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Jana B, Liu X, Dénéréaz J, Park H, Leshchiner D, Liu B, Gallay C, Zhu J, Veening JW, van Opijnen T. CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria. Nat Microbiol 2024:10.1038/s41564-024-01759-x. [PMID: 39030344 DOI: 10.1038/s41564-024-01759-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/12/2024] [Indexed: 07/21/2024]
Abstract
Genetic interactions identify functional connections between genes and pathways, establishing gene functions or druggable targets. Here we use CRISPRi-TnSeq, CRISPRi-mediated knockdown of essential genes alongside TnSeq-mediated knockout of non-essential genes, to map genome-wide interactions between essential and non-essential genes in Streptococcus pneumoniae. Transposon-mutant libraries constructed in 13 CRISPRi strains enabled screening of ~24,000 gene pairs. This identified 1,334 genetic interactions, including 754 negative and 580 positive interactions. Network analyses show that 17 non-essential genes pleiotropically interact with more than half the essential genes tested. Validation experiments confirmed that a 7-gene subset protects against perturbations. Furthermore, we reveal hidden redundancies that compensate for essential gene loss, relationships between cell wall synthesis, integrity and cell division, and show that CRISPRi-TnSeq identifies synthetic and suppressor-type relationships between both functionally linked and disparate genes and pathways. Importantly, in species where CRISPRi and Tn-Seq are established, CRISPRi-TnSeq should be straightforward to implement.
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Affiliation(s)
- Bimal Jana
- Department of Biology, Boston College, Chestnut Hill, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xue Liu
- Department of Pathogen Biology, Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Julien Dénéréaz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Hongshik Park
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | | | - Bruce Liu
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Clément Gallay
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Junhao Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA, USA.
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Weaver A, Taguchi A, Dörr T. Masters of Misdirection: Peptidoglycan Glycosidases in Bacterial Growth. J Bacteriol 2023; 205:e0042822. [PMID: 36757204 PMCID: PMC10029718 DOI: 10.1128/jb.00428-22] [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: 02/10/2023] Open
Abstract
The dynamic composition of the peptidoglycan cell wall has been the subject of intense research for decades, yet how bacteria coordinate the synthesis of new peptidoglycan with the turnover and remodeling of existing peptidoglycan remains elusive. Diversity and redundancy within peptidoglycan synthases and peptidoglycan autolysins, enzymes that degrade peptidoglycan, have often made it challenging to assign physiological roles to individual enzymes and determine how those activities are regulated. For these reasons, peptidoglycan glycosidases, which cleave within the glycan strands of peptidoglycan, have proven veritable masters of misdirection over the years. Unlike many of the broadly conserved peptidoglycan synthetic complexes, diverse bacteria can employ unrelated glycosidases to achieve the same physiological outcome. Additionally, although the mechanisms of action for many individual enzymes have been characterized, apparent conserved homologs in other organisms can exhibit an entirely different biochemistry. This flexibility has been recently demonstrated in the context of three functions critical to vegetative growth: (i) release of newly synthesized peptidoglycan strands from their membrane anchors, (ii) processing of peptidoglycan turned over during cell wall expansion, and (iii) removal of peptidoglycan fragments that interfere with daughter cell separation during cell division. Finally, the regulation of glycosidase activity during these cell processes may be a cumulation of many factors, including protein-protein interactions, intrinsic substrate preferences, substrate availability, and subcellular localization. Understanding the true scope of peptidoglycan glycosidase activity will require the exploration of enzymes from diverse organisms with equally diverse growth and division strategies.
