1
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Koli S, Shetty S. Ribosomal dormancy at the nexus of ribosome homeostasis and protein synthesis. Bioessays 2024; 46:e2300247. [PMID: 38769702 DOI: 10.1002/bies.202300247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/05/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Dormancy or hibernation is a non-proliferative state of cells with low metabolic activity and gene expression. Dormant cells sequester ribosomes in a translationally inactive state, called dormant/hibernating ribosomes. These dormant ribosomes are important for the preservation of ribosomes and translation shut-off. While recent studies attempted to elucidate their modes of formation, the regulation and roles of the diverse dormant ribosomal populations are still largely understudied. The mechanistic details of the formation of dormant ribosomes in stress and especially their disassembly during recovery remain elusive. In this review, we discuss the roles of dormant ribosomes and their potential regulatory mechanisms. Furthermore, we highlight the paradigms that need to be answered in the field of ribosomal dormancy.
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Affiliation(s)
- Saloni Koli
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Sunil Shetty
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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2
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Zhong M, Li Y, Deng L, Fang J, Yu X. Insight into the adaptation mechanisms of high hydrostatic pressure in physiology and metabolism of hadal fungi from the deepest ocean sediment. mSystems 2024; 9:e0108523. [PMID: 38117068 PMCID: PMC10804941 DOI: 10.1128/msystems.01085-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
High hydrostatic pressure (HHP) influences the life processes of organisms living at depth in the oceans. While filamentous fungi are one of the essential members of deep-sea microorganisms, few works have explored their piezotolerance to HHP. Here, we obtained three homogeneous Aspergillus sydowii from terrestrial, shallow, and hadal areas, respectively, to compare their pressure resistance. A set of all-around evaluation methods including determination of growth rate, metabolic activity, and microscopic staining observation was established and indicated that A. sydowii DM1 from the hadal area displayed significant piezotolerance. Global analysis of transcriptome data under elevated HHP revealed that A. sydowii DM1 proactively modulated cell membrane permeability, hyphae morphology, and septal quantities for seeking a better livelihood under mild pressure. Besides, differentially expressed genes were mainly enriched in the biosynthesis of amino acids, carbohydrate metabolism, cell process, etc., implying how the filamentous fungi respond to elevated pressure at the molecular level. We speculated that A. sydowii DM1 could acclimatize itself to HHP by adopting several strategies, including environmental response pathway HOG-MAPK, stress proteins, and cellular metabolisms.IMPORTANCEFungi play an ecological and biological function in marine environments, while the physiology of filamentous fungi under high hydrostatic pressure (HHP) is an unknown territory due to current technologies. As filamentous fungi are found in various niches, Aspergillus sp. from deep-sea inspire us to the physiological trait of eukaryotes under HHP, which can be considered as a prospective research model. Here, the evaluation methods we constructed would be universal for most filamentous fungi to assess their pressure resistance, and we found that Aspergillus sydowii DM1 from the hadal area owned better piezotolerance and the active metabolisms under HHP indicated the existence of undiscovered metabolic strategies for hadal fungi. Since pressure-related research of marine fungi has been unexpectedly neglected, our study provided an enlightening strategy for them under HHP; we believed that understanding their adaptation and ecological function in original niches will be accelerated in the perceivable future.
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Affiliation(s)
- Maosheng Zhong
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Yongqi Li
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Ludan Deng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Xi Yu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
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3
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Yannarell SM, Beaudoin ES, Talley HS, Schoenborn AA, Orr G, Anderton CR, Chrisler WB, Shank EA. Extensive cellular multi-tasking within Bacillus subtilis biofilms. mSystems 2023; 8:e0089122. [PMID: 37527273 PMCID: PMC10469600 DOI: 10.1128/msystems.00891-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/08/2023] [Indexed: 08/03/2023] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells "multi-task," simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms. IMPORTANCE Many microbes differentiate, expressing diverse phenotypes to ensure their survival in various environments. However, studies on phenotypic differentiation have typically examined only a few phenotypes at one time, thus limiting our knowledge about the extent of differentiation and phenotypic overlap in the population. We investigated the spatial organization and gene expression relationships for genes important in B. subtilis biofilms. In doing so, we mapped spatial gene expression patterns and expanded the number of cell populations described in the B. subtilis literature. It is likely that other bacteria also display complex differentiation patterns within their biofilms. Studying the extent of cellular differentiation in other microbes may be important when designing therapies for disease-causing bacteria, where studying only a single phenotype may be masking underlying phenotypic differentiation relevant to infection outcomes.
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Affiliation(s)
- Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eric S. Beaudoin
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Hunter S. Talley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William B. Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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4
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Măgălie A, Schwartz DA, Lennon JT, Weitz JS. Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching. J Theor Biol 2023; 561:111413. [PMID: 36639023 DOI: 10.1016/j.jtbi.2023.111413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/01/2023] [Accepted: 01/05/2023] [Indexed: 01/12/2023]
Abstract
Organisms have evolved different mechanisms in response to periods of environmental stress, including dormancy - a reversible state of reduced metabolic activity. Transitions to and from dormancy can be random or induced by changes in environmental conditions. Prior theoretical work has shown that stochastic transitioning between active and dormant states at the individual level can maximize fitness at the population level. However, such theories of 'bet-hedging' strategies typically neglect certain physiological features of transitions to dormancy, including time lags to gain protective benefits. Here, we construct and analyze a dynamic model that couples stochastic changes in environmental state with the population dynamics of organisms that can initiate dormancy after an explicit time delay. Stochastic environments are simulated using a multi-state Markov chain through which the mean and variance of environmental residence time can be adjusted. In the absence of time lags (or in the limit of very short lags), we find that bet-hedging strategy transition probabilities scale inversely with the mean environmental residence times, consistent with prior theory. We also find that increasing delays in dormancy decreases optimal transitioning probabilities, an effect that can be influenced by the correlations of environmental noise. When environmental residence times - either good or bad - are uncorrelated, the maximum population level fitness is obtained given low levels of transitioning between active and dormant states. However when environmental residence times are correlated, optimal dormancy initiation and termination probabilities increase insofar as the mean environmental persistent time is longer than the delay to reach dormancy. We also find that bet hedging is no longer advantageous when delays to enter dormancy exceed the mean environmental residence times. Altogether, these results show how physiological limits to dormancy and environmental dynamics shape the evolutionary benefits and even viability of bet hedging strategies at population scales.
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Affiliation(s)
- Andreea Măgălie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | | | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Physics, Georgia Institute of Technology, Atlanta, GA, USA; Institut de Biologie, École Normale Supérieure, Paris, France.
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5
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Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
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Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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6
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Zhang JY, Lian ZH, Narsing Rao MP, Wang P, Liu L, Fang BZ, Li MM, Liu ZT, Lv AP, Tan S, Dong L, Li JL, Jiao JY, Li WJ. Insights into the effects of drying treatments on cultivable microbial diversity of marine sediments. Microbiol Res 2023; 266:127214. [DOI: 10.1016/j.micres.2022.127214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
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7
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Iven H, Walker TWN, Anthony M. Biotic Interactions in Soil are Underestimated Drivers of Microbial Carbon Use Efficiency. Curr Microbiol 2022; 80:13. [PMID: 36459292 PMCID: PMC9718865 DOI: 10.1007/s00284-022-02979-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/05/2022] [Indexed: 12/05/2022]
Abstract
Microbial carbon use efficiency (CUE)-the balance between microbial growth and respiration-strongly impacts microbial mediated soil carbon storage and is sensitive to many well-studied abiotic environmental factors. However, surprisingly, little work has examined how biotic interactions in soil may impact CUE. Here, we review the theoretical and empirical lines of evidence exploring how biotic interactions affect CUE through the lens of life history strategies. Fundamentally, the CUE of a microbial population is constrained by population density and carrying capacity, which, when reached, causes species to grow more quickly and less efficiently. When microbes engage in interspecific competition, they accelerate growth rates to acquire limited resources and release secondary chemicals toxic to competitors. Such processes are not anabolic and thus constrain CUE. In turn, antagonists may activate one of a number of stress responses that also do not involve biomass production, potentially further reducing CUE. In contrast, facilitation can increase CUE by expanding species realized niches, mitigating environmental stress and reducing production costs of extracellular enzymes. Microbial interactions at higher trophic levels also influence CUE. For instance, predation on microbes can positively or negatively impact CUE by changing microbial density and the outcomes of interspecific competition. Finally, we discuss how plants select for more or less efficient microbes under different contexts. In short, this review demonstrates the potential for biotic interactions to be a strong regulator of microbial CUE and additionally provides a blueprint for future research to address key knowledge gaps of ecological and applied importance for carbon sequestration.
