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Bardetti P, Barber F, Rojas ER. Non-linear stress-softening of the bacterial cell wall confers cell shape homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.03.611099. [PMID: 39282265 PMCID: PMC11398337 DOI: 10.1101/2024.09.03.611099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The bacillus - or rod - is a pervasive cellular morphology among bacteria. Rod-shaped cells elongate without widening by reinforcing their cell wall anisotropically to prevent turgor pressure from inflating cell width. Here, we demonstrate that a constrictive force is also essential for avoiding pressure-driven widening in Gram-positive bacteria. Specifically, super-resolution measurements of the nonlinear mechanical properties of the cell wall revealed that across a range of turgor pressure cell elongation directly causes width constriction, similar to a "finger trap" toy. As predicted by theory, this property depends on cell-wall anisotropy and is precisely correlated with the cell's ability to maintain a rod shape. Furthermore, the acute non-linearities in the dependence between cell length and width deformation result in a negative-feedback mechanism that confers cell-width homeostasis. That is, the Gram-positive cell wall is a "smart material" whose exotic mechanical properties are exquisitely adapted to execute cellular morphogenesis.
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Affiliation(s)
- Paola Bardetti
- Department of Biology, New York University, New York, New York, 10003, USA
| | - Felix Barber
- Department of Biology, New York University, New York, New York, 10003, USA
| | - Enrique R Rojas
- Department of Biology, New York University, New York, New York, 10003, USA
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2
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Li R, Chu R, Ban R. The characteristics of autolysins associated with cell separation in Bacillus subtilis. J Bacteriol 2024; 206:e0013324. [PMID: 39012109 PMCID: PMC11340307 DOI: 10.1128/jb.00133-24] [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: 04/01/2024] [Accepted: 06/12/2024] [Indexed: 07/17/2024] Open
Abstract
The peptidoglycan hydrolases responsible for the cell separation of Bacillus subtilis cells are collectively referred to as autolysins. However, the role of each autolysin in the cell separation of B. subtilis is not fully understood. In this study, we constructed a series of cell separation-associated autolysin deficient strains and strains overexpressing the transcription factors SlrR and SinR, and the morphological changes of these strains in liquid culture were observed. The results showed that the absence of D,L-endopeptidases CwlS and LytF only increased the cell chain length in the early exponential phase. The absence of D,L-endopeptidase LytE or N-acetylmuramyl-L-alanine amidase LytC can cause cells to form chains throughout the growth of B. subtilis, although the cell chain length was significantly shortened during the stationary phase. However, the absence of peptidoglycan N-acetylglucosaminidase LytD only caused minor defect in cell separation. Therefore, we concluded that LytE and LytC were the major autolysins that ensure the timely separation of B. subtilis daughter cells, whereas CwlS, LytF, and LytD were the minor autolysins. In addition, overexpression of the transcription factors SinR and SlrR in the cwlS lytF lytC lytE mutant enabled B. subtilis cells to form ultra-long chains in the vegetative phase, and its biomass level was basically the same as that of the wild type. This led to the conclusion that besides inhibiting the expression of lytC and lytF, the SinR-SlrR complex also has other potential mechanisms to inhibit cell separation.IMPORTANCEIn this study, the effects of CwlS, LytC, LytD, LytF, LytE, and SinR-SlrR complex on the cell separation of Bacillus subtilis at different growth phases were studied, and an ultra-long-chained B. subtilis strain was constructed. In microbial fermentation, due to its large cell size, this ultra-long-chained B. subtilis strain may be more likely to be precipitated or intercepted during the removal of bacterial process with centrifugation and membrane filtration as the main methods, which is crucial to improve the purity of the product.
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Affiliation(s)
- Rui Li
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Ronghao Chu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Rui Ban
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
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3
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Dunn CM, Foust D, Gao Y, Biteen JS, Shaw SL, Kearns DB. Nascent flagellar basal bodies are immobilized by rod assembly in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606393. [PMID: 39211283 PMCID: PMC11360914 DOI: 10.1101/2024.08.02.606393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Flagella are complex, trans-envelope nanomachines that localize to species- specific cellular addresses. Here we study the localization dynamics of the earliest stage of basal body formation in Bacillus subtilis using a fluorescent fusion to the C-ring protein FliM. We find that B. subtilis basal bodies do not exhibit dynamic subunit exchange and are largely stationary at steady state, consistent with flagellar assembly through the peptidoglycan. Rare basal bodies were observed to be mobile however, and the frequency of basal body mobility is elevated both early in basal body assembly and when the rod is mutated. Thus, basal body mobility is a precursor to patterning and we propose that rod polymerization probes the peptidoglycan superstructure for pores of sufficient diameter that permit rod completion. Furthermore, mutation of the rod also disrupts basal body patterning in a way that phenocopies mutation of the cytoplasmic flagellar patterning protein FlhF. We infer that conformational changes in the basal body exchange information between rod synthesis and the cytoplasmic patterning proteins to restrict assembly at certain pores established by a grid-like pattern pre-existent in the peptidoglycan itself. IMPORTANCE Bacteria insert flagella in a species-specific pattern on the cell body, but how patterns are achieved is poorly understood. In bacteria with a single polar flagellum, a marker protein localizes to the cell pole and nucleates the assembly of the flagellum at that site. Bacillus subtilis assembles ∼15 flagella over the length of the cell body in a grid-like pattern and lacks all proteins associated with targeted assembly in polarly flagellated bacteria. Here we show that B. subtilis basal bodies are mobile soon after assembly and become immobilized when the flagellar rod transits the peptidoglycan wall. Moreover, defects in the flagellar rod lead to an asymmetric distribution of flagella with respect to the midcell. We conclude that the patterning of flagella is different in B. subtilis , and we infer that the B. subtilis rod probes the peptidoglycan for holes that can accommodate the machine.
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Velle KB, Swafford AJM, Garner E, Fritz-Laylin LK. Actin network evolution as a key driver of eukaryotic diversification. J Cell Sci 2024; 137:jcs261660. [PMID: 39120594 DOI: 10.1242/jcs.261660] [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] [Indexed: 08/10/2024] Open
Abstract
Eukaryotic cells have been evolving for billions of years, giving rise to wildly diverse cell forms and functions. Despite their variability, all eukaryotic cells share key hallmarks, including membrane-bound organelles, heavily regulated cytoskeletal networks and complex signaling cascades. Because the actin cytoskeleton interfaces with each of these features, understanding how it evolved and diversified across eukaryotic phyla is essential to understanding the evolution and diversification of eukaryotic cells themselves. Here, we discuss what we know about the origin and diversity of actin networks in terms of their compositions, structures and regulation, and how actin evolution contributes to the diversity of eukaryotic form and function.
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Affiliation(s)
- Katrina B Velle
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | | | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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5
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Dersch S, Graumann PL. Adaptation of Bacillus subtilis MreB Filaments to Osmotic Stress Depends on Influx of Potassium Ions. Microorganisms 2024; 12:1309. [PMID: 39065078 PMCID: PMC11279060 DOI: 10.3390/microorganisms12071309] [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: 05/02/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
The circumferential motion of MreB filaments plays a key role in cell shape maintenance in many bacteria. It has recently been shown that filament formation of MreB filaments in Bacillus subtilis is influenced by stress conditions. In response to osmotic upshift, MreB molecules were released from filaments, as seen by an increase in freely diffusive molecules, and the peptidoglycan synthesis pattern became less organized, concomitant with slowed-down cell extension. In this study, biotic and abiotic factors were analysed with respect to a possible function in the adaptation of MreB filaments to stress conditions. We show that parallel to MreB, its interactor RodZ becomes more diffusive following osmotic stress, but the remodeling of MreB filaments is not affected by a lack of RodZ. Conversely, mutant strains that prevent efficient potassium influx into cells following osmotic shock show a failure to disassemble MreB filaments, accompanied by less perturbed cell wall extension than is observed in wild type cells. Because potassium ions are known to negatively affect MreB polymerization in vitro, our data indicate that polymer disassembly is directly mediated by the physical consequences of the osmotic stress response. The lack of an early potassium influx response strongly decreases cell survival following stress application, suggesting that the disassembly of MreB filaments may ensure slowed-down cell wall extension to allow for efficient adaptation to new osmotic conditions.
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Affiliation(s)
| | - Peter L. Graumann
- Centre for Synthetic Microbiology (SYNMIKRO), Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany;
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Middlemiss S, Blandenet M, Roberts DM, McMahon A, Grimshaw J, Edwards JM, Sun Z, Whitley KD, Blu T, Strahl H, Holden S. Molecular motor tug-of-war regulates elongasome cell wall synthesis dynamics in Bacillus subtilis. Nat Commun 2024; 15:5411. [PMID: 38926336 PMCID: PMC11208587 DOI: 10.1038/s41467-024-49785-x] [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: 05/10/2023] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Most rod-shaped bacteria elongate by inserting new cell wall material into the inner surface of the cell sidewall. This is performed by class A penicillin binding proteins (PBPs) and a highly conserved protein complex, the elongasome, which moves processively around the cell circumference and inserts long glycan strands that act as barrel-hoop-like reinforcing structures, thereby giving rise to a rod-shaped cell. However, it remains unclear how elongasome synthesis dynamics and termination events are regulated to determine the length of these critical cell-reinforcing structures. To address this, we developed a method to track individual elongasome complexes around the entire circumference of Bacillus subtilis cells for minutes-long periods using single-molecule fluorescence microscopy. We found that the B. subtilis elongasome is highly processive and that processive synthesis events are frequently terminated by rapid reversal or extended pauses. We found that cellular levels of RodA regulate elongasome processivity, reversal and pausing. Our single-molecule data, together with stochastic simulations, show that elongasome dynamics and processivity are regulated by molecular motor tug-of-war competition between several, likely two, oppositely oriented peptidoglycan synthesis complexes associated with the MreB filament. Altogether these results demonstrate that molecular motor tug-of-war is a key regulator of elongasome dynamics in B. subtilis, which likely also regulates the cell shape via modulation of elongasome processivity.
