51
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Degeneration of industrial bacteria caused by genetic instability. World J Microbiol Biotechnol 2020; 36:119. [DOI: 10.1007/s11274-020-02901-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
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52
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Ardaševa A, Gatenby RA, Anderson ARA, Byrne HM, Maini PK, Lorenzi T. A Mathematical Dissection of the Adaptation of Cell Populations to Fluctuating Oxygen Levels. Bull Math Biol 2020; 82:81. [PMID: 32556703 DOI: 10.1007/s11538-020-00754-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/27/2020] [Indexed: 12/17/2022]
Abstract
The disordered network of blood vessels that arises from tumour angiogenesis results in variations in the delivery of oxygen into the tumour tissue. This brings about regions of chronic hypoxia (i.e. sustained low oxygen levels) and regions with alternating periods of low and relatively higher oxygen levels, and makes it necessary for cancer cells to adapt to fluctuating environmental conditions. We use a phenotype-structured model to dissect the evolutionary dynamics of cell populations exposed to fluctuating oxygen levels. In this model, the phenotypic state of every cell is described by a continuous variable that provides a simple representation of its metabolic phenotype, ranging from fully oxidative to fully glycolytic, and cells are grouped into two competing populations that undergo heritable, spontaneous phenotypic variations at different rates. Model simulations indicate that, depending on the rate at which oxygen is consumed by the cells, dynamic nonlinear interactions between cells and oxygen can stimulate chronic hypoxia and cycling hypoxia. Moreover, the model supports the idea that under chronic-hypoxic conditions lower rates of phenotypic variation lead to a competitive advantage, whereas higher rates of phenotypic variation can confer a competitive advantage under cycling-hypoxic conditions. In the latter case, the numerical results obtained show that bet-hedging evolutionary strategies, whereby cells switch between oxidative and glycolytic phenotypes, can spontaneously emerge. We explain how these results can shed light on the evolutionary process that may underpin the emergence of phenotypic heterogeneity in vascularised tumours.
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Affiliation(s)
- Aleksandra Ardaševa
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Robert A Gatenby
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Alexander R A Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Tommaso Lorenzi
- School of Mathematics and Statistics, University of St Andrews, St Andrews, KY16 9SS, UK. .,Department of Mathematical Sciences "G. L. Lagrange", Dipartimento di Eccellenza, 2018-2022, Politecnico di Torino, 10129, Turin, Italy.
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53
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Vourc'h T, Léopoldès J, Peerhossaini H. Clustering of bacteria with heterogeneous motility. Phys Rev E 2020; 101:022612. [PMID: 32168693 DOI: 10.1103/physreve.101.022612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/05/2020] [Indexed: 11/07/2022]
Abstract
We study the clustering of a model cyanobacterium Synechocystis into microcolonies. The bacteria are allowed to diffuse onto surfaces of different hardness and interact with the others by aggregation and detachment. We find that soft surfaces give rise to more microcolonies than hard ones. This effect is related to the amount of heterogeneity of bacteria's dynamics as given by the proportion of motile cells. A kinetic model that emphasizes specific interactions between cells, complemented by extensive numerical simulations considering various amounts of motility, describes the experimental results adequately. The high proportion of motile cells enhances dispersion rather than aggregation.
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Affiliation(s)
- T Vourc'h
- Laboratoire AstroParticules et Cosmologie, CNRS, Université Paris-Diderot, Université de Paris, 5 rue Thomas Mann 75013 Paris, France
| | - J Léopoldès
- ESPCI Paris, PSL Research University, CNRS, Institut Langevin, 1 rue Jussieu, F-75005 Paris, France.,Université Paris-Est Marne-la-Vallée, 5 Bd Descartes, Champs sur Marne, Marne-la-Vallée Cedex 2, France
| | - H Peerhossaini
- Laboratoire AstroParticules et Cosmologie, CNRS, Université Paris-Diderot, Université de Paris, 5 rue Thomas Mann 75013 Paris, France.,Mechanics of Active Fluids Laboratory, Department of Civil and Environmental Engineering, Department of Mechanical and Materials Engineering, University of Western Ontario, London, Ontario, Canada N6A3K7
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54
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Ardaševa A, Gatenby RA, Anderson ARA, Byrne HM, Maini PK, Lorenzi T. Evolutionary dynamics of competing phenotype-structured populations in periodically fluctuating environments. J Math Biol 2020; 80:775-807. [PMID: 31641842 PMCID: PMC7028828 DOI: 10.1007/s00285-019-01441-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/14/2019] [Indexed: 12/20/2022]
Abstract
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in ecology, which is used to explain how species may survive when faced with the evolutionary risks associated with temporally varying environments. In order to support a deeper understanding of the adaptive role of spontaneous phenotypic variations in fluctuating environments, we consider a system of non-local partial differential equations modelling the evolutionary dynamics of two competing phenotype-structured populations in the presence of periodically oscillating nutrient levels. The two populations undergo heritable, spontaneous phenotypic variations at different rates. The phenotypic state of each individual is represented by a continuous variable, and the phenotypic landscape of the populations evolves in time due to variations in the nutrient level. Exploiting the analytical tractability of our model, we study the long-time behaviour of the solutions to obtain a detailed mathematical depiction of the evolutionary dynamics. The results suggest that when nutrient levels undergo small and slow oscillations, it is evolutionarily more convenient to rarely undergo spontaneous phenotypic variations. Conversely, under relatively large and fast periodic oscillations in the nutrient levels, which bring about alternating cycles of starvation and nutrient abundance, higher rates of spontaneous phenotypic variations confer a competitive advantage. We discuss the implications of our results in the context of cancer metabolism.
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Affiliation(s)
- Aleksandra Ardaševa
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG UK
| | - Robert A. Gatenby
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL USA
| | | | - Helen M. Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG UK
| | - Philip K. Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG UK
| | - Tommaso Lorenzi
- School of Mathematics and Statistics, University of St Andrews, St Andrews, KY16 9SS UK
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55
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Yu JR, Feng TJ, Zheng XD, Chen DH, Tao Y. Transitions in the cell-fate induction induced by colored noise associated with the inductive stimulus. J Theor Biol 2020; 484:110018. [PMID: 31550442 DOI: 10.1016/j.jtbi.2019.110018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/15/2022]
Abstract
The cell-fate induction based on the saddle-node bifurcation is undoubtedly a very important concept in developmental biology, which provides a possible mechanism to explain the intrinsic irreversibility in the developmental process. In this paper, the effect of a colored noise, which is associated with the inductive stimulus, on the saddle-node landscape of cell-fate induction is investigated, especially, the effect of the change of correlation time of colored noise on cell-fate induction. The main results show clearly that the change of correlation time of colored noise could induce the transitions of the system. This implies that the colored noise associated with inductive stimulus may have a profound effect on the saddle-node bifurcation landscape of cell-fate induction. This will also help us to understand more deeply the role of cell-fate induction in developmental biology.
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Affiliation(s)
- Jie-Ru Yu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China; Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tian-Jiao Feng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Systems Science, Beijing Normal University, Beijing 100875, China
| | - Xiu-Deng Zheng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Da-Hua Chen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Tao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
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56
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Gumuscu B, Herr AE. Separation-encoded microparticles for single-cell western blotting. LAB ON A CHIP 2020; 20:64-73. [PMID: 31773114 PMCID: PMC7029799 DOI: 10.1039/c9lc00917e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Direct measurement of proteins from single cells has been realized at the microscale using microfluidic channels, capillaries, and semi-enclosed microwell arrays. Although powerful, these formats are constrained, with the enclosed geometries proving cumbersome for multistage assays, including electrophoresis followed by immunoprobing. We introduce a hybrid microfluidic format that toggles between a planar microwell array and a suspension of microparticles. The planar array is stippled in a thin sheet of polyacrylamide gel, for efficient single-cell isolation and protein electrophoresis of hundreds-to-thousands of cells. Upon mechanical release, array elements become a suspension of separation-encoded microparticles for more efficient immunoprobing due to enhanced mass transfer. Dehydrating microparticles offer improved analytical sensitivity owing to in-gel concentration of fluorescence signal for high-throughput single-cell targeted proteomics.
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Affiliation(s)
- Burcu Gumuscu
- Department of Bioengineering, University of California Berkeley, Berkeley, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California Berkeley, Berkeley, USA.
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57
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Intracellular Energy Variability Modulates Cellular Decision-Making Capacity. Sci Rep 2019; 9:20196. [PMID: 31882965 PMCID: PMC6934696 DOI: 10.1038/s41598-019-56587-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
Cells generate phenotypic diversity both during development and in response to stressful and changing environments, aiding survival. Functionally vital cell fate decisions from a range of phenotypic choices are made by regulatory networks, the dynamics of which rely on gene expression and hence depend on the cellular energy budget (and particularly ATP levels). However, despite pronounced cell-to-cell ATP differences observed across biological systems, the influence of energy availability on regulatory network dynamics is often overlooked as a cellular decision-making modulator, limiting our knowledge of how energy budgets affect cell behaviour. Here, we consider a mathematical model of a highly generalisable, ATP-dependent, decision-making regulatory network, and show that cell-to-cell ATP variability changes the sets of decisions a cell can make. Our model shows that increasing intracellular energy levels can increase the number of supported stable phenotypes, corresponding to increased decision-making capacity. Model cells with sub-threshold intracellular energy are limited to a singular phenotype, forcing the adoption of a specific cell fate. We suggest that energetic differences between cells may be an important consideration to help explain observed variability in cellular decision-making across biological systems.