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Affiliation(s)
- Hélène Iven
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, 8006, Zurich, Switzerland.
| | - Tom W N Walker
- Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8006, Zurich, Switzerland
| | - Mark Anthony
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8006, Zurich, Switzerland
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8
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Lombardino J, Burton BM. An electric alarm clock for spores. Science 2022; 378:25-26. [PMID: 36201570 DOI: 10.1126/science.ade3921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Inactive spores integrate stimuli over time through stored electrochemical potential.
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Affiliation(s)
- Jonathan Lombardino
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, WI, USA.,Bacteriology Department, University of Wisconsin-Madison, WI, USA
| | - Briana M Burton
- Bacteriology Department, University of Wisconsin-Madison, WI, USA
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9
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Camacho Mateu J, Sireci M, Muñoz MA. Phenotypic-dependent variability and the emergence of tolerance in bacterial populations. PLoS Comput Biol 2021; 17:e1009417. [PMID: 34555011 PMCID: PMC8492070 DOI: 10.1371/journal.pcbi.1009417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 10/05/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well-documented to intersperse much more tightly than traditionally assumed, especially in communities of microorganisms. Advancing the development of mathematical and computational approaches to shed novel light onto eco-evolutionary problems is a challenge of utmost relevance. With this motivation in mind, here we scrutinize recent experimental results showing evidence of rapid evolution of tolerance by lag in bacterial populations that are periodically exposed to antibiotic stress in laboratory conditions. In particular, the distribution of single-cell lag times-i.e., the times that individual bacteria from the community remain in a dormant state to cope with stress-evolves its average value to approximately fit the antibiotic-exposure time. Moreover, the distribution develops right-skewed heavy tails, revealing the presence of individuals with anomalously large lag times. Here, we develop a parsimonious individual-based model mimicking the actual demographic processes of the experimental setup. Individuals are characterized by a single phenotypic trait: their intrinsic lag time, which is transmitted with variation to the progeny. The model-in a version in which the amplitude of phenotypic variations grows with the parent's lag time-is able to reproduce quite well the key empirical observations. Furthermore, we develop a general mathematical framework allowing us to describe with good accuracy the properties of the stochastic model by means of a macroscopic equation, which generalizes the Crow-Kimura equation in population genetics. Even if the model does not account for all the biological mechanisms (e.g., genetic changes) in a detailed way-i.e., it is a phenomenological one-it sheds light onto the eco-evolutionary dynamics of the problem and can be helpful to design strategies to hinder the emergence of tolerance in bacterial communities. From a broader perspective, this work represents a benchmark for the mathematical framework designed to tackle much more general eco-evolutionary problems, thus paving the road to further research avenues.
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Affiliation(s)
- José Camacho Mateu
- Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Matteo Sireci
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
| | - Miguel A. Muñoz
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
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10
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Modi S, Dey S, Singh A. Noise suppression in stochastic genetic circuits using PID controllers. PLoS Comput Biol 2021; 17:e1009249. [PMID: 34319990 PMCID: PMC8360635 DOI: 10.1371/journal.pcbi.1009249] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/12/2021] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Inside individual cells, protein population counts are subject to molecular noise due to low copy numbers and the inherent probabilistic nature of biochemical processes. We investigate the effectiveness of proportional, integral and derivative (PID) based feedback controllers to suppress protein count fluctuations originating from two noise sources: bursty expression of the protein, and external disturbance in protein synthesis. Designs of biochemical reactions that function as PID controllers are discussed, with particular focus on individual controllers separately, and the corresponding closed-loop system is analyzed for stochastic controller realizations. Our results show that proportional controllers are effective in buffering protein copy number fluctuations from both noise sources, but this noise suppression comes at the cost of reduced static sensitivity of the output to the input signal. In contrast, integral feedback has no effect on the protein noise level from stochastic expression, but significantly minimizes the impact of external disturbances, particularly when the disturbance comes at low frequencies. Counter-intuitively, integral feedback is found to amplify external disturbances at intermediate frequencies. Next, we discuss the design of a coupled feedforward-feedback biochemical circuit that approximately functions as a derivate controller. Analysis using both analytical methods and Monte Carlo simulations reveals that this derivative controller effectively buffers output fluctuations from bursty stochastic expression, while maintaining the static input-output sensitivity of the open-loop system. In summary, this study provides a systematic stochastic analysis of biochemical controllers, and paves the way for their synthetic design and implementation to minimize deleterious fluctuations in gene product levels. In the noisy cellular environment, biochemical species such as genes, RNAs and proteins that often occur at low molecular counts, are subject to considerable stochastic fluctuations in copy numbers over time. How cellular biochemical processes function reliably in the face of such randomness is an intriguing fundamental problem. Increasing evidence suggests that random fluctuations (noise) in protein copy numbers play important functional roles, such as driving genetically identical cells to different cell fates. Moreover, many disease states have been attributed to elevated noise levels in specific proteins. Here we systematically investigate design of biochemical systems that function as proportional, integral and derivative-based feedback controllers to suppress protein count fluctuations arising from bursty expression of the protein and external disturbance in protein synthesis. Our results show that different controllers are effective in buffering different noise components, and identify ranges of feedback gain for minimizing deleterious fluctuations in protein levels.
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Affiliation(s)
- Saurabh Modi
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, United States of America
| | - Supravat Dey
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, United States of America
| | - Abhyudai Singh
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, United States of America
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, United States of America
- * E-mail:
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11
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Blath J, Hermann F, Slowik M. A branching process model for dormancy and seed banks in randomly fluctuating environments. J Math Biol 2021; 83:17. [PMID: 34279717 PMCID: PMC8289800 DOI: 10.1007/s00285-021-01639-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 06/17/2021] [Accepted: 06/27/2021] [Indexed: 11/25/2022]
Abstract
The goal of this article is to contribute towards the conceptual and quantitative understanding of the evolutionary benefits for (microbial) populations to maintain a seed bank consisting of dormant individuals when facing fluctuating environmental conditions. To this end, we discuss a class of '2-type' branching processes describing populations of individuals that may switch between 'active' and 'dormant' states in a random environment oscillating between a 'healthy' and a 'harsh' state. We incorporate different switching strategies and suggest a method of 'fair comparison' to incorporate potentially varying reproductive costs. We then use this concept to compare the fitness of the different strategies in terms of maximal Lyapunov exponents. This gives rise to a 'fitness map' depicting the environmental regimes where certain switching strategies are uniquely supercritical.
