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De Baets J, De Paepe B, De Mey M. Delaying production with prokaryotic inducible expression systems. Microb Cell Fact 2024; 23:249. [PMID: 39272067 DOI: 10.1186/s12934-024-02523-w] [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: 06/20/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Engineering bacteria with the purpose of optimizing the production of interesting molecules often leads to a decrease in growth due to metabolic burden or toxicity. By delaying the production in time, these negative effects on the growth can be avoided in a process called a two-stage fermentation. MAIN TEXT During this two-stage fermentation process, the production stage is only activated once sufficient cell mass is obtained. Besides the possibility of using external triggers, such as chemical molecules or changing fermentation parameters to induce the production stage, there is a renewed interest towards autoinducible systems. These systems, such as quorum sensing, do not require the extra interference with the fermentation broth to start the induction. In this review, we discuss the different possibilities of both external and autoinduction methods to obtain a two-stage fermentation. Additionally, an overview is given of the tuning methods that can be applied to optimize the induction process. Finally, future challenges and prospects of (auto)inducible expression systems are discussed. CONCLUSION There are numerous methods to obtain a two-stage fermentation process each with their own advantages and disadvantages. Even though chemically inducible expression systems are well-established, an increasing interest is going towards autoinducible expression systems, such as quorum sensing. Although these newer techniques cannot rely on the decades of characterization and applications as is the case for chemically inducible promoters, their advantages might lead to a shift in future inducible expression systems.
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Affiliation(s)
- Jasmine De Baets
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Brecht De Paepe
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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2
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Matteau D, Duval A, Baby V, Rodrigue S. Mesoplasma florum: a near-minimal model organism for systems and synthetic biology. Front Genet 2024; 15:1346707. [PMID: 38404664 PMCID: PMC10884336 DOI: 10.3389/fgene.2024.1346707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Mesoplasma florum is an emerging model organism for systems and synthetic biology due to its small genome (∼800 kb) and fast growth rate. While M. florum was isolated and first described almost 40 years ago, many important aspects of its biology have long remained uncharacterized due to technological limitations, the absence of dedicated molecular tools, and since this bacterial species has not been associated with any disease. However, the publication of the first M. florum genome in 2004 paved the way for a new era of research fueled by the rise of systems and synthetic biology. Some of the most important studies included the characterization and heterologous use of M. florum regulatory elements, the development of the first replicable plasmids, comparative genomics and transposon mutagenesis, whole-genome cloning in yeast, genome transplantation, in-depth characterization of the M. florum cell, as well as the development of a high-quality genome-scale metabolic model. The acquired data, knowledge, and tools will greatly facilitate future genome engineering efforts in M. florum, which could next be exploited to rationally design and create synthetic cells to advance fundamental knowledge or for specific applications.
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Affiliation(s)
- Dominick Matteau
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Anthony Duval
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Vincent Baby
- Centre de diagnostic vétérinaire de l'Université de Montréal, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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3
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Govers SK, Campos M, Tyagi B, Laloux G, Jacobs-Wagner C. Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle. Cell Syst 2024; 15:19-36.e5. [PMID: 38157847 DOI: 10.1016/j.cels.2023.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; de Duve Institute, UCLouvain, Brussels, Belgium; Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Toulouse, France
| | - Bhavyaa Tyagi
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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4