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Affiliation(s)
- Stuart Middlemiss
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Matthieu Blandenet
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - David M Roberts
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, UK
| | - Andrew McMahon
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, UK
| | - James Grimshaw
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Joshua M Edwards
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, UK
| | - Zikai Sun
- Department of Electronic Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Kevin D Whitley
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Thierry Blu
- Department of Electronic Engineering, The Chinese University of Hong Kong, Hong Kong, China
- Dept of Electrical Engineering, National Taiwan University, Taipei City, Taiwan
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Séamus Holden
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, UK.
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Perez AJ, Lamanna MM, Bruce KE, Touraev MA, Page JE, Shaw SL, Tsui HCT, Winkler ME. Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2024; 121:e2401831121. [PMID: 38875147 PMCID: PMC11194595 DOI: 10.1073/pnas.2401831121] [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: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/16/2024] Open
Abstract
Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed nonprocessive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.
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Affiliation(s)
- Amilcar J. Perez
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Melissa M. Lamanna
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Kevin E. Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Marc A. Touraev
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Julia E. Page
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Sidney L. Shaw
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | | | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
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8
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Perez AJ, Lamanna MM, Bruce KE, Touraev MA, Page JE, Shaw SL, Tsui HCT, Winkler ME. Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575112. [PMID: 38328058 PMCID: PMC10849506 DOI: 10.1101/2024.01.10.575112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed non-processive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.
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9
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Alvarado Obando M, Rey-Varela D, Cava F, Dörr T. Genetic interaction mapping reveals functional relationships between peptidoglycan endopeptidases and carboxypeptidases. PLoS Genet 2024; 20:e1011234. [PMID: 38598601 PMCID: PMC11034669 DOI: 10.1371/journal.pgen.1011234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/22/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulators in Vibrio cholerae. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. dacA1 is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in dacA1. A subsequent suppressor screen to restore viability of ΔdacA1 in LB medium identified hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote EP activation. Our data thus reveal a more complex role of DacA1 in maintaining PG homeostasis than previously assumed.
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Affiliation(s)
- Manuela Alvarado Obando
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Diego Rey-Varela
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host-Microbe Interactions and Disease (CIHMID), Ithaca, New York, United States of America
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10
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Howard CB, Rabinovitch A, Yehezkel G, Zaritsky A. Tight coupling of cell width to nucleoid structure in Escherichia coli. Biophys J 2024; 123:502-508. [PMID: 38243596 PMCID: PMC10912912 DOI: 10.1016/j.bpj.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/24/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
Cell dimensions of rod-shaped bacteria such as Escherichia coli are connected to mass growth and chromosome replication. During their interdivision cycle (τ min), cells enlarge by elongation only, but at faster growth in richer media, they are also wider. Changes in width W upon nutritional shift-up (shortening τ) occur during the division process. The elusive signal directing the mechanism for W determination is likely related to the tightly linked duplications of the nucleoid (DNA) and the sacculus (peptidoglycan), the only two structures (macromolecules) existing in a single copy that are coupled, temporally and spatially. Six known parameters related to the nucleoid structure and replication are reasonable candidates to convey such a signal, all simple functions of the key number of replication positions n(=C/τ), the ratio between the rates of growth (τ-1) and of replication (C-1). The current analysis of available literature-recorded data discovered that, of these, nucleoid complexity NC[=(2n-1)/(n×ln2)] is by far the most likely parameter affecting cell width W. The exceedingly high correlations found between these two seemingly unrelated measures (NC and W) indicate that coupling between them is of major importance to the species' survival. As an exciting corollary, to the best of our knowledge, a new, indirect approach to estimate DNA replication rate is revealed. Potential involvement of DNA topoisomerases in W determination is also proposed and discussed.
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Affiliation(s)
- Charles B Howard
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Avinoam Rabinovitch
- Department of Physics, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Galit Yehezkel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Arieh Zaritsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel.
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11
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Shrestha S, Taib N, Gribaldo S, Shen A. Diversification of division mechanisms in endospore-forming bacteria revealed by analyses of peptidoglycan synthesis in Clostridioides difficile. Nat Commun 2023; 14:7975. [PMID: 38042849 PMCID: PMC10693644 DOI: 10.1038/s41467-023-43595-3] [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: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
The bacterial enzymes FtsW and FtsI, encoded in the highly conserved dcw gene cluster, are considered to be universally essential for the synthesis of septal peptidoglycan (PG) during cell division. Here, we show that the pathogen Clostridioides difficile lacks a canonical FtsW/FtsI pair, and its dcw-encoded PG synthases have undergone a specialization to fulfill sporulation-specific roles, including synthesizing septal PG during the sporulation-specific mode of cell division. Although these enzymes are directly regulated by canonical divisome components during this process, dcw-encoded PG synthases and their divisome regulators are dispensable for cell division during normal growth. Instead, C. difficile uses a bifunctional class A penicillin-binding protein as the core divisome PG synthase, revealing a previously unreported role for this class of enzymes. Our findings support that the emergence of endosporulation in the Firmicutes phylum facilitated the functional repurposing of cell division factors. Moreover, they indicate that C. difficile, and likely other clostridia, assemble a distinct divisome that therefore may represent a unique target for therapeutic interventions.
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Affiliation(s)
- Shailab Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Najwa Taib
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell Unit, Paris, France
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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12
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Lenoir C, Pelletier A, Manuse S, Millat H, Ducret A, Galinier A, Doan T, Grangeasse C. The morphogenic protein CopD controls the spatio-temporal dynamics of PBP1a and PBP2b in Streptococcus pneumoniae. mBio 2023; 14:e0141123. [PMID: 37728370 PMCID: PMC10653890 DOI: 10.1128/mbio.01411-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Penicillin-binding proteins (PBPs) are essential for proper bacterial cell division and morphogenesis. The genome of Streptococcus pneumoniae encodes for two class B PBPs (PBP2x and 2b), which are required for the assembly of the peptidoglycan framework and three class A PBPs (PBP1a, 1b and 2a), which remodel the peptidoglycan mesh during cell division. Therefore, their activities should be finely regulated in space and time to generate the pneumococcal ovoid cell shape. To date, two proteins, CozE and MacP, are known to regulate the function of PBP1a and PBP2a, respectively. In this study, we describe a novel regulator (CopD) that acts on both PBP1a and PBP2b. These findings provide valuable information for understanding bacterial cell division. Furthermore, knowing that ß-lactam antibiotic resistance often arises from PBP mutations, the characterization of such a regulator represents a promising opportunity to develop new strategies to resensitize resistant strains.
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Affiliation(s)
- Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Sylvie Manuse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Hugo Millat
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR, Aix-Marseille Université, CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, UMR, Aix-Marseille Université, Marseille, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
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13
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Wilson SA, Tank RKJ, Hobbs JK, Foster SJ, Garner EC. An exhaustive multiple knockout approach to understanding cell wall hydrolase function in Bacillus subtilis. mBio 2023; 14:e0176023. [PMID: 37768080 PMCID: PMC10653849 DOI: 10.1128/mbio.01760-23] [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: 07/12/2023] [Accepted: 08/03/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE In order to grow, bacterial cells must both create and break down their cell wall. The enzymes that are responsible for these processes are the target of some of our best antibiotics. Our understanding of the proteins that break down the wall- cell wall hydrolases-has been limited by redundancy among the large number of hydrolases many bacteria contain. To solve this problem, we identified 42 cell wall hydrolases in Bacillus subtilis and created a strain lacking 40 of them. We show that cells can survive using only a single cell wall hydrolase; this means that to understand the growth of B. subtilis in standard laboratory conditions, it is only necessary to study a very limited number of proteins, simplifying the problem substantially. We additionally show that the ∆40 strain is a research tool to characterize hydrolases, using it to identify three "helper" hydrolases that act in certain stress conditions.
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Affiliation(s)
- Sean A. Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Raveen K. J. Tank
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Jamie K. Hobbs
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Simon J. Foster
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ethan C. Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
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14
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Mao W, Renner LD, Cornilleau C, Li de la Sierra-Gallay I, Afensiss S, Benlamara S, Ah-Seng Y, Van Tilbeurgh H, Nessler S, Bertin A, Chastanet A, Carballido-Lopez R. On the role of nucleotides and lipids in the polymerization of the actin homolog MreB from a Gram-positive bacterium. eLife 2023; 12:e84505. [PMID: 37818717 PMCID: PMC10718530 DOI: 10.7554/elife.84505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/08/2023] [Indexed: 10/12/2023] Open
Abstract
In vivo, bacterial actin MreB assembles into dynamic membrane-associated filamentous structures that exhibit circumferential motion around the cell. Current knowledge of MreB biochemical and polymerization properties in vitro remains limited and is mostly based on MreB proteins from Gram-negative species. In this study, we report the first observation of organized protofilaments by electron microscopy and the first 3D-structure of MreB from a Gram-positive bacterium. We show that Geobacillus stearothermophilus MreB forms straight pairs of protofilaments on lipid surfaces in the presence of ATP or GTP, but not in the presence of ADP, GDP or non-hydrolysable ATP analogs. We demonstrate that membrane anchoring is mediated by two spatially close short hydrophobic sequences while electrostatic interactions also contribute to lipid binding, and show that the population of membrane-bound protofilament doublets is in steady-state. In solution, protofilament doublets were not detected in any condition tested. Instead, MreB formed large sheets regardless of the bound nucleotide, albeit at a higher critical concentration. Altogether, our results indicate that both lipids and ATP are facilitators of MreB polymerization, and are consistent with a dual effect of ATP hydrolysis, in promoting both membrane binding and filaments assembly/disassembly.
