracted 8 h after exposure, during lag phase, to capture gene transcription changes during adaptation to the organic acid stress. Significant differential transcription of 1,041 genes in H7858 and 640 genes in F6854 was observed in at least one pair of the 4 different treatments. The effects of combined treatment with lactate and diacetate included (i) synergistic transcription differences for 474 and 209 genes in H7858 and F6854, respectively, (ii) differential transcription of genes encoding cation transporters and ABC transporters of metals, and (iii) altered metabolism, including induction of a nutrient-limiting stress response, reduction of menaquinone biosynthesis, and a shift from fermentative production of acetate and lactate to energetically less favorable, neutral acetoin. These data suggest that additional treatments that interfere with cellular energy generation processes could more efficiently inhibit the growth of L. monocytogenes.
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18
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Roux AL, Sivadon-Tardy V, Bauer T, Lortat-Jacob A, Herrmann JL, Gaillard JL, Rottman M. Diagnosis of prosthetic joint infection by beadmill processing of a periprosthetic specimen. Clin Microbiol Infect 2010; 17:447-50. [PMID: 20825439 DOI: 10.1111/j.1469-0691.2010.03359.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a microbiological process for the documentation of prosthetic joint infection (PJI). Intraoperative periprosthetic tissue samples from 92 consecutive patients undergoing revision surgery for PJI were submitted to mechanized beadmill processing: specimens were aseptically collected in polypropylene vials, filled with sterile water and glass beads and submitted to mechanized agitation with a beadmill. The documentation rate of PJI following culture on solid and liquid media was 83.7% and the contamination rate 8.7%. Final documentation was obtained after overnight culture for 51.9% of cases and with 7 days of broth culture for all documented cases.
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Affiliation(s)
- A-L Roux
- Université de Versailles Saint-Quentin-en-Yvelines, EA3647, Garches, France
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19
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Ksiazek K. Bacterial aging: from mechanistic basis to evolutionary perspective. Cell Mol Life Sci 2010; 67:3131-7. [PMID: 20526791 PMCID: PMC11115482 DOI: 10.1007/s00018-010-0417-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/22/2010] [Accepted: 05/12/2010] [Indexed: 01/08/2023]
Abstract
Aging-defined as the progressive impairment of an organism's functional capacity, resulting from deleterious changes in cells, organs, and biological systems-is one of the most fundamental features of Eukaryotes, from humans to the unicellular budding yeast Saccharomyces cerevisiae. It has recently been reported that this may also be the case for certain (if not all) types of bacteria. In this paper, the current view on the mechanistic background and evolutionary significance of bacterial kind of aging is presented, with particular emphasis on the role of asymmetric cell division, the characteristics of stationary growth phase, and the role of oxidative protein damage.
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Affiliation(s)
- Krzysztof Ksiazek
- Department of Pathophysiology, University of Medical Sciences, Swiecickiego 6, 60-781, Poznań, Poland.
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20
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Książek K. Let's stop overlooking bacterial aging. Biogerontology 2010; 11:717-23. [PMID: 20440559 DOI: 10.1007/s10522-010-9278-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 04/19/2010] [Indexed: 02/02/2023]
Abstract
It has long been believed that bacteria, the organisms displaying symmetrical pattern of divisions, cannot age, and thereby constitute essentially immortal creatures. In recent years, the discovery of morphologically (Caulobacter crescentus) and functionally (Escherichia coli) asymmetrical cell fission as well as an observation of cell behavior in the stationary growth phase (Escherichia coli) overthrew, at least partly, the myth of bacterial immortality. In fact, the body of evidence has accumulated that bacteria may also get old similarly as eukaryotic cells and organisms do. In this paper a brief overview of the state-of-art in the field of bacterial aging is discussed, and the major challenges and limitations in these research are delineated.
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Affiliation(s)
- Krzysztof Książek
- Department of Pathophysiology, Poznan University of Medical Sciences, Poland.
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21
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Muñoz-Cuevas M, Fernández PS, George S, Pin C. Modeling the lag period and exponential growth of Listeria monocytogenes under conditions of fluctuating temperature and water activity values. Appl Environ Microbiol 2010; 76:2908-15. [PMID: 20208022 PMCID: PMC2863444 DOI: 10.1128/aem.02572-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 02/22/2010] [Indexed: 11/20/2022] Open
Abstract
The dynamic model for the growth of a bacterial population described by Baranyi and Roberts (J. Baranyi and T. A. Roberts, Int. J. Food Microbiol. 23:277-294, 1994) was applied to model the lag period and exponential growth of Listeria monocytogenes under conditions of fluctuating temperature and water activity (a(w)) values. To model the duration of the lag phase, the dependence of the parameter h(0), which quantifies the amount of work done during the lag period, on the previous and current environmental conditions was determined experimentally. This parameter depended not only on the magnitude of the change between the previous and current environmental conditions but also on the current growth conditions. In an exponentially growing population, any change in the environment requiring a certain amount of work to adapt to the new conditions initiated a lag period that lasted until that work was finished. Observations for several scenarios in which exponential growth was halted by a sudden change in the temperature and/or a(w) were in good agreement with predictions. When a population already in a lag period was subjected to environmental fluctuations, the system was reset with a new lag phase. The work to be done during the new lag phase was estimated to be the workload due to the environmental change plus the unfinished workload from the uncompleted previous lag phase.
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Affiliation(s)
- Marina Muñoz-Cuevas
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Pablo S. Fernández
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Susan George
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Carmen Pin
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
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