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Schultes FPJ, Haarmann M, Tischler D, Mügge C. Primary alcohols as substrates or products in whole-cell biocatalysis: Toxicity for Escherichia coli expression strains. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.112979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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5
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Water Stress-Driven Changes in Bacterial Cell Surface Properties. Appl Environ Microbiol 2022; 88:e0073222. [PMID: 36226960 PMCID: PMC9642014 DOI: 10.1128/aem.00732-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Increased drought intensity and frequency exposes soil bacteria to prolonged water stress. While numerous studies reported on behavioral and physiological mechanisms of bacterial adaptation to water stress, changes in bacterial cell surface properties during adaptation are not well researched. We studied adaptive changes in cell surface hydrophobicity (CSH) after exposure to osmotic (NaCl) and matric stress (polyethylene glycol 8000 [PEG 8000]) for six typical soil bacteria (Bacillus subtilis, Arthrobacter chlorophenolicus, Pseudomonas fluorescens, Novosphingobium aromaticivorans, Rhodococcus erythropolis, and Mycobacterium pallens) covering a wide range of cell surface properties. Additional physicochemical parameters (surface chemical composition, surface charge, cell size and stiffness) of B. subtilis and P. fluorescens were analyzed to understand their possible contribution to CSH development. Changes in CSH caused by osmotic and matric stress depend on strain and stress type. CSH of B. subtilis and P. fluorescens increased with stress intensity, R. erythropolis and M. pallens exhibited a generally high but constant contact angle, while the response of A. chlorophenolicus and N. aromaticivorans depended on growth conditions and stress type. Osmotically driven changes in CSH of B. subtilis and P. fluorescens are accompanied by increasing surface N/C ratio, suggesting an increase in protein concentration within the cell wall. Cell envelope proteins thus presumably control bacterial CSH in two ways: (i) by increases in the relative density of surface proteins due to efflux of cytoplasmic water and subsequent cell shrinkage, and (ii) by destabilization of cell wall proteins, resulting in conformational changes which render the surface more hydrophobic. IMPORTANCE Changes in precipitation frequency, intensity, and temporal distribution are projected to result in increased frequency and intensity of droughts and heavy rainfall events. Prolonged droughts can promote the development of soil water repellency (SWR); this impacts the infiltration and distribution of water in the soil profile, exposing soil microorganisms to water stress. Exposure to water stress has recently been reported to result in increased cell surface hydrophobicity. However, the mechanism of this development is poorly understood. This study investigates the changes in the physicochemical properties of bacterial cell surfaces under water stress as a possible mechanism of increased surface hydrophobicity. Our results improve understanding of the microbial response to water stress in terms of surface properties, the variations in stress response depending on cell wall composition, and its contribution to the development of SWR.
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6
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Czerwińska-Główka D, Krukiewicz K. Guidelines for a Morphometric Analysis of Prokaryotic and Eukaryotic Cells by Scanning Electron Microscopy. Cells 2021; 10:3304. [PMID: 34943812 PMCID: PMC8699492 DOI: 10.3390/cells10123304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/11/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
The invention of a scanning electron microscopy (SEM) pushed the imaging methods and allowed for the observation of cell details with a high resolution. Currently, SEM appears as an extremely useful tool to analyse the morphology of biological samples. The aim of this paper is to provide a set of guidelines for using SEM to analyse morphology of prokaryotic and eukaryotic cells, taking as model cases Escherichia coli bacteria and B-35 rat neuroblastoma cells. Herein, we discuss the necessity of a careful sample preparation and provide an optimised protocol that allows to observe the details of cell ultrastructure (≥ 50 nm) with a minimum processing effort. Highlighting the versatility of morphometric descriptors, we present the most informative parameters and couple them with molecular processes. In this way, we indicate the wide range of information that can be collected through SEM imaging of biological materials that makes SEM a convenient screening method to detect cell pathology.