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Affiliation(s)
- Jochen Blath
- Present Address: Institute of Mathematics, Technische Universität Berlin, Strasse des 17. Juni 136, 10623 Berlin, Germany
| | - Felix Hermann
- Present Address: Institute of Mathematics, Technische Universität Berlin, Strasse des 17. Juni 136, 10623 Berlin, Germany
| | - Martin Slowik
- Present Address: Mathematical Institute, University of Mannheim, B6, 26, 68159 Mannheim, Germany
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12
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Bakshi S, Leoncini E, Baker C, Cañas-Duarte SJ, Okumus B, Paulsson J. Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence. Nat Microbiol 2021; 6:783-791. [PMID: 34017106 DOI: 10.1038/s41564-021-00900-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/29/2021] [Indexed: 02/03/2023]
Abstract
As bacteria transition from exponential to stationary phase, they change substantially in size, morphology, growth and expression profiles. These responses also vary between individual cells, but it has proved difficult to track cell lineages along the growth curve to determine the progression of events or correlations between how individual cells enter and exit dormancy. Here, we developed a platform for tracking more than 105 parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track batch populations. Initial applications show that for both Escherichia coli and Bacillus subtilis, growth changes from an 'adder' mode in exponential phase to mixed 'adder-timers' entering stationary phase, and then a near-perfect 'sizer' upon exit-creating broadly distributed cell sizes in stationary phase but rapidly returning to narrowly distributed sizes upon exit. Furthermore, cells that undergo more divisions when entering stationary phase suffer reduced survival after long periods of dormancy but are the only cells observed that persist following antibiotic treatment.
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Affiliation(s)
- Somenath Bakshi
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA. .,Department of Engineering, Cambridge University, Cambridge, UK.
| | - Emanuele Leoncini
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Charles Baker
- Biophysics Program, Harvard University, Boston, MA, USA
| | | | - Burak Okumus
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,XCellCure, LLC., Saint Louis, MO, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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13
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Abstract
Clostridioides difficile is a leading cause of health care-associated infections worldwide. These infections are transmitted by C. difficile′s metabolically dormant, aerotolerant spore form. Functional spore formation depends on the assembly of two protective layers, a thick layer of modified peptidoglycan known as the cortex layer and a multilayered proteinaceous meshwork known as the coat. We previously identified two spore morphogenetic proteins, SpoIVA and SipL, that are essential for recruiting coat proteins to the developing forespore and making functional spores. While SpoIVA and SipL directly interact, the identities of the proteins they recruit to the forespore remained unknown. Here, we used mass spectrometry-based affinity proteomics to identify proteins that interact with the SpoIVA-SipL complex. These analyses identified the Peptostreptococcaceae family-specific, sporulation-induced bitopic membrane protein CD3457 (renamed SpoVQ) as a protein that interacts with SipL and SpoIVA. Loss of SpoVQ decreased heat-resistant spore formation by ∼5-fold and reduced cortex thickness ∼2-fold; the thinner cortex layer of ΔspoVQ spores correlated with higher levels of spontaneous germination (i.e., in the absence of germinant). Notably, loss of SpoVQ in either spoIVA or sipL mutants prevented cortex synthesis altogether and greatly impaired the localization of a SipL-mCherry fusion protein around the forespore. Thus, SpoVQ is a novel regulator of C. difficile cortex synthesis that appears to link cortex and coat formation. The identification of SpoVQ as a spore morphogenetic protein further highlights how Peptostreptococcaceae family-specific mechanisms control spore formation in C. difficile. IMPORTANCE The Centers for Disease Control has designated Clostridioides difficile as an urgent threat because of its intrinsic antibiotic resistance. C. difficile persists in the presence of antibiotics in part because it makes metabolically dormant spores. While recent work has shown that preventing the formation of infectious spores can reduce C. difficile disease recurrence, more selective antisporulation therapies are needed. The identification of spore morphogenetic factors specific to C. difficile would facilitate the development of such therapies. In this study, we identified SpoVQ (CD3457) as a spore morphogenetic protein specific to the Peptostreptococcaceae family that regulates the formation of C. difficile’s protective spore cortex layer. SpoVQ acts in concert with the known spore coat morphogenetic factors, SpoIVA and SipL, to link formation of the protective coat and cortex layers. These data reveal a novel pathway that could be targeted to prevent the formation of infectious C. difficile spores.
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14
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Pokhrel N, Sela-Donenfeld D, Cinnamon Y. The chick blastoderm during diapause, a landmark for optimization of preincubation storage conditions. Poult Sci 2021; 100:101227. [PMID: 34175796 PMCID: PMC8242057 DOI: 10.1016/j.psj.2021.101227] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 11/24/2022] Open
Abstract
At the time of oviposition, the chicken embryo is in its blastodermal stage. The blastoderm displays the unique ability to undergo developmental arrest at low temperatures in a process called “embryonic diapause.” In the wild, diapause occurs in freshly laid eggs until the last egg of the clutch has been laid, providing an evolutionary advantage to hens that can synchronously hatch their eggs. The poultry industry utilizes the diapause phenomenon to store eggs before incubation, thereby mitigating their logistic problems. The embryos can only be stored at particular embryonic stages—termed “diapause developmental window” (DW)—if they are to continue to develop normally thereafter. Both cellular and molecular mechanisms define the limits of this DW which broadly comply with onset of blastulation to early gastrulation. Storage conditions affect the cellular and molecular characteristics of the embryo during this window and their ability to successfully resume development (SRD). At storage temperatures of ~12°C to 18°C, embryos can undergo diapause for a short period (up to 7 days (d)) without affecting SRD. However, following longer period of diapause (up to 28 d), embryo stored at ~12°C, but not at ~18°C, can resume development normally. Moreover, eggs can be heated before or during the storage period which will lead to their commencing in development; however, unlike the non-heated embryos, the storage temperature for heated embryos, which are more advance in developing, is not clear. Thus, based on SRD, this review brings evidence supporting the notion that a lower storage temperature is beneficial for early-stage blastoderms whereas a higher storage temperature is favorable for later-stage/gastrulating embryos. Our understanding of the molecular mechanisms underlying the relationship between storage temperature and development stage within the DW is rather limited. However, it is expected to become relevant in light of the effect of selective breeding of modern avian birds on the advancement of embryonic development stage. Thus, this review discusses parameters that are regulated during the DW and affect SRD, and presents the need to adopt new storage techniques. The pre-managerial decision of required duration of storage with manipulation of storage temperature in the currently used storage techniques may improve SRD characteristics.
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Affiliation(s)
- N Pokhrel
- Agricultural Research Organization, Volcani Center, Department of Poultry and Aquaculture Science, Rishon LeTsiyon, Israel; Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - D Sela-Donenfeld
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Y Cinnamon
- Agricultural Research Organization, Volcani Center, Department of Poultry and Aquaculture Science, Rishon LeTsiyon, Israel.
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15
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Maire T, Allertz T, Betjes MA, Youk H. Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability. Mol Syst Biol 2020; 16:e9245. [PMID: 33206464 PMCID: PMC7673291 DOI: 10.15252/msb.20199245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 11/28/2022] Open
Abstract
Dormancy is colloquially considered as extending lifespan by being still. Starved yeasts form dormant spores that wake-up (germinate) when nutrients reappear but cannot germinate (die) after some time. What sets their lifespans and how they age are open questions because what processes occur-and by how much-within each dormant spore remains unclear. With single-cell-level measurements, we discovered how dormant yeast spores age and die: spores have a quantifiable gene-expressing ability during dormancy that decreases over days to months until it vanishes, causing death. Specifically, each spore has a different probability of germinating that decreases because its ability to-without nutrients-express genes decreases, as revealed by a synthetic circuit that forces GFP expression during dormancy. Decreasing amounts of molecules required for gene expression-including RNA polymerases-decreases gene-expressing ability which then decreases chances of germinating. Spores gradually lose these molecules because they are produced too slowly compared with their degradations, causing gene-expressing ability to eventually vanish and, thus, death. Our work provides a systems-level view of dormancy-to-death transition.