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Affiliation(s)
- Wei Mao
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Lars D Renner
- Leibniz Institute of Polymer Research, and the Max-Bergmann-Center of BiomaterialsDresdenGermany
| | - Charlène Cornilleau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSGif-sur-YvetteFrance
| | - Sana Afensiss
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Sarah Benlamara
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Yoan Ah-Seng
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Herman Van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSGif-sur-YvetteFrance
| | - Sylvie Nessler
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSGif-sur-YvetteFrance
| | - Aurélie Bertin
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Sorbonne Université, 75005ParisFrance
| | - Arnaud Chastanet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Rut Carballido-Lopez
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
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15
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Bramkamp M, Scheffers DJ. Bacterial membrane dynamics: Compartmentalization and repair. Mol Microbiol 2023; 120:490-501. [PMID: 37243899 DOI: 10.1111/mmi.15077] [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: 03/31/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]
Abstract
In every bacterial cell, the plasma membrane plays a key role in viability as it forms a selective barrier between the inside of the cell and its environment. This barrier function depends on the physical state of the lipid bilayer and the proteins embedded or associated with the bilayer. Over the past decade or so, it has become apparent that many membrane-organizing proteins and principles, which were described in eukaryote systems, are ubiquitous and play important roles in bacterial cells. In this minireview, we focus on the enigmatic roles of bacterial flotillins in membrane compartmentalization and bacterial dynamins and ESCRT-like systems in membrane repair and remodeling.
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Affiliation(s)
- Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dirk-Jan Scheffers
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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16
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Castanheira S, García-Del Portillo F. Evidence of two differentially regulated elongasomes in Salmonella. Commun Biol 2023; 6:923. [PMID: 37689828 PMCID: PMC10492807 DOI: 10.1038/s42003-023-05308-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: 06/23/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023] Open
Abstract
Cell shape is genetically inherited by all forms of life. Some unicellular microbes increase niche adaptation altering shape whereas most show invariant morphology. A universal system of peptidoglycan synthases guided by cytoskeletal scaffolds defines bacterial shape. In rod-shaped bacteria, this system consists of two supramolecular complexes, the elongasome and divisome, which insert cell wall material along major and minor axes. Microbes with invariant shape are thought to use a single morphogenetic system irrespective of the occupied niche. Here, we provide evidence for two elongasomes that generate (rod) shape in the same bacterium. This phenomenon was unveiled in Salmonella, a pathogen that switches between extra- and intracellular lifestyles. The two elongasomes can be purified independently, respond to different environmental cues, and are directed by distinct peptidoglycan synthases: the canonical PBP2 and the pathogen-specific homologue PBP2SAL. The PBP2-elongasome responds to neutral pH whereas that directed by PBP2SAL assembles in acidic conditions. Moreover, the PBP2SAL-elongasome moves at a lower speed. Besides Salmonella, other human, animal, and plant pathogens encode alternative PBPs with predicted morphogenetic functions. Therefore, contrasting the view of morphological plasticity facilitating niche adaptation, some pathogens may have acquired alternative systems to preserve their shape in the host.
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Affiliation(s)
- Sónia Castanheira
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, Darwin 3, 28049, Madrid, Spain
| | - Francisco García-Del Portillo
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, Darwin 3, 28049, Madrid, Spain.
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17
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Prindle JR, de Cuba OIC, Gahlmann A. Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects. J Chem Phys 2023; 159:071002. [PMID: 37589409 PMCID: PMC10908566 DOI: 10.1063/5.0155638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/06/2023] [Indexed: 08/18/2023] Open
Abstract
Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.
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Affiliation(s)
- Joshua Robert Prindle
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Olivia Isabella Christiane de Cuba
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
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18
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Kawai Y, Kawai M, Mackenzie ES, Dashti Y, Kepplinger B, Waldron KJ, Errington J. On the mechanisms of lysis triggered by perturbations of bacterial cell wall biosynthesis. Nat Commun 2023; 14:4123. [PMID: 37433811 DOI: 10.1038/s41467-023-39723-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/20/2023] [Indexed: 07/13/2023] Open
Abstract
Inhibition of bacterial cell wall synthesis by antibiotics such as β-lactams is thought to cause explosive lysis through loss of cell wall integrity. However, recent studies on a wide range of bacteria have suggested that these antibiotics also perturb central carbon metabolism, contributing to death via oxidative damage. Here, we genetically dissect this connection in Bacillus subtilis perturbed for cell wall synthesis, and identify key enzymatic steps in upstream and downstream pathways that stimulate the generation of reactive oxygen species through cellular respiration. Our results also reveal the critical role of iron homeostasis for the oxidative damage-mediated lethal effects. We show that protection of cells from oxygen radicals via a recently discovered siderophore-like compound uncouples changes in cell morphology normally associated with cell death, from lysis as usually judged by a phase pale microscopic appearance. Phase paling appears to be closely associated with lipid peroxidation.
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Affiliation(s)
- Yoshikazu Kawai
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Maki Kawai
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Eilidh Sohini Mackenzie
- Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Yousef Dashti
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Bernhard Kepplinger
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, 50-383, Wrocław, Poland
| | - Kevin John Waldron
- Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia.
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19
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Shlosman I, Fivenson EM, Gilman MSA, Sisley TA, Walker S, Bernhardt TG, Kruse AC, Loparo JJ. Allosteric activation of cell wall synthesis during bacterial growth. Nat Commun 2023; 14:3439. [PMID: 37301887 PMCID: PMC10257715 DOI: 10.1038/s41467-023-39037-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The peptidoglycan (PG) cell wall protects bacteria against osmotic lysis and determines cell shape, making this structure a key antibiotic target. Peptidoglycan is a polymer of glycan chains connected by peptide crosslinks, and its synthesis requires precise spatiotemporal coordination between glycan polymerization and crosslinking. However, the molecular mechanism by which these reactions are initiated and coupled is unclear. Here we use single-molecule FRET and cryo-EM to show that an essential PG synthase (RodA-PBP2) responsible for bacterial elongation undergoes dynamic exchange between closed and open states. Structural opening couples the activation of polymerization and crosslinking and is essential in vivo. Given the high conservation of this family of synthases, the opening motion that we uncovered likely represents a conserved regulatory mechanism that controls the activation of PG synthesis during other cellular processes, including cell division.
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Affiliation(s)
- Irina Shlosman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Tyler A Sisley
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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20
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Kawai Y, Errington J. Dissecting the roles of peptidoglycan synthetic and autolytic activities in the walled to L-form bacterial transition. Front Microbiol 2023; 14:1204979. [PMID: 37333659 PMCID: PMC10272550 DOI: 10.3389/fmicb.2023.1204979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023] Open
Abstract
Bacterial cells are surrounded by a peptidoglycan (PG) wall, which is a crucial target for antibiotics. It is well known that treatment with cell wall-active antibiotics occasionally converts bacteria to a non-walled "L-form" state that requires the loss of cell wall integrity. L-forms may have an important role in antibiotic resistance and recurrent infection. Recent work has revealed that inhibition of de novo PG precursor synthesis efficiently induces the L-form conversion in a wide range of bacteria, but the molecular mechanisms remain poorly understood. Growth of walled bacteria requires the orderly expansion of the PG layer, which involves the concerted action not just of synthases but also degradative enzymes called autolysins. Most rod-shaped bacteria have two complementary systems for PG insertion, the Rod and aPBP systems. Bacillus subtilis has two major autolysins, called LytE and CwlO, which are thought to have partially redundant functions. We have dissected the functions of autolysins, relative to the Rod and aPBP systems, during the switch to L-form state. Our results suggest that when de novo PG precursor synthesis is inhibited, residual PG synthesis occurs specifically via the aPBP pathway, and that this is required for continued autolytic activity by LytE/CwlO, resulting in cell bulging and efficient L-form emergence. The failure of L-form generation in cells lacking aPBPs was rescued by enhancing the Rod system and in this case, emergence specifically required LytE but was not associated with cell bulging. Our results suggest that two distinct pathways of L-form emergence exist depending on whether PG synthesis is being supported by the aPBP or RodA PG synthases. This work provides new insights into mechanisms of L-form generation, and specialisation in the roles of essential autolysins in relation to the recently recognised dual PG synthetic systems of bacteria.
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21
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Zhu X, Zhang K, Luo H, Wu J. Overexpression of the class A penicillin-binding protein PonA in Bacillus improves recombinant protein production. BIORESOURCE TECHNOLOGY 2023; 383:129219. [PMID: 37217145 DOI: 10.1016/j.biortech.2023.129219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
The bottleneck of recombinant protein production in microbial cell factories is sometimes determined by limited manipulable targets and the lack of gene annotation related to protein expression. PonA is the major class A penicillin-binding protein in Bacillus, which polymerizes and cross-links peptidoglycan. Here, we described its novel functions during recombinant protein expression in Bacillus subtilis and analyzed the mechanism of its chaperone activity. When PonA was overexpressed, the expression of hyperthermophilic amylase significantly increased 3.96- and 1.26-fold in shake flasks and fed-batch processes, respectively. Increased cell diameter and reinforced cell walls were observed in PonA-overexpressing strains. Furthermore, the FN3 structural domain and the natural dimeric structure of PonA may be critical for exerting its chaperone activity. These data suggest that PonA can be an effective target for modification of the expression of recombinant proteins in B. subtilis.
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Affiliation(s)
- Xuyang Zhu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Kang Zhang
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Hui Luo
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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22
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Keller MR, Dörr T. Bacterial metabolism and susceptibility to cell wall-active antibiotics. Adv Microb Physiol 2023; 83:181-219. [PMID: 37507159 PMCID: PMC11024984 DOI: 10.1016/bs.ampbs.2023.04.002] [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] [Indexed: 07/30/2023]
Abstract
Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.