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58
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Zhang R, Slamti L, Tong L, Verplaetse E, Ma L, Lemy C, Peng Q, Guo S, Zhang J, Song F, Lereclus D. The stationary phase regulator CpcR activates cry gene expression in non-sporulating cells of Bacillus thuringiensis. Mol Microbiol 2019; 113:740-754. [PMID: 31793098 DOI: 10.1111/mmi.14439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/29/2022]
Abstract
Cell differentiation within an isogenic population allows the specialisation of subpopulations and a division of labour. Bacillus thuringiensis is a spore-forming bacterium that produces insecticidal crystal proteins (Cry proteins) in sporulating cells. We recently reported that strain B. thuringiensis LM1212 presents the unique ability to differentiate into two subpopulations during the stationary phase: spore-formers and crystal-producers. Here, we characterised the transcriptional regulator CpcR responsible for this differentiation and the expression of the cry genes. cpcR is located on a plasmid that also harbours cry genes. The alignment of LM1212 cry gene promoters revealed the presence of a conserved DNA sequence upstream from the -35 region. This presumed CpcR box was also found in the promoter of cpcR and we showed that cpcR transcription is positively autoregulated. Electrophoretic mobility shift assays suggested that CpcR directly controls the transcription of its target genes by binding to the CpcR box. We showed that CpcR was able to direct the production of a crystal consisting of a heterologous insecticidal Cry protein in non-sporulating cells of a typical B. thuringiensis kurstaki strain. Moreover, the expression of cpcR induced a reduction in the sporulation of this B. thuringiensis strain, suggesting an interaction between CpcR and the sporulation regulatory networks.
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Affiliation(s)
- Ruibin Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.,Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Leyla Slamti
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Lei Tong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Emilie Verplaetse
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Lixia Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.,Beijing Institute of Technology, Beijing, P. R. China
| | - Christelle Lemy
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Qi Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Shuyuan Guo
- Beijing Institute of Technology, Beijing, P. R. China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Didier Lereclus
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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59
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Manina G, Griego A, Singh LK, McKinney JD, Dhar N. Preexisting variation in DNA damage response predicts the fate of single mycobacteria under stress. EMBO J 2019; 38:e101876. [PMID: 31583725 PMCID: PMC6856624 DOI: 10.15252/embj.2019101876] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/06/2019] [Accepted: 09/16/2019] [Indexed: 11/09/2022] Open
Abstract
Clonal microbial populations are inherently heterogeneous, and this diversification is often considered as an adaptation strategy. In clinical infections, phenotypic diversity is found to be associated with drug tolerance, which in turn could evolve into genetic resistance. Mycobacterium tuberculosis, which ranks among the top ten causes of mortality with high incidence of drug-resistant infections, exhibits considerable phenotypic diversity. In this study, we quantitatively analyze the cellular dynamics of DNA damage responses in mycobacteria using microfluidics and live-cell fluorescence imaging. We show that individual cells growing under optimal conditions experience sporadic DNA-damaging events manifested by RecA expression pulses. Single-cell responses to these events occur as transient pulses of fluorescence expression, which are dependent on the gene-network structure but are triggered by extrinsic signals. We demonstrate that preexisting subpopulations, with discrete levels of DNA damage response, are associated with differential susceptibility to fluoroquinolones. Our findings reveal that the extent of DNA integrity prior to drug exposure impacts the drug activity against mycobacteria, with conceivable therapeutic implications.
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Affiliation(s)
- Giulia Manina
- Microbial Individuality and Infection GroupCell Biology and Infection DepartmentInstitut PasteurParisFrance
- School of Life SciencesSwiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Anna Griego
- Microbial Individuality and Infection GroupCell Biology and Infection DepartmentInstitut PasteurParisFrance
- Université Paris DescartesSorbonne Paris CitéParisFrance
| | - Lalit Kumar Singh
- Microbial Individuality and Infection GroupCell Biology and Infection DepartmentInstitut PasteurParisFrance
| | - John D McKinney
- School of Life SciencesSwiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Neeraj Dhar
- School of Life SciencesSwiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
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60
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Torres MA, Terraf MCL, Minahk CJ, Delgado MA. Stability of the Salmonella Typhimurium rcsC11 mutant under different stress conditions. MICROBIOLOGY-SGM 2019; 166:157-168. [PMID: 31714197 DOI: 10.1099/mic.0.000873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The virulence genes of Salmonella are modulated during infection by several regulatory systems, and the RcsCDB system is one of the most important of these. The S. Typhimurium EG14873 (rcsC11) strain harbours the rcsC11 point mutation, displaying a constitutive activation of this system, which is characterized by mucoid colonies and attenuated virulence phenotypes. In this work, the stability of the rcsC11 mutation was analysed under stress conditions. Under acid and anaerobic stresses, we observed the appearance of small and non-mucoid colonies of the rcsC11 strain. The sequencing of the rcsC gene from these colonies showed that the mutation is conserved. Moreover, we found that small colonies were also generated when the wild-type strain grew in acid and anaerobic conditions. It is worth noting that the transition from normal to atypical colonies of both strains only took place after several days of incubation and was not observed during eukaryotic cell infection. Therefore, the appearance of these atypical colonies is a characteristic feature of S. Typhimurium strains under stressful situations and does not involve a reversion of the rcsC11 allele and nor does it imply any risk to mammalian cells. Therefore, we propose that the S. Typhimurium rcsC11 strain is a good candidate for the development of attenuated vaccines.
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Affiliation(s)
- Mariela A Torres
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica 'Dr. Bernabé Bloj', Facultad de Bioquímica, Química y Farmacia, UNT Chacabuco 461, T4000ILI - San Miguel de Tucumán, Argentina
| | - María C Leccese Terraf
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica 'Dr. Bernabé Bloj', Facultad de Bioquímica, Química y Farmacia, UNT Chacabuco 461, T4000ILI - San Miguel de Tucumán, Argentina
| | - Carlos J Minahk
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica 'Dr. Bernabé Bloj', Facultad de Bioquímica, Química y Farmacia, UNT Chacabuco 461, T4000ILI - San Miguel de Tucumán, Argentina
| | - Mónica A Delgado
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica 'Dr. Bernabé Bloj', Facultad de Bioquímica, Química y Farmacia, UNT Chacabuco 461, T4000ILI - San Miguel de Tucumán, Argentina
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61
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Gasperotti A, Brameyer S, Fabiani F, Jung K. Phenotypic heterogeneity of microbial populations under nutrient limitation. Curr Opin Biotechnol 2019; 62:160-167. [PMID: 31698311 DOI: 10.1016/j.copbio.2019.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
Abstract
Phenotypic heterogeneity is a phenomenon in which genetically identical individuals have different characteristics. This behavior can also be found in bacteria, even if they grow as monospecies in well-mixed environments such as bioreactors. Here it is discussed how phenotypic heterogeneity is generated by internal factors and how it is promoted under nutrient-limited growth conditions. A better understanding of the molecular levels that control phenotypic heterogeneity could improve biotechnological production processes.
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Affiliation(s)
- Ana Gasperotti
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Florian Fabiani
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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62
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Jung K, Brameyer S, Fabiani F, Gasperotti A, Hoyer E. Phenotypic Heterogeneity Generated by Histidine Kinase-Based Signaling Networks. J Mol Biol 2019; 431:4547-4558. [DOI: 10.1016/j.jmb.2019.03.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 01/16/2023]
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63
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Influence of Phenotypic Dissociation in Bacillus subtilis Strain ET-1 on Iturin A Production. Curr Microbiol 2019; 76:1487-1494. [PMID: 31494740 DOI: 10.1007/s00284-019-01764-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/26/2019] [Indexed: 10/26/2022]
Abstract
Iturin A is a very important cyclic lipopeptide produced by several B. subtilis strains and has large commercial and therapeutic application potentials but its production on industrial scale has not been realized yet. In the present study, we have observed that the strain ET-1 of Bacillus subtilis, a producer of Iturin A, can present at least three different colony morphologies, which we arbitrarily called Rough, Smooth, and Mucoid morphotypes (R-, S-, and M-form). Performing HPLC analysis, a significant difference between the amounts of Iturin A produced by the three morphotypes was found. The morphotype R-form showed the highest productivity with yields about 10 and 100 times higher than morphotypes S and M, respectively. The results show that the production of Iturin A by B. subtilis could be strongly influenced by the phenotypic heterogeneity of cells within the inoculum. Indeed, we have observed that, pasteurizing the inoculum before seeding in order to improve the homogeneity removing the phenotypes less able to synthesize the Iturin A, its yields in a bench-scale production could be significantly improved. This can represent an important control factor also at industrial scale to improve the Iturin A yields, the robustness, the replicability, and consequently the cost-effectiveness of fermentation processes.
