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Liu X, de Bakker V, Heggenhougen MV, Mårli MT, Frøynes AH, Salehian Z, Porcellato D, Morales Angeles D, Veening JW, Kjos M. Genome-wide CRISPRi screens for high-throughput fitness quantification and identification of determinants for dalbavancin susceptibility in Staphylococcus aureus. mSystems 2024:e0128923. [PMID: 38837392 DOI: 10.1128/msystems.01289-23] [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: 12/04/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024] Open
Abstract
Antibiotic resistance and tolerance remain a major problem for the treatment of staphylococcal infections. Identifying genes that influence antibiotic susceptibility could open the door to novel antimicrobial strategies, including targets for new synergistic drug combinations. Here, we developed a genome-wide CRISPR interference library for Staphylococcus aureus, demonstrated its use by quantifying gene fitness in different strains through CRISPRi-seq, and used it to identify genes that modulate susceptibility to the lipoglycopeptide dalbavancin. By exposing the library to sublethal concentrations of dalbavancin using both CRISPRi-seq and direct selection methods, we not only found genes previously reported to be involved in antibiotic susceptibility but also identified genes thus far unknown to affect antibiotic tolerance. Importantly, some of these genes could not have been detected by more conventional transposon-based knockout approaches because they are essential for growth, stressing the complementary value of CRISPRi-based methods. Notably, knockdown of a gene encoding the uncharacterized protein KapB specifically sensitizes the cells to dalbavancin, but not to other antibiotics of the same class, whereas knockdown of the Shikimate pathway showed the opposite effect. The results presented here demonstrate the promise of CRISPRi-seq screens to identify genes and pathways involved in antibiotic susceptibility and pave the way to explore alternative antimicrobial treatments through these insights.IMPORTANCEAntibiotic resistance is a challenge for treating staphylococcal infections. Identifying genes that affect how antibiotics work could help create new treatments. In our study, we made a CRISPR interference library for Staphylococcus aureus and used this to find which genes are critical for growth and also mapped genes that are important for antibiotic sensitivity, focusing on the lipoglycopeptide antibiotic dalbavancin. With this method, we identified genes that altered the sensitivity to dalbavancin upon knockdown, including genes involved in different cellular functions. CRISPRi-seq offers a means to uncover untapped antibiotic targets, including those that conventional screens would disregard due to their essentiality. This paves the way for the discovery of new ways to fight infections.
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Affiliation(s)
- Xue Liu
- Department of Pathogen, Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Department of Fundamental Microbiology, University of Lausanne, , Switzerland
| | - Vincent de Bakker
- Department of Fundamental Microbiology, University of Lausanne, , Switzerland
| | | | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
| | - Anette Heidal Frøynes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
| | - Zhian Salehian
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
| | - Danae Morales Angeles
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, University of Lausanne, , Switzerland
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
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Seo J, Kim JH, Ko N, Kim J, Moon K, Kim IS, Lee W. Development of novel indole-quinoline hybrid molecules targeting bacterial proton motive force. J Appl Microbiol 2024; 135:lxae104. [PMID: 38678002 DOI: 10.1093/jambio/lxae104] [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: 03/04/2024] [Revised: 04/01/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
AIMS This study aimed to develop an editable structural scaffold for improving drug development, including pharmacokinetics and pharmacodynamics of antibiotics by using synthetic compounds derived from a (hetero)aryl-quinoline hybrid scaffold. METHODS AND RESULTS In this study, 18 CF3-substituted (hetero)aryl-quinoline hybrid molecules were examined for their potential antibacterial activity against Staphylococcus aureus by determining minimal inhibitory concentrations. These 18 synthetic compounds represent modifications to key regions of the quinoline N-oxide scaffold, enabling us to conduct a structure-activity relationship analysis for antibacterial potency. Among the compounds, 3 m exhibited potency against with both methicillin resistant S. aureus strains, as well as other Gram-positive bacteria, including Enterococcus faecalis and Bacillus subtilis. We demonstrated that 3 m disrupted the bacterial proton motive force (PMF) through monitoring the PMF and conducting the molecular dynamics simulations. Furthermore, we show that this mechanism of action, disrupting PMF, is challenging for S. aureus to overcome. We also validated this PMF inhibition mechanism of 3 m in an Acinetobacter baumannii strain with weaken lipopolysaccharides. Additionally, in Gram-negative bacteria, we demonstrated that 3 m exhibited a synergistic effect with colistin that disrupts the outer membrane of Gram-negative bacteria. CONCLUSIONS Our approach to developing editable synthetic novel antibacterials underscores the utility of CF3-substituted (hetero)aryl-quinoline scaffold for designing compounds targeting the bacterial proton motive force, and for further drug development, including pharmacokinetics and pharmacodynamics.
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Affiliation(s)
- Jinbeom Seo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ji-Hoon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Nayoung Ko
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jihyeon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kyeongwon Moon
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - In Su Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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3
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Kim SJ, Jo J, Kim J, Ko KS, Lee W. Polymyxin B nonapeptide potentiates the eradication of Gram-negative bacterial persisters. Microbiol Spectr 2024; 12:e0368723. [PMID: 38391225 PMCID: PMC10986493 DOI: 10.1128/spectrum.03687-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Antibiotic-resistant Gram-negative bacteria remain a globally leading cause of bacterial infection-associated mortality, and it is imperative to identify novel therapeutic strategies. Recently, the advantage of using antibacterials selective against Gram-negative bacteria has been demonstrated with polymyxins that specifically target the lipopolysaccharides of Gram-negative bacteria. However, the severe cytotoxicity of polymyxins limits their clinical use. Here, we demonstrate that polymyxin B nonapeptide (PMBN), a polymyxin B derivative without the terminal amino acyl residue, can significantly enhance the effectiveness of commonly used antibiotics against only Gram-negative bacteria and their persister cells. We show that although PMBN itself does not exhibit antibacterial activity or cytotoxicity well above the 100-fold minimum inhibitory concentration of polymyxin B, PMBN can increase the potency of co-treated antibiotics. We also demonstrate that using PMBN in combination with other antibiotics significantly reduces the frequency of resistant mutant formation. Together, this work provides evidence of the utilities of PMBN as a novel potentiator for antibiotics against Gram-negative bacteria and insights for the eradication of bacterial persister cells during antibiotic treatment. IMPORTANCE The significance of our study lies in addressing the problem of antibiotic-resistant Gram-negative bacteria, which continue to be a global cause of mortality associated with bacterial infections. Therefore, identifying innovative therapeutic approaches is an urgent need. Recent research has highlighted the potential of selective antibacterials like polymyxins, which specifically target the lipopolysaccharides of Gram-negative bacteria. However, the clinical use of polymyxins is limited by their severe cytotoxicity. This study unveils the effectiveness of polymyxin B nonapeptide (PMBN) in significantly enhancing the eradication of persister cells in Gram-negative bacteria. Although PMBN itself does not exhibit antibacterial activity or cytotoxicity, it remarkably reduces persister cells during the treatment of antibiotics. Moreover, combining PMBN with other antibiotics reduces the emergence of resistant mutants. Our research emphasizes the utility of PMBN as a novel potentiator to decrease persister cells during antibiotic treatments for Gram-negative bacteria.