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Affiliation(s)
- Megan Renee Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States; Department of Microbiology, Cornell University, Ithaca, NY, United States; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States.
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23
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Koyano Y, Okajima K, Mihara M, Yamamoto H. Visualization of Wall Teichoic Acid Decoration in Bacillus subtilis. J Bacteriol 2023; 205:e0006623. [PMID: 37010431 PMCID: PMC10127673 DOI: 10.1128/jb.00066-23] [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: 02/14/2023] [Accepted: 03/16/2023] [Indexed: 04/04/2023] Open
Abstract
Teichoic acids are important for the maintenance of cell shape and growth in Gram-positive bacteria. Bacillus subtilis produces major and minor forms of wall teichoic acid (WTA) and lipoteichoic acid during vegetative growth. We found that newly synthesized WTA attachment to peptidoglycan occurs in a patch-like manner on the sidewall with the fluorescent labeling compound of the concanavalin A lectin. Similarly, WTA biosynthesis enzymes fused to the epitope tags were localized in similar patch-like patterns on the cylindrical part of the cell, and WTA transporter TagH was frequently colocalized with WTA polymerase TagF, WTA ligase TagT, and actin homolog MreB, respectively. Moreover, we found that the nascent cell wall patches, decorated with the newly glucosylated WTA, were colocalized with TagH and WTA ligase TagV. In the cylindrical part, the newly glucosylated WTA patchily inserted into the bottom of the cell wall layer and finally reached the outermost layer of the cell wall after approximately half an hour. Incorporation of newly glucosylated WTA was arrested with the addition of vancomycin but restored with the removal of the antibiotic. These results are consistent with the prevailing model that WTA precursors are attached to newly synthesized peptidoglycan. IMPORTANCE In Gram-positive bacteria, the cell wall is composed of mesh-like peptidoglycan and covalently linked wall teichoic acid (WTA). It is unclear where WTA decorates peptidoglycan to create a cell wall architecture. Here, we demonstrate that nascent WTA decoration occurred in a patch-like manner at the peptidoglycan synthesis sites on the cytoplasmic membrane. The incorporated cell wall with newly glucosylated WTA in the cell wall layer then reached the outermost layer of the cell wall after approximately half an hour. Incorporation of newly glucosylated WTA was arrested with the addition of vancomycin but restored with the removal of the antibiotic. These results are consistent with the prevailing model that WTA precursors are attached to newly synthesized peptidoglycan.
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Affiliation(s)
- Yutaka Koyano
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano, Japan
| | - Kiyoshirou Okajima
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano, Japan
| | - Mako Mihara
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano, Japan
| | - Hiroki Yamamoto
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano, Japan
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24
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Willdigg JR, Patel Y, Helmann JD. A Decrease in Fatty Acid Synthesis Rescues Cells with Limited Peptidoglycan Synthesis Capacity. mBio 2023; 14:e0047523. [PMID: 37017514 PMCID: PMC10128001 DOI: 10.1128/mbio.00475-23] [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: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Proper synthesis and maintenance of a multilayered cell envelope are critical for bacterial fitness. However, whether mechanisms exist to coordinate synthesis of the membrane and peptidoglycan layers is unclear. In Bacillus subtilis, synthesis of peptidoglycan (PG) during cell elongation is mediated by an elongasome complex acting in concert with class A penicillin-binding proteins (aPBPs). We previously described mutant strains limited in their capacity for PG synthesis due to a loss of aPBPs and an inability to compensate by upregulation of elongasome function. Growth of these PG-limited cells can be restored by suppressor mutations predicted to decrease membrane synthesis. One suppressor mutation leads to an altered function repressor, FapR*, that functions as a super-repressor and leads to decreased transcription of fatty acid synthesis (FAS) genes. Consistent with fatty acid limitation mitigating cell wall synthesis defects, inhibition of FAS by cerulenin also restored growth of PG-limited cells. Moreover, cerulenin can counteract the inhibitory effect of β-lactams in some strains. These results imply that limiting PG synthesis results in impaired growth, in part, due to an imbalance of PG and cell membrane synthesis and that B. subtilis lacks a robust physiological mechanism to reduce membrane synthesis when PG synthesis is impaired. IMPORTANCE Understanding how a bacterium coordinates cell envelope synthesis is essential to fully appreciate how bacteria grow, divide, and resist cell envelope stresses, such as β-lactam antibiotics. Balanced synthesis of the peptidoglycan cell wall and the cell membrane is critical for cells to maintain shape and turgor pressure and to resist external cell envelope threats. Using Bacillus subtilis, we show that cells deficient in peptidoglycan synthesis can be rescued by compensatory mutations that decrease the synthesis of fatty acids. Further, we show that inhibiting fatty acid synthesis with cerulenin is sufficient to restore growth of cells deficient in peptidoglycan synthesis. Understanding the coordination of cell wall and membrane synthesis may provide insights relevant to antimicrobial treatment.
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Affiliation(s)
| | - Yesha Patel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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25
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Galinier A, Delan-Forino C, Foulquier E, Lakhal H, Pompeo F. Recent Advances in Peptidoglycan Synthesis and Regulation in Bacteria. Biomolecules 2023; 13:biom13050720. [PMID: 37238589 DOI: 10.3390/biom13050720] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Bacteria must synthesize their cell wall and membrane during their cell cycle, with peptidoglycan being the primary component of the cell wall in most bacteria. Peptidoglycan is a three-dimensional polymer that enables bacteria to resist cytoplasmic osmotic pressure, maintain their cell shape and protect themselves from environmental threats. Numerous antibiotics that are currently used target enzymes involved in the synthesis of the cell wall, particularly peptidoglycan synthases. In this review, we highlight recent progress in our understanding of peptidoglycan synthesis, remodeling, repair, and regulation in two model bacteria: the Gram-negative Escherichia coli and the Gram-positive Bacillus subtilis. By summarizing the latest findings in this field, we hope to provide a comprehensive overview of peptidoglycan biology, which is critical for our understanding of bacterial adaptation and antibiotic resistance.
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Affiliation(s)
- Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS/Aix-Marseille Univ, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Clémentine Delan-Forino
- Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS/Aix-Marseille Univ, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Elodie Foulquier
- Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS/Aix-Marseille Univ, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Hakima Lakhal
- Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS/Aix-Marseille Univ, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS/Aix-Marseille Univ, 31 Chemin Joseph Aiguier, 13009 Marseille, France
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26
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Sun Y, Hürlimann S, Garner E. Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis. Nat Microbiol 2023; 8:469-480. [PMID: 36797487 DOI: 10.1038/s41564-023-01329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/13/2023] [Indexed: 02/18/2023]
Abstract
How bacteria link their growth rate to external nutrient conditions is unknown. To investigate how Bacillus subtilis cells alter the rate at which they expand their cell walls as they grow, we compared single-cell growth rates of cells grown under agar pads with the density of moving MreB filaments under a variety of growth conditions. MreB filament density increases proportionally with growth rate. We show that both MreB filament density and growth rate depend on the abundance of Lipid II and murAA, the first gene in the biosynthetic pathway creating the cell wall precursor Lipid II. Lipid II is sensed by the serine/threonine kinase PrkC, which phosphorylates RodZ and other proteins. We show that phosphorylated RodZ increases MreB filament density, which in turn increases cell growth rate. We also show that increasing the activity of this pathway in nutrient-poor media results in cells that elongate faster than wild-type cells, which means that B. subtilis contains spare 'growth capacity'. We conclude that PrkC functions as a cellular rheostat, enabling fine-tuning of cell growth rates in response to Lipid II in different nutrient conditions.
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Affiliation(s)
- Yingjie Sun
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Sylvia Hürlimann
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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27
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Ferrando J, Filluelo O, Zeigler DR, Picart P. Barriers to simultaneous multilocus integration in Bacillus subtilis tumble down: development of a straightforward screening method for the colorimetric detection of one-step multiple gene insertion using the CRISPR-Cas9 system. Microb Cell Fact 2023; 22:21. [PMID: 36721198 PMCID: PMC9890709 DOI: 10.1186/s12934-023-02032-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Despite recent advances in genetic engineering tools for effectively regulating and manipulating genes, efficient simultaneous multigene insertion methods have not been established in Bacillus subtilis. To date, multilocus integration systems in B. subtilis, which is one of the main industrial enzyme producers and a GRAS (generally regarded as safe) microbial host, rely on iterative rounds of plasmid construction for sequential insertions of genes into the B. subtilis chromosome, which is tedious and time consuming. RESULTS In this study, we present development and proof-of-concept of a novel CRISPR-Cas9-based genome-editing strategy for the colorimetric detection of one-step multiple gene insertion in B. subtilis. First, up to three copies of the crtMN operon from Staphylococcus aureus, encoding a yellow pigment, were incorporated at three ectopic sites within the B. subtilis chromosome, rendering engineered strains able to form yellow colonies. Second, a single CRISPR-Cas9-based plasmid carrying a highly specific single guide RNA (sgRNA) targeting crtMN operon and a changeable editing template was constructed to facilitate simultaneous insertion of multiple gene-copies through homology-directed repair (HDR). Upon transformation of engineered strains with engineered plasmids, strains harboring up to three gene copies integrated into the chromosome formed white colonies because of the removal of the crtMN operon, clearly distinguishable from yellow colonies harboring undesired genetic modifications. As a result, construction of a plasmid-less, marker-free, high-expression stable producer B. subtilis strain can be completed in only seven days, demonstrating the potential that the implementation of this technology may bring for biotechnology purposes. CONCLUSIONS The novel technology expands the genome-editing toolset for B. subtilis and means a substantial improvement over current methodology, offering new application possibilities that we envision should significantly boost the development of B. subtilis as a chassis in the field of synthetic biology.