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64
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Khlebodarova TM, Likhoshvai VA. Molecular Mechanisms of Non-Inherited Antibiotic Tolerance in Bacteria and Archaea. Mol Biol 2019. [DOI: 10.1134/s0026893319040058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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65
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Izri Z, Garenne D, Noireaux V, Maeda YT. Gene Expression in on-Chip Membrane-Bound Artificial Cells. ACS Synth Biol 2019; 8:1705-1712. [PMID: 31268305 DOI: 10.1021/acssynbio.9b00247] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Artificial cells made of molecular components and lipid membrane are emerging platforms to characterize living systems properties. Cell-free transcription-translation (TXTL) offers advantages for the bottom-up synthesis of cellular reactors. Yet, scaling up their design within well-defined geometries remains challenging. We present a microfluidic device hosting TXTL reactions of a reporter gene in thousands of microwells separated from an external buffer by a phospholipid membrane. In the presence of nutrients in the buffer, microreactors are stable beyond 24 h and yield a few mg/mL of proteins. Nutrients in the external solution feed the TXTL reaction at the picoliter scale via passive transport across the phospholipid membrane of each microfluidic well, despite the absence of pores. Replacing nutrients with an inert polymer and fatty acids at an isotonic concentration reduces microreactors efficiency, and a significant fraction yields no protein. This emphasizes the crucial role of the membrane for designing cell-free TXTL microreactors as efficient artificial cells.
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Affiliation(s)
- Ziane Izri
- Department of Physics , Kyushu University , Fukuoka , 819-0395 , Japan
| | - David Garenne
- School of Physics and Astronomy , University of Minnesota , Minneapolis , Minnesota 55455 United States
| | - Vincent Noireaux
- School of Physics and Astronomy , University of Minnesota , Minneapolis , Minnesota 55455 United States
| | - Yusuke T Maeda
- Department of Physics , Kyushu University , Fukuoka , 819-0395 , Japan
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66
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Weiss CA, Hoberg JA, Liu K, Tu BP, Winkler WC. Single-Cell Microscopy Reveals That Levels of Cyclic di-GMP Vary among Bacillus subtilis Subpopulations. J Bacteriol 2019; 201:e00247-19. [PMID: 31138629 PMCID: PMC6657594 DOI: 10.1128/jb.00247-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/21/2019] [Indexed: 11/20/2022] Open
Abstract
The synthesis of signaling molecules is one strategy bacteria employ to sense alterations in their environment and rapidly adjust to those changes. In Gram-negative bacteria, bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulates the transition from a unicellular motile state to a multicellular sessile state. However, c-di-GMP signaling has been less intensively studied in Gram-positive organisms. To that end, we constructed a fluorescent yfp reporter based on a c-di-GMP-responsive riboswitch to visualize the relative abundance of c-di-GMP for single cells of the Gram-positive model organism Bacillus subtilis Coupled with cell-type-specific fluorescent reporters, this riboswitch reporter revealed that c-di-GMP levels are markedly different among B. subtilis cellular subpopulations. For example, cells that have made the decision to become matrix producers maintain higher intracellular c-di-GMP concentrations than motile cells. Similarly, we find that c-di-GMP levels differ between sporulating and competent cell types. These results suggest that biochemical measurements of c-di-GMP abundance are likely to be inaccurate for a bulk ensemble of B. subtilis cells, as such measurements will average c-di-GMP levels across the population. Moreover, the significant variation in c-di-GMP levels between cell types hints that c-di-GMP might play an important role during B. subtilis biofilm formation. This study therefore emphasizes the importance of using single-cell approaches for analyzing metabolic trends within ensemble bacterial populations.IMPORTANCE Many bacteria have been shown to differentiate into genetically identical yet morphologically distinct cell types. Such population heterogeneity is especially prevalent among biofilms, where multicellular communities are primed for unexpected environmental conditions and can efficiently distribute metabolic responsibilities. Bacillus subtilis is a model system for studying population heterogeneity; however, a role for c-di-GMP in these processes has not been thoroughly investigated. Herein, we introduce a fluorescent reporter, based on a c-di-GMP-responsive riboswitch, to visualize the relative abundance of c-di-GMP for single B. subtilis cells. Our analysis shows that c-di-GMP levels are conspicuously different among B. subtilis cellular subtypes, suggesting a role for c-di-GMP during biofilm formation. These data highlight the utility of riboswitches as tools for imaging metabolic changes within individual bacterial cells. Analyses such as these offer new insight into c-di-GMP-regulated phenotypes, especially given that other biofilms also consist of multicellular communities.
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Affiliation(s)
- Cordelia A Weiss
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Jakob A Hoberg
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Kuanqing Liu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Benjamin P Tu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
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67
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van Gestel J, Ackermann M, Wagner A. Microbial life cycles link global modularity in regulation to mosaic evolution. Nat Ecol Evol 2019; 3:1184-1196. [PMID: 31332330 DOI: 10.1038/s41559-019-0939-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 06/03/2019] [Indexed: 11/09/2022]
Abstract
Microbes are exposed to changing environments, to which they can respond by adopting various lifestyles such as swimming, colony formation or dormancy. These lifestyles are often studied in isolation, thereby giving a fragmented view of the life cycle as a whole. Here, we study lifestyles in the context of this whole. We first use machine learning to reconstruct the expression changes underlying life cycle progression in the bacterium Bacillus subtilis, based on hundreds of previously acquired expression profiles. This yields a timeline that reveals the modular organization of the life cycle. By analysing over 380 Bacillales genomes, we then show that life cycle modularity gives rise to mosaic evolution in which life stages such as motility and sporulation are conserved and lost as discrete units. We postulate that this mosaic conservation pattern results from habitat changes that make these life stages obsolete or detrimental. Indeed, when evolving eight distinct Bacillales strains and species under laboratory conditions that favour colony growth, we observe rapid and parallel losses of the sporulation life stage across species, induced by mutations that affect the same global regulator. We conclude that a life cycle perspective is pivotal to understanding the causes and consequences of modularity in both regulation and evolution.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland. .,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,The Santa Fe Institute, Santa Fe, NM, USA.
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68
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Müller J, Spriewald S, Stecher B, Stadler E, Fuchs TM. Evolutionary Stability of Salmonella Competition with the Gut Microbiota: How the Environment Fosters Heterogeneity in Exploitative and Interference Competition. J Mol Biol 2019; 431:4732-4748. [PMID: 31260689 DOI: 10.1016/j.jmb.2019.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 11/27/2022]
Abstract
Following ingestion, gastrointestinal pathogens compete against the gastrointestinal microbiota and overcome host immune defenses in order to cause infections. Besides employing direct killing mechanisms, the commensal microbiota occupies metabolic niches to outcompete invading pathogens. Salmonella enterica serovar Typhimurium (S. Typhimurium) uses several strategies to successfully colonize the gut and establish infection, of which an increasing number is based on phenotypic heterogeneity within the S. Typhimurium population. The utilization of myo-inositol (MI) and the production of colicin confer a selective advantage over the microbiota in terms of exploitative and interference competition, respectively. In this review, we summarize the genetic basis underlying bistability of MI catabolism and colicin production. As demonstrated by single-cell analyses, a stochastic switch in the expression of the genes responsible for colicin production and MI degradation constitutes the heterogeneity of the two phenotypes. Both genetic systems are tightly regulated to avoid their expression under non-appropriate conditions and possible detrimental effects on bacterial fitness. Moreover, evolutionary mechanisms underlying formation and stability of these phenotypes in S. Typhimurium are discussed. We propose that both MI catabolism and colicin production create a bet-hedging strategy, which provides an adaptive benefit for S. Typhimurium in the fluctuating environment of the mammalian gut.
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Affiliation(s)
- Johannes Müller
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany; Institute for Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Stefanie Spriewald
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Eva Stadler
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institut für Molekulare Pathogenese, Naumburger Str. 96a, 07743 Jena, Germany.
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69
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García-Betancur JC, Lopez D. Cell Heterogeneity in Staphylococcal Communities. J Mol Biol 2019; 431:4699-4711. [PMID: 31220460 DOI: 10.1016/j.jmb.2019.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
The human pathogen Staphylococcus aureus is a gram-positive bacterium that causes difficult-to-treat infections. One of the reasons why S. aureus is such as successful pathogen is due to the cell-to-cell physiological variability that exists within microbial communities. Many laboratories around the world study the genetic mechanisms involved in S. aureus cell heterogeneity to better understand infection mechanism of this bacterium. It was recently shown that the Agr quorum-sensing system, which antagonistically regulates biofilm-associated or acute bacteremia infections, is expressed in a subpopulation of specialized cells. In this review, we discuss the different genetic mechanism for bacterial cell differentiation and the physiological properties of the distinct cell types that are already described in S. aureus communities, as well as the role that these cell types play during an infection process.
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Affiliation(s)
- Juan Carlos García-Betancur
- Research Center for Infectious Diseases ZINF, University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology IMIB, University of Würzburg, 97080 Würzburg, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology IMIB, University of Würzburg, 97080 Würzburg, Germany; National Centre for Biotechnology (CNB-CSIC), 28050 Madrid, Spain.
