1
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Enright AL, Heelan WJ, Ward RD, Peters JM. CRISPRi functional genomics in bacteria and its application to medical and industrial research. Microbiol Mol Biol Rev 2024; 88:e0017022. [PMID: 38809084 PMCID: PMC11332340 DOI: 10.1128/mmbr.00170-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
SUMMARYFunctional genomics is the use of systematic gene perturbation approaches to determine the contributions of genes under conditions of interest. Although functional genomic strategies have been used in bacteria for decades, recent studies have taken advantage of CRISPR (clustered regularly interspaced short palindromic repeats) technologies, such as CRISPRi (CRISPR interference), that are capable of precisely modulating expression of all genes in the genome. Here, we discuss and review the use of CRISPRi and related technologies for bacterial functional genomics. We discuss the strengths and weaknesses of CRISPRi as well as design considerations for CRISPRi genetic screens. We also review examples of how CRISPRi screens have defined relevant genetic targets for medical and industrial applications. Finally, we outline a few of the many possible directions that could be pursued using CRISPR-based functional genomics in bacteria. Our view is that the most exciting screens and discoveries are yet to come.
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Affiliation(s)
- Amy L. Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - William J. Heelan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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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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3
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Hao A, Suo Y, Lee SY. Structural insights into the FtsEX-EnvC complex regulation on septal peptidoglycan hydrolysis in Vibrio cholerae. Structure 2024; 32:188-199.e5. [PMID: 38070498 DOI: 10.1016/j.str.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/02/2023] [Accepted: 11/14/2023] [Indexed: 02/04/2024]
Abstract
During bacterial cell division, hydrolysis of septal peptidoglycan (sPG) is crucial for cell separation. This sPG hydrolysis is performed by the enzyme amidases whose activity is regulated by the integral membrane protein complex FtsEX-EnvC. FtsEX is an ATP-binding cassette transporter, and EnvC is a long coiled-coil protein that interacts with and activates the amidases. The molecular mechanism by which the FtsEX-EnvC complex activates amidases remains largely unclear. We present the cryo-electron microscopy structure of the FtsEX-EnvC complex from the pathogenic bacteria V. cholerae (FtsEX-EnvCVC). FtsEX-EnvCVC in the presence of ADP adopts a distinct conformation where EnvC is "horizontally extended" rather than "vertically extended". Subsequent structural studies suggest that EnvC can swing between these conformations in space in a nucleotide-dependent manner. Our structural analysis and functional studies suggest that FtsEX-EnvCVC employs spatial control of EnvC for amidase activation, providing mechanistic insights into the FtsEX-EnvC regulation on septal peptidoglycan hydrolysis.
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Affiliation(s)
- Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Yang Suo
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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4
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Elgrably-Weiss M, Hussain F, Georg J, Shraiteh B, Altuvia S. Balanced cell division is secured by two different regulatory sites in OxyS RNA. RNA (NEW YORK, N.Y.) 2024; 30:124-135. [PMID: 38071477 PMCID: PMC10798246 DOI: 10.1261/rna.079836.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/09/2023] [Indexed: 01/18/2024]
Abstract
The hydrogen peroxide-induced small RNA OxyS has been proposed to originate from the 3' UTR of a peroxide mRNA. Unexpectedly, phylogenetic OxyS targetome predictions indicate that most OxyS targets belong to the category of "cell cycle," including cell division and cell elongation. Previously, we reported that Escherichia coli OxyS inhibits cell division by repressing expression of the essential transcription termination factor nusG, thereby leading to the expression of the KilR protein, which interferes with the function of the major cell division protein, FtsZ. By interfering with cell division, OxyS brings about cell-cycle arrest, thus allowing DNA damage repair. Cell division and cell elongation are opposing functions to the extent that inhibition of cell division requires a parallel inhibition of cell elongation for the cells to survive. In this study, we report that in addition to cell division, OxyS inhibits mepS, which encodes an essential peptidoglycan endopeptidase that is responsible for cell elongation. Our study indicates that cell-cycle arrest and balancing between cell division and cell elongation are important and conserved functions of the oxidative stress-induced sRNA OxyS.