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Affiliation(s)
- Anna Weaver
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Atsushi Taguchi
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
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Haubrich BA, Nayyab S, Gallati M, Hernandez J, Williams C, Whitman A, Zimmerman T, Li Q, Chen Y, Zhou CZ, Basu A, Reid CW. Inhibition of Streptococcus pneumoniae growth by masarimycin. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35467499 DOI: 10.1099/mic.0.001182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Despite renewed interest, development of chemical biology methods to study peptidoglycan metabolism has lagged in comparison to the glycobiology field in general. To address this, a panel of diamides were screened against the Gram-positive bacterium Streptococcus pneumoniae to identify inhibitors of bacterial growth. The screen identified the diamide masarimycin as a bacteriostatic inhibitor of S. pneumoniae growth with an MIC of 8 µM. The diamide inhibited detergent-induced autolysis in a concentration-dependent manner, indicating perturbation of peptidoglycan degradation as the mode-of-action. Cell based screening of masarimycin against a panel of autolysin mutants, identified a higher MIC against a ΔlytB strain lacking an endo-N-acetylglucosaminidase involved in cell division. Subsequent biochemical and phenotypic analyses suggested that the higher MIC was due to an indirect interaction with LytB. Further analysis of changes to the cell surface in masarimycin treated cells identified the overexpression of several moonlighting proteins, including elongation factor Tu which is implicated in regulating cell shape. Checkerboard assays using masarimycin in concert with additional antibiotics identified an antagonistic relationship with the cell wall targeting antibiotic fosfomycin, which further supports a cell wall mode-of-action.
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Affiliation(s)
- Brad A Haubrich
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA.,Department of Basic Sciences, Touro University Nevada, College of Osteopathic Medicine, Henderson, NV 89014, USA
| | - Saman Nayyab
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA.,Amherst Department of Molecular and Cellular Biology, University of Massachusetts, 230 Stockbridge Rd Amherst, MA, USA
| | - Mika Gallati
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Jazmeen Hernandez
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Caroline Williams
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Andrew Whitman
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Tahl Zimmerman
- Department of Family and Consumer Sciences, North Carolina A&T State University, Greensboro, NC, USA
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Amit Basu
- Department of Chemistry, Brown University, Providence, RI, USA
| | - Christopher W Reid
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
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HONGBO Z, HASEBE A, ALAM A, YUNQING L, HOSHIKA S, YAMAUTI M, SANO H. Antibacterial potential of colloidal platinum nanoparticles against Streptococcus mutans . Dent Mater J 2022; 41:368-375. [DOI: 10.4012/dmj.2021-203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhang HONGBO
- Department of Restorative Dentistry, Division of Oral Health Science, Hokkaido University Graduate School of Dental Medicine
| | - Akira HASEBE
- Department of Oral Molecular Microbiology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University
| | - Arefin ALAM
- Department of Restorative Dentistry, Division of Oral Health Science, Hokkaido University Graduate School of Dental Medicine
| | - Liu YUNQING
- Department of Restorative Dentistry, Division of Oral Health Science, Hokkaido University Graduate School of Dental Medicine
| | - Shuhei HOSHIKA
- Department of Restorative Dentistry, Division of Oral Health Science, Hokkaido University Graduate School of Dental Medicine
| | - Monica YAMAUTI
- Department of Restorative Dentistry, Division of Oral Health Science, Hokkaido University Graduate School of Dental Medicine
| | - Hidehiko SANO
- Department of Restorative Dentistry, Division of Oral Health Science, Hokkaido University Graduate School of Dental Medicine
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Briggs NS, Bruce KE, Naskar S, Winkler ME, Roper DI. The Pneumococcal Divisome: Dynamic Control of Streptococcus pneumoniae Cell Division. Front Microbiol 2021; 12:737396. [PMID: 34737730 PMCID: PMC8563077 DOI: 10.3389/fmicb.2021.737396] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022] Open
Abstract
Cell division in Streptococcus pneumoniae (pneumococcus) is performed and regulated by a protein complex consisting of at least 14 different protein elements; known as the divisome. Recent findings have advanced our understanding of the molecular events surrounding this process and have provided new understanding of the mechanisms that occur during the division of pneumococcus. This review will provide an overview of the key protein complexes and how they are involved in cell division. We will discuss the interaction of proteins in the divisome complex that underpin the control mechanisms for cell division and cell wall synthesis and remodelling that are required in S. pneumoniae, including the involvement of virulence factors and capsular polysaccharides.