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Affiliation(s)
| | - Katarzyna Krukiewicz
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, 44-100 Gliwice, Poland;
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7
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Francis N, Laishram RS. Transgenesis of mammalian PABP reveals mRNA polyadenylation as a general stress response mechanism in bacteria. iScience 2021; 24:103119. [PMID: 34646982 PMCID: PMC8496165 DOI: 10.1016/j.isci.2021.103119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/23/2021] [Accepted: 09/09/2021] [Indexed: 12/01/2022] Open
Abstract
In eukaryotes, mRNA 3′-polyadenylation triggers poly(A) binding protein (PABP) recruitment and stabilization. In a stark contrast, polyadenylation marks mRNAs for degradation in bacteria. To study this difference, we trans-express the mammalian nuclear PABPN1 chromosomally and extra-chromosomally in Escherichia coli. Expression of PABPN1 but not the mutant PABPN1 stabilizes polyadenylated mRNAs and improves their half-lives. In the presence of PABPN1, 3′-exonuclease PNPase is not detected on PA-tailed mRNAs compromising the degradation. We show that PABPN1 trans-expression phenocopies pcnB (that encodes poly(A) polymerase, PAPI) mutation and regulates plasmid copy number. Genome-wide RNA-seq analysis shows a general up-regulation of polyadenylated mRNAs on PABPN1 expression, the largest subset of which are those involved in general stress response. However, major global stress regulators are unaffected on PABPN1 expression. Concomitantly, PABPN1 expression or pcnB mutation imparts cellular tolerance to multiple stresses. This study establishes mRNA 3′-polyadenylation as a general stress response mechanism in E. coli. Trans expression of mammalian PABPN1 stabilizes polyadenyated mRNAs in E. coli PABPN1 expression phenocopies pcnB mutation and regulates plasmid copy number 3′-polyadenylation acts as a general stress response mechanism in bacteria This study indicates an evolutionary significance of PABP in mRNA metabolism
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Affiliation(s)
- Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Trivandrum 695014, India
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8
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Romanova N, Niemann T, Greiner JFW, Kaltschmidt B, Kaltschmidt C, Noll T. Hyperosmolality in CHO culture: Effects on cellular behavior and morphology. Biotechnol Bioeng 2021; 118:2348-2359. [PMID: 33751545 DOI: 10.1002/bit.27747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/23/2021] [Accepted: 03/08/2021] [Indexed: 01/02/2023]
Abstract
Exposure of Chinese hamster ovary cells (CHO) to highly concentrated feed solution during fed-batch cultivation is known to result in an unphysiological osmolality increase (>300 mOsm/kg), affecting cell physiology and morphology. Extending previous observation on osmotic adaptation, the present study investigates for the first time potential effects of hyperosmolality on CHO cells on both population and single-cell level. We intentionally exposed CHO cells to hyperosmolality of up to 545 mOsm/kg during fed-batch cultivation. In concordance with existing research data, hyperosmolality-exposed CHO cells showed a nearly triplicated volume accompanied by ablation of proliferation. On the molecular level, we observed a strong hyperosmolality-dependent increase in mitochondrial activity in CHO cells compared to control. In contrast to mitochondrial activity, hyperosmolality-dependent proliferation arrest of CHO cells was not accompanied by DNA accumulation or caspase-3/7-mediated apoptosis. Notably, we demonstrate for the first time a formation of up to eight multiple, small nuclei in single hyperosmolality-stressed CHO cells. The here presented observations reveal previously unknown hyperosmolality-dependent morphological changes in CHO cells and support existing data on the osmotic response in mammalian cells.
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Affiliation(s)
- Nadiya Romanova
- Cell Culture Technology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Tarek Niemann
- AG Molecular Neurobiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Cell Biology, Faculty of Biology, University of Bielefeld, Universitaetsstrasse 25, Bielefeld, 33615, Germany
| | - Johannes F W Greiner
- Department of Cell Biology, Faculty of Biology, University of Bielefeld, Universitaetsstrasse 25, Bielefeld, 33615, Germany
| | - Barbara Kaltschmidt
- AG Molecular Neurobiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Cell Biology, Faculty of Biology, University of Bielefeld, Universitaetsstrasse 25, Bielefeld, 33615, Germany
| | - Christian Kaltschmidt
- Department of Cell Biology, Faculty of Biology, University of Bielefeld, Universitaetsstrasse 25, Bielefeld, 33615, Germany
| | - Thomas Noll
- Cell Culture Technology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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9
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Matteau D, Lachance J, Grenier F, Gauthier S, Daubenspeck JM, Dybvig K, Garneau D, Knight TF, Jacques P, Rodrigue S. Integrative characterization of the near-minimal bacterium Mesoplasma florum. Mol Syst Biol 2020; 16:e9844. [PMID: 33331123 PMCID: PMC7745072 DOI: 10.15252/msb.20209844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/11/2022] Open
Abstract
The near-minimal bacterium Mesoplasma florum is an interesting model for synthetic genomics and systems biology due to its small genome (~ 800 kb), fast growth rate, and lack of pathogenic potential. However, fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. We investigated several physical and physiological parameters of this bacterium, including cell size, growth kinetics, and biomass composition of the cell. We also performed the first genome-wide analysis of its transcriptome and proteome, notably revealing a conserved promoter motif, the organization of transcription units, and the transcription and protein expression levels of all protein-coding sequences. We converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts provide a strong experimental foundation for the development of a genome-scale model for M. florum and will guide future genome engineering endeavors in this simple organism.