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Affiliation(s)
- Jordi Ferrando
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | - Oriana Filluelo
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | | | - Pere Picart
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
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28
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Schulz LM, Rothe P, Halbedel S, Gründling A, Rismondo J. Imbalance of peptidoglycan biosynthesis alters the cell surface charge of Listeria monocytogenes. Cell Surf 2022; 8:100085. [PMID: 36304571 PMCID: PMC9593813 DOI: 10.1016/j.tcsw.2022.100085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 02/09/2023] Open
Abstract
The bacterial cell wall is composed of a thick layer of peptidoglycan and cell wall polymers, which are either embedded in the membrane or linked to the peptidoglycan backbone and referred to as lipoteichoic acid (LTA) and wall teichoic acid (WTA), respectively. Modifications of the peptidoglycan or WTA backbone can alter the susceptibility of the bacterial cell towards cationic antimicrobials and lysozyme. The human pathogen Listeria monocytogenes is intrinsically resistant towards lysozyme, mainly due to deacetylation and O-acetylation of the peptidoglycan backbone via PgdA and OatA. Recent studies identified additional factors, which contribute to the lysozyme resistance of this pathogen. One of these is the predicted ABC transporter, EslABC. An eslB mutant is hyper-sensitive towards lysozyme, likely due to the production of thinner and less O-acetylated peptidoglycan. Using a suppressor screen, we show here that suppression of eslB phenotypes could be achieved by enhancing peptidoglycan biosynthesis, reducing peptidoglycan hydrolysis or alterations in WTA biosynthesis and modification. The lack of EslB also leads to a higher negative surface charge, which likely stimulates the activity of peptidoglycan hydrolases and lysozyme. Based on our results, we hypothesize that the portion of cell surface exposed WTA is increased in the eslB mutant due to the thinner peptidoglycan layer and that latter one could be caused by an impairment in UDP-N-acetylglucosamine (UDP-GlcNAc) production or distribution.
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Affiliation(s)
- Lisa Maria Schulz
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Patricia Rothe
- FG11, Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany
| | - Sven Halbedel
- FG11, Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Leipziger Straße 44, 39120 Magdeburg, Germany
| | - Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jeanine Rismondo
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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29
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Kepplinger B, Wen X, Tyler AR, Kim BY, Brown J, Banks P, Dashti Y, Mackenzie ES, Wills C, Kawai Y, Waldron KJ, Allenby NEE, Wu LJ, Hall MJ, Errington J. Mirubactin C rescues the lethal effect of cell wall biosynthesis mutations in Bacillus subtilis. Front Microbiol 2022; 13:1004737. [PMID: 36312962 PMCID: PMC9609785 DOI: 10.3389/fmicb.2022.1004737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/22/2022] [Indexed: 01/29/2023] Open
Abstract
Growth of most rod-shaped bacteria is accompanied by the insertion of new peptidoglycan into the cylindrical cell wall. This insertion, which helps maintain and determine the shape of the cell, is guided by a protein machine called the rod complex or elongasome. Although most of the proteins in this complex are essential under normal growth conditions, cell viability can be rescued, for reasons that are not understood, by the presence of a high (mM) Mg2+ concentration. We screened for natural product compounds that could rescue the growth of mutants affected in rod-complex function. By screening > 2,000 extracts from a diverse collection of actinobacteria, we identified a compound, mirubactin C, related to the known iron siderophore mirubactin A, which rescued growth in the low micromolar range, and this activity was confirmed using synthetic mirubactin C. The compound also displayed toxicity at higher concentrations, and this effect appears related to iron homeostasis. However, several lines of evidence suggest that the mirubactin C rescuing activity is not due simply to iron sequestration. The results support an emerging view that the functions of bacterial siderophores extend well beyond simply iron binding and uptake.
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Affiliation(s)
- Bernhard Kepplinger
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Xin Wen
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew Robert Tyler
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Byung-Yong Kim
- Odyssey Therapeutics Inc., Newcastle upon Tyne, United Kingdom
| | - James Brown
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter Banks
- Faculty of Medical Sciences, Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yousef Dashti
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eilidh Sohini Mackenzie
- Faculty of Medical Sciences, Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Corinne Wills
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshikazu Kawai
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kevin John Waldron
- Faculty of Medical Sciences, Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael John Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
- Odyssey Therapeutics Inc., Newcastle upon Tyne, United Kingdom
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30
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Knapp BD, Ward MD, Bowman GR, Shi H, Huang KC. Multiple conserved states characterize the twist landscape of the bacterial actin homolog MreB. Comput Struct Biotechnol J 2022; 20:5838-5846. [PMID: 36382191 PMCID: PMC9627593 DOI: 10.1016/j.csbj.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 12/01/2022] Open
Abstract
Filament formation by cytoskeletal proteins is critical to their involvement in myriad cellular processes. The bacterial actin homolog MreB, which is essential for cell-shape determination in many rod-shaped bacteria, has served as a model system for studying the mechanics of cytoskeletal filaments. Previous molecular dynamics (MD) simulations revealed that the twist of MreB double protofilaments is dependent on the bound nucleotide, as well as binding to the membrane or the accessory protein RodZ, and MreB mutations that modulate twist also affect MreB spatial organization and cell shape. Here, we show that MreB double protofilaments can adopt multiple twist states during microsecond-scale MD simulations. A deep learning algorithm trained only on high- and low-twist states robustly identified all twist conformations across most perturbations of ATP-bound MreB, suggesting the existence of a conserved set of states whose occupancy is affected by each perturbation to MreB. Simulations replacing ATP with ADP indicated that twist states were generally stable after hydrolysis. These findings suggest a rich twist landscape that could provide the capacity to tune MreB activity and therefore its effects on cell shape.
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Affiliation(s)
| | - Michael D. Ward
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63130, USA
- Center for the Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Gregory R. Bowman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63130, USA
- Center for the Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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31
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Lamanna MM, Manzoor I, Joseph M, Ye ZA, Benedet M, Zanardi A, Ren Z, Wang X, Massidda O, Tsui HT, Winkler ME. Roles of RodZ and class A PBP1b in the assembly and regulation of the peripheral peptidoglycan elongasome in ovoid-shaped cells of Streptococcus pneumoniae D39. Mol Microbiol 2022; 118:336-368. [PMID: 36001060 PMCID: PMC9804626 DOI: 10.1111/mmi.14969] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/17/2023]
Abstract
RodZ of rod-shaped bacteria functions to link MreB filaments to the Rod peptidoglycan (PG) synthase complex that moves circumferentially perpendicular to the long cell axis, creating hoop-like sidewall PG. Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus; Spn) that lack MreB, use a different modality for peripheral PG elongation that emanates from the midcell of dividing cells. Yet, S. pneumoniae encodes a RodZ homolog similar to RodZ in rod-shaped bacteria. We show here that the helix-turn-helix and transmembrane domains of RodZ(Spn) are essential for growth at 37°C. ΔrodZ mutations are suppressed by Δpbp1a, mpgA(Y488D), and ΔkhpA mutations that suppress ΔmreC, but not ΔcozE. Consistent with a role in PG elongation, RodZ(Spn) co-localizes with MreC and aPBP1a throughout the cell cycle and forms complexes and interacts with PG elongasome proteins and regulators. Depletion of RodZ(Spn) results in aberrantly shaped, non-growing cells and mislocalization of elongasome proteins MreC, PBP2b, and RodA. Moreover, Tn-seq reveals that RodZ(Spn), but not MreCD(Spn), displays a specific synthetic-viable genetic relationship with aPBP1b, whose function is unknown. We conclude that RodZ(Spn) acts as a scaffolding protein required for elongasome assembly and function and that aPBP1b, like aPBP1a, plays a role in elongasome regulation and possibly peripheral PG synthesis.
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Affiliation(s)
- Melissa M. Lamanna
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Irfan Manzoor
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Merrin Joseph
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Ziyun A. Ye
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Mattia Benedet
- Department of Cellular, Computational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Alessia Zanardi
- Department of Cellular, Computational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Zhongqing Ren
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Xindan Wang
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Orietta Massidda
- Department of Cellular, Computational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Ho‐Ching T. Tsui
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Malcolm E. Winkler
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
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32
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Nierhaus T, McLaughlin SH, Bürmann F, Kureisaite-Ciziene D, Maslen SL, Skehel JM, Yu CWH, Freund SMV, Funke LFH, Chin JW, Löwe J. Bacterial divisome protein FtsA forms curved antiparallel double filaments when binding to FtsN. Nat Microbiol 2022; 7:1686-1701. [PMID: 36123441 PMCID: PMC7613929 DOI: 10.1038/s41564-022-01206-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/19/2022] [Indexed: 11/08/2022]
Abstract
During bacterial cell division, filaments of tubulin-like FtsZ form the Z-ring, which is the cytoplasmic scaffold for divisome assembly. In Escherichia coli, the actin homologue FtsA anchors the Z-ring to the membrane and recruits divisome components, including bitopic FtsN. FtsN regulates the periplasmic peptidoglycan synthase FtsWI. To characterize how FtsA regulates FtsN, we applied electron microscopy to show that E. coli FtsA forms antiparallel double filaments on lipid monolayers when bound to the cytoplasmic tail of FtsN. Using X-ray crystallography, we demonstrate that Vibrio maritimus FtsA crystallizes as an equivalent double filament. We identified an FtsA-FtsN interaction site in the IA-IC interdomain cleft of FtsA using X-ray crystallography and confirmed that FtsA forms double filaments in vivo by site-specific cysteine cross-linking. FtsA-FtsN double filaments reconstituted in or on liposomes prefer negative Gaussian curvature, like those of MreB, the actin-like protein of the elongasome. We propose that curved antiparallel FtsA double filaments together with treadmilling FtsZ filaments organize septal peptidoglycan synthesis in the division plane.