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Affiliation(s)
- Nicholas S. Briggs
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kevin E. Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Souvik Naskar
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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Looks can be deceiving: Bacterial enzymes work through unanticipated mechanism. Proc Natl Acad Sci U S A 2021; 118:2114568118. [PMID: 34526405 DOI: 10.1073/pnas.2114568118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
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Biochemical reconstitution defines new functions for membrane-bound glycosidases in assembly of the bacterial cell wall. Proc Natl Acad Sci U S A 2021; 118:2103740118. [PMID: 34475211 DOI: 10.1073/pnas.2103740118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 07/30/2021] [Indexed: 01/25/2023] Open
Abstract
The peptidoglycan cell wall is a macromolecular structure that encases bacteria and is essential for their survival. Proper assembly of the cell wall requires peptidoglycan synthases as well as membrane-bound cleavage enzymes that control where new peptidoglycan is made and inserted. Previous studies have shown that two membrane-bound proteins in Streptococcus pneumoniae, here named MpgA and MpgB, are important in maintaining cell wall integrity. MpgA was predicted to be a lytic transglycosylase based on its homology to Escherichia coli MltG, while the enzymatic activity of MpgB was unclear. Using nascent peptidoglycan substrates synthesized in vitro from the peptidoglycan precursor Lipid II, we report that both MpgA and MpgB are muramidases. We show that replacing a single amino acid in E. coli MltG with the corresponding amino acid from MpgA results in muramidase activity, allowing us to predict from the presence of this amino acid that other putative lytic transglycosylases actually function as muramidases. Strikingly, we report that MpgA and MpgB cut nascent peptidoglycan at different positions along the sugar backbone relative to the reducing end, with MpgA producing much longer peptidoglycan oligomers. We show that the cleavage site selectivity of MpgA is controlled by the LysM-like subdomain, which is required for its full functionality in cells. We propose that MltG's ability to complement the loss of MpgA in S. pneumoniae despite performing different cleavage chemistry is because it can cleave nascent peptidoglycan at the same distance from the lipid anchor.
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Kuru E, Radkov A, Meng X, Egan A, Alvarez L, Dowson A, Booher G, Breukink E, Roper DI, Cava F, Vollmer W, Brun Y, VanNieuwenhze MS. Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis. ACS Chem Biol 2019; 14:2745-2756. [PMID: 31743648 PMCID: PMC6929685 DOI: 10.1021/acschembio.9b00664] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Bacteria exhibit a myriad of different morphologies,
through the
synthesis and modification of their essential peptidoglycan (PG) cell
wall. Our discovery of a fluorescent D-amino acid (FDAA)-based PG labeling approach provided a powerful method
for observing how these morphological changes occur. Given that PG
is unique to bacterial cells and a common target for antibiotics,
understanding the precise mechanism(s) for incorporation of (F)DAA-based
probes is a crucial determinant in understanding the role of PG synthesis
in bacterial cell biology and could provide a valuable tool in the
development of new antimicrobials to treat drug-resistant antibacterial
infections. Here, we systematically investigate the mechanisms of
FDAA probe incorporation into PG using two model organisms Escherichia coli (Gram-negative) and Bacillus subtilis (Gram-positive). Our in vitro and in vivo data unequivocally demonstrate
that these bacteria incorporate FDAAs using two extracytoplasmic pathways:
through activity of their D,D-transpeptidases, and,
if present, by their L,D-transpeptidases and not
via cytoplasmic incorporation into a D-Ala-D-Ala
dipeptide precursor. Our data also revealed the unprecedented finding
that the DAA-drug, D-cycloserine, can be incorporated into
peptide stems by each of these transpeptidases, in addition to its
known inhibitory activity against D-alanine racemase and D-Ala-D-Ala ligase. These mechanistic findings enabled
development of a new, FDAA-based, in vitro labeling approach that
reports on subcellular distribution of muropeptides, an especially
important attribute to enable the study of bacteria with poorly defined
growth modes. An improved understanding of the incorporation mechanisms
utilized by DAA-based probes is essential when interpreting results
from high resolution experiments and highlights the antimicrobial
potential of synthetic DAAs.
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Affiliation(s)
- Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Atanas Radkov
- Department of Biochemistry and Biophysics, UCSF School of Medicine, San Francisco, California 94158, United States
| | - Xin Meng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alexander Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Laura Alvarez
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Amanda Dowson
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Garrett Booher
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Eefjan Breukink
- Department of Chemistry, Utrecht University, 3584 CH, Utrecht, Netherlands
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Yves Brun
- Department of Microbiology, Infectious Diseases, and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Michael S. VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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