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70
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Bettenworth V, Steinfeld B, Duin H, Petersen K, Streit WR, Bischofs I, Becker A. Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems. J Mol Biol 2019; 431:4530-4546. [PMID: 31051177 DOI: 10.1016/j.jmb.2019.04.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/11/2022]
Abstract
Quorum sensing is usually thought of as a collective behavior in which all members of a population partake. However, over the last decade, several reports of phenotypic heterogeneity in quorum sensing-related gene expression have been put forward, thus challenging this view. In the respective systems, cells of isogenic populations did not contribute equally to autoinducer production or target gene activation, and in some cases, the fraction of contributing cells was modulated by environmental factors. Here, we look into potential origins of these incidences and into how initial cell-to-cell variations might be amplified to establish distinct phenotypic heterogeneity. We furthermore discuss potential functions heterogeneity in bacterial quorum sensing systems could serve: as a preparation for environmental fluctuations (bet hedging), as a more cost-effective way of producing public goods (division of labor), as a loophole for genotypic cooperators when faced with non-contributing mutants (cheat protection), or simply as a means to fine-tune the output of the population as a whole (output modulation). We illustrate certain aspects of these recent developments with the model organisms Sinorhizobium meliloti, Sinorhizobium fredii and Bacillus subtilis, which possess quorum sensing systems of different complexity, but all show phenotypic heterogeneity therein.
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Affiliation(s)
- Vera Bettenworth
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35043 Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany.
| | - Benedikt Steinfeld
- BioQuant Center of the University of Heidelberg, 69120 Heidelberg, Germany; Center for Molecular Biology (ZMBH), University of Heidelberg, 69120 Heidelberg, Germany; Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
| | - Hilke Duin
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Katrin Petersen
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Ilka Bischofs
- BioQuant Center of the University of Heidelberg, 69120 Heidelberg, Germany; Center for Molecular Biology (ZMBH), University of Heidelberg, 69120 Heidelberg, Germany; Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35043 Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany.
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71
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Serra DO, Hengge R. A c-di-GMP-Based Switch Controls Local Heterogeneity of Extracellular Matrix Synthesis which Is Crucial for Integrity and Morphogenesis of Escherichia coli Macrocolony Biofilms. J Mol Biol 2019; 431:4775-4793. [PMID: 30954572 DOI: 10.1016/j.jmb.2019.04.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
The extracellular matrix in macrocolony biofilms of Escherichia coli is arranged in a complex large-scale architecture, with homogenic matrix production close to the surface, whereas zones further below display pronounced local heterogeneity of matrix production, which results in distinct three-dimensional architectural structures. Combining genetics, cryosectioning and fluorescence microscopy of macrocolony biofilms, we demonstrate here in situ that this local matrix heterogeneity is generated by a c-di-GMP-dependent molecular switch characterized by several nested positive and negative feedback loops. In this switch, the trigger phosphodiesterase PdeR is the key component for establishing local heterogeneity in the activation of the transcription factor MlrA, which in turn activates expression of the major matrix regulator CsgD. Upon its release of direct inhibition by PdeR, the second switch component, the diguanylate cyclase DgcM, activates MlrA by direct interaction. Antagonistically acting PdeH and DgcE provide for a PdeR-sensed c-di-GMP input into this switch and-via their spatially differentially controlled expression-generate the long-range vertical asymmetry of the matrix architecture. Using flow cytometry, we show heterogeneity of CsgD expression to also occur in spatially unstructured planktonic cultures, where it is controlled by the same c-di-GMP circuitry as in macrocolony biofilms. Quantification by flow cytometry also showed CsgDON subpopulations with distinct CsgD expression levels and revealed an additional fine-tuning feedback within the PdeR/DgcM-mediated switch that depends on c-di-GMP synthesis by DgcM. Finally, local heterogeneity of matrix production was found to be crucial for the tissue-like elasticity that allows for large-scale wrinkling and folding of macrocolony biofilms.
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Affiliation(s)
- Diego O Serra
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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72
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Sawato T, Saito N, Yamaguchi M. Chemical Systems Involving Two Competitive Self-Catalytic Reactions. ACS OMEGA 2019; 4:5879-5899. [PMID: 31459737 PMCID: PMC6648109 DOI: 10.1021/acsomega.9b00133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/13/2019] [Indexed: 06/10/2023]
Abstract
Self-catalytic reactions are chemical phenomena, in which a product catalyzes the reactions of substrates further to yield products. A significant amplification of product concentration occurs during the reactions in a dilute solution, which exhibit notable properties such as sigmoidal kinetics, seeding effects, and thermal hysteresis. Chemical systems involving two competitive self-catalytic reactions can be considered, in which the competitive formation of two products occurs, which is affected by environmental changes, subtle perturbations, and fluctuations, and notable chemical phenomena appear such as formation of different structures in response to slow/fast temperature changes, chiral symmetry breaking, shortcut in reaction time, homogeneous-heterogeneous transitions, and mechanical responses. Studies on such chemical systems provide understanding on biological systems and can also be extended to the development of novel functional materials.
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73
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Schoenfelder SMK, Lange C, Prakash SA, Marincola G, Lerch MF, Wencker FDR, Förstner KU, Sharma CM, Ziebuhr W. The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities. PLoS Pathog 2019; 15:e1007618. [PMID: 30870530 PMCID: PMC6435200 DOI: 10.1371/journal.ppat.1007618] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/26/2019] [Accepted: 02/04/2019] [Indexed: 12/15/2022] Open
Abstract
RsaE is a conserved small regulatory RNA (sRNA) which was previously reported to represent a riboregulator of central carbon flow and other metabolic pathways in Staphylococcus aureus and Bacillus subtilis. Here we show that RsaE contributes to extracellular (e)DNA release and biofilm-matrix switching towards polysaccharide intercellular adhesin (PIA) production in a hypervariable Staphylococcus epidermidis isolate. Transcriptome analysis through differential RNA sequencing (dRNA-seq) in combination with confocal laser scanning microscopy (CLSM) and reporter gene fusions demonstrate that S. epidermidis protein- and PIA-biofilm matrix producers differ with respect to RsaE and metabolic gene expression. RsaE is spatiotemporally expressed within S. epidermidis PIA-mediated biofilms, and its overexpression triggers a PIA biofilm phenotype as well as eDNA release in an S. epidermidis protein biofilm matrix-producing strain background. dRNA-seq and Northern blot analyses revealed RsaE to exist as a major full-length 100-nt transcript and a minor processed species lacking approximately 20 nucleotides at the 5'-end. RsaE processing results in expansion of the mRNA target spectrum. Thus, full-length RsaE interacts with S. epidermidis antiholin-encoding lrgA mRNA, facilitating bacterial lysis and eDNA release. Processed RsaE, however, interacts with the 5'-UTR of icaR and sucCD mRNAs, encoding the icaADBC biofilm operon repressor IcaR and succinyl-CoA synthetase of the tricarboxylic acid (TCA) cycle, respectively. RsaE augments PIA-mediated biofilm matrix production, most likely through activation of icaADBC operon expression via repression of icaR as well as by TCA cycle inhibition and re-programming of staphylococcal central carbon metabolism towards PIA precursor synthesis. Additionally, RsaE supports biofilm formation by mediating the release of eDNA as stabilizing biofilm matrix component. As RsaE itself is heterogeneously expressed within biofilms, we consider this sRNA to function as a factor favoring phenotypic heterogeneity and supporting division of labor in S. epidermidis biofilm communities. Bacterial biofilms are highly organized structures which functionally emulate multicellular organisms, last but not least through heterogeneous gene expression patterns displayed by biofilm subpopulations. Here we analyzed the functions of the non-coding RNA RsaE in Staphylococcus epidermidis biofilm communities. RsaE exerted unexpected influences on S. epidermidis biofilm matrix composition by triggering localized eDNA release and facilitating PIA expression. RsaE accomplishes these effects by targeting mRNAs involved in bacterial lysis control, icaADBC expression and TCA cycle activity, with RsaE undergoing processing to exploit its full target potential. Interestingly, RsaE interaction with lysis-engaged lrgA mRNA is specific for S. epidermidis lrgA, but does not occur with lrgA mRNA from S. aureus, suggesting species-specific differences in staphylococcal lysis control. We speculate that RsaE-mediated bacterial lysis might represent a form of bacterial altruism contributing to biofilm structuring by providing nutrients to neighboring bacterial cells as well as by releasing eDNA as stabilizing biofilm matrix component. Due to its heterogeneous expression, we consider RsaE as a supporting factor that facilitates population diversity. Together, the data give insight into an unanticipated role of sRNAs as players in S. epidermidis biofilm organization.