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Affiliation(s)
- Sun Ju Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jeongwoo Jo
- Department of Microbiology, School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jihyeon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kwan Soo Ko
- Department of Microbiology, School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
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4
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Bartlett TM, Sisley TA, Mychack A, Walker S, Baker RW, Rudner DZ, Bernhardt TG. FacZ is a GpsB-interacting protein that prevents aberrant division-site placement in Staphylococcus aureus. Nat Microbiol 2024; 9:801-813. [PMID: 38443581 PMCID: PMC10914604 DOI: 10.1038/s41564-024-01607-y] [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: 04/24/2023] [Accepted: 01/15/2024] [Indexed: 03/07/2024]
Abstract
Staphylococcus aureus is a Gram-positive pathogen responsible for antibiotic-resistant infections. To identify vulnerabilities in cell envelope biogenesis that may overcome resistance, we enriched for S. aureus transposon mutants with defects in cell surface integrity or cell division by sorting for cells that stain with propidium iodide or have increased light-scattering properties, respectively. Transposon sequencing of the sorted populations identified more than 20 previously uncharacterized factors impacting these processes. Cells inactivated for one of these proteins, factor preventing extra Z-rings (FacZ, SAOUHSC_01855), showed aberrant membrane invaginations and multiple FtsZ cytokinetic rings. These phenotypes were suppressed in mutants lacking the conserved cell-division protein GpsB, which forms an interaction hub bridging envelope biogenesis factors with the cytokinetic ring in S. aureus. FacZ was found to interact directly with GpsB in vitro and in vivo. We therefore propose that FacZ is an envelope biogenesis factor that antagonizes GpsB function to prevent aberrant division events in S. aureus.
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Affiliation(s)
- Thomas M Bartlett
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Tyler A Sisley
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Aaron Mychack
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Suzanne Walker
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Richard W Baker
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Z Rudner
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Thomas G Bernhardt
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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5
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Henriksen C, Baek KT, Wacnik K, Gallay C, Veening JW, Foster SJ, Frees D. The ClpX chaperone and a hypermorphic FtsA variant with impaired self-interaction are mutually compensatory for coordinating Staphylococcus aureus cell division. Mol Microbiol 2024; 121:98-115. [PMID: 38041395 DOI: 10.1111/mmi.15200] [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: 08/28/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
Bacterial cell division requires the coordinated assembly and disassembly of a large protein complex called the divisome; however, the exact role of molecular chaperones in this critical process remains unclear. We here provide genetic evidence that ClpX unfoldase activity is a determinant for proper coordination of bacterial cell division by showing the growth defect of a Staphylococcus aureus clpX mutant is rescued by a spontaneously acquired G325V substitution in the ATP-binding domain of the essential FtsA cell division protein. The polymerization state of FtsA is thought to control initiation of bacterial septum synthesis and, while restoring the aberrant FtsA dynamics in clpX cells, the FtsAG325V variant displayed reduced ability to interact with itself and other cell division proteins. In wild-type cells, the ftsAG325V allele shared phenotypes with Escherichia coli superfission ftsA mutants and accelerated the cell cycle, increased the risk of daughter cell lysis, and conferred sensitivity to heat and antibiotics inhibiting cell wall synthesis. Strikingly, lethality was mitigated by spontaneous mutations that inactivate ClpX. Taken together, our results suggest that ClpX promotes septum synthesis by antagonizing FtsA interactions and illuminates the critical role of a protein unfoldase in coordinating bacterial cell division.
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Affiliation(s)
- Camilla Henriksen
- Department of Veterinary and Animal Disease, University of Copenhagen, Frederiksberg, Denmark
| | - Kristoffer T Baek
- Department of Veterinary and Animal Disease, University of Copenhagen, Frederiksberg, Denmark
| | | | - Clement Gallay
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Simon J Foster
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Dorte Frees
- Department of Veterinary and Animal Disease, University of Copenhagen, Frederiksberg, Denmark
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6
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Bartlett TM, Sisley TA, Mychack A, Walker S, Baker RW, Rudner DZ, Bernhardt TG. Identification of FacZ as a division site placement factor in Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538170. [PMID: 37162900 PMCID: PMC10168275 DOI: 10.1101/2023.04.24.538170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Staphylococcus aureus is a gram-positive pathogen responsible for life-threatening infections that are difficult to treat due to antibiotic resistance. The identification of new vulnerabilities in essential processes like cell envelope biogenesis represents a promising avenue towards the development of anti-staphylococcal therapies that overcome resistance. To this end, we performed cell sorting-based enrichments for S. aureus mutants with defects in envelope integrity and cell division. We identified many known envelope biogenesis factors as well as a large collection of new factors with roles in this process. Mutants inactivated for one of the hits, the uncharacterized SAOUHSC_01855 protein, displayed aberrant membrane invaginations and multiple FtsZ cytokinetic ring structures. This factor is broadly distributed among Firmicutes, and its inactivation in B. subtilis similarly caused division and membrane defects. We therefore renamed the protein FacZ (Firmicute-associated coordinator of Z-rings). In S. aureus, inactivation of the conserved cell division protein GpsB suppressed the division and morphological defects of facZ mutants. Additionally, FacZ and GpsB were found to interact directly in a purified system. Thus, FacZ is a novel antagonist of GpsB function with a conserved role in controlling division site placement in S. aureus and other Firmicutes.
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Affiliation(s)
- Thomas M. Bartlett
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Tyler A. Sisley
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Aaron Mychack
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard W. Baker
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Z. Rudner
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
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7
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Sit B, Srisuknimit V, Bueno E, Zingl FG, Hullahalli K, Cava F, Waldor MK. Undecaprenyl phosphate translocases confer conditional microbial fitness. Nature 2023; 613:721-728. [PMID: 36450355 PMCID: PMC9876793 DOI: 10.1038/s41586-022-05569-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022]
Abstract
The microbial cell wall is essential for maintenance of cell shape and resistance to external stressors1. The primary structural component of the cell wall is peptidoglycan, a glycopolymer with peptide crosslinks located outside of the cell membrane1. Peptidoglycan biosynthesis and structure are responsive to shifting environmental conditions such as pH and salinity2-6, but the mechanisms underlying such adaptations are incompletely understood. Precursors of peptidoglycan and other cell surface glycopolymers are synthesized in the cytoplasm and then delivered across the cell membrane bound to the recyclable lipid carrier undecaprenyl phosphate7 (C55-P, also known as UndP). Here we identify the DUF368-containing and DedA transmembrane protein families as candidate C55-P translocases, filling a critical gap in knowledge of the proteins required for the biogenesis of microbial cell surface polymers. Gram-negative and Gram-positive bacteria lacking their cognate DUF368-containing protein exhibited alkaline-dependent cell wall and viability defects, along with increased cell surface C55-P levels. pH-dependent synthetic genetic interactions between DUF368-containing proteins and DedA family members suggest that C55-P transporter usage is dynamic and modulated by environmental inputs. C55-P transporter activity was required by the cholera pathogen for growth and cell shape maintenance in the intestine. We propose that conditional transporter reliance provides resilience in lipid carrier recycling, bolstering microbial fitness both inside and outside the host.
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Affiliation(s)
- Brandon Sit
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Veerasak Srisuknimit
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Franz G Zingl
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Karthik Hullahalli
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA. .,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Howard Hughes Medical Institute, Bethesda, MD, USA.