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Affiliation(s)
- Maya Elgrably-Weiss
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120 Jerusalem, Israel
| | - Fayyaz Hussain
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, 79104 Freiburg, Germany
| | - Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, 79104 Freiburg, Germany
| | - Bushra Shraiteh
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120 Jerusalem, Israel
| | - Shoshy Altuvia
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120 Jerusalem, Israel
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5
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Jager K, Orozco-Hidalgo MT, Springstein BL, Joly-Smith E, Papazotos F, McDonough E, Fleming E, McCallum G, Yuan AH, Hilfinger A, Hochschild A, Potvin-Trottier L. Measuring prion propagation in single bacteria elucidates a mechanism of loss. Proc Natl Acad Sci U S A 2023; 120:e2221539120. [PMID: 37738299 PMCID: PMC10523482 DOI: 10.1073/pnas.2221539120] [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: 01/13/2023] [Accepted: 07/26/2023] [Indexed: 09/24/2023] Open
Abstract
Prions are self-propagating protein aggregates formed by specific proteins that can adopt alternative folds. Prions were discovered as the cause of the fatal transmissible spongiform encephalopathies in mammals, but prions can also constitute nontoxic protein-based elements of inheritance in fungi and other species. Prion propagation has recently been shown to occur in bacteria for more than a hundred cell divisions, yet a fraction of cells in these lineages lost the prion through an unknown mechanism. Here, we investigate prion propagation in single bacterial cells as they divide using microfluidics and fluorescence microscopy. We show that the propagation occurs in two distinct modes. In a fraction of the population, cells had multiple small visible aggregates and lost the prion through random partitioning of aggregates to one of the two daughter cells at division. In the other subpopulation, cells had a stable large aggregate localized to the pole; upon division the mother cell retained this polar aggregate and a daughter cell was generated that contained small aggregates. Extending our findings to prion domains from two orthologous proteins, we observe similar propagation and loss properties. Our findings also provide support for the suggestion that bacterial prions can form more than one self-propagating state. We implement a stochastic version of the molecular model of prion propagation from yeast and mammals that recapitulates all the observed single-cell properties. This model highlights challenges for prion propagation that are unique to prokaryotes and illustrates the conservation of fundamental characteristics of prion propagation.
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Affiliation(s)
- Krista Jager
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | | | - Euan Joly-Smith
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
| | - Fotini Papazotos
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | - Eleanor Fleming
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Giselle McCallum
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | - Andy H. Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Department of Mathematics, University of Toronto, Toronto, ONM5S 2E4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
| | - Ann Hochschild
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Laurent Potvin-Trottier
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
- Department of Physics, Concordia University, Montréal, QCH4B 1R6, Canada
- Center for Applied Synthetic Biology, Concordia University, Montréal, QCH4B 1R6, Canada
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6
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Griffin ME, Klupt S, Espinosa J, Hang HC. Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions. Cell Chem Biol 2023; 30:436-456. [PMID: 36417916 PMCID: PMC10192474 DOI: 10.1016/j.chembiol.2022.11.001] [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: 05/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall is composed of a highly crosslinked matrix of glycopeptide polymers known as peptidoglycan that dictates bacterial cell morphology and protects against environmental stresses. Regulation of peptidoglycan turnover is therefore crucial for bacterial survival and growth and is mediated by key protein complexes and enzyme families. Here, we review the prevalence, structure, and activity of NlpC/P60 peptidases, a family of peptidoglycan hydrolases that are crucial for cell wall turnover and division as well as interactions with antibiotics and different hosts. Understanding the molecular functions of NlpC/P60 peptidases should provide important insight into bacterial physiology, their interactions with different kingdoms of life, and the development of new therapeutic approaches.