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Affiliation(s)
- Tim Nierhaus
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Jason W Chin
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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33
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Navarro PP, Vettiger A, Ananda VY, Llopis PM, Allolio C, Bernhardt TG, Chao LH. Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli. Nat Microbiol 2022; 7:1621-1634. [PMID: 36097171 PMCID: PMC9519445 DOI: 10.1038/s41564-022-01210-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/21/2022] [Indexed: 01/19/2023]
Abstract
The bacterial division apparatus catalyses the synthesis and remodelling of septal peptidoglycan (sPG) to build the cell wall layer that fortifies the daughter cell poles. Understanding of this essential process has been limited by the lack of native three-dimensional views of developing septa. Here, we apply state-of-the-art cryogenic electron tomography (cryo-ET) and fluorescence microscopy to visualize the division site architecture and sPG biogenesis dynamics of the Gram-negative bacterium Escherichia coli. We identify a wedge-like sPG structure that fortifies the ingrowing septum. Experiments with strains defective in sPG biogenesis revealed that the septal architecture and mode of division can be modified to more closely resemble that of other Gram-negative (Caulobacter crescentus) or Gram-positive (Staphylococcus aureus) bacteria, suggesting that a conserved mechanism underlies the formation of different septal morphologies. Finally, analysis of mutants impaired in amidase activation (ΔenvC ΔnlpD) showed that cell wall remodelling affects the placement and stability of the cytokinetic ring. Taken together, our results support a model in which competition between the cell elongation and division machineries determines the shape of cell constrictions and the poles they form. They also highlight how the activity of the division system can be modulated to help generate the diverse array of shapes observed in the bacterial domain.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Virly Y Ananda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Christoph Allolio
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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34
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Kitahara Y, Oldewurtel ER, Wilson S, Sun Y, Altabe S, de Mendoza D, Garner EC, van Teeffelen S. The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis. PNAS NEXUS 2022; 1:pgac134. [PMID: 36082236 PMCID: PMC9437589 DOI: 10.1093/pnasnexus/pgac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/21/2022] [Indexed: 01/29/2023]
Abstract
All cells must increase their volumes in response to biomass growth to maintain intracellular mass density within physiologically permissive bounds. Here, we investigate the regulation of volume growth in the Gram-positive bacterium Bacillus subtilis. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. First, we demonstrate that cell-volume growth is determined indirectly, by expanding their envelopes in proportion to mass growth, similarly to the Gram-negative Escherichia coli, despite their fundamentally different envelope structures. Next, we studied, which pathways might be responsible for robust surface-to-mass coupling: We found that both peptidoglycan synthesis and membrane synthesis are required for proper surface-to-mass coupling. However, surprisingly, neither pathway is solely rate-limiting, contrary to wide-spread belief, since envelope growth continues at a reduced rate upon complete inhibition of either process. To arrest cell-envelope growth completely, the simultaneous inhibition of both envelope-synthesis processes is required. Thus, we suggest that multiple envelope-synthesis pathways collectively confer an important aspect of volume regulation, the coordination between surface growth, and biomass growth.
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Affiliation(s)
- Yuki Kitahara
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada,Université de Paris, Paris, France,Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Enno R Oldewurtel
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Yingjie Sun
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Silvia Altabe
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Conicet- and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Conicet- and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
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35
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Abstract
Bacteria have evolved to develop multiple strategies for antibiotic resistance by effectively reducing intracellular antibiotic concentrations or antibiotic binding affinities, but the role of cell morphology in antibiotic resistance remains poorly understood. By analyzing cell morphological data for different bacterial species under antibiotic stress, we find that bacteria increase or decrease the cell surface-to-volume ratio depending on the antibiotic target. Using quantitative modeling, we show that by reducing the surface-to-volume ratio, bacteria can effectively reduce the intracellular antibiotic concentration by decreasing antibiotic influx. The model further predicts that bacteria can increase the surface-to-volume ratio to induce the dilution of membrane-targeting antibiotics, in agreement with experimental data. Using a whole-cell model for the regulation of cell shape and growth by antibiotics, we predict shape transformations that bacteria can utilize to increase their fitness in the presence of antibiotics. We conclude by discussing additional pathways for antibiotic resistance that may act in synergy with shape-induced resistance.
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Affiliation(s)
- Nikola Ojkic
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Diana Serbanescu
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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36
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Melzer ES, Kado T, García-Heredia A, Gupta KR, Meniche X, Morita YS, Sassetti CM, Rego EH, Siegrist MS. Cell Wall Damage Reveals Spatial Flexibility in Peptidoglycan Synthesis and a Nonredundant Role for RodA in Mycobacteria. J Bacteriol 2022; 204:e0054021. [PMID: 35543537 PMCID: PMC9210966 DOI: 10.1128/jb.00540-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/06/2022] [Indexed: 12/28/2022] Open
Abstract
Cell wall peptidoglycan is a heteropolymeric mesh that protects the bacterium from internal turgor and external insults. In many rod-shaped bacteria, peptidoglycan synthesis for normal growth is achieved by two distinct pathways: the Rod complex, comprised of MreB, RodA, and a cognate class B penicillin-binding protein (PBP), and the class A PBPs (aPBPs). In contrast to laterally growing bacteria, pole-growing mycobacteria do not encode an MreB homolog and do not require SEDS protein RodA for in vitro growth. However, RodA contributes to the survival of Mycobacterium tuberculosis in some infection models, suggesting that the protein could have a stress-dependent role in maintaining cell wall integrity. Under basal conditions, we find here that the subcellular distribution of RodA largely overlaps that of the aPBP PonA1 and that both RodA and the aPBPs promote polar peptidoglycan assembly. Upon cell wall damage, RodA fortifies Mycobacterium smegmatis against lysis and, unlike aPBPs, contributes to a shift in peptidoglycan assembly from the poles to the sidewall. Neither RodA nor PonA1 relocalize; instead, the redistribution of nascent cell wall parallels that of peptidoglycan precursor synthase MurG. Our results support a model in which mycobacteria balance polar growth and cell-wide repair via spatial flexibility in precursor synthesis and extracellular insertion. IMPORTANCE Peptidoglycan synthesis is a highly successful target for antibiotics. The pathway has been extensively studied in model organisms under laboratory-optimized conditions. In natural environments, bacteria are frequently under attack. Moreover, the vast majority of bacterial species are unlikely to fit a single paradigm of cell wall assembly because of differences in growth mode and/or envelope structure. Studying cell wall synthesis under nonoptimal conditions and in nonstandard species may improve our understanding of pathway function and suggest new inhibition strategies. Mycobacterium smegmatis, a relative of several notorious human and animal pathogens, has an unusual polar growth mode and multilayered envelope. In this work, we challenged M. smegmatis with cell wall-damaging enzymes to characterize the roles of cell wall-building enzymes when the bacterium is under attack.
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Affiliation(s)
- Emily S. Melzer
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Takehiro Kado
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Xavier Meniche
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - E. Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - M. Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
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37
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Tian J, Xing B, Li M, Xu C, Huo YX, Guo S. Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening of Bacillus subtilis Biofuel Overproducers. Int J Mol Sci 2022; 23:ijms23094853. [PMID: 35563243 PMCID: PMC9099979 DOI: 10.3390/ijms23094853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus subtilis is a versatile microbial cell factory that can produce valuable proteins and value-added chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable host strains. Herein, we develop an efficient CRISPR-Cas9 method for large-scale and scarless genome engineering in the Bacillus subtilis genome, which can delete up to 134.3 kb DNA fragments, 3.5 times as long as the previous report, with a positivity rate of 100%. The effects of using a heterologous NHEJ system, linear donor DNA, and various donor DNA length on the engineering efficiencies were also investigated. The CRISPR-Cas9 method was then utilized for Bacillus subtilis genome simplification and construction of a series of individual and cumulative deletion mutants, which are further screened for overproducer of isobutanol, a new generation biofuel. These results suggest that the method is a powerful genome engineering tool for constructing and screening engineered host strains with enhanced capabilities, highlighting the potential for synthetic biology and metabolic engineering.
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Lamanna MM, Maurelli AT. What Is Motion? Recent Advances in the Study of Molecular Movement Patterns of the Peptidoglycan Synthesis Machines. J Bacteriol 2022; 204:e0059821. [PMID: 34928180 PMCID: PMC9017339 DOI: 10.1128/jb.00598-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
How proteins move through space and time is a fundamental question in biology. While great strides have been made toward a mechanistic understanding of protein movement, many questions remain. We discuss the biological implications of motion in the context of the peptidoglycan (PG) synthesis machines. We reviewed systems in several bacteria, including Escherichia coli, Bacillus subtilis, and Streptococcus pneumoniae, and present a comprehensive view of our current knowledge regarding movement dynamics. Discrepancies are also addressed because "one size does not fit all". For bacteria to divide, new PG is synthesized and incorporated into the growing cell wall by complex multiprotein nanomachines consisting of PG synthases (transglycosylases [TG] and/or transpeptidases [TP]) as well as a variety of regulators and cytoskeletal factors. Advances in imaging capabilities and labeling methods have revealed that these machines are not static but rather circumferentially transit the cell via directed motion perpendicular to the long axis of model rod-shaped bacteria such as E. coli and B. subtilis. The enzymatic activity of the TG:TPs drives motion in some species while motion is mediated by FtsZ treadmilling in others. In addition, both directed and diffusive motion of the PG synthases have been observed using single-particle tracking technology. Here, we examined the biological role of diffusion regarding transit. Lastly, findings regarding the monofunctional transglycosylases (RodA and FtsW) as well as the Class A PG synthases are discussed. This minireview serves to showcase recent advances, broach mechanistic unknowns, and stimulate future areas of study.