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Affiliation(s)
- Théo Maire
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Tim Allertz
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Max A Betjes
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Hyun Youk
- Kavli Institute of NanoscienceDelftThe Netherlands
- CIFARCIFAR Azrieli Global Scholars ProgramTorontoONCanada
- Program in Molecular MedicineUniversity of Massachusetts Medical SchoolWorcesterMAUSA
- Program in Systems BiologyUniversity of Massachusetts Medical SchoolWorcesterMAUSA
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16
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Setlow P, Christie G. Bacterial Spore mRNA - What's Up With That? Front Microbiol 2020; 11:596092. [PMID: 33193276 PMCID: PMC7649253 DOI: 10.3389/fmicb.2020.596092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 01/19/2023] Open
Abstract
Bacteria belonging to the orders Bacillales and Clostridiales form spores in response to nutrient starvation. From a simplified morphological perspective, the spore can be considered as comprising a central protoplast or core, that is, enveloped sequentially by an inner membrane (IM), a peptidoglycan cortex, an outer membrane, and a proteinaceous coat. All of these structures are characterized by unique morphological and/or structural features, which collectively confer metabolic dormancy and properties of environmental resistance to the quiescent spore. These properties are maintained until the spore is stimulated to germinate, outgrow and form a new vegetative cell. Spore germination comprises a series of partially overlapping biochemical and biophysical events - efflux of ions from the core, rehydration and IM reorganization, disassembly of cortex and coat - all of which appear to take place in the absence of de novo ATP and protein synthesis. If the latter points are correct, why then do spores of all species examined to date contain a diverse range of mRNA molecules deposited within the spore core? Are some of these molecules "functional," serving as translationally active units that are required for efficient spore germination and outgrowth, or are they just remnants from sporulation whose sole purpose is to provide a reservoir of ribonucleotides for the newly outgrowing cell? What is the fate of these molecules during spore senescence, and indeed, are conditions within the spore core likely to provide any opportunity for changes in the transcriptional profile of the spore during dormancy? This review encompasses a historical perspective of spore ribonucleotide biology, from the earliest biochemical led analyses - some of which in hindsight have proved to be remarkably prescient - through the transcriptomic era at the turn of this century, to the latest next generation sequencing derived insights. We provide an overview of the key literature to facilitate reasoned responses to the aforementioned questions, and many others, prior to concluding by identifying the major outstanding issues in this crucial area of spore biology.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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17
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Personnic N, Striednig B, Hilbi H. Quorum sensing controls persistence, resuscitation, and virulence of Legionella subpopulations in biofilms. ISME JOURNAL 2020; 15:196-210. [PMID: 32951019 DOI: 10.1038/s41396-020-00774-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/13/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
The water-borne bacterium Legionella pneumophila is the causative agent of Legionnaires' disease. In the environment, the opportunistic pathogen colonizes different niches, including free-living protozoa and biofilms. The physiological state(s) of sessile Legionella in biofilms and their functional consequences are not well understood. Using single-cell techniques and fluorescent growth rate probes as well as promoter reporters, we show here that sessile L. pneumophila exhibits phenotypic heterogeneity and adopts growing and nongrowing ("dormant") states in biofilms and microcolonies. Phenotypic heterogeneity is controlled by the Legionella quorum sensing (Lqs) system, the transcription factor LvbR, and the temperature. The Lqs system and LvbR determine the ratio between growing and nongrowing sessile subpopulations, as well as the frequency of growth resumption ("resuscitation") and microcolony formation of individual bacteria. Nongrowing L. pneumophila cells are metabolically active, express virulence genes and show tolerance toward antibiotics. Therefore, these sessile nongrowers are persisters. Taken together, the Lqs system, LvbR and the temperature control the phenotypic heterogeneity of sessile L. pneumophila, and these factors regulate the formation of a distinct subpopulation of nongrowing, antibiotic tolerant, virulent persisters. Hence, the biofilm niche of L. pneumophila has a profound impact on the ecology and virulence of this opportunistic pathogen.
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Affiliation(s)
- Nicolas Personnic
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland.
| | - Bianca Striednig
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland.
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18
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Frentz Z, Dworkin J. Bioluminescence dynamics in single germinating bacterial spores reveal metabolic heterogeneity. J R Soc Interface 2020; 17:20200350. [PMID: 32900305 DOI: 10.1098/rsif.2020.0350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Spore-forming bacteria modulate their metabolic rate by over five orders of magnitude as they transition between dormant spores and vegetative cells and thus represent an extreme case of phenotypic variation. During environmental changes in nutrient availability, clonal populations of spore-forming bacteria exhibit individual differences in cell fate, the timing of phenotypic transitions and gene expression. One potential source of this variability is metabolic heterogeneity, but this has not yet been measured, as existing single-cell methods are not easily applicable to spores due to their small size and strong autofluorescence. Here, we use the bacterial bioluminescence system and a highly sensitive microscope to measure metabolic dynamics in thousands of B. subtilis spores as they germinate. We observe and quantitate large variations in the bioluminescence dynamics across individual spores that can be decomposed into contributions from variability in germination timing, the amount of endogenously produced luminescence substrate and the intracellular reducing power. This work shows that quantitative measurement of spore metabolism is possible and thus it opens avenues for future study of the thermodynamic nature of dormant states.
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Affiliation(s)
- Zak Frentz
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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19
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Christie G, Setlow P. Bacillus spore germination: Knowns, unknowns and what we need to learn. Cell Signal 2020; 74:109729. [PMID: 32721540 DOI: 10.1016/j.cellsig.2020.109729] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 01/06/2023]
Abstract
How might a microbial cell that is entirely metabolically dormant - and which has the ability to remain so for extended periods of time - irreversibly commit itself to resuming vegetative growth within seconds of being exposed to certain amino acids or sugars? That this process takes place in the absence of any detectable ATP or de novo protein synthesis, and relies upon a pre-formed apparatus that is immobilised, respectively, in a semi-crystalline membrane or multi-layered proteinaceous coat, only exacerbates the challenge facing spores of Bacillales species when stimulated to germinate. Whereas the process by which spores are formed in response to nutrient starvation - sporulation - involves the orchestrated interplay between hundreds of distinct proteins, the process by which spores return to life - germination - is a much simpler affair, requiring a handful of receptor and channel proteins complemented with specialized peptidoglycan lysins. Despite this relative simplicity, and research effort spanning many decades, comprehensive understanding of key molecular and biochemical details and, in particular signal transduction mechanisms associated with spore germination, has remained elusive. In this review we provide an up to date overview of the field while identifying what we consider to be the key gaps in knowledge associated with germination of Bacillales spores, suggesting also technical approaches that may provide fresh insight to this unique biological process.
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Affiliation(s)
- Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 OAS, United Kingdom.
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA.
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20
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Differential effects of 'resurrecting' Csp pseudoproteases during Clostridioides difficile spore germination. Biochem J 2020; 477:1459-1478. [PMID: 32242623 PMCID: PMC7200643 DOI: 10.1042/bcj20190875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 01/02/2023]
Abstract
Clostridioides difficile is a spore-forming bacterial pathogen that is the leading cause of hospital-acquired gastroenteritis. C. difficile infections begin when its spore form germinates in the gut upon sensing bile acids. These germinants induce a proteolytic signaling cascade controlled by three members of the subtilisin-like serine protease family, CspA, CspB, and CspC. Notably, even though CspC and CspA are both pseudoproteases, they are nevertheless required to sense germinants and activate the protease, CspB. Thus, CspC and CspA are part of a growing list of pseudoenzymes that play important roles in regulating cellular processes. However, despite their importance, the structural properties of pseudoenzymes that allow them to function as regulators remain poorly understood. Our recently solved crystal structure of CspC revealed that its pseudoactive site residues align closely with the catalytic triad of CspB, suggesting that it might be possible to ‘resurrect' the ancestral protease activity of the CspC and CspA pseudoproteases. Here, we demonstrate that restoring the catalytic triad to these pseudoproteases fails to resurrect their protease activity. We further show that the pseudoactive site substitutions differentially affect the stability and function of the CspC and CspA pseudoproteases: the substitutions destabilized CspC and impaired spore germination without affecting CspA stability or function. Thus, our results surprisingly reveal that the presence of a catalytic triad does not necessarily predict protease activity. Since homologs of C. difficile CspA occasionally carry an intact catalytic triad, our results indicate that bioinformatic predictions of enzyme activity may underestimate pseudoenzymes in rare cases.