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Affiliation(s)
- Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Steven Klupt
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
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7
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Jager K, Orozco-Hidalgo MT, Springstein BL, Joly-Smith E, Papazotos F, McDonough E, Fleming E, McCallum G, Hilfinger A, Hochschild A, Potvin-Trottier L. Measuring prion propagation in single bacteria elucidates mechanism of loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523042. [PMID: 36712035 PMCID: PMC9882039 DOI: 10.1101/2023.01.11.523042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Prions are self-propagating protein aggregates formed by specific proteins that can adopt alternative folds. Prions were discovered as the cause of the fatal transmissible spongiform encephalopathies in mammals, but prions can also constitute non-toxic protein-based elements of inheritance in fungi and other species. Prion propagation has recently been shown to occur in bacteria for more than a hundred cell divisions, yet a fraction of cells in these lineages lost the prion through an unknown mechanism. Here, we investigate prion propagation in single bacterial cells as they divide using microfluidics and fluorescence microscopy. We show that the propagation occurs in two distinct modes with distinct stability and inheritance characteristics. We find that the prion is lost through random partitioning of aggregates to one of the two daughter cells at division. Extending our findings to prion domains from two orthologous proteins, we observe similar propagation and loss properties. Our findings also provide support for the suggestion that bacterial prions can form more than one self-propagating state. We implement a stochastic version of the molecular model of prion propagation from yeast and mammals that recapitulates all the observed single-cell properties. This model highlights challenges for prion propagation that are unique to prokaryotes and illustrates the conservation of fundamental characteristics of prion propagation across domains of life.
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Affiliation(s)
- Krista Jager
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | | | | | - Euan Joly-Smith
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Fotini Papazotos
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - EmilyKate McDonough
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eleanor Fleming
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Giselle McCallum
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ann Hochschild
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Laurent Potvin-Trottier
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Physics, Concordia University, Montréal, Québec, Canada
- Center for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
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8
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Voedts H, Kennedy SP, Sezonov G, Arthur M, Hugonnet JE. Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli revealed unexpected impacts of β-lactams. Nat Commun 2022; 13:7962. [PMID: 36575173 PMCID: PMC9794725 DOI: 10.1038/s41467-022-35528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/06/2022] [Indexed: 12/28/2022] Open
Abstract
The D,D-transpeptidase activity of penicillin-binding proteins (PBPs) is the well-known primary target of β-lactam antibiotics that block peptidoglycan polymerization. β-lactam-induced bacterial killing involves complex downstream responses whose causes and consequences are difficult to resolve. Here, we use the functional replacement of PBPs by a β-lactam-insensitive L,D-transpeptidase to identify genes essential to mitigate the effects of PBP inactivation by β-lactams in actively dividing bacteria. The functions of the 179 conditionally essential genes identified by this approach extend far beyond L,D-transpeptidase partners for peptidoglycan polymerization to include proteins involved in stress response and in the assembly of outer membrane polymers. The unsuspected effects of β-lactams include loss of the lipoprotein-mediated covalent bond that links the outer membrane to the peptidoglycan, destabilization of the cell envelope in spite of effective peptidoglycan cross-linking, and increased permeability of the outer membrane. The latter effect indicates that the mode of action of β-lactams involves self-promoted penetration through the outer membrane.