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Affiliation(s)
- Melissa Mae Lamanna
- Department of Environmental & Global Health and Emerging Pathogens Institute, University of Floridagrid.15276.37, Gainesville, Florida, USA
| | - Anthony T. Maurelli
- Department of Environmental & Global Health and Emerging Pathogens Institute, University of Floridagrid.15276.37, Gainesville, Florida, USA
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39
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Basaran M, Yaman YI, Yüce TC, Vetter R, Kocabas A. Large-scale orientational order in bacterial colonies during inward growth. eLife 2022; 11:72187. [PMID: 35254257 PMCID: PMC8963879 DOI: 10.7554/elife.72187] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
During colony growth, complex interactions regulate the bacterial orientation, leading to the formation of large-scale ordered structures, including topological defects, microdomains, and branches. These structures may benefit bacterial strains, providing invasive advantages during colonization. Active matter dynamics of growing colonies drives the emergence of these ordered structures. However, additional biomechanical factors also play a significant role during this process. Here, we show that the velocity profile of growing colonies creates strong radial orientation during inward growth when crowded populations invade a closed area. During this process, growth geometry sets virtual confinement and dictates the velocity profile. Herein, flow-induced alignment and torque balance on the rod-shaped bacteria result in a new stable orientational equilibrium in the radial direction. Our analysis revealed that the dynamics of these radially oriented structures, also known as aster defects, depend on bacterial length and can promote the survival of the longest bacteria around localized nutritional hotspots. The present results indicate a new mechanism underlying structural order and provide mechanistic insights into the dynamics of bacterial growth on complex surfaces.
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Affiliation(s)
| | - Y Ilker Yaman
- Department of Physics, Koç University, Istanbul, Turkey
| | | | - Roman Vetter
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Askin Kocabas
- Department of Physics, Koç University, Istanbul, Turkey
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40
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Magnesium rescues the morphology of Bacillus subtilis mreB mutants through its inhibitory effect on peptidoglycan hydrolases. Sci Rep 2022; 12:1137. [PMID: 35064120 PMCID: PMC8782873 DOI: 10.1038/s41598-021-04294-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/06/2021] [Indexed: 02/04/2023] Open
Abstract
Cell wall homeostasis in bacteria is tightly regulated by balanced synthesis and degradation of peptidoglycan (PG), allowing cells to expand their sacculus during growth while maintaining physical integrity. In rod-shaped bacteria, actin-like MreB proteins are key players of the PG elongation machinery known as the Rod complex. In the Gram-positive model bacterium Bacillus subtilis depletion of the essential MreB leads to loss of rod shape and cell lysis. However, millimolar concentrations of magnesium in the growth medium rescue the viability and morphological defects of mreB mutants by an unknown mechanism. Here, we used a combination of cytological, biochemical and biophysical approaches to investigate the cell surface properties of mreB null mutant cells and the interactions of Mg2+ with the cell wall of B. subtilis. We show that ∆mreB cells have rougher and softer surfaces, and changes in PG composition indicative of increased DL- and DD-endopeptidase activities as well as increased deacetylation of the sugar moieties. Increase in DL-endopeptidase activity is mitigated by excess Mg2+ while DD-endopeptidase activity remains high. Visualization of PG degradation in pulse-chase experiments showed anisotropic PG hydrolase activity along the sidewalls of ∆mreB cells, in particular at the sites of increased cell width and bulging, while PG synthesis remained isotropic. Overall, our data support a model in which divalent cations maintain rod shape in ∆mreB cells by inhibiting PG hydrolases, possibly through the formation of crosslinks with carboxyl groups of the PG meshwork that affect the capacity of PG hydrolases to act on their substrate.
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A High-Content Microscopy Screening Identifies New Genes Involved in Cell Width Control in Bacillus subtilis. mSystems 2021; 6:e0101721. [PMID: 34846166 PMCID: PMC8631317 DOI: 10.1128/msystems.01017-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
How cells control their shape and size is a fundamental question of biology. In most bacteria, cell shape is imposed by the peptidoglycan (PG) polymeric meshwork that surrounds the cell. Thus, bacterial cell morphogenesis results from the coordinated action of the proteins assembling and degrading the PG shell. Remarkably, during steady-state growth, most bacteria maintain a defined shape along generations, suggesting that error-proof mechanisms tightly control the process. In the rod-shaped model for the Gram-positive bacterium Bacillus subtilis, the average cell length varies as a function of the growth rate, but the cell diameter remains constant throughout the cell cycle and across growth conditions. Here, in an attempt to shed light on the cellular circuits controlling bacterial cell width, we developed a screen to identify genetic determinants of cell width in B. subtilis. Using high-content screening (HCS) fluorescence microscopy and semiautomated measurement of single-cell dimensions, we screened a library of ∼4,000 single knockout mutants. We identified 13 mutations significantly altering cell diameter, in genes that belong to several functional groups. In particular, our results indicate that metabolism plays a major role in cell width control in B. subtilis. IMPORTANCE Bacterial shape is primarily dictated by the external cell wall, a vital structure that, as such, is the target of countless antibiotics. Our understanding of how bacteria synthesize and maintain this structure is therefore a cardinal question for both basic and applied research. Bacteria usually multiply from generation to generation while maintaining their progenies with rigorously identical shapes. This implies that the bacterial cells constantly monitor and maintain a set of parameters to ensure this perpetuation. Here, our study uses a large-scale microscopy approach to identify at the whole-genome level, in a model bacterium, the genes involved in the control of one of the most tightly controlled cellular parameters, the cell width.
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Acinetobacter baumannii Can Survive with an Outer Membrane Lacking Lipooligosaccharide Due to Structural Support from Elongasome Peptidoglycan Synthesis. mBio 2021; 12:e0309921. [PMID: 34844428 PMCID: PMC8630537 DOI: 10.1128/mbio.03099-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative bacteria resist external stresses due to cell envelope rigidity, which is provided by two membranes and a peptidoglycan layer. The outer membrane (OM) surface contains lipopolysaccharide (LPS; contains O-antigen) or lipooligosaccharide (LOS). LPS/LOS are essential in most Gram-negative bacteria and may contribute to cellular rigidity. Acinetobacter baumannii is a useful tool for testing these hypotheses as it can survive without LOS. Previously, our group found that strains with naturally high levels of penicillin binding protein 1A (PBP1A) could not become LOS deficient unless the gene encoding it was deleted, highlighting the relevance of peptidoglycan biosynthesis and suggesting that high PBP1A levels were toxic during LOS deficiency. Transposon sequencing and follow-up analysis found that axial peptidoglycan synthesis by the elongasome and a peptidoglycan recycling enzyme, ElsL, were vital in LOS-deficient cells. The toxicity of high PBP1A levels during LOS deficiency was clarified to be due to a negative impact on elongasome function. Our data suggest that during LOS deficiency, the strength of the peptidoglycan specifically imparted by elongasome synthesis becomes essential, supporting that the OM and peptidoglycan contribute to cell rigidity.
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43
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Graham CLB, Newman H, Gillett FN, Smart K, Briggs N, Banzhaf M, Roper DI. A Dynamic Network of Proteins Facilitate Cell Envelope Biogenesis in Gram-Negative Bacteria. Int J Mol Sci 2021; 22:12831. [PMID: 34884635 PMCID: PMC8657477 DOI: 10.3390/ijms222312831] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteria must maintain the ability to modify and repair the peptidoglycan layer without jeopardising its essential functions in cell shape, cellular integrity and intermolecular interactions. A range of new experimental techniques is bringing an advanced understanding of how bacteria regulate and achieve peptidoglycan synthesis, particularly in respect of the central role played by complexes of Sporulation, Elongation or Division (SEDs) and class B penicillin-binding proteins required for cell division, growth and shape. In this review we highlight relationships implicated by a bioinformatic approach between the outer membrane, cytoskeletal components, periplasmic control proteins, and cell elongation/division proteins to provide further perspective on the interactions of these cell division, growth and shape complexes. We detail the network of protein interactions that assist in the formation of peptidoglycan and highlight the increasingly dynamic and connected set of protein machinery and macrostructures that assist in creating the cell envelope layers in Gram-negative bacteria.
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Affiliation(s)
- Chris L. B. Graham
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Hector Newman
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Francesca N. Gillett
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Katie Smart
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Nicholas Briggs
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Manuel Banzhaf
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
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44
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Lv X, Jin K, Sun G, Ledesma-Amaro R, Liu L. Microscopy imaging of living cells in metabolic engineering. Trends Biotechnol 2021; 40:752-765. [PMID: 34799183 DOI: 10.1016/j.tibtech.2021.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023]
Abstract
Microscopy imaging of living cells is becoming a pivotal, noninvasive, and highly specific tool in metabolic engineering to visualize molecular dynamics in industrial microorganisms. This review describes the different microscopy methods, from fluorescence to super resolution, with application in microbial bioengineering. Firstly, the role and importance of microscopy imaging is analyzed in the context of strain design. Then, the advantages and disadvantages of different microscopy technologies are discussed, including confocal laser scanning microscopy (CLSM), spatial light interference microscopy (SLIM), and super-resolution microscopy, followed by their applications in synthetic biology. Finally, the future perspectives of live-cell imaging and their potential to transform microbial systems are analyzed. This review provides theoretical guidance and highlights the importance of microscopy in understanding and engineering microbial metabolism.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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45
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Unipolar Peptidoglycan Synthesis in the Rhizobiales Requires an Essential Class A Penicillin-Binding Protein. mBio 2021; 12:e0234621. [PMID: 34544272 PMCID: PMC8546619 DOI: 10.1128/mbio.02346-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the Rhizobiales are polarly growing bacteria that lack homologs of the canonical Rod complex. To investigate the mechanisms underlying polar cell wall synthesis, we systematically probed the function of cell wall synthesis enzymes in the plant pathogen Agrobacterium tumefaciens. The development of fluorescent d-amino acid dipeptide (FDAAD) probes, which are incorporated into peptidoglycan by penicillin-binding proteins in A. tumefaciens, enabled us to monitor changes in growth patterns in the mutants. Use of these fluorescent cell wall probes and peptidoglycan compositional analysis demonstrate that a single class A penicillin-binding protein is essential for polar peptidoglycan synthesis. Furthermore, we find evidence of an additional mode of cell wall synthesis that requires ld-transpeptidase activity. Genetic analysis and cell wall targeting antibiotics reveal that the mechanism of unipolar growth is conserved in Sinorhizobium and Brucella. This work provides insights into unipolar peptidoglycan biosynthesis employed by the Rhizobiales during cell elongation.