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8
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Sionov RV, Banerjee S, Bogomolov S, Smoum R, Mechoulam R, Steinberg D. Targeting the Achilles’ Heel of Multidrug-Resistant Staphylococcus aureus by the Endocannabinoid Anandamide. Int J Mol Sci 2022; 23:ijms23147798. [PMID: 35887146 PMCID: PMC9319909 DOI: 10.3390/ijms23147798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
Antibiotic-resistant Staphylococcus aureus is a major health issue that requires new therapeutic approaches. Accumulating data suggest that it is possible to sensitize these bacteria to antibiotics by combining them with inhibitors targeting efflux pumps, the low-affinity penicillin-binding protein PBP2a, cell wall teichoic acid, or the cell division protein FtsZ. We have previously shown that the endocannabinoid Anandamide (N-arachidonoylethanolamine; AEA) could sensitize drug-resistant S. aureus to a variety of antibiotics, among others, through growth arrest and inhibition of drug efflux. Here, we looked at biochemical alterations caused by AEA. We observed that AEA increased the intracellular drug concentration of a fluorescent penicillin and augmented its binding to membrane proteins with concomitant altered membrane distribution of these proteins. AEA also prevented the secretion of exopolysaccharides (EPS) and reduced the cell wall teichoic acid content, both processes known to require transporter proteins. Notably, AEA was found to inhibit membrane ATPase activity that is necessary for transmembrane transport. AEA did not affect the membrane GTPase activity, and the GTPase cell division protein FtsZ formed the Z-ring of the divisome normally in the presence of AEA. Rather, AEA caused a reduction in murein hydrolase activities involved in daughter cell separation. Altogether, this study shows that AEA affects several biochemical processes that culminate in the sensitization of the drug-resistant bacteria to antibiotics.
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Affiliation(s)
- Ronit Vogt Sionov
- Biofilm Research Laboratory, Institute of Biomedical and Oral Sciences, Faculty of Dentistry, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (S.B.); (S.B.); (D.S.)
- Correspondence:
| | - Shreya Banerjee
- Biofilm Research Laboratory, Institute of Biomedical and Oral Sciences, Faculty of Dentistry, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (S.B.); (S.B.); (D.S.)
| | - Sergei Bogomolov
- Biofilm Research Laboratory, Institute of Biomedical and Oral Sciences, Faculty of Dentistry, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (S.B.); (S.B.); (D.S.)
| | - Reem Smoum
- Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (R.S.); (R.M.)
| | - Raphael Mechoulam
- Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (R.S.); (R.M.)
| | - Doron Steinberg
- Biofilm Research Laboratory, Institute of Biomedical and Oral Sciences, Faculty of Dentistry, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (S.B.); (S.B.); (D.S.)
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9
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Call SN, Andrews LB. CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. Front Genome Ed 2022; 4:892304. [PMID: 35813973 PMCID: PMC9260158 DOI: 10.3389/fgeed.2022.892304] [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: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 01/08/2023] Open
Abstract
CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) have become ubiquitous approaches to control gene expression in bacteria due to their simple design and effectiveness. By regulating transcription of a target gene(s), CRISPRi/a can dynamically engineer cellular metabolism, implement transcriptional regulation circuitry, or elucidate genotype-phenotype relationships from smaller targeted libraries up to whole genome-wide libraries. While CRISPRi/a has been primarily established in the model bacteria Escherichia coli and Bacillus subtilis, a growing numbering of studies have demonstrated the extension of these tools to other species of bacteria (here broadly referred to as non-model bacteria). In this mini-review, we discuss the challenges that contribute to the slower creation of CRISPRi/a tools in diverse, non-model bacteria and summarize the current state of these approaches across bacterial phyla. We find that despite the potential difficulties in establishing novel CRISPRi/a in non-model microbes, over 190 recent examples across eight bacterial phyla have been reported in the literature. Most studies have focused on tool development or used these CRISPRi/a approaches to interrogate gene function, with fewer examples applying CRISPRi/a gene regulation for metabolic engineering or high-throughput screens and selections. To date, most CRISPRi/a reports have been developed for common strains of non-model bacterial species, suggesting barriers remain to establish these genetic tools in undomesticated bacteria. More efficient and generalizable methods will help realize the immense potential of programmable CRISPR-based transcriptional control in diverse bacteria.
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Affiliation(s)
- Stephanie N. Call
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, United States
- *Correspondence: Lauren B. Andrews,
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10
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Abstract
Cell division and cell wall synthesis in staphylococci need to be precisely coordinated and controlled to allow the cell to multiply while maintaining its nearly spherical shape. The mechanisms ensuring correct placement of the division plane and synthesis of new cell wall have been studied intensively. However, hitherto unknown factors and proteins are likely to play key roles in this complex interplay. Here, we identified and investigated a protein with a major influence on cell morphology in Staphylococcus aureus. The protein, named SmdA (for staphylococcal morphology determinant A), is a membrane protein with septum-enriched localization. By CRISPRi knockdown and overexpression combined with different microscopy techniques, we demonstrated that proper levels of SmdA were necessary for cell division, including septum formation and cell splitting. We also identified conserved residues in SmdA that were critical for its functionality. Pulldown and bacterial two-hybrid interaction experiments showed that SmdA interacted with several known cell division and cell wall synthesis proteins, including penicillin-binding proteins (PBPs) and EzrA. Notably, SmdA also affected susceptibility to cell wall targeting antibiotics, particularly in methicillin-resistant S. aureus (MRSA). Together, our results showed that S. aureus was dependent on balanced amounts of membrane attached SmdA to carry out proper cell division.
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11
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Liu Q, Li D, Wang N, Guo G, Shi Y, Zou Q, Zhang X. Identification and Application of a Panel of Constitutive Promoters for Gene Overexpression in Staphylococcus aureus. Front Microbiol 2022; 13:818307. [PMID: 35295303 PMCID: PMC8918988 DOI: 10.3389/fmicb.2022.818307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus is a leading pathogen that is currently the most common cause of infection in hospitalized patients. An in-depth genetic analysis of S. aureus virulence genes contributing to pathogenesis is needed to develop novel antimicrobial therapies. However, tools for genetic manipulation in S. aureus are limited, particularly those for gene expression. Here, 38 highly expressed genes were identified in S. aureus USA300_FPR3757 via RNA-seq. Promoter regions from 30 of these genes were successfully cloned, of which 20 promoters exhibited a wide range of activity. By utilizing these active promoters, 20 S. aureus-Escherichia coli shuttle vectors were constructed and evaluated by expressing an egfp reporter gene. Expression of the egfp gene under the control of different promoters was confirmed and quantified by Western blotting and qPCR, which suggested that the activity of these promoters varied from 18 to 650% of the activity of PsarA, a widely used promoter for gene expression. In addition, our constructed vectors were verified to be highly compatible with gene expression in different S. aureus strains. Furthermore, these vectors were evaluated and used to overexpress two endogenous proteins in S. aureus, namely, catalase and the transcriptional repressor of purine biosynthesis (PurR). Meanwhile, the physiological functions and phenotypes of overexpressed PurR and catalase in S. aureus were validated. Altogether, this evidence indicates that our constructed vectors provide a wide range of promoter activity on gene expression in S. aureus. This set of vectors carrying different constitutive promoters developed here will provide a powerful tool for the direct analysis of target gene function in staphylococcal cells.