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Affiliation(s)
| | - Claudia Lange
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | | | - Gabriella Marincola
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Maike F. Lerch
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Freya D. R. Wencker
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Konrad U. Förstner
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Cynthia M. Sharma
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Wilma Ziebuhr
- University of Würzburg, Institute of Molecular Infection Biology, Würzburg, Germany
- * E-mail:
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74
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Guo X, Silva KPT, Boedicker JQ. Single-cell variability of growth interactions within a two-species bacterial community. Phys Biol 2019; 16:036001. [DOI: 10.1088/1478-3975/ab005f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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75
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Stress-induced protein aggregates shape population heterogeneity in bacteria. Curr Genet 2019; 65:865-869. [PMID: 30820637 DOI: 10.1007/s00294-019-00947-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 02/07/2023]
Abstract
The concept of phenotypic heterogeneity preparing a subpopulation of isogenic cells to better cope with anticipated stresses has been well established. However, less is known about how stress itself can drive subsequent cellular individualization in clonal populations. In this perspective, we focus on the impact of stress-induced cellular protein aggregates, and how their segregation and disaggregation can act as a deterministic incentive for heterogeneity in the population emerging from a stressed ancestor.
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76
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Abstract
To survive unpredictable environmental change, many organisms adopt bet-hedging strategies that are initially costly but provide a long-term fitness benefit. The temporal extent of these deferred fitness benefits determines whether bet-hedging organisms can survive long enough to realize them. In this article, we examine a model of microbial bet hedging in which there are two paths to extinction: unpredictable environmental change and demographic stochasticity. In temporally correlated environments, these drivers of extinction select for different switching strategies. Rapid phenotype switching ensures survival in the face of unpredictable environmental change, while slower-switching organisms become extinct. However, when both switching strategies are present in the same population, then demographic stochasticity-enforced by a limited population size-leads to extinction of the faster-switching organism. As a result, we find a novel form of evolutionary suicide whereby selection in a fluctuating environment can favor bet-hedging strategies that ultimately increase the risk of extinction. Population structures with multiple subpopulations and dispersal can reduce the risk of extinction from unpredictable environmental change and shift the balance so as to facilitate the evolution of slower-switching organisms.
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77
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Willis A, Chuang AW, Dyhrman S, Burford MA. Differential expression of phosphorus acquisition genes in response to phosphorus stress in two Raphidiopsis raciborskii strains. HARMFUL ALGAE 2019; 82:19-25. [PMID: 30928007 DOI: 10.1016/j.hal.2018.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
The cyanobacterium Raphidiopsis raciborskii is a nuisance in freshwater ecosystems. Strains vary in their physiological responses to environmental drivers, thus a greater understanding of the magnitude of strain variation is required to characterize the species. In this study, two strains of R. raciborskii isolated from a tropical Australian water reservoir were grown with and without phosphorus (P) to determine any relative response to P stress. The strains had the same growth rates and under P free conditions, cells grew at the same rate as P replete conditions until day 9 when cell growth ceased. There was no difference in the alkaline phosphatase activity per cell for the P replete and P free conditions, but the level of activity per cell was greater in CS-505 than CS-506. P acquisition genes were identified from the sequenced genomes; both strains contained the same genes, but with differences in copy number of phoA (7 and 6), phnK (3 and 1) and phnH (2 and 1) between CS-505 and CS-506 (respectively). The expression of P acquisition genes under P stress was measured throughout the experiment and shown to vary in magnitude and timing across strains, and in P replete versus P free cultures. In strain CS-505, upregulation of the pstS1 and phoA genes occurred late in the growth phase and into senescence. These genes are involved in phosphate uptake and use of various forms of organic P. For strain CS-506, there was upregulation of the phosphate uptake gene, pit, and organic P utilization genes, phoA, phoU, phnD and phnK, commencing late in the growth phase. Our study shows that despite the fact that these two strains were isolated from the same waterbody, they differed markedly in their gene expression response to P free conditions. This capacity of R. raciborskii to vary in strain responses to P conditions gives the organism flexibility in responding to environmental change, particularly P stress conditions.
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Affiliation(s)
- Anusuya Willis
- Australian Rivers Institute, Griffith University, Nathan, 4111 Queensland, Australia.
| | - Ann W Chuang
- Australian Rivers Institute, Griffith University, Nathan, 4111 Queensland, Australia
| | - Sonya Dyhrman
- Department of Earth and Environmental Sciences, and the Lamont-Doherty Earth Observatory, Columbia University, Palisades NY, 10964, USA
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, Nathan, 4111 Queensland, Australia
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78
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Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin-antitoxin system. Curr Genet 2019; 65:133-138. [PMID: 30132188 PMCID: PMC6343021 DOI: 10.1007/s00294-018-0879-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022]
Abstract
Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin-antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin-antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin-antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.
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Affiliation(s)
- Nela Nikolic
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria.
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79
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Pasotti L, Bellato M, Politi N, Casanova M, Zucca S, Cusella De Angelis MG, Magni P. A Synthetic Close-Loop Controller Circuit for the Regulation of an Extracellular Molecule by Engineered Bacteria. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2019; 13:248-258. [PMID: 30489274 DOI: 10.1109/tbcas.2018.2883350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Feedback control is ubiquitous in biological systems. It can also play a crucial role in the design of synthetic circuits implementing novel functions in living systems, to achieve self-regulation of gene expression, noise reduction, rise time decrease, or adaptive pathway control. Despite in vitro, in vivo, and ex vivo implementations have been successfully reported, the design of biological close-loop systems with quantitatively predictable behavior is still a major challenge. In this work, we tested a model-based bottom-up design of a synthetic close-loop controller in engineered Escherichia coli, aimed to automatically regulate the concentration of an extracellular molecule, N-(3-oxohexanoyl)-L-homoserine lactone (HSL), by rewiring the elements of heterologous quorum sensing/quenching networks. The synthetic controller was successfully constructed and experimentally validated. Relying on mathematical model and experimental characterization of individual regulatory parts and enzymes, we evaluated the predictability of the interconnected system behavior in vivo. The culture was able to reach an HSL steady-state level of 72 nM, accurately predicted by the model, and showed superior capabilities in terms of robustness against cell density variation and disturbance rejection, compared with a corresponding open-loop circuit. This engineering-inspired design approach may be adopted for the implementation of other close-loop circuits for different applications and contribute to decreasing trial-and-error steps.
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80
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Li H, Mei X, Liu B, Xie G, Ren N, Xing D. Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:166. [PMID: 31297154 PMCID: PMC6598285 DOI: 10.1186/s13068-019-1511-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/19/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND H2-ethanol-coproducing bacteria, as primary fermenters, play important roles in the microbiome of bioreactors for bioenergy production from organic wastewater or solid wastes. Ethanoligenens harbinense YUAN-3 is an anaerobic ethanol-H2-fermenting bacterium. Ethanol is one of the main end-products of strain YUAN-3 that influence its fermentative process. Until recently, the molecular mechanism of metabolic regulation in strain YUAN-3 during ethanol accumulation has still been unclear. This study aims to elucidate the metabolic regulation mechanisms in strain YUAN-3, which contributes to effectively shape the microbiome for biofuel and bioenergy production from waste stream. RESULTS This study reports that ethanol stress altered the distribution of end-product yields in the H2-ethanol-coproducing Ethanoligenens harbinense strain YUAN-3. Decreasing trends of hydrogen yield from 1888.6 ± 45.8 to 837 ± 64.7 mL L-1 and acetic acid yield from 1767.7 ± 45 to 160.6 ± 44.7 mg L-1 were observed in strain YUAN-3 with increasing exogenous ethanol (0 mM-200 mM). However, the ethanol yield of strain YUAN-3 increased by 15.1%, 30.1%, and 27.4% in 50 mM, 100 mM, and 200 mM ethanol stress, respectively. The endogenous ethanol accounted for 96.1% (w/w) in liquid end-products when exogenous ethanol of 200 mM was added. The molar ratio of ethanol to acetic acid increased 14 times (exogenous ethanol of 200 mM) compared to the control. iTRAQ-based quantitative proteomic analysis indicated that 263 proteins of strain YUAN-3 were differentially expressed in 50 mM, 100 mM, and 200 mM of exogenous ethanol. These proteins are mainly involved in amino acid transport and metabolism, central carbon metabolism, and oxidative stress response. CONCLUSION These differentially expressed proteins play important roles in metabolic changes necessary for growth and survival of strain YUAN-3 during ethanol stress. The up-regulation of bifunctional acetaldehyde-CoA/alcohol dehydrogenase (ADHE) was the main reason why ethanol production was enhanced, while hydrogen gas and acetic acid yields declined in strain YUAN-3 during ethanol stress. This study also provides a new approach for the enhancement of ethanologenesis by H2-ethanol-coproducing bacteria through exogenous ethanol addition.