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21
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Ten Brink H, Gremer JR, Kokko H. Optimal germination timing in unpredictable environments: the importance of dormancy for both among- and within-season variation. Ecol Lett 2020. [PMID: 31994356 DOI: 10.1111/ele.1346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
For organisms living in unpredictable environments, timing important life-history events is challenging. One way to deal with uncertainty is to spread the emergence of offspring across multiple years via dormancy. However, timing of emergence is not only important among years, but also within each growing season. Here, we study the evolutionary interactions between germination strategies that deal with among- and within-season uncertainty. We use a modelling approach that considers among-season dormancy and within-season germination phenology of annual plants as potentially independent traits and study their separate and joint evolution in a variable environment. We find that higher among-season dormancy selects for earlier germination within the growing season. Furthermore, our results indicate that more unpredictable natural environments can counter-intuitively select for less risk-spreading within the season. Furthermore, strong priority effects select for earlier within-season germination phenology which in turn increases the need for bet hedging through among-season dormancy.
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Affiliation(s)
- Hanna Ten Brink
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jennifer R Gremer
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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22
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Ten Brink H, Gremer JR, Kokko H. Optimal germination timing in unpredictable environments: the importance of dormancy for both among- and within-season variation. Ecol Lett 2020; 23:620-630. [PMID: 31994356 PMCID: PMC7079161 DOI: 10.1111/ele.13461] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/09/2019] [Accepted: 12/22/2019] [Indexed: 01/19/2023]
Abstract
For organisms living in unpredictable environments, timing important life‐history events is challenging. One way to deal with uncertainty is to spread the emergence of offspring across multiple years via dormancy. However, timing of emergence is not only important among years, but also within each growing season. Here, we study the evolutionary interactions between germination strategies that deal with among‐ and within‐season uncertainty. We use a modelling approach that considers among‐season dormancy and within‐season germination phenology of annual plants as potentially independent traits and study their separate and joint evolution in a variable environment. We find that higher among‐season dormancy selects for earlier germination within the growing season. Furthermore, our results indicate that more unpredictable natural environments can counter‐intuitively select for less risk‐spreading within the season. Furthermore, strong priority effects select for earlier within‐season germination phenology which in turn increases the need for bet hedging through among‐season dormancy.
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Affiliation(s)
- Hanna Ten Brink
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jennifer R Gremer
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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23
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Wright ES, Vetsigian KH. Stochastic exits from dormancy give rise to heavy‐tailed distributions of descendants in bacterial populations. Mol Ecol 2019; 28:3915-3928. [DOI: 10.1111/mec.15200] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Erik S. Wright
- Department of Biomedical Informatics University of Pittsburgh Pittsburgh PA USA
| | - Kalin H. Vetsigian
- Wisconsin Institute for Discovery University of Wisconsin‐Madison Madison WI USA
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24
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Rohlfing AE, Eckenroth BE, Forster ER, Kevorkian Y, Donnelly ML, Benito de la Puebla H, Doublié S, Shen A. The CspC pseudoprotease regulates germination of Clostridioides difficile spores in response to multiple environmental signals. PLoS Genet 2019; 15:e1008224. [PMID: 31276487 PMCID: PMC6636752 DOI: 10.1371/journal.pgen.1008224] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/17/2019] [Accepted: 05/31/2019] [Indexed: 12/18/2022] Open
Abstract
The gastrointestinal pathogen, Clostridioides difficile, initiates infection when its metabolically dormant spore form germinates in the mammalian gut. While most spore-forming bacteria use transmembrane germinant receptors to sense nutrient germinants, C. difficile is thought to use the soluble pseudoprotease, CspC, to detect bile acid germinants. To gain insight into CspC's unique mechanism of action, we solved its crystal structure. Guided by this structure, we identified CspC mutations that confer either hypo- or hyper-sensitivity to bile acid germinant. Surprisingly, hyper-sensitive CspC variants exhibited bile acid-independent germination as well as increased sensitivity to amino acid and/or calcium co-germinants. Since mutations in specific residues altered CspC's responsiveness to these different signals, CspC plays a critical role in regulating C. difficile spore germination in response to multiple environmental signals. Taken together, these studies implicate CspC as being intimately involved in the detection of distinct classes of co-germinants in addition to bile acids and thus raises the possibility that CspC functions as a signaling node rather than a ligand-binding receptor.
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Affiliation(s)
- Amy E. Rohlfing
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Brian E. Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Emily R. Forster
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Yuzo Kevorkian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - M. Lauren Donnelly
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hector Benito de la Puebla
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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25
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Spanka DT, Konzer A, Edelmann D, Berghoff BA. High-Throughput Proteomics Identifies Proteins With Importance to Postantibiotic Recovery in Depolarized Persister Cells. Front Microbiol 2019; 10:378. [PMID: 30894840 PMCID: PMC6414554 DOI: 10.3389/fmicb.2019.00378] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial populations produce phenotypic variants called persisters to survive harmful conditions. Persisters are highly tolerant to antibiotics and repopulate environments after the stress has vanished. In order to resume growth, persisters have to recover from the persistent state, but the processes behind recovery remain mostly elusive. Deciphering these processes is an essential step toward understanding the persister phenomenon in its entirety. High-throughput proteomics by mass spectrometry is a valuable tool to assess persister physiology during any stage of the persister life cycle, and is expected to considerably contribute to our understanding of the recovery process. In the present study, an Escherichia coli strain, that overproduces the membrane-depolarizing toxin TisB, was established as a model for persistence by the use of high-throughput proteomics. Labeling of TisB persisters with stable isotope-containing amino acids (pulsed-SILAC) revealed an active translational response to ampicillin, including several RpoS-dependent proteins. Subsequent investigation of the persister proteome during postantibiotic recovery by label-free quantitative proteomics identified proteins with importance to the recovery process. Among them, AhpF, a component of alkyl hydroperoxide reductase, and the outer membrane porin OmpF were found to affect the persistence time of TisB persisters. Assessing the role of AhpF and OmpF in TisB-independent persisters demonstrated that the importance of a particular protein for the recovery process strongly depends on the physiological condition of a persister cell. Our study provides important insights into persister physiology and the processes behind recovery of depolarized cells.
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Affiliation(s)
- Daniel-Timon Spanka
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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26
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Extreme slow growth as alternative strategy to survive deep starvation in bacteria. Nat Commun 2019; 10:890. [PMID: 30792386 PMCID: PMC6385201 DOI: 10.1038/s41467-019-08719-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 01/18/2019] [Indexed: 12/04/2022] Open
Abstract
Bacteria can become dormant or form spores when they are starved for nutrients. Here, we find that non-sporulating Bacillus subtilis cells can survive deep starvation conditions for many months. During this period, cells adopt an almost coccoid shape and become tolerant to antibiotics. Unexpectedly, these cells appear to be metabolically active and show a transcriptome profile very different from that of stationary phase cells. We show that these starved cells are not dormant but are growing and dividing, albeit with a doubling time close to 4 days. Very low nutrient levels, comparable to 10,000-fold diluted lysogeny broth (LB), are sufficient to sustain this growth. This extreme slow growth, which we propose to call ‘oligotrophic growth state’, provides an alternative strategy for B. subtilis to endure nutrient depletion and environmental stresses. Further work is warranted to test whether this state can be found in other bacterial species to survive deep starvation conditions. Bacteria can become dormant or form spores when starved for nutrients. Here, Gray et al. describe an alternative strategy, or ‘oligotrophic growth state’, showing that non-sporulating Bacillus subtilis cells can survive deep starvation conditions by adopting an almost coccoid shape and extremely low growth rates.