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46
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Tank RG, Lund VA, Kumar S, Turner RD, Lafage L, Pasquina Lemonche L, Bullough PA, Cadby A, Foster SJ, Hobbs JK. Correlative Super-Resolution Optical and Atomic Force Microscopy Reveals Relationships Between Bacterial Cell Wall Architecture and Synthesis in Bacillus subtilis. ACS NANO 2021; 15:16011-16018. [PMID: 34533301 PMCID: PMC8552488 DOI: 10.1021/acsnano.1c04375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Understanding how bacteria grow and divide requires insight into both the molecular-level dynamics of ultrastructure and the chemistry of the constituent components. Atomic force microscopy (AFM) can provide near molecular resolution images of biological systems but typically provides limited chemical information. Conversely, while super-resolution optical microscopy allows localization of particular molecules and chemistries, information on the molecular context is difficult to obtain. Here, we combine these approaches into STORMForce (stochastic optical reconstruction with atomic force microscopy) and the complementary SIMForce (structured illumination with atomic force microscopy), to map the synthesis of the bacterial cell wall structural macromolecule, peptidoglycan, during growth and division in the rod-shaped bacterium Bacillus subtilis. Using "clickable" d-amino acid incorporation, we fluorescently label and spatially localize a short and controlled period of peptidoglycan synthesis and correlate this information with high-resolution AFM of the resulting architecture. During division, septal synthesis occurs across its developing surface, suggesting a two-stage process with incorporation at the leading edge and with considerable in-filling behind. During growth, the elongation of the rod occurs through bands of synthesis, spaced by ∼300 nm, and corresponds to denser regions of the internal cell wall as revealed by AFM. Combining super-resolution optics and AFM can provide insights into the synthesis processes that produce the complex architectures of bacterial structural biopolymers.
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Affiliation(s)
- Raveen
K. G. Tank
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - Victoria A. Lund
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Sandip Kumar
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Robert D. Turner
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
- Department
of Computer Science, University of Sheffield, Sheffield, S1 4DP, United Kingdom
| | - Lucia Lafage
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Laia Pasquina Lemonche
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Per A. Bullough
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Ashley Cadby
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - Simon J. Foster
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jamie K. Hobbs
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
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47
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Abstract
The purpose of this review is to explore self-organizing mechanisms that pattern microtubules (MTs) and spatially organize animal cell cytoplasm, inspired by recent experiments in frog egg extract. We start by reviewing conceptual distinctions between self-organizing and templating mechanisms for subcellular organization. We then discuss self-organizing mechanisms that generate radial MT arrays and cell centers in the absence of centrosomes. These include autocatalytic MT nucleation, transport of minus ends, and nucleation from organelles such as melanosomes and Golgi vesicles that are also dynein cargoes. We then discuss mechanisms that partition the cytoplasm in syncytia, in which multiple nuclei share a common cytoplasm, starting with cytokinesis, when all metazoan cells are transiently syncytial. The cytoplasm of frog eggs is partitioned prior to cytokinesis by two self-organizing modules, protein regulator of cytokinesis 1 (PRC1)-kinesin family member 4A (KIF4A) and chromosome passenger complex (CPC)-KIF20A. Similar modules may partition longer-lasting syncytia, such as early Drosophila embryos. We end by discussing shared mechanisms and principles for the MT-based self-organization of cellular units.
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Affiliation(s)
- Timothy J Mitchison
- Harvard Medical School, Boston, Massachusetts 02115, USA; ,
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Christine M Field
- Harvard Medical School, Boston, Massachusetts 02115, USA; ,
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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48
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van Teeseling MCF. Elongation at Midcell in Preparation of Cell Division Requires FtsZ, but Not MreB nor PBP2 in Caulobacter crescentus. Front Microbiol 2021; 12:732031. [PMID: 34512611 PMCID: PMC8429850 DOI: 10.3389/fmicb.2021.732031] [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: 06/28/2021] [Accepted: 08/09/2021] [Indexed: 02/04/2023] Open
Abstract
Controlled growth of the cell wall is a key prerequisite for bacterial cell division. The existing view of the canonical rod-shaped bacterial cell dictates that newborn cells first elongate throughout their side walls using the elongasome protein complex, and subsequently use the divisome to coordinate constriction of the dividing daughter cells. Interestingly, another growth phase has been observed in between elongasome-mediated elongation and constriction, during which the cell elongates from the midcell outward. This growth phase, that has been observed in Escherichia coli and Caulobacter crescentus, remains severely understudied and its mechanisms remain elusive. One pressing open question is which role the elongasome key-component MreB plays in this respect. This study quantitatively investigates this growth phase in C. crescentus and focuses on the role of both divisome and elongasome components. This growth phase is found to initiate well after MreB localizes at midcell, although it does not require its presence at this subcellular location nor the action of key elongasome components. Instead, the divisome component FtsZ seems to be required for elongation at midcell. This study thus shines more light on this growth phase in an important model organism and paves the road to more in-depth studies.
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Affiliation(s)
- Muriel C F van Teeseling
- Junior Research Group Prokaryotic Cell Biology, Department Microbial Interactions, Institute of Microbiology, Friedrich-Schiller-Universität, Jena, Germany.,Department of Biology, University of Marburg, Marburg, Germany
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49
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Wong F, Wilson S, Helbig R, Hegde S, Aftenieva O, Zheng H, Liu C, Pilizota T, Garner EC, Amir A, Renner LD. Understanding Beta-Lactam-Induced Lysis at the Single-Cell Level. Front Microbiol 2021; 12:712007. [PMID: 34421870 PMCID: PMC8372035 DOI: 10.3389/fmicb.2021.712007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022] Open
Abstract
Mechanical rupture, or lysis, of the cytoplasmic membrane is a common cell death pathway in bacteria occurring in response to β-lactam antibiotics. A better understanding of the cellular design principles governing the susceptibility and response of individual cells to lysis could indicate methods of potentiating β-lactam antibiotics and clarify relevant aspects of cellular physiology. Here, we take a single-cell approach to bacterial cell lysis to examine three cellular features—turgor pressure, mechanosensitive channels, and cell shape changes—that are expected to modulate lysis. We develop a mechanical model of bacterial cell lysis and experimentally analyze the dynamics of lysis in hundreds of single Escherichia coli cells. We find that turgor pressure is the only factor, of these three cellular features, which robustly modulates lysis. We show that mechanosensitive channels do not modulate lysis due to insufficiently fast solute outflow, and that cell shape changes result in more severe cellular lesions but do not influence the dynamics of lysis. These results inform a single-cell view of bacterial cell lysis and underscore approaches of combatting antibiotic tolerance to β-lactams aimed at targeting cellular turgor.
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Affiliation(s)
- Felix Wong
- Department of Biological Engineering, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, United States.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States.,Center for Systems Biology, Harvard University, Cambridge, MA, United States
| | - Ralf Helbig
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
| | - Smitha Hegde
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Olha Aftenieva
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
| | - Hai Zheng
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chenli Liu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States.,Center for Systems Biology, Harvard University, Cambridge, MA, United States
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
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Delisle J, Cordier B, Audebert S, Pophillat M, Cluzel C, Espinosa L, Grangeasse C, Galinier A, Doan T. Characterization of TseB: A new actor in cell wall elongation in Bacillus subtilis. Mol Microbiol 2021; 116:1099-1112. [PMID: 34411374 DOI: 10.1111/mmi.14798] [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: 02/26/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Penicillin-binding proteins (PBPs) are crucial enzymes of peptidoglycan assembly and targets of β-lactam antibiotics. However, little is known about their regulation. Recently, membrane proteins were shown to regulate the bifunctional transpeptidases/glycosyltransferases aPBPs in some bacteria. However, up to now, regulators of monofunctional transpeptidases bPBPs have yet to be revealed. Here, we propose that TseB could be such a PBP regulator. This membrane protein was previously found to suppress tetracycline sensitivity of a Bacillus subtilis strain deleted for ezrA, a gene encoding a regulator of septation ring formation. In this study, we show that TseB is required for B. subtilis normal cell shape, tseB mutant cells being shorter and wider than wild-type cells. We observed that TseB interacts with PBP2A, a monofunctional transpeptidase. While TseB is not required for PBP2A activity, stability, and localization, we show that the overproduction of PBP2A is deleterious in the absence of TseB. In addition, we showed that TseB is necessary not only for efficient cell wall elongation during exponential phase but also during spore outgrowth, as it was also observed for PBP2A. Altogether, our results suggest that TseB is a new member of the elongasome that regulates PBP2A function during cell elongation and spore germination.
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Affiliation(s)
- Jordan Delisle
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Baptiste Cordier
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Stéphane Audebert
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Matthieu Pophillat
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS/Université Lyon I, Lyon, France
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Université Lyon I, Lyon, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Thierry Doan
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
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