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Affiliation(s)
- Qiang Liu
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Qiang Liu,
| | - Daiyu Li
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Ning Wang
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Guo
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Shi
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Xiaokai Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
- Xiaokai Zhang,
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12
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Yu JS, Kim JH, Rashan L, Kim I, Lee W, Kim KH. Potential Antimicrobial Activity of Galloyl-Flavonoid Glycosides From Woodfordia uniflora Against Methicillin-Resistant Staphylococcus aureus. Front Microbiol 2021; 12:784504. [PMID: 34899667 PMCID: PMC8662356 DOI: 10.3389/fmicb.2021.784504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/05/2021] [Indexed: 11/20/2022] Open
Abstract
Antibiotic-resistant infections are a growing problem; to combat multi-drug resistant bacterial infections, antibiotics with novel mechanisms of action are needed. Identification of potent bioactive natural products is an attractive avenue for developing novel therapeutic strategies against bacterial infections. As part of our ongoing research to explore bioactive natural products from diverse resources, we investigated the antimicrobial compounds from Woodfordia uniflora, a flowering shrub unique to the Dhofar region of Oman. The plant has been used as a remedy for skin infections in Oman. However, to date, no study has examined the antimicrobial compounds in W. uniflora. Phytochemical analysis of the methanolic extract of W. uniflora leaves in combination with LC/MS-based analysis allowed us to isolate and identify four flavonoid-type analogs (1–4), procyanidin B3-3-O-gallate (1), rhamnetin 3-O-(6″-galloyl)-β-D-glucopyranoside (2), rhamnetin 3-O-α-L-rhamnopyranoside (3), and quercetin 3-O-(6″-galloyl)-β-D-glucopyranoside (4). The isolates have a novel mechanism of action; the compounds inhibit biofilm formation in methicillin-resistant Staphylococcus aureus (MRSA) and synergize with methicillin. Our metabolite analysis revealed that this synergizing activity by compounds was achieved by remodeling metabolism including central carbon metabolism and glutamine biosynthesis that resulted in abnormal cell formation and reduction in biofilm formation of MRSA. Taken together, these findings provide experimental evidence that rhamnetin 3-O-(6″-galloyl)-β-D-glucopyranoside (2) and quercetin 3-O-(6″-galloyl)-β-D-glucopyranoside (4) can be considered as potential therapeutic agents for the treatment of methicillin-resistant S. aureus-associated diseases.
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Affiliation(s)
- Jae Sik Yu
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Ji-Hoon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Luay Rashan
- Biodiversity Unit, Research Center, Dhofar University, Salalah, Oman
| | - Inseo Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
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13
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Zhang R, Shebes MA, Kho K, Scaffidi SJ, Meredith TC, Yu W. Spatial regulation of protein A in Staphylococcus aureus. Mol Microbiol 2021; 116:589-605. [PMID: 33949015 DOI: 10.1111/mmi.14734] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/31/2022]
Abstract
Surface proteins of Staphylococcus aureus play vital roles in bacterial physiology and pathogenesis. Recent work suggests that surface proteins are spatially regulated by a YSIRK/GXXS signal peptide that promotes cross-wall targeting at the mid-cell, though the mechanisms remain unclear. We previously showed that protein A (SpA), a YSIRK/GXXS protein and key staphylococcal virulence factor, mis-localizes in a ltaS mutant deficient in lipoteichoic acid (LTA) production. Here, we identified that SpA contains another cross-wall targeting signal, the LysM domain, which, in addition to the YSIRK/GXXS signal peptide, significantly enhances SpA cross-wall targeting. We show that LTA synthesis, but not LtaS, is required for SpA septal anchoring and cross-wall deposition. Interestingly, LTA is predominantly found at the peripheral cell membrane and is diminished at the septum of dividing staphylococcal cells, suggesting a restriction mechanism for SpA septal localization. Finally, we show that D-alanylation of LTA abolishes SpA cross-wall deposition by disrupting SpA distribution in the peptidoglycan layer without altering SpA septal anchoring. Our study reveals that multiple factors contribute to the spatial regulation and cross-wall targeting of SpA via different mechanisms, which coordinately ensures efficient incorporation of surface proteins into the growing peptidoglycan during the cell cycle.
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Affiliation(s)
- Ran Zhang
- Department of Cell Biology, Microbiology and Molecular Biology (CMMB), University of South Florida, Tampa, FL, USA
| | - Mac A Shebes
- Department of Cell Biology, Microbiology and Molecular Biology (CMMB), University of South Florida, Tampa, FL, USA
| | - Kelvin Kho
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Salvatore J Scaffidi
- Department of Cell Biology, Microbiology and Molecular Biology (CMMB), University of South Florida, Tampa, FL, USA
| | - Timothy C Meredith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Wenqi Yu
- Department of Cell Biology, Microbiology and Molecular Biology (CMMB), University of South Florida, Tampa, FL, USA
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14
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Fergestad ME, Stamsås GA, Morales Angeles D, Salehian Z, Wasteson Y, Kjos M. Penicillin-binding protein PBP2a provides variable levels of protection toward different β-lactams in Staphylococcus aureus RN4220. Microbiologyopen 2020; 9:e1057. [PMID: 32419377 PMCID: PMC7424258 DOI: 10.1002/mbo3.1057] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/21/2020] [Accepted: 04/25/2020] [Indexed: 12/31/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is resistant to most β-lactams due to the expression of an extra penicillin-binding protein, PBP2a, with low β-lactam affinity. It has long been known that heterologous expression of the PBP2a-encoding mecA gene in methicillin-sensitive S. aureus (MSSA) provides protection towards β-lactams, however, some reports suggest that the degree of protection can vary between different β-lactams. To test this more systematically, we introduced an IPTG-inducible mecA into the MSSA laboratory strain RN4220. We confirm, by growth assays as well as single-cell microfluidics time-lapse microscopy experiments, that PBP2a expression protects against β-lactams in S. aureus RN4220. By testing a panel of ten different β-lactams, we conclude that there is also a great variation in the level of protection conferred by PBP2a. Expression of PBP2a resulted in an only fourfold increase in minimum inhibitory concentration (MIC) for imipenem, while a 32-fold increase in MIC was observed for cefaclor and cephalexin. Interestingly, in our experimental setup, PBP2a confers the highest protection against cefaclor and cephalexin-two β-lactams that are known to have a high specific affinity toward the transpeptidase PBP3 of S. aureus. Notably, using a single-cell microfluidics setup we demonstrate a considerable phenotypic variation between cells upon β-lactam exposure and show that mecA-expressing S. aureus can survive β-lactam concentrations much higher than the minimal inhibitory concentrations. We discuss possible explanations and implications of these results including important aspects regarding treatment of infection.
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Affiliation(s)
- Marte Ekeland Fergestad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Gro Anita Stamsås
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Danae Morales Angeles
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Zhian Salehian
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Yngvild Wasteson
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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15
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Chan H, Söderström B, Skoglund U. Spo0J and SMC are required for normal chromosome segregation in Staphylococcus aureus. Microbiologyopen 2020; 9:e999. [PMID: 31990138 PMCID: PMC7142367 DOI: 10.1002/mbo3.999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 12/22/2022] Open
Abstract
Bacterial chromosome segregation is an essential cellular process that is particularly elusive in spherical bacteria such as the opportunistic human pathogen Staphylococcus aureus. In this study, we examined the functional significance of a ParB homologue, Spo0J, in staphylococcal chromosome segregation and investigated the role of the structural maintenance of chromosomes (SMC) bacterial condensin in this process. We show that neither spo0J nor smc is essential in S. aureus; however, their absence causes abnormal chromosome segregation. We demonstrate that formation of complexes containing Spo0J and SMC is required for efficient S. aureus chromosome segregation and that SMC localization is dependent on Spo0J. Furthermore, we found that cell division and cell cycle progression are unaffected by the absence of spo0J or smc. Our results verify the role of Spo0J and SMC in ensuring accurate staphylococcal chromosome segregation and also imply functional redundancy or the involvement of additional mechanisms that might contribute to faithful chromosome inheritance.