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27
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Zhou P, Chen Y, Lu Q, Qin H, Ou H, He B, Ye J. Cellular metabolism network of Bacillus thuringiensis related to erythromycin stress and degradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 160:328-341. [PMID: 29857237 DOI: 10.1016/j.ecoenv.2018.05.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/15/2018] [Accepted: 05/20/2018] [Indexed: 06/08/2023]
Abstract
Erythromycin is one of the most widely used macrolide antibiotics. To present a system-level understanding of erythromycin stress and degradation, proteome, phospholipids and membrane potentials were investigated after the erythromycin degradation. Bacillus thuringiensis could effectively remove 77% and degrade 53% of 1 µM erythromycin within 24 h. The 36 up-regulated and 22 down-regulated proteins were mainly involved in spore germination, chaperone and nucleic acid binding. Up-regulated ribose-phosphate pyrophosphokinase and ribosomal proteins confirmed that the synthesis of protein, DNA and RNA were enhanced after the erythromycin degradation. The reaction network of glycolysis/gluconeogenesis was activated, whereas, the activity of spore germination was decreased. The increased synthesis of phospholipids, especially, palmitoleic acid and oleic acid, altered the membrane permeability for erythromycin transport. Ribose-phosphate pyrophosphokinase and palmitoleic acid could be biomarkers to reflect erythromycin exposure. Lipids, disease, pyruvate metabolism and citrate cycle in human cells could be the target pathways influenced by erythromycin. The findings presented novel insights to the interaction among erythromycin stress, protein interaction and metabolism network, and provided a useful protocol for investigating cellular metabolism responses under pollutant stress.
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Affiliation(s)
- Pulin Zhou
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Ya Chen
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Qiying Lu
- College of Biology and Food Engineering, Guangdong University of Education, Guangzhou 510303, Guangdong, China
| | - Huaming Qin
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Huase Ou
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Baoyan He
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jinshao Ye
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China.
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28
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Kell DB, Pretorius E. No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. Biol Rev Camb Philos Soc 2018; 93:1518-1557. [PMID: 29575574 PMCID: PMC6055827 DOI: 10.1111/brv.12407] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 12/11/2022]
Abstract
Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.
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Affiliation(s)
- Douglas B. Kell
- School of ChemistryThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- The Manchester Institute of BiotechnologyThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
| | - Etheresia Pretorius
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
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29
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Fowler AC, Winstanley HF. Microbial dormancy and boom-and-bust population dynamics under starvation stress. Theor Popul Biol 2018; 120:114-120. [PMID: 29447840 DOI: 10.1016/j.tpb.2018.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/20/2018] [Accepted: 02/05/2018] [Indexed: 11/16/2022]
Abstract
We propose a model for the growth of microbial populations in the presence of a rate-limiting nutrient which accounts for the switching of cells to a dormant phase at low densities in response to decreasing concentration of a putative biochemical signal. We then show that in conditions of nutrient starvation, self-sustained oscillations can occur, thus providing a natural explanation for such phenomena as plankton blooms. However, unlike results of previous studies, the microbial population minima do not become unrealistically small, being buffered during minima by an increased dormant phase population. We also show that this allows microbes to survive in extreme environments for very long periods, consistent with observation. The mechanism provides a natural vehicle for other such sporadic outbreaks, such as viral epidemics.
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Affiliation(s)
- A C Fowler
- MACSI, University of Limerick, Limerick, Ireland; OCIAM, University of Oxford, Oxford, UK.
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30
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Mutlu A, Trauth S, Ziesack M, Nagler K, Bergeest JP, Rohr K, Becker N, Höfer T, Bischofs IB. Phenotypic memory in Bacillus subtilis links dormancy entry and exit by a spore quantity-quality tradeoff. Nat Commun 2018; 9:69. [PMID: 29302032 PMCID: PMC5754360 DOI: 10.1038/s41467-017-02477-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/04/2017] [Indexed: 12/15/2022] Open
Abstract
Some bacteria, such as Bacillus subtilis, withstand starvation by forming dormant spores that revive when nutrients become available. Although sporulation and spore revival jointly determine survival in fluctuating environments, the relationship between them has been unclear. Here we show that these two processes are linked by a phenotypic “memory” that arises from a carry-over of molecules from the vegetative cell into the spore. By imaging life histories of individual B. subtilis cells using fluorescent reporters, we demonstrate that sporulation timing controls nutrient-induced spore revival. Alanine dehydrogenase contributes to spore memory and controls alanine-induced outgrowth, thereby coupling a spore’s revival capacity to the gene expression and growth history of its progenitors. A theoretical analysis, and experiments with signaling mutants exhibiting altered sporulation timing, support the hypothesis that such an intrinsically generated memory leads to a tradeoff between spore quantity and spore quality, which could drive the emergence of complex microbial traits. Bacillus subtilis withstands starvation by forming dormant spores that revive when nutrients become available. Here, Mutlu et al. show that sporulation timing controls spore revival through a phenotypic ‘memory’ that arises from the carry-over of a metabolic enzyme from the vegetative cell into the spore.
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Affiliation(s)
- Alper Mutlu
- 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
| | - Stephanie Trauth
- 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
| | - Marika Ziesack
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Katja Nagler
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jan-Philip Bergeest
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Karl Rohr
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Nils Becker
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Thomas Höfer
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Ilka B 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.
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31
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Carvalhais V, Pérez-Cabezas B, Oliveira C, Vitorino R, Vilanova M, Cerca N. Tetracycline and rifampicin induced a viable but nonculturable state in Staphylococcus epidermidis biofilms. Future Microbiol 2017; 13:27-36. [PMID: 29227161 DOI: 10.2217/fmb-2017-0107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM The goal of this study was to determine the effectiveness of antibiotics on Staphylococcus epidermidis biofilms with different proportions of dormant bacteria, using clinical and commensal isolates. MATERIALS & METHODS The ability of S. epidermidis isolates to develop a dormant state was determined. The susceptibility of biofilms with prevented or induced dormancy to antibiotics was evaluated by enumeration of viable and cultivable cells, and confocal microscopy. RESULTS Dormancy was observed in the majority of tested strains. Tetracycline and rifampicin enhanced the development of a viable but noncultivable biofilm state. CONCLUSION Biofilms with induced dormancy were more likely to survive rifampicin. Furthermore, we found that the reduction of cultivable cells was not sufficient to reach definite conclusions on antimicrobial effectiveness.
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Affiliation(s)
- Virginia Carvalhais
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Begoña Pérez-Cabezas
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Cátia Oliveira
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Rui Vitorino
- iBiMED - Department of Medical Sciences, Institute for Biomedicine, University of Aveiro, Campus Universitário de Santiago, Agra do Crasto, 3810-193, Aveiro, Portugal.,Department of Physiology & Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Manuel Vilanova
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde & IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal
| | - Nuno Cerca
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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32
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Bobek J, Šmídová K, Čihák M. A Waking Review: Old and Novel Insights into the Spore Germination in Streptomyces. Front Microbiol 2017; 8:2205. [PMID: 29180988 PMCID: PMC5693915 DOI: 10.3389/fmicb.2017.02205] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/26/2017] [Indexed: 01/02/2023] Open
Abstract
The complex development undergone by Streptomyces encompasses transitions from vegetative mycelial forms to reproductive aerial hyphae that differentiate into chains of single-celled spores. Whereas their mycelial life – connected with spore formation and antibiotic production – is deeply investigated, spore germination as the counterpoint in their life cycle has received much less attention. Still, germination represents a system of transformation from metabolic zero point to a new living lap. There are several aspects of germination that may attract our attention: (1) Dormant spores are strikingly well-prepared for the future metabolic restart; they possess stable transcriptome, hydrolytic enzymes, chaperones, and other required macromolecules stabilized in a trehalose milieu; (2) Germination itself is a specific sequence of events leading to a complete morphological remodeling that include spore swelling, cell wall reconstruction, and eventually germ tube emergences; (3) Still not fully unveiled are the strategies that enable the process, including a single cell’s signal transduction and gene expression control, as well as intercellular communication and the probability of germination across the whole population. This review summarizes our current knowledge about the germination process in Streptomyces, while focusing on the aforementioned points.