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Affiliation(s)
- Henri Voedts
- grid.417925.cCentre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France
| | - Sean P. Kennedy
- Institut Pasteur, Université Paris Cité, Département Biologie Computationnelle, F-75015 Paris, France
| | - Guennadi Sezonov
- grid.417925.cCentre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France
| | - Michel Arthur
- grid.417925.cCentre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France
| | - Jean-Emmanuel Hugonnet
- grid.417925.cCentre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, F-75006 Paris, France
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9
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Sloan R, Surber J, Roy EJ, Hartig E, Morgenstein RM. Enzyme 1 of the phosphoenolpyruvate:sugar phosphotransferase system is involved in resistance to MreB disruption in wild-type and ∆envC cells. Mol Microbiol 2022; 118:588-600. [PMID: 36199205 PMCID: PMC9671846 DOI: 10.1111/mmi.14988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 01/12/2023]
Abstract
Cell wall synthesis in bacteria is determined by two protein complexes: the elongasome and divisome. The elongasome is coordinated by the actin homolog MreB while the divisome is organized by the tubulin homolog FtsZ. While these two systems must coordinate with each other to ensure that elongation and division are coregulated, this cross talk has been understudied. Using the MreB depolymerizing agent, A22, we found that multiple gene deletions result in cells exhibiting increased sensitivity to MreB depolymerization. One of those genes encodes for EnvC, a part of the divisome that is responsible for splitting daughter cells after the completion of cytokinesis through the activation of specific amidases. Here we show this increased sensitivity to A22 works through two known amidase targets of EnvC: AmiA and AmiB. In addition, suppressor analysis revealed that mutations in enzyme 1 of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) can suppress the effects of A22 in both wild-type and envC deletion cells. Together this work helps to link elongation, division, and metabolism.
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Affiliation(s)
- Ryan Sloan
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Jacob Surber
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Emma J. Roy
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Ethan Hartig
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
| | - Randy M. Morgenstein
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahomaUSA
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10
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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] [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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11
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Tan WB, Chng SS. Genetic interaction mapping highlights key roles of the Tol-Pal complex. Mol Microbiol 2022; 117:921-936. [PMID: 35066953 DOI: 10.1111/mmi.14882] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
The conserved Tol-Pal trans-envelope complex is important for outer membrane (OM) stability and cell division in Gram-negative bacteria. It is proposed to mediate OM constriction during cell division via cell wall tethering. Yet, recent studies suggest the complex has additional roles in OM lipid homeostasis and septal wall separation. How Tol-Pal facilitates all these processes is unclear. To gain insights into its function(s), we applied transposon-insertion sequencing, and report here a detailed network of genetic interactions with the tol-pal locus in Escherichia coli. We found one positive and >20 negative strong interactions based on fitness. Disruption osmoregulated-periplasmic glucan biosynthesis restores fitness and OM barrier function, but not proper division, in tol-pal mutants. In contrast, deleting genes involved in OM homeostasis and cell wall remodeling cause synthetic growth defects in strains lacking Tol-Pal, especially exacerbating OM barrier and/or division phenotypes. Notably, the ΔtolA mutant having additional defects in OM protein assembly (ΔbamB) exhibited severe division phenotypes, even when single mutants divided normally; this highlights the possibility for OM phenotypes to indirectly impact cell division. Overall, our work underscores the intricate nature of Tol-Pal function, and reinforces its key roles in cell wall-OM tethering, cell wall remodeling, and in particular, OM homeostasis.
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Affiliation(s)
- Wee Boon Tan
- Department of Chemistry, National University of Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore
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12
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A New Class of Cell Wall-Recycling l,d-Carboxypeptidase Determines β-Lactam Susceptibility and Morphogenesis in Acinetobacter baumannii. mBio 2021; 12:e0278621. [PMID: 34872350 PMCID: PMC8649774 DOI: 10.1128/mbio.02786-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hospital-acquired pathogen Acinetobacter baumannii possesses a complex cell envelope that is key to its multidrug resistance and virulence. The bacterium, however, lacks many canonical enzymes that build the envelope in model organisms. Instead, A. baumannii contains a number of poorly annotated proteins that may allow alternative mechanisms of envelope biogenesis. We demonstrated previously that one of these unusual proteins, ElsL, is required for maintaining a characteristic short rod shape and for withstanding antibiotics that attack the septal cell wall. Curiously, ElsL is composed of a leaderless YkuD-family domain usually found in secreted, cell wall-modifying l,d-transpeptidases (LDTs). Here, we show that, rather than being an LDT, ElsL is actually a new class of cytoplasmic l,d-carboxypeptidase (LDC) that provides a critical step in cell wall recycling previously thought to be missing from A. baumannii. Absence of ElsL impairs cell wall integrity, morphology, and intrinsic resistance due to buildup of murein tetrapeptide precursors, toxicity of which is bypassed by preventing muropeptide recycling. Multiple pathways in the cell become sites of vulnerability when ElsL is inactivated, including l,d-cross-link formation, cell division, and outer membrane lipid homoeostasis, reflecting its pleiotropic influence on envelope physiology. We thus reveal a novel class of cell wall-recycling LDC critical to growth and homeostasis of A. baumannii and likely many other bacteria.