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Affiliation(s)
- Huahua Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, P.O. Box 2614, No. 73 Huanghe Road, Nangang District, Harbin, 150090 Heilongjiang China
| | - Xiaoxue Mei
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, P.O. Box 2614, No. 73 Huanghe Road, Nangang District, Harbin, 150090 Heilongjiang China
| | - Bingfeng Liu
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, P.O. Box 2614, No. 73 Huanghe Road, Nangang District, Harbin, 150090 Heilongjiang China
| | - Guojun Xie
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, P.O. Box 2614, No. 73 Huanghe Road, Nangang District, Harbin, 150090 Heilongjiang China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, P.O. Box 2614, No. 73 Huanghe Road, Nangang District, Harbin, 150090 Heilongjiang China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, P.O. Box 2614, No. 73 Huanghe Road, Nangang District, Harbin, 150090 Heilongjiang China
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81
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Zacchetti B, Wösten HA, Claessen D. Multiscale heterogeneity in filamentous microbes. Biotechnol Adv 2018; 36:2138-2149. [DOI: 10.1016/j.biotechadv.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/15/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
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82
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Hoang Y, Kroos L. Ultrasensitive Response of Developing Myxococcus xanthus to the Addition of Nutrient Medium Correlates with the Level of MrpC. J Bacteriol 2018; 200:e00456-18. [PMID: 30181127 PMCID: PMC6199472 DOI: 10.1128/jb.00456-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022] Open
Abstract
Upon depletion of nutrients, Myxococcus xanthus forms mounds on a solid surface. The differentiation of rod-shaped cells into stress-resistant spores within mounds creates mature fruiting bodies. The developmental process can be perturbed by the addition of nutrient medium before the critical period of commitment to spore formation. The response was investigated by adding a 2-fold dilution series of nutrient medium to starving cells. An ultrasensitive response was observed, as indicated by a steep increase in the spore number after the addition of 12.5% versus 25% nutrient medium. The level of MrpC, which is a key transcription factor in the gene regulatory network, correlated with the spore number after nutrient medium addition. The MrpC level decreased markedly by 3 h after adding nutrient medium but recovered more after the addition of 12.5% than after 25% nutrient medium addition. The difference in MrpC levels was greatest midway during the period of commitment to sporulation, and mound formation was restored after 12.5% nutrient medium addition but not after adding 25% nutrient medium. Although the number of spores formed after 12.5% nutrient medium addition was almost normal, the transcript levels of "late" genes in the regulatory network failed to rise normally during the commitment period. However, at later times, expression from a reporter gene fused to a late promoter was higher after adding 12.5% than after adding 25% nutrient medium, consistent with the spore numbers. The results suggest that a threshold level of MrpC must be achieved in order for mounds to persist and for cells within to differentiate into spores.IMPORTANCE Many signaling and gene regulatory networks convert graded stimuli into all-or-none switch-like responses. Such ultrasensitivity can produce bistability in cell populations, leading to different cell fates and enhancing survival. We discovered an ultrasensitive response of M. xanthus to nutrient medium addition during development. A small change in nutrient medium concentration caused a profound change in the developmental process. The level of the transcription factor MrpC correlated with multicellular mound formation and differentiation into spores. A threshold level of MrpC is proposed to be necessary to initiate mound formation and create a positive feedback loop that may explain the ultrasensitive response. Understanding how this biological switch operates will provide a paradigm for the broadly important topic of cellular behavior in microbial communities.
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Affiliation(s)
- Y Hoang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Lee Kroos
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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83
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Choudhury D, Gayen K, Saini S. Dynamic control of arabinose and xylose utilization in E. coli. CAN J CHEM ENG 2018. [DOI: 10.1002/cjce.23197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Debika Choudhury
- Department of Chemical Engineering; IIT Bombay; Mumbai Maharashtra 400076 India
| | - Kalyan Gayen
- Department of Chemical Engineering; NIT Agartala; Tripura 799055 India
| | - Supreet Saini
- Department of Chemical Engineering; IIT Bombay; Mumbai Maharashtra 400076 India
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84
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Genetic diversity and phenotypic plasticity of AHL-mediated Quorum sensing in environmental strains of Vibrio mediterranei. ISME JOURNAL 2018; 13:159-169. [PMID: 30116040 DOI: 10.1038/s41396-018-0260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/12/2018] [Accepted: 07/24/2018] [Indexed: 01/28/2023]
Abstract
N-Acyl homoserine lactone (AHL)-mediated Quorum sensing (QS) is one of the most studied social behavior among Proteobacteria. However, despite the current knowledge on QS-associated phenotypes such as bioluminescence, biofilm formation, or pathogenesis, the characterization of environmental factors driving QS in realistic ecological settings remains scarce. We investigated the dynamics of AHL and AHL-producing Vibrio among 840 isolates collected fortnightly from the Salses-Leucate Mediterranean lagoon in spring and summer 2015 and 2016. Vibrio isolates were characterized by gyrB gene sequencing, Enterobacterial repetitive intergenic consensus polymerase chain reaction, and genome sequencing, and AHL production was investigated by a biosensors-based UHPLC-HRMS/MS approach. Our results revealed, for the first time, a succession of V. mediterranei isolates with different AHL production phenotypes over time and this dynamics was observed in a single genotype (average genomic nucleotide identity >99.9). A multivariate DistLM analysis revealed that 83.4% of the temporal variation of V. mediterranei QS phenotypes was explained by environmental variables. Overall, our results suggest that isolates of a single genotype are able to change their QS phenotypes in response to environmental conditions, highlighting the phenotypic plasticity of bacterial communication in the environment.
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85
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Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis. Nat Commun 2018; 9:3043. [PMID: 30072730 PMCID: PMC6072776 DOI: 10.1038/s41467-018-05466-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022] Open
Abstract
Writing artificial logic and dynamic function into complex cellular background to achieve desired phenotypes or improved outputs calls for the development of new genetic tools as well as their innovative use. In this study, we present a sensor-regulator and RNAi-based bifunctional dynamic control network that can provide simultaneous upregulation and downregulation of cellular metabolism for engineered biosynthesis. The promoter-regulator-mediated upregulation function and its transduced downregulation function through RNAi are systematically verified and characterized. We apply this dynamic control network to regulate the phosphoenolpyruvate metabolic node in Escherichia coli and achieve autonomous distribution of carbon flux between its native metabolism and the engineered muconic acid biosynthetic pathway. This allows muconic acid biosynthesis to reach 1.8 g L−1. This study also suggests the circumstances where dynamic control approaches are likely to take effects. Engineering dynamic control can improve microbial production of target chemicals. Here, the authors design a sensor-regulator and RNAi based bifunctional dynamic control network that can simultaneously and independently turn up and down cellular metabolism for engineered muconic acid production in E. coli.
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86
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Li T, Dong Y, Zhang X, Ji X, Luo C, Lou C, Zhang HM, Ouyang Q. Engineering of a genetic circuit with regulatable multistability. Integr Biol (Camb) 2018; 10:474-482. [DOI: 10.1039/c8ib00030a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tingting Li
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
| | - Yiming Dong
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
| | - Xuanqi Zhang
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
| | - Xiangyu Ji
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100871, China
| | - Chunxiong Luo
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Chunbo Lou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100871, China
| | - Haoqian M. Zhang
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
- Bluepha Co., Ltd., Beijing 102206, China
| | - Qi Ouyang
- Centre for Quantitative Biology and Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
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87
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Abstract
A growing body of research suggests bacterial metabolism and membrane bioenergetics affect the lethality of a broad spectrum of antibiotics. Electrochemical gradients spanning energy-transducing membranes are the foundation of the chemiosmotic hypothesis and are essential for life; accordingly, their dysfunction appears to be a critical factor in bacterial death. Proton flux across energy-transducing membranes is central for cellular homeostasis as vectorial proton translocation generates a proton motive force used for ATP synthesis, pH homeostasis, and maintenance of solute gradients. Our recent investigations indicate that maintenance of pH homeostasis is a critical factor in antibiotic killing and suggest an imbalance in proton flux initiates disruptions in chemiosmotic gradients that lead to cell death. The complex and interconnected relationships between electron transport systems, central carbon metabolism, oxidative stress generation, pH homeostasis, and electrochemical gradients provide challenging obstacles to deciphering the roles for each of these processes in antibiotic lethality. In this chapter, we will present evidence for the pH homeostasis hypothesis of antibiotic lethality that bactericidal activity flows from disruption of cellular energetics and loss of chemiosmotic homeostasis. A holistic understanding of the interconnection of energetic processes and antibiotic activity may direct future research toward the development of more effective therapeutic interventions.
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88
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Prusa J, Zhu DX, Stallings CL. The stringent response and Mycobacterium tuberculosis pathogenesis. Pathog Dis 2018; 76:5035815. [PMID: 29947752 PMCID: PMC7191866 DOI: 10.1093/femspd/fty054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/08/2018] [Indexed: 12/23/2022] Open
Abstract
During infection, the host restrains Mycobacterium tuberculosis (Mtb) from proliferating by imposing an arsenal of stresses. Despite this onslaught of attacks, Mtb is able to persist for the lifetime of the host, indicating that this pathogen has substantial molecular mechanisms to resist host-inflicted damage. The stringent response is a conserved global stress response in bacteria that involves the production of the hyperphosphorylated guanine nucleotides ppGpp and pppGpp (collectively called (p)ppGpp). (p)ppGpp then regulates a number of cellular processes to adjust the physiology of the bacteria to promote survival in different environments. Survival in the presence of host-generated stresses is an essential quality of successful pathogens, and the stringent response is critical for the intracellular survival of a number of pathogenic bacteria. In addition, the stringent response has been linked to virulence gene expression, persistence, latency and drug tolerance. In Mtb, (p)ppGpp synthesis is required for survival in low nutrient conditions, long term culture and during chronic infection in animal models, all indicative of a strict requirement for (p)ppGpp during exposure to stresses associated with infection. In this review we discuss (p)ppGpp metabolism and how this functions as a critical regulator of Mtb virulence.