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Affiliation(s)
- Jan Bobek
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czechia.,Chemistry Department, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Ústí nad Labem, Czechia.,Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Klára Šmídová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czechia.,Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Matouš Čihák
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czechia
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33
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Revisiting the Role of Csp Family Proteins in Regulating Clostridium difficile Spore Germination. J Bacteriol 2017; 199:JB.00266-17. [PMID: 28874406 DOI: 10.1128/jb.00266-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/23/2017] [Indexed: 02/07/2023] Open
Abstract
Clostridium difficile causes considerable health care-associated gastrointestinal disease that is transmitted by its metabolically dormant spore form. Upon entering the gut, C. difficile spores germinate and outgrow to produce vegetative cells that release disease-causing toxins. C. difficile spore germination depends on the Csp family of (pseudo)proteases and the cortex hydrolase SleC. The CspC pseudoprotease functions as a bile salt germinant receptor that activates the protease CspB, which in turn proteolytically activates the SleC zymogen. Active SleC degrades the protective cortex layer, allowing spores to outgrow and resume metabolism. We previously showed that the CspA pseudoprotease domain, which is initially produced as a fusion to CspB, controls the incorporation of the CspC germinant receptor in mature spores. However, study of the individual Csp proteins has been complicated by the polar effects of TargeTron-based gene disruption on the cspBA-cspC operon. To overcome these limitations, we have used pyrE-based allelic exchange to create individual deletions of the regions encoding CspB, CspA, CspBA, and CspC in strain 630Δerm Our results indicate that stable CspA levels in sporulating cells depend on CspB and confirm that CspA maximizes CspC incorporation into spores. Interestingly, we observed that csp and sleC mutants spontaneously germinate more frequently in 630Δerm than equivalent mutants in the JIR8094 and UK1 strain backgrounds. Analyses of this phenomenon suggest that only a subpopulation of C. difficile 630Δerm spores can spontaneously germinate, in contrast with Bacillus subtilis spores. We also show that C. difficile clinical isolates that encode truncated CspBA variants have sequencing errors that actually produce full-length CspBA.IMPORTANCEClostridium difficile is a leading cause of health care-associated infections. Initiation of C. difficile infection depends on spore germination, a process controlled by Csp family (pseudo)proteases. The CspC pseudoprotease is a germinant receptor that senses bile salts and activates the CspB protease, which activates a hydrolase required for germination. Previous work implicated the CspA pseudoprotease in controlling CspC incorporation into spores but relied on plasmid-based overexpression. Here we have used allelic exchange to study the functions of CspB and CspA. We determined that CspA production and/or stability depends on CspB and confirmed that CspA maximizes CspC incorporation into spores. Our data also suggest that a subpopulation of C. difficile spores spontaneously germinates in the absence of bile salt germinants and/or Csp proteins.
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34
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Zanchi C, Johnston PR, Rolff J. Evolution of defence cocktails: Antimicrobial peptide combinations reduce mortality and persistent infection. Mol Ecol 2017; 26:5334-5343. [PMID: 28762573 DOI: 10.1111/mec.14267] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 01/26/2023]
Abstract
The simultaneous expression of costly immune effectors such as multiple antimicrobial peptides is a hallmark of innate immunity of multicellular organisms, yet the adaptive advantage remains unresolved. Here, we test current hypotheses on the evolution of such defence cocktails. We use RNAi gene knock-down to explore, the effects of three highly expressed antimicrobial peptides, displaying different degrees of activity in vitro against Staphylococcus aureus, during an infection in the beetle Tenebrio molitor. We find that a defensin confers no survival benefit but reduces bacterial loads. A coleoptericin contributes to host survival without affecting bacterial loads. An attacin has no individual effect. Simultaneous knock-down of the defensin with the other AMPs results in increased mortality and elevated bacterial loads. Contrary to common expectations, the effects on host survival and bacterial load can be independent. The expression of multiple AMPs increases host survival and contributes to the control of persisting infections and tolerance. This is an emerging property that explains the adaptive benefit of defence cocktails.
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Affiliation(s)
- Caroline Zanchi
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany.,Westfälische Wilhelms-Universität Münster, Institute of Evolution and Biodiversity, Münster, Germany
| | - Paul R Johnston
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jens Rolff
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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35
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Abstract
The interaction between the host and the pathogen is extremely complex and is affected by anatomical, physiological, and immunological diversity in the microenvironments, leading to phenotypic diversity of the pathogen. Phenotypic heterogeneity, defined as nongenetic variation observed in individual members of a clonal population, can have beneficial consequences especially in fluctuating stressful environmental conditions. This is all the more relevant in infections caused by Mycobacterium tuberculosis wherein the pathogen is able to survive and often establish a lifelong persistent infection in the host. Recent studies in tuberculosis patients and in animal models have documented the heterogeneous and diverging trajectories of individual lesions within a single host. Since the fate of the individual lesions appears to be determined by the local tissue environment rather than systemic response of the host, studying this heterogeneity is very relevant to ensure better control and complete eradication of the pathogen from individual lesions. The heterogeneous microenvironments greatly enhance M. tuberculosis heterogeneity influencing the growth rates, metabolic potential, stress responses, drug susceptibility, and eventual lesion resolution. Single-cell approaches such as time-lapse microscopy using microfluidic devices allow us to address cell-to-cell variations that are often lost in population-average measurements. In this review, we focus on some of the factors that could be considered as drivers of phenotypic heterogeneity in M. tuberculosis as well as highlight some of the techniques that are useful in addressing this issue.
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36
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Abstract
Dormant Bacillales and Clostridiales spores begin to grow when small molecules (germinants) trigger germination, potentially leading to food spoilage or disease. Germination-specific proteins sense germinants, transport small molecules, and hydrolyze specific bonds in cortex peptidoglycan and specific proteins. Major events in germination include (a) germinant sensing; (b) commitment to germinate; (c) release of spores' depot of dipicolinic acid (DPA); (d) hydrolysis of spores' peptidoglycan cortex; and (e) spore core swelling and water uptake, cell wall peptidoglycan remodeling, and restoration of core protein and inner spore membrane lipid mobility. Germination is similar between Bacillales and Clostridiales, but some species differ in how germinants are sensed and how cortex hydrolysis and DPA release are triggered. Despite detailed knowledge of the proteins and signal transduction pathways involved in germination, precisely what some germination proteins do and how they do it remain unclear.
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Affiliation(s)
- Peter Setlow
- Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut 06030-3305;
| | - Shiwei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Yong-Qing Li
- Department of Physics, East Carolina University, Greenville, North Carolina 27858-4353;
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37
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Berghoff BA, Wagner EGH. RNA-based regulation in type I toxin-antitoxin systems and its implication for bacterial persistence. Curr Genet 2017; 63:1011-1016. [PMID: 28560584 PMCID: PMC5668327 DOI: 10.1007/s00294-017-0710-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 02/02/2023]
Abstract
Bacterial dormancy is a valuable survival strategy upon challenging environmental conditions. Dormant cells tolerate the consequences of high stress levels and may re-populate the environment upon return to favorable conditions. Antibiotic-tolerant bacteria—termed persisters—regularly cause relapsing infections, increase the likelihood of antibiotic resistance, and, therefore, earn increasing attention. Their generation often depends on toxins from chromosomal toxin–antitoxin systems. Here, we review recent insights concerning RNA-based control of toxin synthesis, and discuss possible implications for persister generation.