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Cho H. Transposon insertion site sequencing (TIS) of Pseudomonas aeruginosa. J Microbiol 2021; 59:1067-1074. [PMID: 34865196 DOI: 10.1007/s12275-021-1565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 10/19/2022]
Abstract
Transposon insertion site sequencing (TIS) is a technique that determines the insertion profile of a transposon mutant library by massive parallel sequencing of transposon-genomic DNA junctions. Because the transposon insertion profile reflects the abundance of each mutant in the library, it provides information to assess the fitness contribution of each genetic locus of a bacterial genome in a specific growth condition or strain background. Although introduced only about a dozen years ago, TIS has become an important tool in bacterial genetics that provides clues to study biological functions and regulatory mechanisms. Here, I describe a protocol for generating high density transposon insertion mutant libraries and preparing Illumina sequencing samples for mapping the transposon junctions of the transposon mutant libraries using Pseudomonas aeruginosa as an example.
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Affiliation(s)
- Hongbaek Cho
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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Voedts H, Dorchêne D, Lodge A, Vollmer W, Arthur M, Hugonnet JE. Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes in Escherichia coli. EMBO J 2021; 40:e108126. [PMID: 34382698 DOI: 10.15252/embj.2021108126] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria resist to the turgor pressure of the cytoplasm through a net-like macromolecule, the peptidoglycan, made of glycan strands connected via peptides cross-linked by penicillin-binding proteins (PBPs). We recently reported the emergence of β-lactam resistance resulting from a bypass of PBPs by the YcbB L,D-transpeptidase (LdtD), which form chemically distinct 3→3 cross-links compared to 4→3 formed by PBPs. Here we show that peptidoglycan expansion requires controlled hydrolysis of cross-links and identify among eight endopeptidase paralogues the minimum enzyme complements essential for bacterial growth with 4→3 (MepM) and 3→3 (MepM and MepK) cross-links. Purified Mep endopeptidases unexpectedly displayed a 4→3 and 3→3 dual specificity implying recognition of a common motif in the two cross-link types. Uncoupling of the polymerization of glycan chains from the 4→3 cross-linking reaction was found to facilitate the bypass of PBPs by YcbB. These results illustrate the plasticity of the peptidoglycan polymerization machinery in response to the selective pressure of β-lactams.
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Affiliation(s)
- Henri Voedts
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
| | - Delphine Dorchêne
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
| | - Adam Lodge
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
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Abstract
Most bacteria are surrounded by a peptidoglycan cell wall that defines their shape and protects them from osmotic lysis. The expansion and division of this structure therefore plays an integral role in bacterial growth and division. Additionally, the biogenesis of the peptidoglycan layer is the target of many of our most effective antibiotics. Thus, a better understanding of how the cell wall is built will enable the development of new therapies to combat the rise of drug-resistant bacterial infections. This review covers recent advances in defining the mechanisms involved in assembling the peptidoglycan layer with an emphasis on discoveries related to the function and regulation of the cell elongation and division machineries in the model organisms Escherichia coli and Bacillus subtilis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Patricia D A Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Current affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, 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
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