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Affiliation(s)
- Helena Chan
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Bill Söderström
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Ulf Skoglund
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
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16
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Do T, Schaefer K, Santiago AG, Coe KA, Fernandes PB, Kahne D, Pinho MG, Walker S. Staphylococcus aureus cell growth and division are regulated by an amidase that trims peptides from uncrosslinked peptidoglycan. Nat Microbiol 2020; 5:291-303. [PMID: 31932712 PMCID: PMC7046134 DOI: 10.1038/s41564-019-0632-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 11/05/2019] [Indexed: 12/16/2022]
Abstract
Bacteria are protected by a polymer of peptidoglycan that serves as an exoskeleton1. In Staphylococcus aureus, the peptidoglycan assembly enzymes relocate during the cell cycle from the periphery, where they are active during growth, to the division site where they build the partition between daughter cells2-4. But how peptidoglycan synthesis is regulated throughout the cell cycle is poorly understood5,6. Here, we used a transposon screen to identify a membrane protein complex that spatially regulates S. aureus peptidoglycan synthesis. This complex consists of an amidase that removes stem peptides from uncrosslinked peptidoglycan and a partner protein that controls its activity. Amidases typically hydrolyse crosslinked peptidoglycan between daughter cells so that they can separate7. However, this amidase controls cell growth. In its absence, peptidoglycan synthesis becomes spatially dysregulated, which causes cells to grow so large that cell division is defective. We show that the cell growth and division defects due to loss of this amidase can be mitigated by attenuating the polymerase activity of the major S. aureus peptidoglycan synthase. Our findings lead to a model wherein the amidase complex regulates the density of peptidoglycan assembly sites to control peptidoglycan synthase activity at a given subcellular location. Removal of stem peptides from peptidoglycan at the cell periphery promotes peptidoglycan synthase relocation to midcell during cell division. This mechanism ensures that cell expansion is properly coordinated with cell division.
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Affiliation(s)
- Truc Do
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Kaitlin Schaefer
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Kathryn A Coe
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Pedro B Fernandes
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Mariana G Pinho
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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17
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Staphylococcus aureus ClpX localizes at the division septum and impacts transcription of genes involved in cell division, T7-secretion, and SaPI5-excision. Sci Rep 2019; 9:16456. [PMID: 31712583 PMCID: PMC6848492 DOI: 10.1038/s41598-019-52823-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/12/2019] [Indexed: 11/25/2022] Open
Abstract
In all living cells, molecular chaperones are essential for facilitating folding and unfolding of proteins. ClpX is a highly conserved ATP-dependent chaperone that besides functioning as a classical chaperone can associate with ClpP to form the ClpXP protease. To investigate the relative impact of the ClpXP protease and the ClpX chaperone in cell physiology of the important pathogenic bacterium Staphylococcus aureus, we assessed the transcriptional changes induced by inactivating only ClpXP, or by completely deleting ClpX. This analysis revealed that ClpX has a profound impact on S. aureus cell physiology that is mediated primarily via ClpXP-dependent pathways. As an example, ClpX impacts expression of virulence genes entirely via ClpXP-dependent mechanisms. Furthermore, ClpX controls a high number of genes and sRNAs via pathways involving both ClpXP protease and ClpX chaperone activities; an interesting example being genes promoting excision and replication of the pathogenicity island SaPI5. Independently of ClpP, ClpX, impacts transcription of only a restricted number of genes involved in peptidoglycan synthesis, cell division, and type seven secretion. Finally, we demonstrate that ClpX localizes in single foci in close proximity to the division septum lending support to the idea that ClpX plays a role in S. aureus cell division.
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18
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Jensen C, Bæk KT, Gallay C, Thalsø-Madsen I, Xu L, Jousselin A, Ruiz Torrubia F, Paulander W, Pereira AR, Veening JW, Pinho MG, Frees D. The ClpX chaperone controls autolytic splitting of Staphylococcus aureus daughter cells, but is bypassed by β-lactam antibiotics or inhibitors of WTA biosynthesis. PLoS Pathog 2019; 15:e1008044. [PMID: 31518377 PMCID: PMC6760813 DOI: 10.1371/journal.ppat.1008044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/25/2019] [Accepted: 08/26/2019] [Indexed: 12/02/2022] Open
Abstract
β-lactam antibiotics interfere with cross-linking of the bacterial cell wall, but the killing mechanism of this important class of antibiotics is not fully understood. Serendipitously we found that sub-lethal doses of β-lactams rescue growth and prevent spontaneous lysis of Staphylococcus aureus mutants lacking the widely conserved chaperone ClpX, and we reasoned that a better understanding of the clpX phenotypes could provide novel insights into the downstream effects of β-lactam binding to the PBP targets. Super-resolution imaging revealed that clpX cells display aberrant septum synthesis, and initiate daughter cell separation prior to septum completion at 30°C, but not at 37°C, demonstrating that ClpX becomes critical for coordinating the S. aureus cell cycle as the temperature decreases. FtsZ localization and dynamics were not affected in the absence of ClpX, suggesting that ClpX affects septum formation and autolytic activation downstream of Z-ring formation. Interestingly, oxacillin antagonized the septum progression defects of clpX cells and prevented lysis of prematurely splitting clpX cells. Strikingly, inhibitors of wall teichoic acid (WTA) biosynthesis that work synergistically with β-lactams to kill MRSA synthesis also rescued growth of the clpX mutant, as did genetic inactivation of the gene encoding the septal autolysin, Sle1. Taken together, our data support a model in which Sle1 causes premature splitting and lysis of clpX daughter cells unless Sle1-dependent lysis is antagonized by β-lactams or by inhibiting an early step in WTA biosynthesis. The finding that β-lactams and inhibitors of WTA biosynthesis specifically prevent lysis of a mutant with dysregulated autolytic activity lends support to the idea that PBPs and WTA biosynthesis play an important role in coordinating cell division with autolytic splitting of daughter cells, and that β-lactams do not kill S. aureus simply by weakening the cell wall. The bacterium Staphylococcus aureus is a major cause of human disease, and the rapid spread of S. aureus strains that are resistant to almost all β-lactam antibiotics has made treatment increasingly difficult. β-lactams interfere with cross-linking of the bacterial cell wall but the killing mechanism of this important class of antibiotics is not fully understood. Here we provide novel insight into this topic by examining a defined S. aureus mutant that has the unusual property of growing markedly better in the presence of β-lactams. Without β-lactams this mutant dies spontaneously at a high frequency due to premature separation of daughter cells during cell division. Cell death of the mutant can, however, be prevented either by exposure to β-lactam antibiotics or by inhibiting synthesis of wall teichoic acid, a major component of the cell wall in Gram-positive bacteria with a conserved role in activation of autolytic splitting of daughter cells. The finding that β-lactam antibiotics can prevent lysis of a mutant with deregulated activity of autolytic enzymes involved in daughter cell splitting, emphasizes the idea that β-lactams interfere with the coordination between cell division and daughter cell splitting, and do not kill S. aureus simply by weakening the cell wall.
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Affiliation(s)
- Camilla Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer T. Bæk
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Clement Gallay
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ida Thalsø-Madsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lijuan Xu
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ambre Jousselin
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Fernando Ruiz Torrubia
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wilhelm Paulander
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana R. Pereira
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Mariana G. Pinho
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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19
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Stamsås GA, Myrbråten IS, Straume D, Salehian Z, Veening JW, Håvarstein LS, Kjos M. CozEa and CozEb play overlapping and essential roles in controlling cell division in Staphylococcus aureus. Mol Microbiol 2018; 109:615-632. [PMID: 29884993 DOI: 10.1111/mmi.13999] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2018] [Indexed: 01/07/2023]
Abstract
Staphylococcus aureus needs to control the position and timing of cell division and cell wall synthesis to maintain its spherical shape. We identified two membrane proteins, named CozEa and CozEb, which together are important for proper cell division in S. aureus. CozEa and CozEb are homologs of the cell elongation regulator CozESpn of Streptococcus pneumoniae. While cozEa and cozEb were not essential individually, the ΔcozEaΔcozEb double mutant was lethal. To study the functions of cozEa and cozEb, we constructed a CRISPR interference (CRISPRi) system for S. aureus, allowing transcriptional knockdown of essential genes. CRISPRi knockdown of cozEa in the ΔcozEb strain (and vice versa) causes cell morphological defects and aberrant nucleoid staining, showing that cozEa and cozEb have overlapping functions and are important for normal cell division. We found that CozEa and CozEb interact with and possibly influence localization of the cell division protein EzrA. Furthermore, the CozE-EzrA interaction is conserved in S. pneumoniae, and cell division is mislocalized in cozESpn -depleted S. pneumoniae cells. Together, our results show that CozE proteins mediate control of cell division in S. aureus and S. pneumoniae, likely via interactions with key cell division proteins such as EzrA.