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Affiliation(s)
- Dominick Matteau
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | | | - Frédéric Grenier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Samuel Gauthier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | | | - Kevin Dybvig
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamALUSA
| | - Daniel Garneau
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
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10
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de Graaff DR, van Loosdrecht MCM, Pronk M. Trehalose as an osmolyte in Candidatus Accumulibacter phosphatis. Appl Microbiol Biotechnol 2020; 105:379-388. [PMID: 33074418 PMCID: PMC7778627 DOI: 10.1007/s00253-020-10947-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/30/2020] [Accepted: 10/04/2020] [Indexed: 11/30/2022]
Abstract
Abstract Candidatus Accumulibacter phosphatis is an important microorganism for enhanced biological phosphorus removal (EBPR). In a previous study, we found a remarkable flexibility regarding salinity, since this same microorganism could thrive in both freshwater- and seawater-based environments, but the mechanism for the tolerance to saline conditions remained unknown. Here, we identified and described the role of trehalose as an osmolyte in Ca. Accumulibacter phosphatis. A freshwater-adapted culture was exposed to a single batch cycle of hyperosmotic and hypo-osmotic shock, which led to the release of trehalose up to 5.34 mg trehalose/g volatile suspended solids (VSS). Long-term adaptation to 30% seawater-based medium in a sequencing batch reactor (SBR) gave a stable operation with complete anaerobic uptake of acetate and propionate along with phosphate release of 0.73 Pmol/Cmol, and complete aerobic uptake of phosphate. Microbial analysis showed Ca. Accumulibacter phosphatis clade I as the dominant organism in both the freshwater- and seawater-adapted cultures (> 90% presence). Exposure of the seawater-adapted culture to a single batch cycle of hyperosmotic incubation and hypo-osmotic shock led to an increase in trehalose release upon hypo-osmotic shock when higher salinity is used for the hyperosmotic incubation. Maximum trehalose release upon hypo-osmotic shock was achieved after hyperosmotic incubation with 3× salinity increase relative to the salinity in the SBR adaptation reactor, resulting in the release of 11.9 mg trehalose/g VSS. Genome analysis shows the possibility of Ca. Accumulibacter phosphatis to convert glycogen into trehalose by the presence of treX, treY, and treZ genes. Addition of trehalose to the reactor led to its consumption, both during anaerobic and aerobic phases. These results indicate the flexibility of the metabolism of Ca. Accumulibacter phosphatis towards variations in salinity. Key points • Trehalose is identified as an osmolyte in Candidatus Accumulibacter phosphatis. • Ca. Accumulibacter phosphatis can convert glycogen into trehalose. • Ca. Accumulibacter phosphatis clade I is present and active in both seawater and freshwater. Electronic supplementary material The online version of this article (10.1007/s00253-020-10947-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Danny R de Graaff
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands. .,Royal HaskoningDHV, Laan1914 35, 3800 AL, Amersfoort, The Netherlands.