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Affiliation(s)
- Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Dennis X Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
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89
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Sommer RJ, Dardiry M, Lenuzzi M, Namdeo S, Renahan T, Sieriebriennikov B, Werner MS. The genetics of phenotypic plasticity in nematode feeding structures. Open Biol 2018; 7:rsob.160332. [PMID: 28298309 PMCID: PMC5376706 DOI: 10.1098/rsob.160332] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/10/2017] [Indexed: 12/15/2022] Open
Abstract
Phenotypic plasticity has been proposed as an ecological and evolutionary concept. Ecologically, it can help study how genes and the environment interact to produce robust phenotypes. Evolutionarily, as a facilitator it might contribute to phenotypic novelty and diversification. However, the discussion of phenotypic plasticity remains contentious in parts due to the absence of model systems and rigorous genetic studies. Here, we summarize recent work on the nematode Pristionchus pacificus, which exhibits a feeding plasticity allowing predatory or bacteriovorous feeding. We show feeding plasticity to be controlled by developmental switch genes that are themselves under epigenetic control. Phylogenetic and comparative studies support phenotypic plasticity and its role as a facilitator of morphological novelty and diversity.
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Affiliation(s)
- Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Mohannad Dardiry
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Masa Lenuzzi
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Suryesh Namdeo
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Tess Renahan
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Michael S Werner
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
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90
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Son M, Kaspar J, Ahn SJ, Burne RA, Hagen SJ. Threshold regulation and stochasticity from the MecA/ClpCP proteolytic system in Streptococcus mutans competence. Mol Microbiol 2018; 110:914-930. [PMID: 29873131 PMCID: PMC6281771 DOI: 10.1111/mmi.13992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2018] [Indexed: 12/28/2022]
Abstract
Many bacterial species use the MecA/ClpCP proteolytic system to block entry into genetic competence. In Streptococcus mutans, MecA/ClpCP degrades ComX (also called SigX), an alternative sigma factor for the comY operon and other late competence genes. Although the mechanism of MecA/ClpCP has been studied in multiple Streptococcus species, its role within noisy competence pathways is poorly understood. S. mutans competence can be triggered by two different peptides, CSP and XIP, but it is not known whether MecA/ClpCP acts similarly for both stimuli, how it affects competence heterogeneity, and how its regulation is overcome. We have studied the effect of MecA/ClpCP on the activation of comY in individual S. mutans cells. Our data show that MecA/ClpCP is active under both XIP and CSP stimulation, that it provides threshold control of comY, and that it adds noise in comY expression. Our data agree quantitatively with a model in which MecA/ClpCP prevents adventitious entry into competence by sequestering or intercepting low levels of ComX. Competence is permitted when ComX levels exceed a threshold, but cell‐to‐cell heterogeneity in MecA levels creates variability in that threshold. Therefore, MecA/ClpCP provides a stochastic switch, located downstream of the already noisy comX, that enhances phenotypic diversity.
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Affiliation(s)
- M Son
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
| | - J Kaspar
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - S J Ahn
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - R A Burne
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - S J Hagen
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
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91
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Gangwe Nana GY, Ripoll C, Cabin-Flaman A, Gibouin D, Delaune A, Janniere L, Grancher G, Chagny G, Loutelier-Bourhis C, Lentzen E, Grysan P, Audinot JN, Norris V. Division-Based, Growth Rate Diversity in Bacteria. Front Microbiol 2018; 9:849. [PMID: 29867792 PMCID: PMC5958220 DOI: 10.3389/fmicb.2018.00849] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/12/2018] [Indexed: 01/19/2023] Open
Abstract
To investigate the nature and origins of growth rate diversity in bacteria, we grew Escherichia coli and Bacillus subtilis in liquid minimal media and, after different periods of 15N-labeling, analyzed and imaged isotope distributions in individual cells with Secondary Ion Mass Spectrometry. We find a striking inter- and intra-cellular diversity, even in steady state growth. This is consistent with the strand-dependent, hyperstructure-based hypothesis that a major function of the cell cycle is to generate coherent, growth rate diversity via the semi-conservative pattern of inheritance of strands of DNA and associated macromolecular assemblies. We also propose quantitative, general, measures of growth rate diversity for studies of cell physiology that include antibiotic resistance.
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Affiliation(s)
- Ghislain Y Gangwe Nana
- Laboratory of Microbiology Signals and Microenvironment, Department of Biology, University of Rouen, Mont Saint Aignan, France
| | - Camille Ripoll
- Department of Biology, University of Rouen, Mont Saint Aignan, France
| | - Armelle Cabin-Flaman
- Groupe de Physique des Matériaux, Centre National de la Recherche Scientifique, Département de Biologie, Université de Rouen Normandie, Saint-Etienne du Rouvray, France
| | - David Gibouin
- Groupe de Physique des Matériaux, Centre National de la Recherche Scientifique, Département de Biologie, Université de Rouen Normandie, Saint-Etienne du Rouvray, France
| | - Anthony Delaune
- Groupe de Physique des Matériaux, Centre National de la Recherche Scientifique, Département de Biologie, Université de Rouen Normandie, Saint-Etienne du Rouvray, France
| | | | - Gerard Grancher
- R. Salem Laboratory of Maths, UMR 6085 Centre National de la Recherche Scientifique-University of Rouen, Saint Etienne du Rouvray, France
| | - Gaelle Chagny
- R. Salem Laboratory of Maths, UMR 6085 Centre National de la Recherche Scientifique-University of Rouen, Saint Etienne du Rouvray, France
| | - Corinne Loutelier-Bourhis
- UMR Centre National de la Recherche Scientifique, 6014 COBRA, University of Rouen, Mont Saint Aignan, France
| | - Esther Lentzen
- Material Research & Technology Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Patrick Grysan
- Material Research & Technology Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Jean-Nicolas Audinot
- Material Research & Technology Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Department of Biology, University of Rouen, Mont Saint Aignan, France
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92
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Nikolic N, Bergmiller T, Vandervelde A, Albanese TG, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Res 2018; 46:2918-2931. [PMID: 29432616 PMCID: PMC5888573 DOI: 10.1093/nar/gky079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 12/30/2017] [Accepted: 01/27/2018] [Indexed: 01/24/2023] Open
Abstract
The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin-antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.
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Affiliation(s)
- Nela Nikolic
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Tobias Bergmiller
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Alexandra Vandervelde
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
| | - Tanino G Albanese
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
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93
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Abstract
The ability of bacterial cells to adjust their gene expression program in response to environmental perturbation is often critical for their survival. Recent experimental advances allowing us to quantitatively record gene expression dynamics in single cells and in populations coupled with mathematical modeling enable mechanistic understanding on how these responses are shaped by the underlying regulatory networks. Here, we review how the combination of local and global factors affect dynamical responses of gene regulatory networks. Our goal is to discuss the general principles that allow extrapolation from a few model bacteria to less understood microbes. We emphasize that, in addition to well-studied effects of network architecture, network dynamics are shaped by global pleiotropic effects and cell physiology.
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Affiliation(s)
- David L Shis
- Department of Biosciences, Rice University, Houston, Texas 77005, USA;
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, USA; .,Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Oleg A Igoshin
- Department of Biosciences, Rice University, Houston, Texas 77005, USA; .,Department of Bioengineering, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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94
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Novelli-Rousseau A, Espagnon I, Filiputti D, Gal O, Douet A, Mallard F, Josso Q. Culture-free Antibiotic-susceptibility Determination From Single-bacterium Raman Spectra. Sci Rep 2018; 8:3957. [PMID: 29500449 PMCID: PMC5834538 DOI: 10.1038/s41598-018-22392-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/14/2018] [Indexed: 01/07/2023] Open
Abstract
Raman spectrometry appears to be an opportunity to perform rapid tests in microbiological diagnostics as it provides phenotype-related information from single bacterial cells thus holding the promise of direct analysis of clinical specimens without any time-consuming growth phase. Here, we demonstrate the feasibility of a rapid antibiotic-susceptibility determination based on the use of Raman spectra acquired on single bacterial cells. After a two-hour preculture step, one susceptible and two resistant E. coli strains were incubated, for only two hours, in the presence of different bactericidal antibiotics (gentamicin, ciprofloxacin, amoxicillin) in a range of concentrations that included the clinical breakpoints used as references in microbial diagnostic. Spectra were acquired and processed to isolate spectral modifications associated with the antibiotic effect. We evidenced an “antibiotic effect signature” which is expressed with specific Raman peaks and the coexistence of three spectral populations in the presence of antibiotic. We devised an algorithm and a test procedure that overcome single-cell heterogeneities to estimate the MIC and determinate the susceptibility phenotype of the tested bacteria using only a few single-cell spectra in four hours only if including the preculture step.