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Affiliation(s)
- Gro Anita Stamsås
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ine Storaker Myrbråten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Zhian Salehian
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Leiv Sigve Håvarstein
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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20
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Lee W, Do T, Zhang G, Kahne D, Meredith TC, Walker S. Antibiotic Combinations That Enable One-Step, Targeted Mutagenesis of Chromosomal Genes. ACS Infect Dis 2018. [PMID: 29534563 DOI: 10.1021/acsinfecdis.8b00017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Targeted modification of bacterial chromosomes is necessary to understand new drug targets, investigate virulence factors, elucidate cell physiology, and validate results of -omics-based approaches. For some bacteria, reverse genetics remains a major bottleneck to progress in research. Here, we describe a compound-centric strategy that combines new negative selection markers with known positive selection markers to achieve simple, efficient one-step genome engineering of bacterial chromosomes. The method was inspired by the observation that certain nonessential metabolic pathways contain essential late steps, suggesting that antibiotics targeting a late step can be used to select for the absence of genes that control flux into the pathway. Guided by this hypothesis, we have identified antibiotic/counterselectable markers to accelerate reverse engineering of two increasingly antibiotic-resistant pathogens, Staphylococcus aureus and Acinetobacter baumannii. For S. aureus, we used wall teichoic acid biosynthesis inhibitors to select for the absence of tarO and for A. baumannii, we used colistin to select for the absence of lpxC. We have obtained desired gene deletions, gene fusions, and promoter swaps in a single plating step with perfect efficiency. Our method can also be adapted to generate markerless deletions of genes using FLP recombinase. The tools described here will accelerate research on two important pathogens, and the concept we outline can be readily adapted to any organism for which a suitable target pathway can be identified.
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Affiliation(s)
- Wonsik Lee
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Truc Do
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Ge Zhang
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Timothy C. Meredith
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
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21
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Santiago M, Lee W, Fayad AA, Coe KA, Rajagopal M, Do T, Hennessen F, Srisuknimit V, Müller R, Meredith TC, Walker S. Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic. Nat Chem Biol 2018; 14:601-608. [PMID: 29662210 PMCID: PMC5964011 DOI: 10.1038/s41589-018-0041-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 02/27/2018] [Indexed: 12/11/2022]
Abstract
Identifying targets of antibacterial compounds remains a challenging step in antibiotic development. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivation mutants. We treated a Staphylococcus aureus transposon library containing 690,000 unique insertions with 32 antibiotics. Upregulation signatures, identified from directional biases in insertions, revealed known molecular targets and resistance mechanisms for the majority of these. Because single gene upregulation does not always confer resistance, we used a complementary machine learning approach to predict mechanism from inactivation mutant fitness profiles. This approach suggested the cell wall precursor Lipid II as the molecular target of the lysocins, a mechanism we have confirmed. We conclude that docking to membrane-anchored Lipid II precedes the selective bacteriolysis that distinguishes these lytic natural products, showing the utility of our approach for nominating antibiotic mechanism of action.
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Affiliation(s)
- Marina Santiago
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wonsik Lee
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Antoine Abou Fayad
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Kathryn A Coe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Mithila Rajagopal
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Truc Do
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Fabienne Hennessen
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Veerasak Srisuknimit
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.
| | - Timothy C Meredith
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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22
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Ney Y, Jawad Nasim M, Kharma A, Youssef LA, Jacob C. Small Molecule Catalysts with Therapeutic Potential. Molecules 2018; 23:E765. [PMID: 29584669 PMCID: PMC6017662 DOI: 10.3390/molecules23040765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 01/21/2023] Open
Abstract
Catalysts are employed in many areas of research and development where they combine high efficiency with often astonishing selectivity for their respective substrates. In biology, biocatalysts are omnipresent. Enzymes facilitate highly controlled, sophisticated cellular processes, such as metabolic conversions, sensing and signalling, and are prominent targets in drug development. In contrast, the therapeutic use of catalysts per se is still rather limited. Recent research has shown that small molecule catalytic agents able to modulate the redox state of the target cell bear considerable promise, particularly in the context of inflammatory and infectious diseases, stroke, ageing and even cancer. Rather than being "active" on their own in a more traditional sense, such agents develop their activity by initiating, promoting, enhancing or redirecting reactions between biomolecules already present in the cell, and their activity therefore depends critically on the predisposition of the target cell itself. Redox catalysts, for instance, preferably target cells with a distinct sensitivity towards changes in an already disturbed redox balance and/or increased levels of reactive oxygen species. Indeed, certain transition metal, chalcogen and quinone agents may activate an antioxidant response in normal cells whilst at the same time triggering apoptosis in cancer cells with a different pre-existing "biochemical redox signature" and closer to the internal redox threshold. In pharmacy, catalysts therefore stand out as promising lead structures, as sensor/effector agents which are highly effective, fairly selective, active in catalytic, i.e., often nanomolar concentrations and also very flexible in their structural design.
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Affiliation(s)
- Yannick Ney
- Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, D-66123 Saarbruecken, Germany.
| | - Muhammad Jawad Nasim
- Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, D-66123 Saarbruecken, Germany.
| | - Ammar Kharma
- Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, D-66123 Saarbruecken, Germany.
| | - Lama A Youssef
- Department of Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, Damascus University, Damascus, Syria.
| | - Claus Jacob
- Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, D-66123 Saarbruecken, Germany.
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Bottomley AL, Liew ATF, Kusuma KD, Peterson E, Seidel L, Foster SJ, Harry EJ. Coordination of Chromosome Segregation and Cell Division in Staphylococcus aureus. Front Microbiol 2017; 8:1575. [PMID: 28878745 PMCID: PMC5572376 DOI: 10.3389/fmicb.2017.01575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/03/2017] [Indexed: 12/03/2022] Open
Abstract
Productive bacterial cell division and survival of progeny requires tight coordination between chromosome segregation and cell division to ensure equal partitioning of DNA. Unlike rod-shaped bacteria that undergo division in one plane, the coccoid human pathogen Staphylococcus aureus divides in three successive orthogonal planes, which requires a different spatial control compared to rod-shaped cells. To gain a better understanding of how this coordination between chromosome segregation and cell division is regulated in S. aureus, we investigated proteins that associate with FtsZ and the divisome. We found that DnaK, a well-known chaperone, interacts with FtsZ, EzrA and DivIVA, and is required for DivIVA stability. Unlike in several rod shaped organisms, DivIVA in S. aureus associates with several components of the divisome, as well as the chromosome segregation protein, SMC. This data, combined with phenotypic analysis of mutants, suggests a novel role for S. aureus DivIVA in ensuring cell division and chromosome segregation are coordinated.