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11
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Abstract
Single-celled organisms must adapt their physiology to persist and propagate across a wide range of environmental conditions. The growth and division of bacterial cells depend on continuous synthesis of an essential extracellular barrier: the peptidoglycan cell wall, a polysaccharide matrix that counteracts turgor pressure and confers cell shape. Unlike many other essential processes and structures within the bacterial cell, the peptidoglycan cell wall and its synthesis machinery reside at the cell surface and are thus uniquely vulnerable to the physicochemical environment and exogenous threats. In addition to the diversity of stressors endangering cell wall integrity, defects in peptidoglycan metabolism require rapid repair in order to prevent osmotic lysis, which can occur within minutes. Here, we review recent work that illuminates mechanisms that ensure robust peptidoglycan metabolism in response to persistent and acute environmental stress. Advances in our understanding of bacterial cell wall quality control promise to inform the development and use of antimicrobial agents that target the synthesis and remodeling of this essential macromolecule.IMPORTANCE Nearly all bacteria are encased in a peptidoglycan cell wall, an essential polysaccharide structure that protects the cell from osmotic rupture and reinforces cell shape. The integrity of this protective barrier must be maintained across the diversity of environmental conditions wherein bacteria replicate. However, at the cell surface, the cell wall and its synthesis machinery face unique challenges that threaten their integrity. Directly exposed to the extracellular environment, the peptidoglycan synthesis machinery encounters dynamic and extreme physicochemical conditions, which may impair enzymatic activity and critical protein-protein interactions. Biotic and abiotic stressors-including host defenses, cell wall active antibiotics, and predatory bacteria and phage-also jeopardize peptidoglycan integrity by introducing lesions, which must be rapidly repaired to prevent cell lysis. Here, we review recently discovered mechanisms that promote robust peptidoglycan synthesis during environmental and acute stress and highlight the opportunities and challenges for the development of cell wall active therapeutics.
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12
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Warmbold B, Ronzheimer S, Freibert SA, Seubert A, Hoffmann T, Bremer E. Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress. Front Microbiol 2020; 11:1700. [PMID: 32849357 PMCID: PMC7396694 DOI: 10.3389/fmicb.2020.01700] [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: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 02/01/2023] Open
Abstract
Bacillus subtilis adjusts to high osmolarity surroundings through the amassing of compatible solutes. It synthesizes the compatible solute glycine betaine from prior imported choline and scavenges many pre-formed osmostress protectants, including glycine betaine, from environmental sources. Choline is imported through the substrate-restricted ABC transporter OpuB and the closely related, but promiscuous, OpuC system, followed by its GbsAB-mediated oxidation to glycine betaine. We have investigated the impact of two MarR-type regulators, GbsR and OpcR, on gbsAB, opuB, and opuC expression. Judging by the position of the previously identified OpcR operator in the regulatory regions of opuB and opuC [Lee et al. (2013) Microbiology 159, 2087−2096], and that of the GbsR operator identified in the current study, we found that the closely related GbsR and OpcR repressors use different molecular mechanisms to control transcription. OpcR functions by sterically hindering access of RNA-polymerase to the opuB and opuC promoters, while GbsR operates through a roadblock mechanism to control gbsAB and opuB transcription. Loss of GbsR or OpcR de-represses opuB and opuC transcription, respectively. With respect to the osmotic control of opuB and opuC expression, we found that this environmental cue operates independently of the OpcR and GbsR regulators. When assessed over a wide range of salinities, opuB and opuC exhibit a surprisingly different transcriptional profile. Expression of opuB increases monotonously in response to incrementally increase in salinity, while opuC transcription levels decrease after an initial up-regulation at moderate salinities. Transcription of the gbsR and opcR regulatory genes is up-regulated in response to salt stress, and is also affected through auto-regulatory processes. The opuB and opuC operons have evolved through a gene duplication event. However, evolution has shaped their mode of genetic regulation, their osmotic-stress dependent transcriptional profile, and the substrate specificity of the OpuB and OpuC ABC transporters in a distinctive fashion.