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Affiliation(s)
- A Novelli-Rousseau
- bioMérieux, Technological Research Department, 5 rue des Berges, 38024, Grenoble, France.
| | - I Espagnon
- CEA, LIST, Département Métrologie, Instrumentation et Information, 91191, Gif-sur-Yvette, France.
| | - D Filiputti
- bioMérieux, Technological Research Department, 5 rue des Berges, 38024, Grenoble, France
| | - O Gal
- CEA, LIST, Département Métrologie, Instrumentation et Information, 91191, Gif-sur-Yvette, France
| | - A Douet
- Bioaster, 40 avenue Tony Garnier, 69007, Lyon, France
| | - F Mallard
- bioMérieux, Technological Research Department, 5 rue des Berges, 38024, Grenoble, France
| | - Q Josso
- bioMérieux, Technological Research Department, 5 rue des Berges, 38024, Grenoble, France.
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95
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Carey JN, Mettert EL, Roggiani M, Myers KS, Kiley PJ, Goulian M. Regulated Stochasticity in a Bacterial Signaling Network Permits Tolerance to a Rapid Environmental Change. Cell 2018; 173:196-207.e14. [PMID: 29502970 DOI: 10.1016/j.cell.2018.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/01/2017] [Accepted: 02/01/2018] [Indexed: 12/25/2022]
Abstract
Microbial populations can maximize fitness in dynamic environments through bet hedging, a process wherein a subpopulation assumes a phenotype not optimally adapted to the present environment but well adapted to an environment likely to be encountered. Here, we show that oxygen induces fluctuating expression of the trimethylamine oxide (TMAO) respiratory system of Escherichia coli, diversifying the cell population and enabling a bet-hedging strategy that permits growth following oxygen loss. This regulation by oxygen affects the variance in gene expression but leaves the mean unchanged. We show that the oxygen-sensitive transcription factor IscR is the key regulator of variability. Oxygen causes IscR to repress expression of a TMAO-responsive signaling system, allowing stochastic effects to have a strong effect on the output of the system and resulting in heterogeneous expression of the TMAO reduction machinery. This work reveals a mechanism through which cells regulate molecular noise to enhance fitness.
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Affiliation(s)
- Jeffrey N Carey
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin L Mettert
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Manuela Roggiani
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin S Myers
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA.
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96
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Willis A, Woodhouse JN, Ongley SE, Jex AR, Burford MA, Neilan BA. Genome variation in nine co-occurring toxic Cylindrospermopsis raciborskii strains. HARMFUL ALGAE 2018; 73:157-166. [PMID: 29602504 DOI: 10.1016/j.hal.2018.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/26/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria form harmful algal blooms and are highly adapted to a range of habitats, in part due to their phenotype plasticity. This plasticity is partially the result of co-existence of multiple strains within a single population. The toxic cyanobacterium Cylindrospermopsis raciborskii has remarkable phenotypic plasticity, strain variation and environmental adaptation resulting in an expansion of its global range. To understand the genetic basis of the high level of plasticity within a C. raciborskii population, the genomes of nine co-occurring strains were compared. The strains differed in morphology, toxin cell quotas and physiology, despite being obtained from a single water sample. Comparative genomics showed that three coiled strains were 3.9 Mbp in size, with 3544 ± 11 genes, while straight strains were 3.8 Mbp in size, with 3485 ± 20 genes. The core proteome comprised 86% of the genome and consisted of 2891 orthologous groups (OGs), whereas the variable genome comprised ∼14% (847 OGs), and the strain specific genome only ∼1% (433 OGs).There was a high proportion of variable strain-specific genes for the very closely related strains, which may underpin strain differentiation. The variable genes were associated with environmental responses and adaptation, particularly phage defence, DNA repair, membrane transport, and stress, illustrative of the adaptability of the strains in response to environmental and biological stressors. This study shows that high genomic variability exists between co-occurring strains and may be the basis of strain phenotypic differences and plasticity of populations. Therefore management and prediction of blooms of this harmful species requires different approaches to capture this strain variability.
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Affiliation(s)
- Anusuya Willis
- Australian Rivers Institute, Griffith University, QLD, Australia.
| | - Jason N Woodhouse
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW, Australia
| | - Sarah E Ongley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW, Australia; School of Environmental and Life Sciences, The University of Newcastle, NSW, Australia
| | - Aaron R Jex
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, VIC, Australia; Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | | | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW, Australia; School of Environmental and Life Sciences, The University of Newcastle, NSW, Australia.
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97
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Chakroun I, Mahdhi A, Morcillo P, Cordero H, Cuesta A, Bakhrouf A, Mahdouani K, Esteban MÁ. Motility, biofilm formation, apoptotic effect and virulence gene expression of atypical Salmonella Typhimurium outside and inside Caco-2 cells. Microb Pathog 2018; 114:153-162. [DOI: 10.1016/j.micpath.2017.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/04/2017] [Accepted: 11/09/2017] [Indexed: 12/15/2022]
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98
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Chang TY, Chen C, Lee M, Chang YC, Lu CH, Lu ST, Wang DY, Wang A, Guo CL, Cheng PL. Paxillin facilitates timely neurite initiation on soft-substrate environments by interacting with the endocytic machinery. eLife 2017; 6:31101. [PMID: 29271742 PMCID: PMC5768420 DOI: 10.7554/elife.31101] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022] Open
Abstract
Neurite initiation is the first step in neuronal development and occurs spontaneously in soft tissue environments. Although the mechanisms regulating the morphology of migratory cells on rigid substrates in cell culture are widely known, how soft environments modulate neurite initiation remains elusive. Using hydrogel cultures, pharmacologic inhibition, and genetic approaches, we reveal that paxillin-linked endocytosis and adhesion are components of a bistable switch controlling neurite initiation in a substrate modulus-dependent manner. On soft substrates, most paxillin binds to endocytic factors and facilitates vesicle invagination, elevating neuritogenic Rac1 activity and expression of genes encoding the endocytic machinery. By contrast, on rigid substrates, cells develop extensive adhesions, increase RhoA activity and sequester paxillin from the endocytic machinery, thereby delaying neurite initiation. Our results highlight paxillin as a core molecule in substrate modulus-controlled morphogenesis and define a mechanism whereby neuronal cells respond to environments exhibiting varying mechanical properties.
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Affiliation(s)
- Ting-Ya Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chen Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Min Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Ya-Chu Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Huan Lu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shao-Tzu Lu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - De-Yao Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Aijun Wang
- Surgical Bioengineering Laboratory, Department of Surgery, University of California, Davis, Davis, United States
| | - Chin-Lin Guo
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Pei-Lin Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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99
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Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
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100
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Bacterial-Chromatin Structural Proteins Regulate the Bimodal Expression of the Locus of Enterocyte Effacement (LEE) Pathogenicity Island in Enteropathogenic Escherichia coli. mBio 2017; 8:mBio.00773-17. [PMID: 28790204 PMCID: PMC5550750 DOI: 10.1128/mbio.00773-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In enteropathogenic Escherichia coli (EPEC), the locus of enterocyte effacement (LEE) encodes a type 3 secretion system (T3SS) essential for pathogenesis. This pathogenicity island comprises five major operons (LEE1 to LEE5), with the LEE5 operon encoding T3SS effectors involved in the intimate adherence of bacteria to enterocytes. The first operon, LEE1, encodes Ler (LEE-encoded regulator), an H-NS (nucleoid structuring protein) paralog that alleviates the LEE H-NS silencing. We observed that the LEE5 and LEE1 promoters present a bimodal expression pattern, depending on environmental stimuli. One key regulator of bimodal LEE1 and LEE5 expression is ler expression, which fluctuates in response to different growth conditions. Under conditions in vitro considered to be equivalent to nonoptimal conditions for virulence, the opposing regulatory effects of H-NS and Ler can lead to the emergence of two bacterial subpopulations. H-NS and Ler share nucleation binding sites in the LEE5 promoter region, but H-NS binding results in local DNA structural modifications distinct from those generated through Ler binding, at least in vitro. Thus, we show how two nucleoid-binding proteins can contribute to the epigenetic regulation of bacterial virulence and lead to opposing bacterial fates. This finding implicates for the first time bacterial-chromatin structural proteins in the bimodal regulation of gene expression. Gene expression stochasticity is an emerging phenomenon in microbiology. In certain contexts, gene expression stochasticity can shape bacterial epigenetic regulation. In enteropathogenic Escherichia coli (EPEC), the interplay between H-NS (a nucleoid structuring protein) and Ler (an H-NS paralog) is required for bimodal LEE5 and LEE1 expression, leading to the emergence of two bacterial subpopulations (with low and high states of expression). The two proteins share mutual nucleation binding sites in the LEE5 promoter region. In vitro, the binding of H-NS to the LEE5 promoter results in local structural modifications of DNA distinct from those generated through Ler binding. Furthermore, ler expression is a key parameter modulating the variability of the proportions of bacterial subpopulations. Accordingly, modulating the production of Ler into a nonpathogenic E. coli strain reproduces the bimodal expression of LEE5. Finally, this study illustrates how two nucleoid-binding proteins can reshape the epigenetic regulation of bacterial virulence.
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