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Affiliation(s)
- Amy L Bottomley
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia
| | - Andrew T F Liew
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia
| | - Kennardy D Kusuma
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia
| | - Elizabeth Peterson
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia
| | - Lisa Seidel
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of SheffieldSheffield, United Kingdom
| | - Elizabeth J Harry
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia
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24
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Pang T, Wang X, Lim HC, Bernhardt TG, Rudner DZ. The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus. PLoS Genet 2017; 13:e1006908. [PMID: 28723932 PMCID: PMC5540599 DOI: 10.1371/journal.pgen.1006908] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 08/02/2017] [Accepted: 07/06/2017] [Indexed: 01/05/2023] Open
Abstract
Successive division events in the spherically shaped bacterium Staphylococcus aureus are oriented in three alternating perpendicular planes. The mechanisms that underlie this relatively unique pattern of division and coordinate it with chromosome segregation remain largely unknown. Thus far, the only known spatial regulator of division in this organism is the nucleoid occlusion protein Noc that inhibits assembly of the cytokinetic ring over the chromosome. However, Noc is not essential in S. aureus, indicating that additional regulators are likely to exist. To search for these factors, we screened for mutants that are synthetic lethal with Noc inactivation. Our characterization of these mutants led to the discovery that S. aureus Noc also controls the initiation of DNA replication. We show that cells lacking Noc over-initiate and mutations in the initiator gene dnaA suppress this defect. Importantly, these dnaA mutations also partially suppress the division problems associated with Δnoc. Reciprocally, we show that over-expression of DnaA enhances the over-initiation and cell division phenotypes of the Δnoc mutant. Thus, a single factor both blocks cell division over chromosomes and helps to ensure that new rounds of DNA replication are not initiated prematurely. This degree of economy in coordinating key cell biological processes has not been observed in rod-shaped bacteria and may reflect the challenges posed by the reduced cell volume and complicated division pattern of this spherical pathogen.
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Affiliation(s)
- Ting Pang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Xindan Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Hoong Chuin Lim
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Thomas G. Bernhardt
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
- * E-mail: (DZR); (TGB)
| | - David Z. Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
- * E-mail: (DZR); (TGB)
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25
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A Polymorphism in leuS Confers Reduced Susceptibility to GSK2251052 in a Clinical Isolate of Staphylococcus aureus. Antimicrob Agents Chemother 2016; 60:3219-21. [PMID: 26976861 DOI: 10.1128/aac.02940-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/04/2016] [Indexed: 02/03/2023] Open
Abstract
GSK2251052 is a broad-spectrum antibacterial inhibitor of leucyl tRNA-synthetase (LeuRS) that has been evaluated in phase II clinical trials. Here, we report the identification of a clinical isolate of Staphylococcus aureus that exhibits reduced susceptibility to GSK2251052 without prior exposure to the compound and demonstrate that this phenotype is attributable to a single amino acid polymorphism (P329) within the editing domain of LeuRS.
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26
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Turnbull L, Strauss MP, Liew ATF, Monahan LG, Whitchurch CB, Harry EJ. Super-resolution imaging of the cytokinetic Z ring in live bacteria using fast 3D-structured illumination microscopy (f3D-SIM). J Vis Exp 2014:51469. [PMID: 25286090 PMCID: PMC4672958 DOI: 10.3791/51469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Imaging of biological samples using fluorescence microscopy has advanced substantially with new technologies to overcome the resolution barrier of the diffraction of light allowing super-resolution of live samples. There are currently three main types of super-resolution techniques – stimulated emission depletion (STED), single-molecule localization microscopy (including techniques such as PALM, STORM, and GDSIM), and structured illumination microscopy (SIM). While STED and single-molecule localization techniques show the largest increases in resolution, they have been slower to offer increased speeds of image acquisition. Three-dimensional SIM (3D-SIM) is a wide-field fluorescence microscopy technique that offers a number of advantages over both single-molecule localization and STED. Resolution is improved, with typical lateral and axial resolutions of 110 and 280 nm, respectively and depth of sampling of up to 30 µm from the coverslip, allowing for imaging of whole cells. Recent advancements (fast 3D-SIM) in the technology increasing the capture rate of raw images allows for fast capture of biological processes occurring in seconds, while significantly reducing photo-toxicity and photobleaching. Here we describe the use of one such method to image bacterial cells harboring the fluorescently-labelled cytokinetic FtsZ protein to show how cells are analyzed and the type of unique information that this technique can provide.
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27
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Compound-gene interaction mapping reveals distinct roles for Staphylococcus aureus teichoic acids. Proc Natl Acad Sci U S A 2014; 111:12510-5. [PMID: 25104751 DOI: 10.1073/pnas.1404099111] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureus contains two distinct teichoic acid (TA) polymers, lipoteichoic acid (LTA) and wall teichoic acid (WTA), which are proposed to play redundant roles in regulating cell division. To gain insight into the underlying biology of S. aureus TAs, we used a small molecule inhibitor to screen a highly saturated transposon library for cellular factors that become essential when WTA is depleted. We constructed an interaction network connecting WTAs with genes involved in LTA synthesis, peptidoglycan synthesis, surface protein display, and D-alanine cell envelope modifications. Although LTAs and WTAs are synthetically lethal, we report that they do not have the same synthetic interactions with other cell envelope genes. For example, D-alanylation, a tailoring modification of both WTAs and LTAs, becomes essential when the former, but not the latter, are removed. Therefore, D-alanine-tailored LTAs are required for survival when WTAs are absent. Examination of terminal phenotoypes led to the unexpected discovery that cells lacking both LTAs and WTAs lose their ability to form Z rings and can no longer divide. We have concluded that the presence of either LTAs or WTAs on the cell surface is required for initiation of S. aureus cell division, but these polymers act as part of distinct cellular networks.
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28
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Novel and tightly regulated resorcinol and cumate-inducible expression systems for Streptomyces and other actinobacteria. Appl Microbiol Biotechnol 2014; 98:8641-55. [DOI: 10.1007/s00253-014-5918-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 01/07/2023]
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29
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Reconstruction of mreB expression in Staphylococcus aureus via a collection of new integrative plasmids. Appl Environ Microbiol 2014; 80:3868-78. [PMID: 24747904 DOI: 10.1128/aem.00759-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Protein localization has been traditionally explored in unicellular organisms, whose ease of genetic manipulation facilitates molecular characterization. The two rod-shaped bacterial models Escherichia coli and Bacillus subtilis have been prominently used for this purpose and have displaced other bacteria whose challenges for genetic manipulation have complicated any study of cell biology. Among these bacteria is the spherical pathogenic bacterium Staphylococcus aureus. In this report, we present a new molecular toolbox that facilitates gene deletion in staphylococci in a 1-step recombination process and additional vectors that facilitate the insertion of diverse reporter fusions into newly identified neutral loci of the S. aureus chromosome. Insertion of the reporters does not add any antibiotic resistance genes to the chromosomes of the resultant strains, thereby making them amenable for further genetic manipulations. We used this toolbox to reconstitute the expression of mreB in S. aureus, a gene that encodes an actin-like cytoskeletal protein which is absent in coccal cells and is presumably lost during the course of speciation. We observed that in S. aureus, MreB is organized in discrete structures in association with the membrane, leading to an unusual redistribution of the cell wall material. The production of MreB also caused cell enlargement, but it did not revert staphylococcal shape. We present interactions of MreB with key staphylococcal cell wall-related proteins. This work facilitates the use S. aureus as a model system in exploring diverse aspects of cellular microbiology.
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30
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How to get (a)round: mechanisms controlling growth and division of coccoid bacteria. Nat Rev Microbiol 2013; 11:601-14. [PMID: 23949602 DOI: 10.1038/nrmicro3088] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacteria come in a range of shapes, including round, rod-shaped, curved and spiral cells. This morphological diversity implies that different mechanisms exist to guide proper cell growth, division and chromosome segregation. Although the majority of studies on cell division have focused on rod-shaped cells, the development of new genetic and cell biology tools has provided mechanistic insight into the cell cycles of bacteria with different shapes, allowing us to appreciate the underlying molecular basis for their morphological diversity. In this Review, we discuss recent progress that has advanced our knowledge of the complex mechanisms for chromosome segregation and cell division in bacteria which have, deceptively, the simplest possible shape: the cocci.