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Affiliation(s)
- Bianca Warmbold
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Stefanie Ronzheimer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Sven-Andreas Freibert
- Department of Medicine, Institute for Cytobiology and Cytopathology, Philipps-University Marburg, Marburg, Germany
| | - Andreas Seubert
- Faculty of Chemistry, Analytical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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13
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pH-dependent activation of cytokinesis modulates Escherichia coli cell size. PLoS Genet 2020; 16:e1008685. [PMID: 32203516 PMCID: PMC7117782 DOI: 10.1371/journal.pgen.1008685] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/02/2020] [Accepted: 02/19/2020] [Indexed: 01/21/2023] Open
Abstract
Cell size is a complex trait, derived from both genetic and environmental factors. Environmental determinants of bacterial cell size identified to date primarily target assembly of cytosolic components of the cell division machinery. Whether certain environmental cues also impact cell size through changes in the assembly or activity of extracytoplasmic division proteins remains an open question. Here, we identify extracellular pH as a modulator of cell division and a significant determinant of cell size across evolutionarily distant bacterial species. In the Gram-negative model organism Escherichia coli, our data indicate environmental pH impacts the length at which cells divide by altering the ability of the terminal cell division protein FtsN to localize to the cytokinetic ring where it activates division. Acidic environments lead to enrichment of FtsN at the septum and activation of division at a reduced cell length. Alkaline pH inhibits FtsN localization and suppresses division activation. Altogether, our work reveals a previously unappreciated role for pH in bacterial cell size control. Bacteria are constantly under assault from endogenous and environmental stressors. To ensure viability and reproductive fitness, many bacteria alter their growth and replication in response to stressful conditions. Previous work from many groups has identified regulatory mechanisms linking cell division with nutrient availability and metabolic state. However, comparatively little is known about how the cell division machinery responds to physical and chemical cues in the environment. Here, we identify a fundamental property of the extracellular environment—environmental pH—as a significant contributor to bacterial cell size. Our genetic and cytological data indicate pH-dependent changes in E. coli cell size are in part due to differential localization of the cell division activator FtsN across pH environments. Increased abundance of FtsN at midcell in acidic environments promotes cell division at a reduced cell volume, while decreased abundance of FtsN at midcell in alkaline environments effectively delays cell division until a larger size is reached. Altogether, our work identifies pH as an environmental determinant of E. coli cell division and illuminates FtsN recruitment as a mediator of cell size.
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14
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Abstract
The cytoplasm of bacterial cells is a highly crowded cellular compartment that possesses considerable osmotic potential. As a result, and owing to the semipermeable nature of the cytoplasmic membrane and the semielastic properties of the cell wall, osmotically driven water influx will generate turgor, a hydrostatic pressure considered critical for growth and viability. Both increases and decreases in the external osmolarity inevitably trigger water fluxes across the cytoplasmic membrane, thus impinging on the degree of cellular hydration, molecular crowding, magnitude of turgor, and cellular integrity. Here, we assess mechanisms that permit the perception of osmotic stress by bacterial cells and provide an overview of the systems that allow them to genetically and physiologically cope with this ubiquitous environmental cue. We highlight recent developments implicating the secondary messenger c-di-AMP in cellular adjustment to osmotic stress and the role of osmotic forces in the life of bacteria-assembled in biofilms.
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Affiliation(s)
- Erhard Bremer
- Laboratory for Microbiology, Department of Biology; and Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043 Marburg, Germany;
| | - Reinhard Krämer
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany;
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Decreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress. J Bacteriol 2019; 201:JB.00708-18. [PMID: 30833357 PMCID: PMC6482933 DOI: 10.1128/jb.00708-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/21/2019] [Indexed: 11/20/2022] Open
Abstract
Bacteria adapt to ever-changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm. Escherichia coli adapts to changing environmental osmolality to survive and maintain growth. It has been shown that the diffusion of green fluorescent protein (GFP) in cells adapted to osmotic upshifts is higher than expected from the increase in biopolymer volume fraction. To better understand the physicochemical state of the cytoplasm in adapted cells, we now follow the macromolecular crowding during adaptation with fluorescence resonance energy transfer (FRET)-based sensors. We apply an osmotic upshift and find that after an initial increase, the apparent crowding decreases over the course of hours to arrive at a value lower than that before the osmotic upshift. Crowding relates to cell volume until cell division ensues, after which a transition in the biochemical organization occurs. Analysis of single cells by microfluidics shows that changes in cell volume, elongation, and division are most likely not the cause for the transition in organization. We further show that the decrease in apparent crowding upon adaptation is similar to the apparent crowding in energy-depleted cells. Based on our findings in combination with literature data, we suggest that adapted cells have indeed an altered biochemical organization of the cytoplasm, possibly due to different effective particle size distributions and concomitant nanoscale heterogeneity. This could potentially be a general response to accommodate higher biopolymer fractions yet retaining crowding homeostasis, and it could apply to other species or conditions as well. IMPORTANCE Bacteria adapt to ever-changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm.
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