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Affiliation(s)
- Bork A Berghoff
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, 35392, Giessen, Germany.
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden.
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38
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Bury-Moné S, Sclavi B. Stochasticity of gene expression as a motor of epigenetics in bacteria: from individual to collective behaviors. Res Microbiol 2017; 168:503-514. [PMID: 28427910 DOI: 10.1016/j.resmic.2017.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/07/2017] [Accepted: 03/28/2017] [Indexed: 01/22/2023]
Abstract
Measuring gene expression at the single cell and single molecule level has recently made possible the quantitative measurement of stochasticity of gene expression. This enables identification of the probable sources and roles of noise. Gene expression noise can result in bacterial population heterogeneity, offering specific advantages for fitness and survival in various environments. This trait is therefore selected during the evolution of the species, and is consequently regulated by a specific genetic network architecture. Examples exist in stress-response mechanisms, as well as in infection and pathogenicity strategies, pointing to advantages for multicellularity of bacterial populations.
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Affiliation(s)
- Stéphanie Bury-Moné
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France.
| | - Bianca Sclavi
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, Université Paris-Saclay, F-94235, Cachan, France.
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39
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Xu Y, Vetsigian K. Phenotypic variability and community interactions of germinating Streptomyces spores. Sci Rep 2017; 7:699. [PMID: 28386097 PMCID: PMC5429633 DOI: 10.1038/s41598-017-00792-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/13/2017] [Indexed: 11/17/2022] Open
Abstract
A case can be made for stochastic germination and interactions among germinating spores as beneficial germination strategies in uncertain environments. However, there is little data on how widespread, species-specific or diverse such phenomena are. Focusing on Streptomycetes, a platform was developed for quantification of germination and early growth within communities of spores. We found that the germination process is stochastic at three levels: spores vary in their germination times, mycelium networks grow at different rates, and a fraction of germlings stall their growth shortly after germination. Furthermore, by monitoring how these stochastic properties are affected by spore density and chemicals released from spores, germination interactions were quantified for four species. Stochastically germinating spores were frequently promoted or inhibited by compounds released by spores from the same or different species, and all species had distinct interaction profiles. The spatial distribution patterns were important with clusters of spores behaving differently than individual spores. Aged spores exhibited higher dormancy but could efficiently geminate in the presence of chemicals released during germination. All interactions were specific to germination and only weakly affected growth rates. This work suggests that stochastic germination is commonly affected by the community context and species have adapted diverse germination strategies.
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Affiliation(s)
- Ye Xu
- Department of Bacteriology and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, 53715, USA
| | - Kalin Vetsigian
- Department of Bacteriology and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, 53715, USA.
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40
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Abstract
Many bacteria form metabolically inactive spores to survive harsh conditions. But how do spores decide to germinate when sensing of the environment is hampered by their inactivity? A new study shows how phenotypic variation leads to stochastic germination of spores.
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Affiliation(s)
- Simon van Vliet
- Department of Environmental Systems Sciences, ETH Zurich, Zurich 8006, Switzerland and Department of Environmental Microbiology, Eawag, Dübendorf 8600, Switzerland.
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41
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Kaldalu N, Hauryliuk V, Tenson T. Persisters-as elusive as ever. Appl Microbiol Biotechnol 2016; 100:6545-6553. [PMID: 27262568 PMCID: PMC4939303 DOI: 10.1007/s00253-016-7648-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 12/27/2022]
Abstract
Persisters—a drug-tolerant sub-population in an isogenic bacterial culture—have been featured throughout the last decade due to their important role in recurrent bacterial infections. Numerous investigations detail the mechanisms responsible for the formation of persisters and suggest exciting strategies for their eradication. In this review, we argue that the very term “persistence” is currently used to describe a large and heterogeneous set of physiological phenomena that are functions of bacterial species, strains, growth conditions, and antibiotics used in the experiments. We caution against the oversimplification of the mechanisms of persistence and urge for a more rigorous validation of the applicability of these mechanisms in each case.
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Affiliation(s)
- Niilo Kaldalu
- University of Tartu, Institute of Technology, Nooruse 1, 50411, Tartu, Estonia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, 50411, Tartu, Estonia
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87, Umeå, Sweden
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411, Tartu, Estonia.
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42
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Pompeo F, Foulquier E, Galinier A. Impact of Serine/Threonine Protein Kinases on the Regulation of Sporulation in Bacillus subtilis. Front Microbiol 2016; 7:568. [PMID: 27148245 PMCID: PMC4837961 DOI: 10.3389/fmicb.2016.00568] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
Bacteria possess many kinases that catalyze phosphorylation of proteins on diverse amino acids including arginine, cysteine, histidine, aspartate, serine, threonine, and tyrosine. These protein kinases regulate different physiological processes in response to environmental modifications. For example, in response to nutritional stresses, the Gram-positive bacterium Bacillus subtilis can differentiate into an endospore; the initiation of sporulation is controlled by the master regulator Spo0A, which is activated by phosphorylation. Spo0A phosphorylation is carried out by a multi-component phosphorelay system. These phosphorylation events on histidine and aspartate residues are labile, highly dynamic and permit a temporal control of the sporulation initiation decision. More recently, another kind of phosphorylation, more stable yet still dynamic, on serine or threonine residues, was proposed to play a role in spore maintenance and spore revival. Kinases that perform these phosphorylation events mainly belong to the Hanks family and could regulate spore dormancy and spore germination. The aim of this mini review is to focus on the regulation of sporulation in B. subtilis by these serine and threonine phosphorylation events and the kinases catalyzing them.
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Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
| | - Elodie Foulquier
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
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Widderich N, Rodrigues CDA, Commichau FM, Fischer KE, Ramirez-Guadiana FH, Rudner DZ, Bremer E. Salt-sensitivity of σ(H) and Spo0A prevents sporulation of Bacillus subtilis at high osmolarity avoiding death during cellular differentiation. Mol Microbiol 2016; 100:108-24. [PMID: 26712348 DOI: 10.1111/mmi.13304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2015] [Indexed: 01/15/2023]
Abstract
The spore-forming bacterium Bacillus subtilis frequently experiences high osmolarity as a result of desiccation in the soil. The formation of a highly desiccation-resistant endospore might serve as a logical osmostress escape route when vegetative growth is no longer possible. However, sporulation efficiency drastically decreases concomitant with an increase in the external salinity. Fluorescence microscopy of sporulation-specific promoter fusions to gfp revealed that high salinity blocks entry into the sporulation pathway at a very early stage. Specifically, we show that both Spo0A- and SigH-dependent transcription are impaired. Furthermore, we demonstrate that the association of SigH with core RNA polymerase is reduced under these conditions. Suppressors that modestly increase sporulation efficiency at high salinity map to the coding region of sigH and in the regulatory region of kinA, encoding one the sensor kinases that activates Spo0A. These findings led us to discover that B. subtilis cells that overproduce KinA can bypass the salt-imposed block in sporulation. Importantly, these cells are impaired in the morphological process of engulfment and late forespore gene expression and frequently undergo lysis. Altogether our data indicate that B. subtilis blocks entry into sporulation in high-salinity environments preventing commitment to a developmental program that it cannot complete.
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Affiliation(s)
- Nils Widderich
- Department of Biology, Laboratory for Molecular Microbiology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Christopher D A Rodrigues
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115-5701, USA
| | - Fabian M Commichau
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg August University Göttingen, Griesebachstr, 8, D-37077, Göttingen, Germany
| | - Kathleen E Fischer
- Department of Biology, Laboratory for Molecular Microbiology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Fernando H Ramirez-Guadiana
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115-5701, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115-5701, USA
| | - Erhard Bremer
- Department of Biology, Laboratory for Molecular Microbiology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
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