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31
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Keffer JL, Huecas S, Hammill JT, Wipf P, Andreu JM, Bewley CA. Chrysophaentins are competitive inhibitors of FtsZ and inhibit Z-ring formation in live bacteria. Bioorg Med Chem 2013; 21:5673-8. [PMID: 23932448 PMCID: PMC3768135 DOI: 10.1016/j.bmc.2013.07.033] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 07/06/2013] [Accepted: 07/16/2013] [Indexed: 12/17/2022]
Abstract
The bacterial cell division protein FtsZ polymerizes in a GTP-dependent manner to form a Z-ring that marks the plane of division. As a validated antimicrobial target, considerable efforts have been devoted to identify small molecule FtsZ inhibitors. We recently discovered the chrysophaentins, a novel suite of marine natural products that inhibit FtsZ activity in vitro. These natural products along with a synthetic hemi-chrysophaentin exhibit strong antimicrobial activity toward a broad spectrum of Gram-positive pathogens. To define their mechanisms of FtsZ inhibition and determine their in vivo effects in live bacteria, we used GTPase assays and fluorescence anisotropy to show that hemi-chrysophaentin competitively inhibits FtsZ activity. Furthermore, we developed a model system using a permeable Escherichia coli strain, envA1, together with an inducible FtsZ-yellow fluorescent protein construct to show by fluorescence microscopy that both chrysophaentin A and hemi-chrysophaentin disrupt Z-rings in live bacteria. We tested the E. coli system further by reproducing phenotypes observed for zantrins Z1 and Z3, and demonstrate that the alkaloid berberine, a reported FtsZ inhibitor, exhibits auto-fluorescence, making it incompatible with systems that employ GFP or YFP tagged FtsZ. These studies describe unique examples of nonnucleotide, competitive FtsZ inhibitors that disrupt FtsZ in vivo, together with a model system that should be useful for in vivo testing of FtsZ inhibitor leads that have been identified through in vitro screens but are unable to penetrate the Gram-negative outer membrane.
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Affiliation(s)
- Jessica L. Keffer
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sonia Huecas
- Centro de Investigaciones Biologicas, CSIC, Madrid, Spain
| | - Jared T. Hammill
- Center for Chemical Methodologies and Library Development, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Peter Wipf
- Centro de Investigaciones Biologicas, CSIC, Madrid, Spain
| | - Jose M. Andreu
- Centro de Investigaciones Biologicas, CSIC, Madrid, Spain
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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32
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Brzoska AJ, Firth N. Two-plasmid vector system for independently controlled expression of green and red fluorescent fusion proteins in Staphylococcus aureus. Appl Environ Microbiol 2013; 79:3133-6. [PMID: 23455338 PMCID: PMC3623144 DOI: 10.1128/aem.00144-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/21/2013] [Indexed: 02/07/2023] Open
Abstract
We have constructed a system for the regulated coexpression of green fluorescent protein (GFP) and red fluorescent protein (RFP) fusions in Staphylococcus aureus. It was validated by simultaneous localization of cell division proteins FtsZ and Noc and used to detect filament formation by an actin-like ParM plasmid partitioning protein in its native coccoid host.
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Affiliation(s)
- Anthony J Brzoska
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
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33
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Prax M, Lee CY, Bertram R. An update on the molecular genetics toolbox for staphylococci. MICROBIOLOGY-SGM 2013; 159:421-435. [PMID: 23378573 PMCID: PMC3709823 DOI: 10.1099/mic.0.061705-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Staphylococci are Gram-positive spherical bacteria of enormous clinical and biotechnological relevance. Staphylococcus aureus has been extensively studied as a model pathogen. A plethora of methods and molecular tools has been developed for genetic modification of at least ten different staphylococcal species to date. Here we review recent developments of various genetic tools and molecular methods for staphylococcal research, which include reporter systems and vectors for controllable gene expression, gene inactivation, gene essentiality testing, chromosomal integration and transposon delivery. It is furthermore illustrated how mutant strain construction by homologous or site-specific recombination benefits from sophisticated counterselection methods. The underlying genetic components have been shown to operate in wild-type staphylococci or modified chassis strains. Finally, possible future developments in the field of applied Staphylococcus genetics are highlighted.
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Affiliation(s)
- Marcel Prax
- Department of Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Faculty of Science, University of Tübingen, Waldhäuser Str. 70/8, 72076 Tübingen, Germany
| | - Chia Y Lee
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 511, Little Rock, AR 72205, USA
| | - Ralph Bertram
- Department of Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Faculty of Science, University of Tübingen, Waldhäuser Str. 70/8, 72076 Tübingen, Germany
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34
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3D-SIM super resolution microscopy reveals a bead-like arrangement for FtsZ and the division machinery: implications for triggering cytokinesis. PLoS Biol 2012; 10:e1001389. [PMID: 22984350 PMCID: PMC3439403 DOI: 10.1371/journal.pbio.1001389] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/03/2012] [Indexed: 12/16/2022] Open
Abstract
Super resolution three-dimensional imaging reveals a new picture of how bacterial cell division proteins localize to the division site, including the formation of dynamic bead-like patterns, and explains how the division ring constricts. FtsZ is a tubulin-like GTPase that is the major cytoskeletal protein in bacterial cell division. It polymerizes into a ring, called the Z ring, at the division site and acts as a scaffold to recruit other division proteins to this site as well as providing a contractile force for cytokinesis. To understand how FtsZ performs these functions, the in vivo architecture of the Z ring needs to be established, as well as how this structure constricts to enable cytokinesis. Conventional wide-field fluorescence microscopy depicts the Z ring as a continuous structure of uniform density. Here we use a form of super resolution microscopy, known as 3D-structured illumination microscopy (3D-SIM), to examine the architecture of the Z ring in cells of two Gram-positive organisms that have different cell shapes: the rod-shaped Bacillus subtilis and the coccoid Staphylococcus aureus. We show that in both organisms the Z ring is composed of a heterogeneous distribution of FtsZ. In addition, gaps of fluorescence were evident, which suggest that it is a discontinuous structure. Time-lapse studies using an advanced form of fast live 3D-SIM (Blaze) support a model of FtsZ localization within the Z ring that is dynamic and remains distributed in a heterogeneous manner. However, FtsZ dynamics alone do not trigger the constriction of the Z ring to allow cytokinesis. Lastly, we visualize other components of the divisome and show that they also adopt a bead-like localization pattern at the future division site. Our data lead us to propose that FtsZ guides the divisome to adopt a similar localization pattern to ensure Z ring constriction only proceeds following the assembly of a mature divisome. Because bacterial cells are so small, it is challenging to image the spatial organization of proteins inside them. All the proteins that orchestrate cell division in these organisms localize to the division site prior to division, but it has not so far been possible to obtain a clear highresolution three-dimensional picture of the dynamics of their localization. In this study we use a new type of super resolution microscopy called three-dimensional structured illumination microscopy (3D-SIM) to analyze the localization of proteins involved in cell division in two types of bacteria that have different cell shapes: the rod-shaped Bacillus subtilis and the spherical Staphylococcus aureus. We show that FtsZ, a cytoskeletal protein that serves as a scaffold for the cytokinetic ring, localizes to the division site in a dynamic bead-like pattern, rather than a uniform ring as was previously proposed, in both types of bacteria. Our observations also provide an explanation of how this ring constricts to split a bacterial cell in two and suggests that this spatial organization of division proteins is conserved among bacteria and is crucial for the regulation of this central cellular process.
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35
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Doherty G, Mettrick K, Grainge I, Lewis PJ. Imaging fluorescent protein fusions in live bacteria. J Microbiol Methods 2012. [DOI: 10.1016/b978-0-08-099387-4.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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